Research

13 pages, 2663 KiB

Open AccessArticle

A Comparative Analysis of Molecular Biological Methods for the Detection of SARS-CoV-2 and Testing the In Vitro Infectivity of the Virus

by Kalina Shishkova, Bilyana Sirakova, Stoyan Shishkov, Eliya Stoilova, Hristiyan Mladenov and Ivo Sirakov

Microorganisms 2024, 12(1), 180; https://doi.org/10.3390/microorganisms12010180 - 17 Jan 2024

Viewed by 1146

Abstract

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for [...] Read more.

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for the detection of SARS-CoV-2, which we validated and applied to detect the virus in feline samples. The present study describes the application of the nested PCR test in parallel with LAMP for the detection of the virus in 427 nasopharyngeal and oropharyngeal human samples taken between October 2020 and January 2022. Of the swabs tested, there were 43 positives, accounting for 10.1% of all samples tested, with the negatives numbering 382, i.e., 89.5%, and there were 2 (0.4%) invalid ones. The nPCR results confirmed those obtained by using LAMP, with results concordant in both methods. Nasal swabs tested using nPCR confirmed the results of oropharyngeal and nasopharyngeal swab samples tested using LAMP and nPCR. The focus of the discussion is on the two techniques: the actual practical application of the laboratory-developed assays and the diagnostic value of nasal samples. The nPCR used is a reliable and sensitive technique for the detection of SARS-CoV-2 in nasopharyngeal, oropharyngeal, and nasal swab samples. However, it has some disadvantages related to the duration of the entire process, as well as a risk of contamination. Experiments were performed to demonstrate the infectivity of the virus from the positive isolates in vitro. A discrepancy was reported between direct and indirect methods of testing the virus and accounting for its ability to cause infection in vitro. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 591 KiB

Open AccessArticle

Influence of Source Materials, Concentration, Gastric Digestion, and Encapsulation on the Bioactive Response of Brassicaceae-Derived Samples against Helicobacter pylori

by Paula Garcia-Ibañez, Jose Manuel Silvan, Diego A. Moreno, Micaela Carvajal and Adolfo J. Martinez-Rodriguez

Microorganisms 2024, 12(1), 77; https://doi.org/10.3390/microorganisms12010077 - 30 Dec 2023

Viewed by 813

Abstract

Isothiocyanates may have antibacterial activity against Helicobacter pylori, but there are different variables related to Brassicaceae-derived samples that could affect their efficacy. This work studied the influence of source variety, concentration, gastric digestion, and encapsulation of samples on their bioactive response against [...] Read more.

Isothiocyanates may have antibacterial activity against Helicobacter pylori, but there are different variables related to Brassicaceae-derived samples that could affect their efficacy. This work studied the influence of source variety, concentration, gastric digestion, and encapsulation of samples on their bioactive response against Helicobacter pylori. The antibacterial activity of raw sprouts (red cabbage and red radish) showed the highest antibacterial effect, which was consistent with a higher amount of isothiocyanates. It decreased with gastric digestion, regardless of sample encapsulation. By contrast, adult red radish leaves became antibacterial after gastric digestion. Antioxidant activity on H. pylori-infected gastric cells was similar in all samples and followed an equivalent pattern with the changes in isothiocyanates. Raw samples decreased intracellular reactive oxygen species production, but they lost this capacity after gastric digestion, regardless whether the compounds were free or encapsulated. Red cabbage sprouts, red radish sprouts, and red radish roots produced a decrease in nitric oxide production. It was consistent with a modulation of the inflammatory response and was associated to isothiocyanates concentration. Encapsulated sprout samples retained part of their anti-inflammatory activity after gastric digestion. Adult raw red radish leaves were not active, but after digestion, they became anti-inflammatory. The results obtained in this study have shown that several variables could have a significant impact on the bioactive properties of Brassicaceae-derived samples against H. pylori, providing a starting point for the design and standardization of samples with specific bioactivities (antibacterial, antioxidant, and anti-inflammatory) potentially useful for the treatment of H. pylori infection. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 2865 KiB

Open AccessArticle

Population Pharmacokinetic and Pharmacodynamic Analysis for Maximizing the Effectiveness of Ceftobiprole in the Treatment of Severe Methicillin-Resistant Staphylococcal Infections

by Pier Giorgio Cojutti, Simone Giuliano, Renato Pascale, Jacopo Angelini, Carlo Tascini, Pierluigi Viale and Federico Pea

Microorganisms 2023, 11(12), 2964; https://doi.org/10.3390/microorganisms11122964 - 12 Dec 2023

Viewed by 945

Abstract

Ceftobiprole is a fifth-generation cephalosporin used for different Gram-positive bacterial infections. A population pharmacokinetic analysis was conducted in real-life clinical patients to assess the adequacy of current dosages. Population pharmacokinetics was conducted using non-linear mixed effect modeling. Monte Carlo simulations were performed to [...] Read more.

Ceftobiprole is a fifth-generation cephalosporin used for different Gram-positive bacterial infections. A population pharmacokinetic analysis was conducted in real-life clinical patients to assess the adequacy of current dosages. Population pharmacokinetics was conducted using non-linear mixed effect modeling. Monte Carlo simulations were performed to determine the probability of target attainment (PTA) of free trough or steady-state concentration over MIC (fC_trough/MIC or fC_ss/MIC) ≥ 1 or ≥4 associated with both the standard and intensified dosing regimens adjusted for renal function. Cumulative fraction of response (CFR) against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (MRSE) were also calculated. A total of 132 patients with 503 concentrations were included. Most of them (107/132, 81.1%) had hospital- or community-acquired pneumonia, endocarditis, and bacteremia. A three-compartment model adequately fitted ceftobiprole concentration-time data. Estimated glomerular filtration rate significantly affected drug clearance. Monte Carlo simulations showed that the optimal target of fC_trough/MIC or fC_ss/MIC ≥ 4 is achieved only with the use of the standard dosages administered by continuous infusion (CI) against MRSA infections in patients with preserved renal function. Intensified dosages administered by CI are needed in patients with impaired renal function and/or augmented renal clearance against MRSA and in patients with preserved renal functions against MRSE. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 2860 KiB

Open AccessArticle

All Kinds of Sunny Colors Synthesized from Methane: Genome-Encoded Carotenoid Production by Methylomonas Species

by Igor Y. Oshkin, Ekaterina N. Tikhonova, Ruslan Z. Suleimanov, Aleksandr A. Ashikhmin, Anastasia A. Ivanova, Nikolai V. Pimenov and Svetlana N. Dedysh

Microorganisms 2023, 11(12), 2865; https://doi.org/10.3390/microorganisms11122865 - 26 Nov 2023

Viewed by 866

Abstract

Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display [...] Read more.

Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display fast growth on methane or natural gas, are of particular interest as potential producers of a feed protein enriched with carotenoids. Until recently, Methylomonas strain 16a and Methylomonas sp. ZR1 remained the only representatives of the genus for which detailed carotenoid profile was determined. In this study, we analyzed the genome sequences of five strains of Methylomonas species whose pigmentation varied from white and yellow to orange and red, and identified carotenoids produced by these bacteria. Carotenoids synthesized using four pigmented strains included C30 fraction, primarily composed of 4,4’-diaplycopene-4,4’-dioic acid and 4,4’-diaplycopenoic acid, as well as C40 fraction with the major compound represented by 1,1’-dihydroxy-3,4-didehydrolycopene. The genomes of studied Methylomonas strains varied in size between 4.59 and 5.45 Mb and contained 4201–4735 protein-coding genes. These genomes and 35 reference Methylomonas genomes available in the GenBank were examined for the presence of genes encoding carotenoid biosynthesis. Genomes of all pigmented Methylomonas strains harbored genes necessary for the synthesis of 4,4’-diaplycopene-4,4’-dioic acid. Non-pigmented “Methylomonas montana” MW1^T lacked the crtN gene required for carotenoid production. Nearly all strains possessed phytoene desaturases, which explained their ability to naturally synthesize lycopene. Thus, members of the genus Methylomonas can potentially be considered as producers of C30 and C40 carotenoids from methane. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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19 pages, 3760 KiB

Open AccessArticle

16S and 18S rDNA Amplicon Sequencing Analysis of Aesthetically Problematic Microbial Mats on the Walls of the Petralona Cave: The Use of Essential Oils as a Cleaning Method

by Natalia Tsouggou, Alexandra Oikonomou, Konstantinos Papadimitriou and Panagiotis N. Skandamis

Microorganisms 2023, 11(11), 2681; https://doi.org/10.3390/microorganisms11112681 - 31 Oct 2023

Viewed by 746

Abstract

The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation [...] Read more.

The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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19 pages, 6491 KiB

Open AccessArticle

In Silico Evaluation, Phylogenetic Analysis, and Structural Modeling of the Class II Hydrophobin Family from Different Fungal Phytopathogens

by Nahla A. Bouqellah and Peter F. Farag

Microorganisms 2023, 11(11), 2632; https://doi.org/10.3390/microorganisms11112632 - 26 Oct 2023

Viewed by 1086

Abstract

The class II hydrophobin group (HFBII) is an extracellular group of proteins that contain the HFBII domain and eight conserved cysteine residues. These proteins are exclusively secreted by fungi and have multiple functions with a probable role as effectors. In the present study, [...] Read more.

The class II hydrophobin group (HFBII) is an extracellular group of proteins that contain the HFBII domain and eight conserved cysteine residues. These proteins are exclusively secreted by fungi and have multiple functions with a probable role as effectors. In the present study, a total of 45 amino acid sequences of hydrophobin class II proteins from different phytopathogenic fungi were retrieved from the NCBI database. We used the integration of well-designed bioinformatic tools to characterize and predict their physicochemical parameters, novel motifs, 3D structures, multiple sequence alignment (MSA), evolution, and functions as effector proteins through molecular docking. The results revealed new features for these protein members. The ProtParam tool detected the hydrophobicity properties of all proteins except for one hydrophilic protein (KAI3335996.1). Out of 45 proteins, six of them were detected as GPI-anchored proteins by the PredGPI server. Different 3D structure templates with high pTM scores were designed by Multifold v1, AlphaFold2, and trRosetta. Most of the studied proteins were anticipated as apoplastic effectors and matched with the ghyd5 gene of Fusarium graminearum as virulence factors. A protein–protein interaction (PPI) analysis unraveled the molecular function of this group as GTP-binding proteins, while a molecular docking analysis detected a chitin-binding effector role. From the MSA analysis, it was observed that the HFBII sequences shared conserved 2 Pro (P) and 2 Gly (G) amino acids besides the known eight conserved cysteine residues. The evolutionary analysis and phylogenetic tree provided evidence of episodic diversifying selection at the branch level using the aBSREL tool. A detailed in silico analysis of this family and the present findings will provide a better understanding of the HFBII characters and evolutionary relationships, which could be very useful in future studies. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 2485 KiB

Open AccessArticle

Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the Class Lecanoromycetes

by Gugulethu Mlambo, Tiara Padayachee, David R. Nelson and Khajamohiddin Syed

Microorganisms 2023, 11(10), 2590; https://doi.org/10.3390/microorganisms11102590 - 19 Oct 2023

Viewed by 999

Abstract

Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play [...] Read more.

Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing these metabolites. Despite the critical role of P450s in the biosynthesis of secondary metabolites, the systematic analysis of P450s in lichens has yet to be reported. This study is aimed to address this research gap. A genome-wide analysis of P450s in five lichens from the fungal class Lecanoromycetes revealed the presence of 434 P450s that are grouped into 178 P450 families and 345 P450 subfamilies. The study indicated that none of the P450 families bloomed, and 15 P450 families were conserved in all five Lecanoromycetes. Lecanoromycetes have more P450s and higher P450 family diversity compared to Pezizomycetes. A total of 73 P450s were found to be part of secondary metabolite gene clusters, indicating their potential involvement in the biosynthesis of secondary metabolites. Annotation of P450s revealed that CYP682BG1 and CYP682BG2 from Cladonia grayi and Pseudevernia furfuracea (physodic acid chemotype) are involved in the synthesis of grayanic acid and physodic acid, CYP65FQ2 from Stereocaulon alpinum is involved in the synthesis of atranorin, and CYP6309A2 from Cladonia uncialis is involved in the synthesis of usnic acid. This study serves as a reference for future annotation of P450s in lichens. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 3880 KiB

Open AccessArticle

Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing

by Eloiza May Galon, Adrian Miki Macalanda, Tatsuki Sugi, Kyoko Hayashida, Naoko Kawai, Taishi Kidaka, Rochelle Haidee Ybañez, Paul Franck Adjou Moumouni, Aaron Edmond Ringo, Hang Li, Shengwei Ji, Junya Yamagishi, Adrian Ybañez and Xuenan Xuan

Microorganisms 2023, 11(10), 2584; https://doi.org/10.3390/microorganisms11102584 - 18 Oct 2023

Viewed by 946

Abstract

Molecular assays and capillary electrophoresis sequencing have been used to identify parasites in livestock. The low sample capacity, which increases labor and processing time, is one drawback. Targeted amplicon sequencing (Ampliseq) uses the fast and large sample capacity platform to identify parasites in [...] Read more.

Molecular assays and capillary electrophoresis sequencing have been used to identify parasites in livestock. The low sample capacity, which increases labor and processing time, is one drawback. Targeted amplicon sequencing (Ampliseq) uses the fast and large sample capacity platform to identify parasites in the target host, overcoming this limitation. DNA was extracted from 162 whole blood samples collected from cattle in three provinces in the Philippines. Using Illumina’s Miseq platform, the V4 hypervariable region of the piroplasma 18S rRNA gene was amplified and sequenced. The AMPtk pipeline was used to obtain distinct amplicon sequence variants (ASVs) and the NCBI BLAST non-redundant database was used to assign taxonomy. In total, 95 (58.64%) samples were positive for piroplasma. Using the AMPTk pipeline, 2179 ASVs were obtained. A total of 79 distinct ASVs were obtained after clustering and filtering, which belonged to genera Babesia (n = 58), Theileria (n = 17), Hepatozoon (n = 2), and Sarcocystis (n = 2). The ASV top hits were composed of 10 species: Babesia bovis, B. bigemina, Theileria orientalis, Babesia sp., Hepatozoon canis, Sarcocystis cruzi, T. annulata, T. equi, T. mutans, and Theileria sp. Thung Song. The results generated in this study demonstrated the applicability of Ampliseq in detecting piroplasmid parasites infecting cattle in the Philippines. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 7732 KiB

Open AccessArticle

Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers

by Despoina E. Kiousi, Dimitrios M. Karadedos, Anastasia Sykoudi, Panagiotis Repanas, Christina S. Kamarinou, Anthoula A. Argyri and Alex Galanis

Microorganisms 2023, 11(10), 2553; https://doi.org/10.3390/microorganisms11102553 - 13 Oct 2023

Cited by 1 | Viewed by 1297

Abstract

Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed [...] Read more.

Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 2981 KiB

Open AccessArticle

Rhodoalgimonas zhirmunskyi gen. nov., sp. nov., a Marine Alphaproteobacterium Isolated from the Pacific Red Alga Ahnfeltia tobuchiensis: Phenotypic Characterization and Pan-Genome Analysis

by Olga Nedashkovskaya, Nadezhda Otstavnykh, Larissa Balabanova, Evgenia Bystritskaya, Song-Gun Kim, Natalia Zhukova, Liudmila Tekutyeva and Marina Isaeva

Microorganisms 2023, 11(10), 2463; https://doi.org/10.3390/microorganisms11102463 - 30 Sep 2023

Cited by 1 | Viewed by 1001

Abstract

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 10Alg 79^T, was isolated from the red alga Ahnfeltia tobuchiensis. A phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Roseobacteraceae, [...] Read more.

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 10Alg 79^T, was isolated from the red alga Ahnfeltia tobuchiensis. A phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Roseobacteraceae, class Alphaproteobacteria, phylum Pseudomonadota, where the nearest neighbor was Shimia sediminis ZQ172^T (97.33% of identity). However, a phylogenomic study clearly showed that strain 10Alg 79^T forms a distinct evolutionary lineage at the genus level within the family Roseobacteraceae combining with strains Aquicoccus porphyridii L1 8-17^T, Marimonas arenosa KCTC 52189^T, and Lentibacter algarum DSM 24677^T. The ANI, AAI, and dDDH values between them were 75.63–78.15%, 67.41–73.08%, and 18.8–19.8%, respectively. The genome comprises 3,754,741 bp with a DNA GC content of 62.1 mol%. The prevalent fatty acids of strain 10Alg 79^T were C_{18:1 ω7c} and C_16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. A pan-genome analysis showed that the unique part of the 10Alg 79^T genome consists of 13 genus-specific clusters and 413 singletons. The annotated singletons were more often related to transport protein systems, transcriptional regulators, and enzymes. A functional annotation of the draft genome sequence revealed that this bacterium could be a source of a new phosphorylase, which may be used for phosphoglycoside synthesis. A combination of the genotypic and phenotypic data showed that the bacterial isolate represents a novel species and a novel genus, for which the name Rhodoalgimonas zhirmunskyi gen. nov., sp. nov. is proposed. The type strain is 10Alg 79^T (=KCTC 72611^T = KMM 6723^T). Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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21 pages, 4105 KiB

Open AccessArticle

Immunoinformatic Execution and Design of an Anti-Epstein–Barr Virus Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses

by Naveed Ahmed, Ali A. Rabaan, Ameen S. S. Alwashmi, Hawra Albayat, Mutaib M. Mashraqi, Ahmad A. Alshehri, Mohammed Garout, Wesam A. Abduljabbar, Nik Yusnoraini Yusof and Chan Yean Yean

Microorganisms 2023, 11(10), 2448; https://doi.org/10.3390/microorganisms11102448 - 29 Sep 2023

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Abstract

One of the most important breakthroughs in healthcare is the development of vaccines. The life cycle and its gene expression in the numerous virus-associated disorders must be considered when choosing the target vaccine antigen for Epstein–Barr virus (EBV). The vaccine candidate used in [...] Read more.

One of the most important breakthroughs in healthcare is the development of vaccines. The life cycle and its gene expression in the numerous virus-associated disorders must be considered when choosing the target vaccine antigen for Epstein–Barr virus (EBV). The vaccine candidate used in the current study will also be effective against all other herpesvirus strains, based on the conservancy study, which verified that the protein is present in all herpesviruses. From the screening, two B-cell epitopes, four MHC-I, and five MHC-II restricted epitopes were chosen for further study. The refined epitopes indicated 70.59% coverage of the population in Malaysia and 93.98% worldwide. After removing the one toxin (PADRE) from the original vaccine design, it was projected that the new vaccine would not be similar to the human host and would instead be antigenic, immunogenic, non-allergenic, and non-toxic. The vaccine construct was stable, thermostable, soluble, and hydrophilic. The immunological simulation projected that the vaccine candidate would be subject to a long-lasting active adaptive response and a short-lived active innate response. With IgM concentrations of up to 450 cells per mm³ and active B-cell concentrations of up to 400 cells per mm³, the B-cells remain active for a considerable time. The construct also discovered other conformational epitopes, improving its ability to stimulate an immune response. This suggests that, upon injection, the epitope will target the B-cell surface receptors and elicit a potent immune response. Furthermore, the discotope analysis confirmed that our conformational B-cell epitope was not displaced during the design. Lastly, the docking complex was stable and exhibited little deformability under heat pressure. These computational results are very encouraging for future testing of our proposed vaccine, which may potentially help in the management and prevention of EBV infections worldwide. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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10 pages, 511 KiB

Open AccessArticle

Is Personal Protective Equipment Worth the Hassle? Annual Risk of Cryptosporidiosis to Dairy Farmers and How Personal Protective Equipment and Handwashing Can Mitigate It

by Alexis L. Mraz, Nandini Mutyala, Seana Cleary and Brenda F. Seals

Microorganisms 2023, 11(10), 2413; https://doi.org/10.3390/microorganisms11102413 - 27 Sep 2023

Viewed by 655

Abstract

Cows are known carriers of Cryptosporidium parvum (C. parvum), a protozoa that can cause the gastrointestinal illness cryptosporidiosis in humans. Despite this potential exposure, dairy farmers tend to wear personal protective equipment (PPE) to protect the milk from contamination, rather than [...] Read more.

Cows are known carriers of Cryptosporidium parvum (C. parvum), a protozoa that can cause the gastrointestinal illness cryptosporidiosis in humans. Despite this potential exposure, dairy farmers tend to wear personal protective equipment (PPE) to protect the milk from contamination, rather than to protect themselves from zoonotic diseases, such as cryptosporidiosis. In this study, cow feces were collected from individual cattle on dairy farms and analyzed for C. parvum using qPCR. Quantitative microbial risk assessment (QMRA) was used to determine the risk of cryptosporidiosis to the dairy farmer with and without the use of handwashing and PPE (gloves and masks). The annualized risk of cryptosporidiosis to dairy farmers was 29.08% but was reduced significantly in each of the three interventions. Among the individual interventions, glove use provided the greatest reduction in risk, bringing the annual risk of cryptosporidiosis to 4.82%. Implementing regular handwashing, the use of gloves and a mask brought the annual risk of cryptosporidiosis to 1.29%. This study provides evidence that handwashing and PPE use can significantly reduce the risk of cryptosporidiosis to farmers and is worth implementing despite potential barriers such as discomfort and cost. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 1458 KiB

Open AccessArticle

A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy

by Arcadia Del Rio, Valeria Fox, Narcisa Muresu, Illari Sechi, Andrea Cossu, Alessandra Palmieri, Rossana Scutari, Claudia Alteri, Giovanni Sotgiu, Paolo Castiglia and Andrea Piana

Microorganisms 2023, 11(9), 2354; https://doi.org/10.3390/microorganisms11092354 - 20 Sep 2023

Cited by 1 | Viewed by 998

Abstract

Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant microorganisms. We reported the results of a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which [...] Read more.

Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant microorganisms. We reported the results of a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which causes hospital-acquired infections (HAIs) and is characterized by a marked resistance profile. Methods: Clinical, phenotypic, and genotypic data were collected for the AMR surveillance screening program of the University Hospital of Sassari (Italy) during 2020–2021. Genomic DNA was sequenced using the Illumina Nova Seq 6000 platform. Final assemblies were manually curated and carefully verified for the detection of antimicrobial resistance genes, porin mutations, and virulence factors. A phylogenetic analysis was performed using the maximum likelihood method. Results: All 17 strains analyzed belonged to ST512, and most of them carried the bla_KPC-31 variant bla_OXA-48-like, an OmpK35 truncation, and an OmpK36 mutation. Phenotypic analysis showed a marked resistance profile to all antibiotic classes, including β-lactams, carbapenems, aminoglycosides, fluoroquinolone, sulphonamides, and novel β-lactam/β-lactamase inhibitors (BL/BLI). Conclusion: WGS characterization revealed the presence of several antibiotic resistance determinants and porin mutations in highly resistant K. pneumoniae strains responsible for HAIs. The detection of bla_KPC-31 in our hospital wards highlights the importance of genomic surveillance in hospital settings to monitor the emergence of new clones and the need to improve control and preventive strategies to efficiently contrast AMR. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 2676 KiB

Open AccessArticle

The Mating Type (MAT) and Virulence of Sporothrix schenckii sensu stricto Isolates Maintained in Culture Collection

by Thais Barreira, Danielly Corrêa-Moreira, Cintia de Moraes Borba, Rodrigo Caldas Menezes, Aurea Maria Lage de Moraes and Manoel Marques Evangelista Oliveira

Microorganisms 2023, 11(9), 2335; https://doi.org/10.3390/microorganisms11092335 - 18 Sep 2023

Viewed by 848

Abstract

In an attempt to determine the mating type of different Sporothrix schenckii sensu stricto isolates that remained viable after a long period of preservation in a culture collection and to correlate them with the degree of virulence/pathogenicity, a PCR technique using primers designed [...] Read more.

In an attempt to determine the mating type of different Sporothrix schenckii sensu stricto isolates that remained viable after a long period of preservation in a culture collection and to correlate them with the degree of virulence/pathogenicity, a PCR technique using primers designed for the sequences of MAT1-1-1 and MAT1-2-1 genes and a murine experimental model were used. The results showed that there was no correlation between the mating type and virulence among the isolates. Furthermore, different degrees of virulence/pathogenicity, ranging from high to low, were found among them based on different virulence parameters. It was assumed that the long period of preservation favored the changes, yielding the isolation of variants. Thus, we believe that new technologies for studies on factors can improve our knowledge of the pathogenesis of sporotrichosis. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 9490 KiB

Open AccessArticle

Comparison of the Effects of Feeding Compound Probiotics and Antibiotics on Growth Performance, Gut Microbiota, and Small Intestine Morphology in Yellow-Feather Broilers

by Yuyan Feng, Xiaoting Wu, Dan Hu, Canyang Wang, Qu Chen and Yingdong Ni

Microorganisms 2023, 11(9), 2308; https://doi.org/10.3390/microorganisms11092308 - 13 Sep 2023

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Abstract

This study was devoted to the comparison of the probiotic effect of compound probiotics to antibiotics as a feed additive for chicken. Two hundred and seventy newly hatched yellow-feather broilers were randomly divided into three groups: the control group (Con), probiotics (Pb), and [...] Read more.

This study was devoted to the comparison of the probiotic effect of compound probiotics to antibiotics as a feed additive for chicken. Two hundred and seventy newly hatched yellow-feather broilers were randomly divided into three groups: the control group (Con), probiotics (Pb), and antibiotics group (Ab). The Pb group received compound probiotics (Bifidobacterium, Lactobacillus acidophilus, Streptococcus faecalis, and yeast) via drinking water for 24 days. The Ab group received antibiotics (zinc bacitracin and colistin sulfate) in their diet for 24 days. All broilers were slaughtered on day 42. Compared with the Con group, the body weight was significantly increased on days 13, 28, and 42 in the Pb group (p < 0.05), and markedly increased on day 28 in the Ab group (p < 0.05). Compared with the Ab group, the body weight of the broilers in the Pb group increased significantly on day 13 (p < 0.05). Compared to the Con and Pb groups, the antibiotics treatment reduced the feed intake (p < 0.05), but there was no significant difference in the feed conversion ratio between the Ab and Pb groups (p > 0.05). The feed conversion ratio of the broilers treated with antibiotics or probiotics significantly decreased compared to the Con group (p < 0.05). The depth of duodenum, jejunum, and ileum crypts in the Pb group decreased significantly compared to the Con and Ab group (p < 0.05). The ratio of the villi length to crypt depth of duodenum, jejunum, and ileum epithelium was significantly increased in the Pb group compared to the Con group (p < 0.05). The genera Bacteroides and Barnesiella were the most significantly enriched bacteria in the Ab and Pb groups, respectively (p < 0.05). The expression of the genes related to antibiotic resistance was significantly decreased in the Pb group compared to the Ab group (p < 0.05). Although both compound probiotics and antibiotics can improve growth performance, antibiotics increased the abundance of harmful bacteria and drug-resistant genes, while probiotics increased Barnesiella abundance, which is related to a decrease in the drug-resistant gene expression. Moreover, the probiotics treatment improved small intestinal morphology and fecal emissions, while antibiotics have no significant effect on these indicators, indicating a bright future for probiotics as an alternative to feed antibiotics in the yellow-feather broiler industry. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 2573 KiB

Open AccessArticle

Identification of Virulence Factors in Entomopathogenic Aspergillus flavus Isolated from Naturally Infected Rhipicephalus microplus

by Cesar A. Arreguin-Perez, Estefan Miranda-Miranda, Jorge Luis Folch-Mallol and Raquel Cossío-Bayúgar

Microorganisms 2023, 11(8), 2107; https://doi.org/10.3390/microorganisms11082107 - 18 Aug 2023

Viewed by 1140

Abstract

Aspergillus flavus has been found to be an effective entomopathogenic fungus for various arthropods, including ticks. In particular, natural fungal infections in cattle ticks show promise for biocontrol of the Rhipicephalus (Boophilus) microplus tick, which is a major ectoparasite affecting cattle [...] Read more.

Aspergillus flavus has been found to be an effective entomopathogenic fungus for various arthropods, including ticks. In particular, natural fungal infections in cattle ticks show promise for biocontrol of the Rhipicephalus (Boophilus) microplus tick, which is a major ectoparasite affecting cattle worldwide. Our study aimed to elucidate the specific entomopathogenic virulence factors encoded in the genome of an A. flavus strain isolated from naturally infected cattle ticks. We performed morphological and biochemical phenotyping alongside complete genome sequencing, which revealed that the isolated fungus was A. flavus related to the L morphotype, capable of producing a range of gene-coded entomopathogenic virulence factors, including ribotoxin, aflatoxin, kojic acid, chitinases, killer toxin, and satratoxin. To evaluate the efficacy of this A. flavus strain against ticks, we conducted experimental bioassays using healthy engorged female ticks. A morbidity rate of 90% was observed, starting at a concentration of 10⁵ conidia/mL. At a concentration of 10⁷ conidia/mL, we observed a 50% mortality rate and a 21.5% inhibition of oviposition. The highest levels of hatch inhibition (30.8%) and estimated reproduction inhibition (34.64%) were achieved at a concentration of 10⁸ conidia/mL. Furthermore, the tick larval progeny that hatched from the infected tick egg masses showed evident symptoms of Aspergillus infection after incubation. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 538 KiB

Open AccessArticle

Toxoplasma gondii Seroprevalence and Trends in Women Presenting for Toxoplasma Screening in South-West Romania

by Cristiana Luiza Radoi, Ovidiu Mircea Zlatian, Maria Balasoiu, Lucian Giubelan, Andreea Cristina Stoian, Livia Dragonu, Alexandru Neacsu and Dominic Gabriel Iliescu

Microorganisms 2023, 11(8), 2057; https://doi.org/10.3390/microorganisms11082057 - 10 Aug 2023

Viewed by 1150

Abstract

Toxoplasmosis, caused by the obligate intracellular protozoan parasite Toxoplasma gondii (T. gondii), is a globally prevalent zoonotic disease with potentially severe implications for immunocompromised individuals, pregnant women, and their fetuses/children. This study examined the prevalence of anti-T. gondii IgM and [...] Read more.

Toxoplasmosis, caused by the obligate intracellular protozoan parasite Toxoplasma gondii (T. gondii), is a globally prevalent zoonotic disease with potentially severe implications for immunocompromised individuals, pregnant women, and their fetuses/children. This study examined the prevalence of anti-T. gondii IgM and IgG antibodies in two groups of childbearing age women, including 653 participants in Group 1 (2013–2016) and 3221 participants in Group 2 (2019–2022). Our results revealed a decrease in the overall positivity rate of anti-T. gondii IgM antibodies from 2.32% to 1.06%, suggesting improved public health interventions over time. However, there were variations among different age groups and between rural and urban environments, with a significant decrease in urban areas across all age groups from Group 1 to Group 2. Regarding anti-T. gondii IgG antibodies, we did not observe a significant change in the seropositivity rate between the two groups. In the rural population with an age group over 35 years, we observed the highest positivity rate in Group 2. This study provided information on the risk factors and burden of toxoplasmosis in women of childbearing age with data that can be valuable to public health policies and the planning of healthcare measures for effective toxoplasmosis management. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 3085 KiB

Open AccessArticle

The Unicellular, Parasitic Fungi, Sanchytriomycota, Possess a DNA Sequence Possibly Encoding a Long Tubulin Polymerization Promoting Protein (TPPP) but Not a Fungal-Type One

by Ferenc Orosz

Microorganisms 2023, 11(8), 2029; https://doi.org/10.3390/microorganisms11082029 - 07 Aug 2023

Viewed by 720

Abstract

The unicellular, parasitic fungi of the phylum Sanchytriomycota (sanchytrids) were discovered a few years ago. These unusual chytrid-like fungi parasitize algae. The zoospores of the species of the phylum contain an extremely long kinetosome composed of microtubular singlets or doublets and a non-motile [...] Read more.

The unicellular, parasitic fungi of the phylum Sanchytriomycota (sanchytrids) were discovered a few years ago. These unusual chytrid-like fungi parasitize algae. The zoospores of the species of the phylum contain an extremely long kinetosome composed of microtubular singlets or doublets and a non-motile pseudocilium (i.e., a reduced posterior flagellum). Fungi provide an ideal opportunity to test and confirm the correlation between the occurrence of flagellar proteins (the ciliome) and that of the eukaryotic cilium/flagellum since the flagellum occurs in the early-branching phyla and not in terrestrial fungi. Tubulin polymerization promoting protein (TPPP)-like proteins, which contain a p25alpha domain, were also suggested to belong to the ciliome and are present in flagellated fungi. Although sanchytrids have lost many of the flagellar proteins, here it is shown that they possess a DNA sequence possibly encoding long (animal-type) TPPP, but not the fungal-type one characteristic of chytrid fungi. Phylogenetic analysis of p25alpha domains placed sanchytrids into a sister position to Blastocladiomycota, similarly to species phylogeny, with maximal support. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 1080 KiB

Open AccessArticle

Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin

by Carine Laurence Yehouenou, Bert Bogaerts, Kevin Vanneste, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Arsène A. Kpangon, Dissou Affolabi, Anne Simon, Francis Moise Dossou and Olivia Dalleur

Microorganisms 2023, 11(8), 1954; https://doi.org/10.3390/microorganisms11081954 - 31 Jul 2023

Cited by 1 | Viewed by 1344

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern, with a considerable impact on patients’ health, and substantial healthcare costs. In this study, patients and healthcare workers (HCWs) from six public hospitals in Benin were screened for MRSA. Strains were identified as [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern, with a considerable impact on patients’ health, and substantial healthcare costs. In this study, patients and healthcare workers (HCWs) from six public hospitals in Benin were screened for MRSA. Strains were identified as MRSA using conventional microbiological methods in Benin, and confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in Belgium. Whole-genome sequencing (WGS) was used on the confirmed MRSA isolates, to characterize their genomic content and study their relatedness. Amongst the 305 isolates (304 wound swabs and 61 nasal swabs) that were collected from patients and HCWs, we detected 32 and 15 cases of MRSA, respectively. From this collection, 27 high-quality WGS datasets were obtained, which carried numerous genes and mutations associated with antimicrobial resistance. The mecA gene was detected in all the sequenced isolates. These isolates were assigned to five sequence types (STs), with ST8 (55.56%, n = 15/27), ST152 (18.52%, n = 5/27), and ST121 (18.52%, n = 5/27) being the most common. These 27 isolates carried multiple virulence genes, including the genes encoding the Panton–Valentine leukocidin toxin (48.15%, n = 13/27), and the tst gene (29.63%, n = 8/27), associated with toxic shock syndrome. This study highlights the need to implement a multimodal strategy for reducing the risk of the cross-transmission of MRSA in hospitals. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 1512 KiB

Open AccessArticle

Assessment of Infection Prevalence and Intensity of Disease-Causing Parasitic Protozoans Perkinsus marinus and Haplosporidium nelsoni in Georgia Oysters

by Sarah Batchelor, J. Scott Harrison, Stephen E. Greiman, Laura M. Treible and John M. Carroll

Microorganisms 2023, 11(7), 1808; https://doi.org/10.3390/microorganisms11071808 - 14 Jul 2023

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Abstract

Eastern oysters, Crassostrea virginica, are ecologically and economically important coastal species which provide a commercially valuable food product while also improving water quality through filtration, protecting shorelines, and providing habitat. The protozoan parasites Perkinsus marinus and Haplosporidium nesloni commonly infect oysters along [...] Read more.

Eastern oysters, Crassostrea virginica, are ecologically and economically important coastal species which provide a commercially valuable food product while also improving water quality through filtration, protecting shorelines, and providing habitat. The protozoan parasites Perkinsus marinus and Haplosporidium nesloni commonly infect oysters along the United States Atlantic and Gulf coasts and have been linked to poor oyster health and mass mortality events. In this study, wild oysters were collected from multiple reefs within four tidal creeks along the coast of Georgia to investigate P. marinus and H. nelsoni prevalence and intensity, their potential impact on oyster health, and identify possible drivers of the parasites. A second study occurred on four sites on Sapelo Island, Georgia, with continuous water quality monitoring data to further elucidate potential drivers. Oyster density and condition index, a proxy for health, were measured, and parasites were quantified using a TaqMan probe based quantitative real-time PCR within gill tissue. Real-time PCR showed that 86% of oysters tested were infected by one or both parasites in the coast-wide survey, and 93% of oysters from Sapelo Island were also infected by one or both parasites. Prevalence and infection intensity for both P. marinus and H. nelsoni varied across sites. Overall impacts on oysters were complex—intensity was not linked to oyster metrics in the coastwide study, but oyster condition was negatively correlated with P. marinus prevalence in the Sapelo Island study. Several relationships between both parasites and water quality parameters were identified, providing valuable information about potential drivers that should be investigated further. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 2070 KiB

Open AccessArticle

Minimal Inhibitory Concentrations of Thymol and Carvacrol: Toward a Unified Statistical Approach to Find Common Trends

by Barbara Speranza, Antonio Bevilacqua, Daniela Campaniello, Clelia Altieri, Maria Rosaria Corbo and Milena Sinigaglia

Microorganisms 2023, 11(7), 1774; https://doi.org/10.3390/microorganisms11071774 - 07 Jul 2023

Cited by 3 | Viewed by 1187

Abstract

Thymol and carvacrol are some of the most important and used components of Essential oils (EOs); they are widely studied, and there are much data available in the literature. Their Minimal Inhibitory Concentration (MIC) values found in the literature from 2005 to present [...] Read more.

Thymol and carvacrol are some of the most important and used components of Essential oils (EOs); they are widely studied, and there are much data available in the literature. Their Minimal Inhibitory Concentration (MIC) values found in the literature from 2005 to present were used to assess the bioactivity toward yeasts, molds, Gram-positive bacteria, and Gram-negative bacteria, as well as on some bacterial species/serotypes (Salmonella sp., Escherichia coli, E. coli O157:H7, lactic acid bacteria, Listeria monocytogenes, Staphylococcus aureus, S. epidermidis, etc.) to find possible common trends or differences between the two compounds and among the tested species. The results were quite interesting and pointed out that there is a common range for the MIC of thymol and carvacrol for some bacterial species (150–400 mg/L), with some exceptions to this generalized statement. In addition, the statistics pointed out that bacteria could experience homogeneous (S. epidermidis, E. coli O157:H7) or heterogeneous trends (for example, Salmonella sp.) depending on the existence of possible sub-species or different experimental set-ups. Moreover, this paper suggests that there are some drawbacks and issues that should be solved for the effective use of EOs, which are the strong variability among the microorganisms and the lack of standard protocols and reference strains. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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24 pages, 27751 KiB

Open AccessArticle

Mucus-Trap-Assisted Feeding Is a Common Strategy of the Small Mixoplanktonic Prorocentrum pervagatum and P. cordatum (Prorocentrales, Dinophyceae)

by Urban Tillmann, Aditee Mitra, Kevin J. Flynn and Michaela E. Larsson

Microorganisms 2023, 11(7), 1730; https://doi.org/10.3390/microorganisms11071730 - 01 Jul 2023

Cited by 1 | Viewed by 1778

Abstract

Prorocentrum comprises a diverse group of bloom-forming dinophytes with a worldwide distribution. Although photosynthetic, mixoplanktonic phagotrophy has also been described. Recently, the small P. cf. balticum was shown to use a remarkable feeding strategy by crafting globular mucus traps to capture and immobilize [...] Read more.

Prorocentrum comprises a diverse group of bloom-forming dinophytes with a worldwide distribution. Although photosynthetic, mixoplanktonic phagotrophy has also been described. Recently, the small P. cf. balticum was shown to use a remarkable feeding strategy by crafting globular mucus traps to capture and immobilize potential prey. Here we present evidence showing that two additional related species, the recently described P. pervagatum and the cosmopolitan bloom-forming P. cordatum, also produce large (80–120 µm) mucus traps supporting their mixoplanktonic activity. Prey are captured within the traps either through passive entanglement upon contact with the outside surface, or through active water movement created by rotating Prorocentrum cells eddying particles to the inside surface where trapped live prey cells became immobilized. Entrapment in mucus assisted deployment into the prey of a peduncle extruded from the apical area of the Prorocentrum cell. Phagotrophy by P. pervagatum supported faster growth compared to unfed controls and time series quantification of food vacuoles revealed ingestion rates of ca. 10–12 Teleaulax prey cells day⁻¹. Model calculations show clear advantages of deploying a mucus trap for increasing prey encounter rates. This study demonstrates that the large size and immobilization properties of mucus traps successfully increase the availability of prey for small Prorocentrum species, whose peduncle feeding mode impedes consumption of actively moving prey, and that this strategy is common among certain clades of small planktonic Prorocentrum species. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 2216 KiB

Open AccessArticle

Evaluation of Antibacterial Activity of Selenium Nanoparticles against Food-Borne Pathogens

by Qunying Yuan, Rong Xiao, Mojetoluwa Afolabi, Manjula Bomma and Zhigang Xiao

Microorganisms 2023, 11(6), 1519; https://doi.org/10.3390/microorganisms11061519 - 07 Jun 2023

Cited by 7 | Viewed by 1808

Abstract

Selenium is an essential micronutrient for all mammals and plays an important role in maintaining human physiological functions. Selenium nanoparticles (SeNPs) have been shown to demonstrate antioxidant and antimicrobial activity. The objective of this study was to explore whether SeNPs have the potential [...] Read more.

Selenium is an essential micronutrient for all mammals and plays an important role in maintaining human physiological functions. Selenium nanoparticles (SeNPs) have been shown to demonstrate antioxidant and antimicrobial activity. The objective of this study was to explore whether SeNPs have the potential to be used as food preservatives with which to reduce food spoilage. SeNPs were synthesized through ascorbic acid reduction of sodium selenite (Na₂SeO₃) in the presence of bovine serum albumin (BSA) as a capping and stabilizing agent. The chemically synthesized SeNPs had a spherical conformation with an average diameter of 22.8 ± 4.7 nm. FTIR analysis confirmed that the nanoparticles were covered with BSA. We further tested the antibacterial activity of these SeNPs against ten common food-borne bacteria. A colony-forming unit assay showed that SeNPs exhibited inhibition on the growth of Listeria Monocytogens (ATCC15313) and Staphylococcus epidermidis (ATCC 700583) starting at 0.5 µg/mL, but higher concentrations were required to slow down the growth of Staphylococcus aureus (ATCC12600), Vibrio alginolyticus (ATCC 33787), and Salmonella enterica (ATCC19585). No inhibition was observed on the growth of the other five test bacteria in our study. Our data suggested that the chemically synthesized SeNPs were able to inhibit the growth of some food-borne bacteria. The size and shape of SeNPs, method of synthesis, and combination of SeNPs with other food preservatives should be considered when SeNPs are to be used for the prevention of bacteria-mediated food spoilage. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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24 pages, 42712 KiB

Open AccessArticle

The Tripartite Lichen Ricasolia virens: Involvement of Cyanobacteria and Bacteria in Its Morphogenesis

by Francisco J. García-Breijo, Arantzazu Molins, José Reig-Armiñana and Eva Barreno

Microorganisms 2023, 11(6), 1517; https://doi.org/10.3390/microorganisms11061517 - 07 Jun 2023

Cited by 1 | Viewed by 1501

Abstract

Ricasolia virens is an epiphytic lichen-forming fungus mainly distributed in Western Europe and Macaronesia in well-structured forests with ecological continuity that lack eutrophication. It is considered to be threatened or extinct in many territories in Europe (IUCN). Despite its biological and ecological relevance, [...] Read more.

Ricasolia virens is an epiphytic lichen-forming fungus mainly distributed in Western Europe and Macaronesia in well-structured forests with ecological continuity that lack eutrophication. It is considered to be threatened or extinct in many territories in Europe (IUCN). Despite its biological and ecological relevance, studies on this taxon are scarce. The thalli are tripartite, and the mycobiont has a simultaneous symbiotic relationship with cyanobacteria and green microalgae, which represent interesting models to analyse the strategies and adaptations resulting from the interactions of lichen symbionts. The present study was designed to contribute to a better understanding of this taxon, which has shown a clear decline over the last century. The symbionts were identified by molecular analysis. The phycobiont is Symbiochloris reticulata, and the cyanobionts (Nostoc) are embedded in internal cephalodia. Light, transmission electron and low-temperature scanning microscopy techniques were used to investigate the thallus anatomy, ultrastructure of microalgae and ontogeny of pycnidia and cephalodia. The thalli are very similar to its closest relative, Ricasolia quercizans. The cellular ultrastructure of S. reticulata by TEM is provided. Non-photosynthetic bacteria located outside the upper cortex are introduced through migratory channels into the subcortical zone by the splitting of fungal hyphae. Cephalodia were very abundant, but never as external photosymbiodemes. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 8862 KiB

Open AccessArticle

Sessile Lifestyle Offers Protection against Copper Stress in Saccharolobus solfataricus

by Alejandra Recalde, Gabriela González-Madrid, José Acevedo-López and Carlos A. Jerez

Microorganisms 2023, 11(6), 1421; https://doi.org/10.3390/microorganisms11061421 - 27 May 2023

Cited by 2 | Viewed by 1321

Abstract

Some archaea from the genus Sulfolobus are important for bioleaching of copper, where metal resistant microorganisms are required. Biofilm generation is one of the ways microorganisms cope with some stimuli in nature, including heavy metals. The response to external factors, particularly in the [...] Read more.

Some archaea from the genus Sulfolobus are important for bioleaching of copper, where metal resistant microorganisms are required. Biofilm generation is one of the ways microorganisms cope with some stimuli in nature, including heavy metals. The response to external factors, particularly in the biofilm form of life, is still underexplored in archaea. To explore how model thermoacidophilic archaeon Saccharolobus solfataricus faces copper stress during this lifestyle, changes in biofilms were studied using crystal violet staining, confocal fluorescence microscopy, and qPCR approaches. It was found that biofilm formation reached a maximum at 0.5 mM Cu, before starting to decrease at higher metal concentrations. The morphology of biofilms at 0.5 mM Cu was observed to be different, displaying lower thickness, different sugar patterns, and higher amounts of cells compared to standard growing conditions. Furthermore, copA, which is responsive to intracellular Cu concentration, was downregulated in biofilm cells when compared with planktonic cells exposed to the same metal concentration. The latest results suggests that cells in biofilms are less exposed to Cu than those in planktonic culture. In a PolyP-deficient strain, Cu was not able to induce biofilm formation at 0.5 mM. In summary, the findings reported here suggest that the biofilm form of life confers S. solfataricus advantages to face stress caused by Cu.Biofilm formation remains a relatively unexplored topic in archaeal research. Therefore, this knowledge in model organisms such as S. solfataricus, and how they use it to face stress, could be of great importance to engineer organisms with improved capabilities to be applied in biotechnological processes, such as bioleaching of metals. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 7597 KiB

Open AccessArticle

RNase Y Autoregulates Its Synthesis in Bacillus subtilis

by Anna Korobeinikova, Soumaya Laalami, Clément Berthy and Harald Putzer

Microorganisms 2023, 11(6), 1374; https://doi.org/10.3390/microorganisms11061374 - 24 May 2023

Viewed by 1068

Abstract

The instability of messenger RNA is crucial to the control of gene expression. In Bacillus subtilis, RNase Y is the major decay-initiating endoribonuclease. Here, we show how this key enzyme regulates its own synthesis by modulating the longevity of its mRNA. Autoregulation [...] Read more.

The instability of messenger RNA is crucial to the control of gene expression. In Bacillus subtilis, RNase Y is the major decay-initiating endoribonuclease. Here, we show how this key enzyme regulates its own synthesis by modulating the longevity of its mRNA. Autoregulation is achieved through cleavages in two regions of the rny (RNase Y) transcript: (i) within the first ~100 nucleotides of the open reading frame, immediately inactivating the mRNA for further rounds of translation; (ii) cleavages in the rny 5′ UTR, primarily within the 5′-terminal 50 nucleotides, creating entry sites for the 5′ exonuclease J1 whose progression is blocked around position −15 of the rny mRNA, potentially by initiating ribosomes. This links the functional inactivation of the transcript by RNase J1 to translation efficiency, depending on the ribosome occupancy at the translation initiation site. By these mechanisms, RNase Y can initiate degradation of its own mRNA when the enzyme is not occupied with degradation of other RNAs and thus prevent its overexpression beyond the needs of RNA metabolism. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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22 pages, 4394 KiB

Open AccessArticle

In Vitro Characterization and Antiviral Susceptibility of Ophidian Serpentoviruses

by Steven B. Tillis, Camille Holt, Spencer Havens, Tracey D. Logan, Justin G. Julander and Robert J. Ossiboff

Microorganisms 2023, 11(6), 1371; https://doi.org/10.3390/microorganisms11061371 - 24 May 2023

Cited by 1 | Viewed by 1929

Abstract

Ophidian serpentoviruses, positive-sense RNA viruses in the order Nidovirales, are important infectious agents of both captive and free-ranging reptiles. Although the clinical significance of these viruses can be variable, some serpentoviruses are pathogenic and potentially fatal in captive snakes. While serpentoviral diversity [...] Read more.

Ophidian serpentoviruses, positive-sense RNA viruses in the order Nidovirales, are important infectious agents of both captive and free-ranging reptiles. Although the clinical significance of these viruses can be variable, some serpentoviruses are pathogenic and potentially fatal in captive snakes. While serpentoviral diversity and disease potential are well documented, little is known about the fundamental properties of these viruses, including their potential host ranges, kinetics of growth, environmental stability, and susceptibility to common disinfectants and viricides. To address this, three serpentoviruses were isolated in culture from three unique PCR-positive python species: Ball python (Python regius), green tree python (Morelia viridis), and Stimson’s python (Antaresia stimsoni). A median tissue culture infectious dose (TCID₅₀) was established to characterize viral stability, growth, and susceptibility. All isolates showed an environmental stability of 10–12 days at room temperature (20 °C). While all three viruses produced variable peak titers on three different cell lines when incubated at 32 °C, none of the viruses detectably replicated at 35 °C. All viruses demonstrated a wide susceptibility to sanitizers, with 10% bleach, 2% chlorhexidine, and 70% ethanol inactivating the virus in one minute and 7% peroxide and a quaternary ammonium solution within three minutes. Of seven tested antiviral agents, remdesivir, ribavirin, and NITD-008, showed potent antiviral activity against the three viruses. Finally, the three isolates successfully infected 32 unique tissue culture cell lines representing different diverse reptile taxa and select mammals and birds as detected by epifluorescent immunostaining. This study represents the first characterization of in vitro properties of growth, stability, host range, and inactivation for a serpentovirus. The reported results provide the basis for procedures to mitigate the spread of serpentoviruses in captive snake colonies as well as identify potential non-pharmacologic and pharmacologic treatment options for ophidian serpentoviral infections. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 560 KiB

Open AccessArticle

Plasmids Increase the Competitive Ability of Plasmid-Bearing Cells Even When Transconjugants Are Poor Donors, as Shown by Computer Simulations

by João S. Rebelo, Célia P. F. Domingues, Teresa Nogueira and Francisco Dionisio

Microorganisms 2023, 11(5), 1238; https://doi.org/10.3390/microorganisms11051238 - 08 May 2023

Cited by 2 | Viewed by 1642

Abstract

Bacterial cells often suffer a fitness cost after conjugative plasmids’ entry because these cells replicate slower than plasmid-free cells. Compensatory mutations may appear after tens of or a few hundred generations, reducing or eliminating this cost. A previous work based on a mathematical [...] Read more.

Bacterial cells often suffer a fitness cost after conjugative plasmids’ entry because these cells replicate slower than plasmid-free cells. Compensatory mutations may appear after tens of or a few hundred generations, reducing or eliminating this cost. A previous work based on a mathematical model and computer simulations has shown that plasmid-bearing cells already adapted to the plasmid may gain a fitness advantage when plasmids transfer into neighboring plasmid-free cells because these cells are still unadapted to the plasmid. These slow-growing transconjugants use fewer resources, which can benefit donor cells. However, opportunities for compensatory mutations in transconjugants increase if these cells become numerous (through replication or conjugation). Moreover, transconjugants also gain an advantage when transferring the plasmid, but the original donors may be too distant from conjugation events to gain an advantage. To understand which consequence prevails, we performed further computer simulations allowing versus banning transfer from transconjugants. The advantage to donors is higher if transconjugants do not transfer plasmids, mainly when donors are rare and when the plasmid transfer rate (from donors) is high. These results show that conjugative plasmids are efficient biological weapons even if the transconjugant cells are poor plasmid donors. After some time, conjugative plasmids gain other host-benefit genes, such as virulence and drug-resistance. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 3341 KiB

Open AccessArticle

In-Silico Analysis Highlights the Existence in Members of Burkholderia cepacia Complex of a New Class of Adhesins Possessing Collagen-like Domains

by Ricardo Estevens, Dalila Mil-Homens and Arsenio M. Fialho

Microorganisms 2023, 11(5), 1118; https://doi.org/10.3390/microorganisms11051118 - 25 Apr 2023

Viewed by 1212

Abstract

Burkholderia cenocepacia is a multi-drug-resistant lung pathogen. This species synthesizes various virulence factors, among which cell-surface components (adhesins) are critical for establishing the contact with host cells. This work in the first part focuses on the current knowledge about the adhesion molecules described [...] Read more.

Burkholderia cenocepacia is a multi-drug-resistant lung pathogen. This species synthesizes various virulence factors, among which cell-surface components (adhesins) are critical for establishing the contact with host cells. This work in the first part focuses on the current knowledge about the adhesion molecules described in this species. In the second part, through in silico approaches, we perform a comprehensive analysis of a group of unique bacterial proteins possessing collagen-like domains (CLDs) that are strikingly overrepresented in the Burkholderia species, representing a new putative class of adhesins. We identified 75 CLD-containing proteins in Burkholderia cepacia complex (Bcc) members (Bcc-CLPs). The phylogenetic analysis of Bcc-CLPs revealed the evolution of the core domain denominated “Bacterial collagen-like, middle region”. Our analysis remarkably shows that these proteins are formed by extensive sets of compositionally biased residues located within intrinsically disordered regions (IDR). Here, we discuss how IDR functions may increase their efficiency as adhesion factors. Finally, we provided an analysis of a set of five homologs identified in B. cenocepacia J2315. Thus, we propose the existence in Bcc of a new type of adhesion factors distinct from the described collagen-like proteins (CLPs) found in Gram-positive bacteria. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 3120 KiB

Open AccessArticle

Grass–Legume Mixture with Rhizobium Inoculation Enhanced the Restoration Effects of Organic Fertilizer

by Haijuan Zhang, Kaifu Zheng, Songsong Gu, Yingcheng Wang, Xueli Zhou, Huilin Yan, Kun Ma, Yangan Zhao, Xin Jin, Guangxin Lu and Ye Deng

Microorganisms 2023, 11(5), 1114; https://doi.org/10.3390/microorganisms11051114 - 25 Apr 2023

Cited by 1 | Viewed by 1265

Abstract

The establishment of artificial grassland is crucial in restoring degraded grassland and resolving the forage–livestock conflict, and the application of organic fertilizer and complementary seeding of grass–legume mixture are effective methods to enhance grass growth in practice. However, its mechanism behind the underground [...] Read more.

The establishment of artificial grassland is crucial in restoring degraded grassland and resolving the forage–livestock conflict, and the application of organic fertilizer and complementary seeding of grass–legume mixture are effective methods to enhance grass growth in practice. However, its mechanism behind the underground is largely unclear. Here, by utilizing organic fertilizer in the alpine region of the Qinghai–Tibet Plateau, this study assessed the potential of grass–legume mixtures with and without the inoculation of Rhizobium for the restoration of degraded grassland. The results demonstrated that the application of organic fertilizer can increase the forage yield and soil nutrient contents of degraded grassland, and they were 0.59 times and 0.28 times higher than that of the control check (CK), respectively. The community composition and structure of soil bacteria and fungi were also changed by applying organic fertilizer. Based on this, the grass–legume mixture inoculated with Rhizobium can further increase the contribution of organic fertilizer to soil nutrients and thus enhance the restoration effects for degraded artificial grassland. Moreover, the application of organic fertilizer significantly increased the colonization of gramineous plant by native mycorrhizal fungi, which was ~1.5–2.0 times higher than CK. This study offers a basis for the application of organic fertilizer and grass–legume mixture in the ecological restoration of degraded grassland. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 1827 KiB

Open AccessArticle

In Vitro Probiotic Properties and In Vivo Anti-Ageing Effects of Lactoplantibacillus plantarum PFA2018AU Strain Isolated from Carrots on Caenorhabditis elegans

by Laura Pompa, Arianna Montanari, Alberta Tomassini, Michele Maria Bianchi, Walter Aureli, Alfredo Miccheli, Daniela Uccelletti and Emily Schifano

Microorganisms 2023, 11(4), 1087; https://doi.org/10.3390/microorganisms11041087 - 21 Apr 2023

Cited by 2 | Viewed by 2097

Abstract

Lactic acid bacteria (LAB) share and provide several beneficial effects on human health, such as the release of bioactive metabolites, pathogen competition, and immune stimulation. The two major reservoirs of probiotic microorganisms are the human gastro-intestinal tract and fermented dairy products. However, other [...] Read more.

Lactic acid bacteria (LAB) share and provide several beneficial effects on human health, such as the release of bioactive metabolites, pathogen competition, and immune stimulation. The two major reservoirs of probiotic microorganisms are the human gastro-intestinal tract and fermented dairy products. However, other sources, such as plant-based foods, represent important alternatives thanks to their large distribution and nutritive value. Here, the probiotic potential of autochthonous Lactiplantibacillus plantarum PFA2018AU, isolated from carrots harvested in Fucino highland, Abruzzo (Italy), was investigated through in vitro and in vivo approaches. The strain was sent to the biobank of Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna in Italy for the purpose of patent procedures under the Budapest Treaty. The isolate showed high survival capability under in vitro simulated gastro-intestinal conditions, antibiotic susceptibility, hydrophobicity, aggregation, and the ability to inhibit the in vitro growth of Salmonella enterica serovar Typhimurium, Listeria monocytogenes, Pseudomonas aeruginosa, and Staphylococcus aureus pathogens. Caenorhabditis elegans was used as the in vivo model in order to analyse prolongevity and anti-ageing effects. L. plantarum PFA2018AU significantly colonised the gut of the worms, extended their lifespan, and stimulated their innate immunity. Overall, these results showed that autochthonous LAB from vegetables, such as carrots, have functional features that can be considered novel probiotic candidates. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 1411 KiB

Open AccessArticle

Nitrobenzoates and Nitrothiobenzoates with Activity against M. tuberculosis

by João P. Pais, Olha Antoniuk, Raquel Freire, David Pires, Emília Valente, Elsa Anes and Luis Constantino

Microorganisms 2023, 11(4), 969; https://doi.org/10.3390/microorganisms11040969 - 08 Apr 2023

Viewed by 1124

Abstract

Esters of weak acids have shown improved antimycobacterial activity over the corresponding free acids and nitro benzoates in particular have previously shown to have a very intriguing activity. To expand the potential of nitro-derivatives of benzoic acid as antimycobacterial drugs and explore the [...] Read more.

Esters of weak acids have shown improved antimycobacterial activity over the corresponding free acids and nitro benzoates in particular have previously shown to have a very intriguing activity. To expand the potential of nitro-derivatives of benzoic acid as antimycobacterial drugs and explore the effects of various structural features on the activity of these compounds, we have obtained a library of 64 derivatives containing esters and thioesters of benzoates and studied their activity against M. tuberculosis, the stability of the compounds, their activation by mycobacterial enzymes and the potential cytotoxicity against human monocytic THP-1 cell line. Our results showed that the most active compounds are those with an aromatic nitro substitution, with the 3,5-dinitro esters series being the most active. Also, the greater antitubercular activity for the nitro derivatives was shown to be unrelated to their pKa values or hydrolysis rates. Given the conventional relationship between nitro-containing substances and toxicity, one might anticipate that the great antimicrobial activity of nitro compounds would be associated with high toxicity; yet, we have not found such a relationship. The nitrobenzoate scaffold, particularly the 3,5-dinitrobenzoate scaffold, merits further investigation, because it has the potential to generate future antimycobacterial agents with improved activity. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 2478 KiB

Open AccessArticle

Selecting 16S rRNA Primers for Microbiome Analysis in a Host–Microbe System: The Case of the Jellyfish Rhopilema nomadica

by Noga Barak, Eduard Fadeev, Vera Brekhman, Dikla Aharonovich, Tamar Lotan and Daniel Sher

Microorganisms 2023, 11(4), 955; https://doi.org/10.3390/microorganisms11040955 - 06 Apr 2023

Cited by 2 | Viewed by 2421

Abstract

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when [...] Read more.

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host–microbe associations. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 2149 KiB

Open AccessArticle

Saccharopolyspora sp. NFXS83 in Marine Biotechnological Applications: From Microalgae Growth Promotion to the Production of Secondary Metabolites

by Constança D. F. Bertrand, Rodrigo Martins, Francisco Quintas-Nunes, Pedro Reynolds-Brandão, Maria T. B. Crespo and Francisco X. Nascimento

Microorganisms 2023, 11(4), 902; https://doi.org/10.3390/microorganisms11040902 - 30 Mar 2023

Viewed by 1623

Abstract

Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a [...] Read more.

Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a potential source of these compounds. This study reports the characterization and genomic analysis of Saccharopolyspora sp. NFXS83, a marine bacterium isolated from seawater from the Sado estuary in Portugal. The NFXS83 strain produced multiple functional and stable extracellular enzymes under high-salt conditions, showed the ability to synthesize auxins such as indole-3-acetic acid, and produced diffusible secondary metabolites capable of inhibiting the growth of Staphylococcus aureus. Furthermore, when Phaeodactylum tricornutum was co-cultivated with strain NFXS83 a significant increase in microalgae cell count, cell size, auto-fluorescence, and fucoxanthin content was observed. Detailed analysis revealed the presence of clusters involved in the production of various secondary metabolites, including extracellular enzymes, antimicrobial compounds, terpenes, and carotenoids in the genome of strain NFXS83. Ultimately, these findings indicate that Saccharopolyspora sp. NFXS83 has a significant potential for a wide range of marine biotechnological applications. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 2099 KiB

Open AccessArticle

Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications

by Alessandra Fontana, Irene Falasconi, Paolo Bellassi, Elisabetta Fanfoni, Edoardo Puglisi and Lorenzo Morelli

Microorganisms 2023, 11(3), 587; https://doi.org/10.3390/microorganisms11030587 - 25 Feb 2023

Cited by 1 | Viewed by 2319

Abstract

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their [...] Read more.

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides). Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 1658 KiB

Open AccessArticle

Effects of Two Feeding Patterns on Growth Performance, Rumen Fermentation Parameters, and Bacterial Community Composition in Yak Calves

by Qin Li, Yan Tu, Tao Ma, Kai Cui, Jianxin Zhang, Qiyu Diao and Yanliang Bi

Microorganisms 2023, 11(3), 576; https://doi.org/10.3390/microorganisms11030576 - 24 Feb 2023

Cited by 3 | Viewed by 1383

Abstract

The health of young ruminants is highly dependent on early rumen microbial colonization. In this study, the effects of milk replacer on growth performance, rumen fermentation, and the rumen microflora in yak calves were evaluated. Sixty yak calves (body weight = 22.5 ± [...] Read more.

The health of young ruminants is highly dependent on early rumen microbial colonization. In this study, the effects of milk replacer on growth performance, rumen fermentation, and the rumen microflora in yak calves were evaluated. Sixty yak calves (body weight = 22.5 ± 0.95 kg, age = 30 ± 1 d) were assigned to the CON group (breastfed) or TRT group (milk replacer fed) and evaluated over 120 d. At 120 d, ruminal fluid samples were collected from 14 calves and then conducted for rumen fermentation and microbiota analyses. There was no difference in growth performance; however, calf survival was higher in the TRT group than in the CON group. The concentration of total volatile fatty acids and the molar proportion of butyric acid and lactic acid were increased with milk replacer feed in the TRT group (p < 0.05), but iso-valeric acid concentration was highest in the CON group (p < 0.05). Firmicutes and Bacteroidetes were the most dominant phyla in the CON and TRT groups, respectively. In the TRT group, Bacteroidetes, Prevotellaceae, Bacteroidia, Bacteroidetes, and Prevotella_1 were the dominant flora in the rumen of calves. The relative abundances of various taxa were correlated with rumen fermentation parameters; the relative abundance of Quinella and iso-butyrate levels were positively correlated (r = 0.57). The relative abundances of the Christensenellaceae_R-7_group and A/P were positively correlated (r = 0.57). In summary, milk replacer is conducive to the development of the rumen microflora, the establishment of rumen fermentation function, and the implementation of early weaning in yaks. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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7 pages, 1050 KiB

Open AccessCommunication

Extraction Bottleneck in the Diagnosis of SARS-CoV-2: Evaluation of an Alternative Protocol Derived from Veterinary Use

by Paolo Bottino, Elisa Zanotto, Francesca Sidoti, Lisa Pastrone, Roberto Piva, Elisabetta Mereu, Cristina Costa and Rossana Cavallo

Microorganisms 2023, 11(2), 535; https://doi.org/10.3390/microorganisms11020535 - 20 Feb 2023

Cited by 1 | Viewed by 1109

Abstract

The COVID-19 pandemic represented a challenge for health-care systems, and a major bottleneck in SARS-CoV-2 diagnosis was the unavailability of extraction reagents. To overcome this limitation, we performed a comparative analysis to evaluate the performance of an alternative extraction protocol derived from veterinary [...] Read more.

The COVID-19 pandemic represented a challenge for health-care systems, and a major bottleneck in SARS-CoV-2 diagnosis was the unavailability of extraction reagents. To overcome this limitation, we performed a comparative analysis to evaluate the performance of an alternative extraction protocol derived from veterinary use adapted to an open robotic platform (Testing method). A total of 73 nasopharyngeal swabs collected for diagnosis of SARS-CoV-2 infection were simultaneously extracted with the Testing protocol and the laboratory Standard of Care in order to assess the performance of the first one. The Cohen’s coefficient between both procedures was excellent (K Value = 0.955). Analysis of cycle threshold and linear regression showed a significant correlation between the two methods for each tested genetic target. Although validated for veterinary applications, the Testing method showed excellent performances in RNA extraction, with several advantages: lower sample input volume, the possibility to overcome the lack of deep-well plates and adaptability to robotic liquid handlers. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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18 pages, 6082 KiB

Open AccessArticle

Bio-Converted Spirulina for Nutraceutical Chewing Candy Formulations Rich in L-Glutamic and Gamma-Aminobutyric Acids

by Elena Bartkiene, Ernesta Tolpeznikaite, Dovile Klupsaite, Vytaute Starkute, Vadims Bartkevics, Anna Skrastina, Romans Pavlenko, Ernestas Mockus, Vita Lele, Gabija Batkeviciute, Ausrine Budrikyte, Rusne Janulyte, Ieva Jomantaite, Auguste Kybartaite, Karolina Knystautaite, Aiste Valionyte, Romas Ruibys and João Miguel Rocha

Microorganisms 2023, 11(2), 441; https://doi.org/10.3390/microorganisms11020441 - 09 Feb 2023

Cited by 3 | Viewed by 2340

Abstract

This study aimed at evaluating changes of microalgae Spirulina during its fermentation with Lactiplantibacillus plantarum No. 122 strain, and further at incorporating Spirulina bio-converted for nutraceuticals rich in L-glutamic (L-Glu) and gamma-aminobutyric acids (GABA) into sucrose-free chewing candy (gummy) preparations. Fermented Spirulina had [...] Read more.

This study aimed at evaluating changes of microalgae Spirulina during its fermentation with Lactiplantibacillus plantarum No. 122 strain, and further at incorporating Spirulina bio-converted for nutraceuticals rich in L-glutamic (L-Glu) and gamma-aminobutyric acids (GABA) into sucrose-free chewing candy (gummy) preparations. Fermented Spirulina had higher b* (yellowness) coordinates than untreated (non-fermented), and fermentation duration (24 and 48 h) had a statistically significant effect on colour coordinates. The highest contents of L-glutamic and gamma-aminobutyric acids (4062 and 228.6 mg/kg, respectively) were found in 24 and 48 h-fermented Spirulina, respectively. Fermentation increased the content of saturated fatty acids and omega-3 in Spirulina, while monounsaturated fatty acids and omega-6 were reduced. The addition of fermented Spirulina (FSp) significantly affected hardness, decreased lightness and yellowness, and increased the greenness of chewing candies. All chewing candy samples (with xylitol) prepared with 3 and 5 g of FSp and 0.2 µL of Citrus paradise essential oil received the highest scores for overall acceptability, and the highest intensity (0.052) of emotion “happy” was elicited by the sample group containing xylitol, agar, ascorbic acid, 3 g of FSp, and 0.1 µL of Mentha spicata essential oil. As an outcome of this research, one may conclude that fermented Spirulina has significant potential as an innovative ingredient in the production of healthier sucrose-free nutraceutical chewing candies. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 569 KiB

Open AccessArticle

Incidence and Risk Factors for Clostridioides difficile Infections in Non-COVID and COVID-19 Patients: Experience from a Tertiary Care Hospital

by Ljiljana Markovic-Denic, Vladimir Nikolic, Borislav Toskovic, Marija Brankovic, Bogdan Crnokrak, Viseslav Popadic, Aleksandra Radojevic, Dusan Radovanovic and Marija Zdravkovic

Microorganisms 2023, 11(2), 435; https://doi.org/10.3390/microorganisms11020435 - 08 Feb 2023

Cited by 1 | Viewed by 1526

Abstract

(1) Background: The aim of this study was to assess the incidence and the risk factors for healthcare-associated Clostridioides difficile infection (HA-CDI) in patients with COVID-19 and without this infection. (2) Methods: A single-center, prospective observational study was conducted at the University Clinical [...] Read more.

(1) Background: The aim of this study was to assess the incidence and the risk factors for healthcare-associated Clostridioides difficile infection (HA-CDI) in patients with COVID-19 and without this infection. (2) Methods: A single-center, prospective observational study was conducted at the University Clinical Hospital Center in Belgrade, Serbia, from January 2019 to December 2021. The entire hospital was a COVID-dedicated hospital for 12 months during the study period. The incidence density rates and risk factors for HA-CDI in patients with and without COVID-19 are presented. (3) Results: The incidence rates of HA-CDIs were three times higher in patients with COVID-19. The HA-CDI–COVID-patients were younger (69.9 ± 12.6 vs. 72.5 ± 11.6; p = 0.017), admitted from another hospital (20.5% vs. 2.9; p < 0.001), had antimicrobial therapy before CDI (99.1% vs. 91.3%, p < 0.001), received two or more antibiotics (p = 0.030) during a longer period (p = 0.035), received proton pump inhibitors (95.9% vs. 50.0%, p < 0.001) during a longer period (p = 0.012) and steroids (32.8% vs. 20.4%, p < 0.001). During the last month before their current hospitalization, a higher percentage of patients without COVID-19 disease were hospitalized in our hospital (p < 0.001). Independent predictors for HA-CDIs in patients with COVID-19 were admission from another hospital (p = 0.003), the length of antibiotic administration (0.020), and the use of steroids in therapy (p < 0.001). The HA-CDI predictors in the non-COVID patients were older age (p = 0.017), advanced-stage renal failure (p = 0.005), chemotherapy (p = 0.003), and a low albumin level (0.005). (4) Conclusion: Higher incidence rates of HAI-CDIs in COVID-19 patients did not occur due to reduced infection control precautions and hygiene measures but due to antibiotic therapy and therapy with other drugs used during the pandemic. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 7352 KiB

Open AccessArticle

Activation of MyD88-Dependent TLR Signaling Modulates Immune Response of the Mouse Heart during Pasteurella multocida Infection

by Qiaoyu Fu, Junming Jiang, Xubo Li, Zhe Zhai, Xuemei Wang, Chongrui Li, Qiaoling Chen, Churiga Man, Li Du, Fengyang Wang and Si Chen

Microorganisms 2023, 11(2), 400; https://doi.org/10.3390/microorganisms11020400 - 04 Feb 2023

Viewed by 1558

Abstract

Pasteurella multocida (P. multocida) is an important zoonotic pathogen. In addition to lung lesions, necropsies have revealed macroscopic lesions in the heart in clinical cases. However, most previous studies focused on lung lesions while ignoring heart lesions. Therefore, to investigate the [...] Read more.

Pasteurella multocida (P. multocida) is an important zoonotic pathogen. In addition to lung lesions, necropsies have revealed macroscopic lesions in the heart in clinical cases. However, most previous studies focused on lung lesions while ignoring heart lesions. Therefore, to investigate the immune response of the P. multocida-infected heart, two murine infection models were established by using P. multocida serotype A (Pm HN02) and D (Pm HN01) strains. Histopathological examination revealed heterogeneous inflammatory responses, including immune cell infiltration in the epicardial and myocardial areas of the heart. Transcriptome sequencing was performed on infected cardiac tissues. To explore the traits of immune responses, we performed the functional enrichment analysis of differentially expressed genes, gene set enrichment analysis and gene set variation analysis. The results showed that the innate immune pathways were significantly regulated in both groups, including the NOD-like receptor signaling pathway, the complement and coagulation cascade and cytokine–cytokine receptor interaction. The Toll-like receptor signaling pathway was only significantly activated in the Pm HN02 group. For the Pm HN02 group, immunohistochemistry analysis further verified the significant upregulation of the hub component MyD88 at the protein level. In conclusion, this study reveals critical pathways for host heart recognition and defense against P. multocida serotypes A and D. Moreover, MyD88 was upregulated by P. multocida serotype A in the heart, providing a theoretical basis for future prevention, diagnosis and treatment research. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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18 pages, 2521 KiB

Open AccessArticle

Ultrastructure and Physiological Characterization of Morchella Mitospores and Their Relevance in the Understanding of the Morel Life Cycle

by Wei Liu, Peixin He, Jin Zhang, Liyuan Wu, Lingfang Er, Xiaofei Shi, Zhijia Gu, Fuqiang Yu and Jesús Pérez-Moreno

Microorganisms 2023, 11(2), 345; https://doi.org/10.3390/microorganisms11020345 - 30 Jan 2023

Cited by 3 | Viewed by 2462

Abstract

Morels, which belong to the Ascomycete genus Morchella, are highly valued edible fungi treasured by gourmet chefs worldwide. Some species are saprotrophic and others are able to form facultative mycorrhizal-like associations with plant roots without establishing true ectomycorrhizal symbioses. In general, it [...] Read more.

Morels, which belong to the Ascomycete genus Morchella, are highly valued edible fungi treasured by gourmet chefs worldwide. Some species are saprotrophic and others are able to form facultative mycorrhizal-like associations with plant roots without establishing true ectomycorrhizal symbioses. In general, it is considered that the formation of asexual spores, or mitospores, is an important step in the life cycle of morels. However, ultrastructure characterization and physiological attributes of morel mitospores have received little attention. In this contribution, the mitospores of M. sextelata were successfully induced under laboratory conditions and their ultrastructure, occurrence, germination, physiological characteristics and mating type gene structure were studied. Mitospore production was closely related to aeration, nutrition and humidity conditions. The average germination rate of mitospores on different media and under various induction stimuli was very low, with an average of 1/100,000. Based on the ultrastructure characterization, low germination rate, growth rate decline, rapid aging and mating genotyping, it was concluded that the mitospores of M. sextelata had lost their conventional function as conidia and might act more as mate sperm-like (gamete) structures. Thus, this study contributed to a deeper understanding of the life cycle of the economically and ecologically important morel fungal group. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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10 pages, 1045 KiB

Open AccessArticle

Effect of Savirin or Ticagrelor Treatment on the Expression of Commonly Used Reference Genes in Staphylococcus aureus

by Narayan Pant, Catherine Rush, Jeffrey Warner and Damon P. Eisen

Microorganisms 2023, 11(2), 336; https://doi.org/10.3390/microorganisms11020336 - 29 Jan 2023

Cited by 1 | Viewed by 1231

Abstract

Reference genes are frequently used for the normalization of quantitative reverse transcriptase PCR (qRTPCR) data in gene expression studies. Staphylococcus aureus is one of the most common causes of biofilm-related infections. Savirin and ticagrelor show in vitro as well as in vivo antibiofilm [...] Read more.

Reference genes are frequently used for the normalization of quantitative reverse transcriptase PCR (qRTPCR) data in gene expression studies. Staphylococcus aureus is one of the most common causes of biofilm-related infections. Savirin and ticagrelor show in vitro as well as in vivo antibiofilm activity against S. aureus. The main aim of this study was to identify the most stably expressed reference genes to study the effect of these molecules on genes in a strong biofilm producing S. aureus isolate isolated from biofilm-related infection. Quantitative real-time PCR was performed by using relative quantification method. Four different algorithms, delta Ct, normfinder, bestkeeper, and genorm, followed by a comprehensive analysis was used to identify the most stable reference genes from a list of sixteen different candidate reference genes. All four algorithms reported different results, with some comparable findings among some methods. In the comprehensive analysis of the results of all the algorithms used, the most stable reference genes found were spa, rpoD, and pyk for savirin treatment experiment and gapdH, gyrA, and gmk for ticagrelor treatment experiment. The optimal number of reference genes required was two for both the experimental conditions. Despite having some drawbacks, each algorithm can reliably determine an appropriate reference gene independently. However, based on consensus ranking and the required optimal number of reference genes reported, spa and rpoD were the most appropriate reference genes for savirin treatment experiment, and gapdH and gyrA were most appropriate for ticagrelor treatment experiment. This study provides baseline data on reference genes to study the effect of savirin or ticagrelor treatment on the expression of potential reference genes in S. aureus. We recommend prior re-validation of reference genes on a case-by-case basis before they can be used. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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18 pages, 4525 KiB

Open AccessArticle

Natural Flavonoid Derivatives Have Pan-Coronavirus Antiviral Activity

by Mattia Mori, Deborah Quaglio, Andrea Calcaterra, Francesca Ghirga, Leonardo Sorrentino, Silvia Cammarone, Matteo Fracella, Alessandra D’Auria, Federica Frasca, Elena Criscuolo, Nicola Clementi, Nicasio Mancini, Bruno Botta, Guido Antonelli, Alessandra Pierangeli and Carolina Scagnolari

Microorganisms 2023, 11(2), 314; https://doi.org/10.3390/microorganisms11020314 - 25 Jan 2023

Cited by 7 | Viewed by 2222

Abstract

The SARS-CoV-2 protease (3CLpro) is one of the key targets for the development of efficacious drugs for COVID-19 treatment due to its essential role in the life cycle of the virus and exhibits high conservation among coronaviruses. Recent studies have shown that flavonoids, [...] Read more.

The SARS-CoV-2 protease (3CLpro) is one of the key targets for the development of efficacious drugs for COVID-19 treatment due to its essential role in the life cycle of the virus and exhibits high conservation among coronaviruses. Recent studies have shown that flavonoids, which are small natural molecules, have antiviral activity against coronaviruses (CoVs), including SARS-CoV-2. In this study, we identified the docking sites and binding affinity of several natural compounds, similar to flavonoids, and investigated their inhibitory activity towards 3CLpro enzymatic activity. The selected compounds were then tested in vitro for their cytotoxicity, for antiviral activity against SARS-CoV-2, and the replication of other coronaviruses in different cell lines. Our results showed that Baicalein (100 μg/mL) exerted strong 3CLpro activity inhibition (>90%), whereas Hispidulin and Morin displayed partial inhibition. Moreover, Baicalein, up to 25 μg/mL, hindered >50% of SARS-CoV-2 replication in Vero E6 cultures. Lastly, Baicalein displayed antiviral activity against alphacoronavirus (Feline-CoV) and betacoronavirus (Bovine-CoV and HCoV-OC43) in the cell lines. Our study confirmed the antiviral activity of Baicalein against SARS-CoV-2 and demonstrated clear evidence of its pan-coronaviral activity. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 3965 KiB

Open AccessArticle

Adaptation of Lacticaseibacillus rhamnosus CM MSU 529 to Aerobic Growth: A Proteomic Approach

by Tatiana Yu. Dinarieva, Alena I. Klimko, Jörg Kahnt, Tatiana A. Cherdyntseva and Alexander I. Netrusov

Microorganisms 2023, 11(2), 313; https://doi.org/10.3390/microorganisms11020313 - 25 Jan 2023

Cited by 3 | Viewed by 1624

Abstract

The study describes the effect of aerobic conditions on the proteome of homofermentative lactic acid bacterium Lacticaseibacillus rhamnosus CM MSU 529 grown in a batch culture. Aeration caused the induction of the biosynthesis of 43 proteins, while 14 proteins were downregulated as detected [...] Read more.

The study describes the effect of aerobic conditions on the proteome of homofermentative lactic acid bacterium Lacticaseibacillus rhamnosus CM MSU 529 grown in a batch culture. Aeration caused the induction of the biosynthesis of 43 proteins, while 14 proteins were downregulated as detected by label-free LC-MS/MS. Upregulated proteins are involved in oxygen consumption (Pox, LctO, pyridoxine 5’-phosphate oxidase), xylulose 5-phosphate conversion (Xfp), pyruvate metabolism (PdhD, AlsS, AlsD), reactive oxygen species (ROS) elimination (Tpx, TrxA, Npr), general stress response (GroES, PfpI, universal stress protein, YqiG), antioxidant production (CysK, DkgA), pyrimidine metabolism (CarA, CarB, PyrE, PyrC, PyrB, PyrR), oligopeptide transport and metabolism (OppA, PepO), and maturation and stability of ribosomal subunits (RbfA, VicX). Downregulated proteins participate in ROS defense (AhpC), citrate and pyruvate consumption (CitE, PflB), oxaloacetate production (AvtA), arginine synthesis (ArgG), amino acid transport (GlnQ), and deoxynucleoside biosynthesis (RtpR). The data obtained shed light on mechanisms providing O₂-tolerance and adaptation to aerobic conditions in strain CM MSU 529. The biosynthesis of 39 from 57 differentially abundant proteins was shown to be O₂-sensitive in lactic acid bacteria for the first time. To our knowledge this is the first study on the impact of aerobic cultivation on the proteome of L. rhamnosus. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 2845 KiB

Open AccessArticle

Genome Analysis Identifies a Novel Type III Secretion System (T3SS) Category in Vibrio Species

by Douaa Zakaria, Shigeaki Matsuda, Tetsuya Iida, Tetsuya Hayashi and Masanori Arita

Microorganisms 2023, 11(2), 290; https://doi.org/10.3390/microorganisms11020290 - 22 Jan 2023

Viewed by 3807

Abstract

The nanomachine referred to as the type III secretion system (T3SS) is used by many Gram-negative pathogens or symbionts to inject their effector proteins into host cells to promote their infections or symbioses. Among the genera possessing T3SS is Vibrio, which consists [...] Read more.

The nanomachine referred to as the type III secretion system (T3SS) is used by many Gram-negative pathogens or symbionts to inject their effector proteins into host cells to promote their infections or symbioses. Among the genera possessing T3SS is Vibrio, which consists of diverse species of Gammaproteobacteria including human pathogenic species and inhabits aquatic environments. We describe the genetic overview of the T3SS gene clusters in Vibrio through a phylogenetic analysis from 48 bacterial strains and a gene order analysis of the two previously known categories in Vibrio (T3SS1 and T3SS2). Through this analysis we identified a new T3SS category (named T3SS3) that shares similar core and related proteins (effectors, translocons, and chaperones) with the Ssa-Esc family of T3SSs in Salmonella, Shewanella, and Sodalis. The high similarity between T3SS3 and the Ssa-Esc family suggests a possibility of genetic exchange among marine bacteria with similar habitats. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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20 pages, 4593 KiB

Open AccessArticle

A Cross-Sectional Study of Potential Antimicrobial Resistance and Ecology in Gastrointestinal and Oral Microbial Communities of Young Normoweight Pakistani Individuals

by Maria Batool, Ciara Keating, Sundus Javed, Arshan Nasir, Muhammad Muddassar and Umer Zeeshan Ijaz

Microorganisms 2023, 11(2), 279; https://doi.org/10.3390/microorganisms11020279 - 20 Jan 2023

Cited by 1 | Viewed by 2610

Abstract

Antimicrobial resistance (AMR) is a major global public health concern mainly affecting low- and middle-income countries (LMICs) due to lack of awareness, inadequate healthcare and sanitation infrastructure, and other environmental factors. In this study, we aimed to link microbial assembly and covariates (body [...] Read more.

Antimicrobial resistance (AMR) is a major global public health concern mainly affecting low- and middle-income countries (LMICs) due to lack of awareness, inadequate healthcare and sanitation infrastructure, and other environmental factors. In this study, we aimed to link microbial assembly and covariates (body mass index, smoking, and use of antibiotics) to gut microbiome structure and correlate the predictive antimicrobial gene prevalence (piARG) using PICRUSt2. We examined the gastrointestinal and oral microbial profiles of healthy adults in Pakistan through 16S rRNA gene sequencing with a focus on different ethnicities, antibiotic usage, drinking water type, smoking, and other demographic measures. We then utilised a suite of innovative statistical tools, driven by numerical ecology and machine learning, to address the above aims. We observed that drinking tap water was the main contributor to increased potential AMR signatures in the Pakistani cohort compared to other factors considered. Microbial niche breadth analysis highlighted an aberrant gut microbial signature of smokers with increased age. Moreover, covariates such as smoking and age impact the human microbial community structure in this Pakistani cohort. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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11 pages, 1197 KiB

Open AccessArticle

Development and Application of an Assay to Evaluate the Anti-Parasitic Effect of Humoral Responses against Trypanosoma cruzi

by Nieves Martinez-Peinado, Juan Carlos Gabaldon-Figueira, Ignacio Martinez-Añon, Cristian Rodríguez-Gordo, Raquel Robleda-Castillo, Maria-Jesus Pinazo, Pascal Bigey, Joaquim Gascon and Julio Alonso-Padilla

Microorganisms 2023, 11(2), 241; https://doi.org/10.3390/microorganisms11020241 - 18 Jan 2023

Viewed by 1466

Abstract

Mounting a balanced and robust humoral immune response is of utmost importance for reducing the infectivity of Trypanosoma cruzi. While the role of such a response in controlling the infection is well known, there is a lack of tools that can be [...] Read more.

Mounting a balanced and robust humoral immune response is of utmost importance for reducing the infectivity of Trypanosoma cruzi. While the role of such a response in controlling the infection is well known, there is a lack of tools that can be used to quickly evaluate it. We developed a serum parasite inhibition assay (to evaluate changes in the parasite infection after exposing infective T. cruzi trypomastigotes to serum samples from infected patients). It is based on Vero cells as the hosts and the Tulahuen β-galactosidase parasite strain, genetically engineered to be quantifiable by spectrophotometry. In parallel, we developed an in-house ELISA to correlate the anti-T. cruzi antibody titres of the clinical samples with their observed anti-parasitic effect in the serum parasite inhibition assay. Serum samples from chronically T. cruzi-infected patients significantly inhibited parasite invasion in a titre-dependant manner, regardless of the patient’s clinical status, compared to samples from the non-infected controls. In addition, there was a clear correlation between the reactivity of the samples to the whole-parasite lysates by ELISA and the inhibitory effect. The results of this work confirm the previously described anti-parasitic effect of the serum of individuals exposed to T. cruzi and present a framework for its large-scale evaluation in further studies. The serum parasite inhibition assay represents a reproducible way to evaluate the intensity and anti-parasitic effect of humoral responses against T. cruzi, which could be applied to the evaluation of candidate antigens/epitopes in the design of Chagas disease vaccine candidates. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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22 pages, 3898 KiB

Open AccessArticle

Microbial Dynamics of a Specialty Italian Raw Ewe’s Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

by Giorgia Rampanti, Luca Belleggia, Federica Cardinali, Vesna Milanović, Andrea Osimani, Cristiana Garofalo, Ilario Ferrocino and Lucia Aquilanti

Microorganisms 2023, 11(1), 219; https://doi.org/10.3390/microorganisms11010219 - 15 Jan 2023

Cited by 6 | Viewed by 1720

Abstract

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe’s milk cheese produced in [...] Read more.

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe’s milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe’s milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe’s milk cheeses. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 2827 KiB

Open AccessArticle

Application of Cloning-Free Genome Engineering to Escherichia coli

by Lucia Romeo, Antonia Esposito, Alberto Bernacchi, Daniele Colazzo, Alberto Vassallo, Marco Zaccaroni, Renato Fani and Sara Del Duca

Microorganisms 2023, 11(1), 215; https://doi.org/10.3390/microorganisms11010215 - 15 Jan 2023

Cited by 1 | Viewed by 1935

Abstract

The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to [...] Read more.

The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to use the cloning-free genome editing (CFGE) approach, proposed by Döhlemann and coworkers (2016), for E. coli genetics, and to deepen the knowledge about the homologous recombination mechanism. The E. coli auxotrophic mutant strains FB182 (hisF892) and FB181 (hisI903) were transformed with the circularized wild-type E. coli (i) hisF gene and hisF gene fragments of decreasing length, and (ii) hisIE gene, respectively. His⁺ clones were selected based on their ability to grow in the absence of histidine, and their hisF/hisIE gene sequences were characterized. CFGE method allowed the recombination of wild-type his genes (or fragments of them) within the mutated chromosomal copy, with a different recombination frequency based on the fragment length, and the generation of clones with a variable number of in tandem his genes copies. Data obtained pave the way to further evolutionary studies concerning the homologous recombination mechanism and the fate of in tandem duplicated genes. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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9 pages, 671 KiB

Open AccessArticle

The Association between Mycoplasma pneumoniae Genotype and Cutaneous Disease

by Jasna Rodman Berlot, Tatjana Mrvič, Mitja Košnik and Darja Keše

Microorganisms 2023, 11(1), 205; https://doi.org/10.3390/microorganisms11010205 - 13 Jan 2023

Cited by 1 | Viewed by 1599

Abstract

Mycoplasma pneumoniae (Mp) can cause several extrapulmonary manifestations, most frequently dermatological ones. It is largely unknown whether Mp genotype determines Mp-induced cutaneous disease. The aim of our study was to assess the association between Mp genotype and this clinical outcome. [...] Read more.

Mycoplasma pneumoniae (Mp) can cause several extrapulmonary manifestations, most frequently dermatological ones. It is largely unknown whether Mp genotype determines Mp-induced cutaneous disease. The aim of our study was to assess the association between Mp genotype and this clinical outcome. We performed a retrospective study of children referred with signs of acute Mp infection from 1 January 2014 to 31 December 2014. We compared the characteristics of children presenting as cutaneous disease, upper (URTI) and lower respiratory tract infection (LRTI). In addition, we separately analyzed the data of patients presenting with Mp-induced cutaneous disease. We evaluated data from 435 patients (mean age 7.3 years, SD 3.4 years; 52.0% boys) who had Mp PCR-positive pharyngeal swab, P1 genotype and/or multilocus variable-number tandem-repeat analysis (MLVA) genotype defined and no viral co-detection, presenting as cutaneous disease (38/435), URTI (46/435) or LRTI (351/435). The majority of patients had urticarial (55%, 21/38) or maculopapular eruptions (37%, 14/38). We found no association between Mp genotype and clinical outcome of cutaneous disease, nor any specific dermatological presentation. In the group with cutaneous disease, 18% (7/38) required hospital admission because of rash. We found that infection with MLVA-3,6,6,2 strains was more common in admitted patients than in outpatients (40% vs. 4%, p = 0.017) and significantly affected the likelihood of hospital admission in a logistic regression model. The results of our cohort study suggest that Mp genotype does not determine Mp-induced cutaneous disease or a specific dermatological presentation. Nevertheless, infections with certain MLVA strains could induce more severe cutaneous disease requiring hospitalization. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 327 KiB

Open AccessArticle

Are ELISA and PCR Discrepancies in the Identification of Chlamydia pneumoniae Caused by the Presence of “Chlamydia-Related Bacteria”?

by Martina Smolejová, Jana Krčmáriková, Iveta Cihová and Pavol Sulo

Microorganisms 2023, 11(1), 187; https://doi.org/10.3390/microorganisms11010187 - 11 Jan 2023

Cited by 1 | Viewed by 2257

Abstract

Chlamydia are Gram-negative, intracellular pathogens colonizing the epithelial mucosa. They cause primarily atypical pneumonia and have recently been associated with chronic diseases. Diagnostics rely almost exclusively on serological methods; PCR tests are used rarely because in patients with positive ELISA, it is nearly [...] Read more.

Chlamydia are Gram-negative, intracellular pathogens colonizing the epithelial mucosa. They cause primarily atypical pneumonia and have recently been associated with chronic diseases. Diagnostics rely almost exclusively on serological methods; PCR tests are used rarely because in patients with positive ELISA, it is nearly impossible to identify chlamydial DNA. To understand this issue, we elaborated a reliable and sensitive nested PCR method (panNPCR) for identifying all Chlamydiales species, not only in sputa, but also in clotted blood. Sequencing of the PCR product revealed that 41% of positive sputa samples and 66% of positive blood samples were not infected by Chlamydia but with “Chlamydia-related bacteria” such as Rhabdochlamydia sp., Parachlamydia sp., Protochlamydia sp., Neochlamydia sp., Mesochlamydia elodeae and lacustris, Piscichlamydia salmonis, and Estrella lausannensis. Consequently, we propose that there might be more than four human pathogenic Chlamydia species. We did not find any clear correlation between increased levels of antibodies and the presence of their DNA. Chlamydialles DNA was found in sputa samples from individuals positive for IgG or IgA but not in blood samples. Thus, elevated IgG and IgA levels are not reliable markers of chronic infection, and the presence of persistent forms should be proved by panNPCR. Apparently, the differences between ELISA and DNA amplification results have three main methodological reasons. The first one is the threshold occurrence of chlamydial genetic material in sputum and blood. The second one is the fact that a significant part of the samples can have DNA with sequences different from those of other species of the order Chlamydiales. The third one is the high background characteristic for ELISA, the absence of paired sera, and the vague interpretation of the gray zone. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

14 pages, 1334 KiB

Open AccessArticle

A Questionnaire Integrated with the Digital Medical Record Improved the Coverage of a Control Program for Congenital Chagas Disease in Tuscany, Italy

by Anna Barbiero, Martina Mazzi, Antonia Mantella, Michele Trotta, Gian Maria Rossolini, Alberto Antonelli, Patrizia Bordonaro, Maria Grazia Colao, Anna Rosa Speciale, Tullio Di Benedetto, Mariarosaria Di Tommaso, Elisabetta Mantengoli, Felice Petraglia, Luisa Galli, Marco Pezzati, Carlo Dani, Maria José Caldes Pinilla, Cecilia Berni, Bassam Dannaoui, Pedro Albajar Viñas, Alessandro Bartoloni and Lorenzo Zammarchi Show full author list Hide full author list

Microorganisms 2023, 11(1), 154; https://doi.org/10.3390/microorganisms11010154 - 06 Jan 2023

Cited by 2 | Viewed by 1852

Abstract

The leading route of Chagas disease transmission in nonendemic countries is congenital. However, policies concerning screening, prevention, and management of congenital Chagas disease are rare in these settings. Since 2012, serological screening for Chagas disease should be provided for pregnant women at risk [...] Read more.

The leading route of Chagas disease transmission in nonendemic countries is congenital. However, policies concerning screening, prevention, and management of congenital Chagas disease are rare in these settings. Since 2012, serological screening for Chagas disease should be provided for pregnant women at risk in Tuscany, Italy according to a Regional resolution. Due to difficulties in the implementation, in November 2019, a checklist aimed at identifying pregnant women at risk for Chagas disease was introduced in digital clinical records at Careggi University Hospital, Florence, Italy. In order to evaluate the effectiveness of the “Chagas checklist”, data about the number of deliveries by women at risk and their screening coverage between 2012 and June 2022 were collected. Out of 1348 deliveries by women at risk, 626 (47%) Trypanosoma cruzi serology tests were performed during the study period. The annual screening coverage increased from an average of 40.3% between 2012 and 2019 to 75.7% between 2020 and June 2022, underlining the big impact of the checklist. Four Chagas disease serological tests out of 626 (0.6%) resulted positive, corresponding to 2 affected women. No cases of congenital transmission occurred. The study showed that a simple digital tool led to a tangible improvement in the coverage of the screening program; its application in a setting where digital charts are available will contribute to the control and elimination of congenital Chagas disease. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 1443 KiB

Open AccessArticle

Antiparasitic Activity of Hippeastrum Species and Synergistic Interaction between Montanine and Benznidazole against Trypanosoma cruzi

by Mauricio Piñeiro, Javier E. Ortiz, Renata M. Spina Zapata, Patricia A. Barrera, Miguel A. Sosa, Germán Roitman, Jaume Bastida and Gabriela E. Feresin

Microorganisms 2023, 11(1), 144; https://doi.org/10.3390/microorganisms11010144 - 06 Jan 2023

Cited by 2 | Viewed by 1804

Abstract

Background: Hippeastrum species have a wide range of biological properties. In Argentina, this genus comprises ten widely distributed species. Purpose: To evaluate the antiparasitic and anticholinesterase activities and chemical profiles of seven Argentinean Hippeastrum species and determine the synergism between the major isolated [...] Read more.

Background: Hippeastrum species have a wide range of biological properties. In Argentina, this genus comprises ten widely distributed species. Purpose: To evaluate the antiparasitic and anticholinesterase activities and chemical profiles of seven Argentinean Hippeastrum species and determine the synergism between the major isolated alkaloid—montanine—and benznidazole in anti-Trypanosoma cruzi activity. Methods: The antiparasitic activity was evaluated through antiproliferative and viability assays against T. cruzi epimastigotes. Synergism assays were performed using the Chou–Talalay method. AChE and BuChE inhibitory activities were also assessed. The alkaloid composition was obtained using GC-MS analysis. Results: All extracts showed strong growth inhibition of T. cruzi epimastigote proliferation. The extracts from H. aglaiae, H. aulicum, and H. hybrid stand out for their potent and total growth inhibition, which was comparable to benznidazole. The H. reticulatum extract showed strong Acetylcholinesterase (AChE) inhibitory activities, while five species showed moderate Butyrylcholinesterase (BuChE) inhibition. Fifteen alkaloids were identified by means of GC-MS. Regarding the synergism assessment, the highest synergistic effect was obtained from the combination of montanine and benznidazole. Conclusion: Hippeastrum species bulb extracts from Argentina were shown to be a good source of antiparasitic alkaloids and cholinesterase inhibitors. The synergism between montanine and benznidazole emerges as a potential combination for future studies to treat Chagas disease. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 3896 KiB

Open AccessArticle

Accuracy and Completeness of Long Read Metagenomic Assemblies

by Jeremy Buttler and Devin M. Drown

Microorganisms 2023, 11(1), 96; https://doi.org/10.3390/microorganisms11010096 - 30 Dec 2022

Cited by 1 | Viewed by 2231

Abstract

Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore [...] Read more.

Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library using a VolTRAX V2 and sequenced using a MinION mk1b. We basecalled with Guppy v5.0.7 using the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10× read depth. Polishing assemblies using Medaka had a predictable improvement in quality. We found Flye to be the most robust across taxa and was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 3678 KiB

Open AccessArticle

Bacteriophages as a Strategy to Protect Potato Tubers against Dickeya dianthicola and Pectobacterium carotovorum Soft Rot

by Filip Beňo, Iveta Horsáková, Martin Kmoch, Karel Petrzik, Gabriela Krátká and Rudolf Ševčík

Microorganisms 2022, 10(12), 2369; https://doi.org/10.3390/microorganisms10122369 - 30 Nov 2022

Cited by 5 | Viewed by 2238

Abstract

The protective effect of bacteriophage suspensions (Ds3CZ + Ds20CZ and PcCB7V + PcCB251) on phytopathogenic bacteria causing soft rot of potato tubers, namely Dickeya dianthicola (D50, D200) and Pectobacterium carotovorum (P87, P224), was observed in ex vivo and in vitro experiments. Ex vivo [...] Read more.

The protective effect of bacteriophage suspensions (Ds3CZ + Ds20CZ and PcCB7V + PcCB251) on phytopathogenic bacteria causing soft rot of potato tubers, namely Dickeya dianthicola (D50, D200) and Pectobacterium carotovorum (P87, P224), was observed in ex vivo and in vitro experiments. Ex vivo tests were performed (with air access) on potato slices, on cylindrical cuts from the center of the tubers, and directly in whole potato tubers. In vitro experiments were carried out in a liquid medium using RTS-8 bioreactors, where bacterial growth was monitored as optical density. In particular, the inhibitory effects of phages were confirmed in experiments on potato slices, where suppression of rot development was evident at first glance. Phage treatment against selected bacteria positively affected potato hardness. Hardness of samples treated with bacteria only was statistically significantly reduced (p < 0.05 for D50 and p < 0.001 for D200 and P87). Ex vivo experiments confirmed significant inhibition of P87 symptom development, partial inhibition of D200 and D50 in phage-treated tubers, and no effect was observed for P224. The inhibitory effect of phages against bacteria was not observed in the in vitro experiment. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 1752 KiB

Open AccessArticle

Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources

by Sergio Morgado, Erica Fonseca and Ana Carolina Vicente

Microorganisms 2022, 10(11), 2281; https://doi.org/10.3390/microorganisms10112281 - 17 Nov 2022

Cited by 8 | Viewed by 3155

Abstract

The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by [...] Read more.

The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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13 pages, 2186 KiB

Open AccessArticle

The Marine Compound Tartrolon E Targets the Asexual and Early Sexual Stages of Cryptosporidium parvum

by Alexis Cotto-Rosario, Emma Y. D. Miller, Fernanda G. Fumuso, Jason A. Clement, Matthew J. Todd and Roberta M. O’Connor

Microorganisms 2022, 10(11), 2260; https://doi.org/10.3390/microorganisms10112260 - 15 Nov 2022

Cited by 1 | Viewed by 1548

Abstract

New therapeutic agents for cryptosporidiosis are a critical medical need. The marine organic compound, tartrolon E (trtE), is highly effective against multiple apicomplexan parasites, including Cryptosporidium. Understanding the mechanism of action of trtE is required to advance in the drug development pipeline. [...] Read more.

New therapeutic agents for cryptosporidiosis are a critical medical need. The marine organic compound, tartrolon E (trtE), is highly effective against multiple apicomplexan parasites, including Cryptosporidium. Understanding the mechanism of action of trtE is required to advance in the drug development pipeline. Here, we validate using Nluc C. parvum parasites for the study of trtE and pinpoint the life stage targeted by trtE. Results show that trtE kills Nluc and wild type C. parvum with equal efficiency, confirming the use of the Nluc C. parvum to study this compound. Results revealed that trtE kills the parasite within an hour of treatment and while the compound has no effect on viability of sporozoites, trtE does inhibit establishment of infection. Targeting treatment at particular life cycle stages demonstrated that trtE is effective against asexual of the parasite but has reduced efficacy against mature sexual stages. Gene expression analysis shows that trtE inhibits the early sexual stage of the parasite. Results from these studies will aid the development of trtE as a therapeutic for cryptosporidiosis. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 2033 KiB

Open AccessArticle

Bacterial Communities in Various Parts of Air-Conditioning Units in 17 Japanese Houses

by Kensuke Watanabe, U Yanagi, Yoshiki Shiraishi, Kazuhiro Harada, Fumitoshi Ogino and Koichiro Asano

Microorganisms 2022, 10(11), 2246; https://doi.org/10.3390/microorganisms10112246 - 13 Nov 2022

Cited by 5 | Viewed by 4808

Abstract

HVAC systems have a significant impact on the indoor environment, and microbial contamination in HVAC systems has a significant effect on the indoor air quality. In this study, to gain a better understanding of the microbial contamination inside ACs, we used NGS to [...] Read more.

HVAC systems have a significant impact on the indoor environment, and microbial contamination in HVAC systems has a significant effect on the indoor air quality. In this study, to gain a better understanding of the microbial contamination inside ACs, we used NGS to analyze the 16S rRNA gene of bacteria adhering to AC filters, cooling coils, fans, and air outlet surfaces. The five phyla in terms of the highest relative abundance were Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, and Bacteroidetes. The surface of an AC filter provides a history of indoor airborne bacterial contamination, and of the 10 bacterial genera we detected with the highest abundance (in the following order: Pseudomonas > Staphylococcus > Paracoccus > Corynebacterium > Acinetobacter > Streptococcus > Methylobacterium > Enhydrobacter > Sphingomonas > Actinotignum) on the filter surface, the top 6 genera were Gram-negative bacteria. Furthermore, the seventh-most abundant genus adhering to the filter surface (Methylobacterium) was the second-most abundant genus on the cooling coil and fan, and the ninth-most abundant genus on the air filter (Sphingomonas) was the third-most abundant genus on the cooling coil. Various factors impact the bacterial flora inside AC units, including the location of the house, AC unit usage, and occupant activity. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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Review

Jump to: Research, Other

16 pages, 16500 KiB

Open AccessReview

Past and Ongoing Field-Based Studies of Myxomycetes

by Steven L. Stephenson

Microorganisms 2023, 11(9), 2283; https://doi.org/10.3390/microorganisms11092283 - 11 Sep 2023

Viewed by 1841

Abstract

Evidence from molecular studies indicates that myxomycetes (also called myxogastrids or plasmodial slime molds) have a long evolutionary history, and the oldest known fossil is from the mid-Cretaceous. However, they were not “discovered” until 1654, when a brief description and a woodcut depicting [...] Read more.

Evidence from molecular studies indicates that myxomycetes (also called myxogastrids or plasmodial slime molds) have a long evolutionary history, and the oldest known fossil is from the mid-Cretaceous. However, they were not “discovered” until 1654, when a brief description and a woodcut depicting what is almost certainly the common species Lycogala epidendrum was published. First thought to be fungi, myxomycetes were not universally recognized as completely distinct until well into the twentieth century. Biodiversity surveys for the group being carried out over several years are relatively recent, with what is apparently the first example being carried out in the 1930s. Beginning in the 1980s, a series of such surveys yielded large bodies of data on the occurrence and distribution of myxomycetes in terrestrial ecosystems. The most notable of these were the All Taxa Biodiversity Inventory (ATBI) project carried out in the Great Smoky Mountains National Park, the Planetary Biodiversity Inventory Project (PBI) carried out in localities throughout the world, and the Myxotropic project being carried out throughout the Neotropics. The datasets available from both past and ongoing surveys now allow global and biogeographical patterns of myxomycetes to be assessed for the first time. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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20 pages, 1325 KiB

Open AccessReview

Novel Perspectives on Food-Based Natural Antimicrobials: A Review of Recent Findings Published since 2020

by Taner Sar, Pelin Kiraz, Vjola Braho, Sharareh Harirchi and Meltem Yesilcimen Akbas

Microorganisms 2023, 11(9), 2234; https://doi.org/10.3390/microorganisms11092234 - 05 Sep 2023

Cited by 3 | Viewed by 1821

Abstract

Various fruit and vegetable wastes, particularly peels, seeds, pulp, and unprocessed residues from the food industry, are abundant sources of antioxidants and essential antimicrobial agents. These valuable bioactive compounds recovered from the food industry have a great application in food, agriculture, medicine, and [...] Read more.

Various fruit and vegetable wastes, particularly peels, seeds, pulp, and unprocessed residues from the food industry, are abundant sources of antioxidants and essential antimicrobial agents. These valuable bioactive compounds recovered from the food industry have a great application in food, agriculture, medicine, and pharmacology. Food-derived natural antimicrobials offer advantages such as diminishing microbial loads and prolonging the shelf life of food products particularly prone to microbial spoilage. They not only enrich the foods with antioxidants but also help prevent microbial contamination, thereby prolonging their shelf life. Similarly, incorporating these natural antimicrobials into food packaging products extends the shelf life of meat products. Moreover, in agricultural practices, these natural antimicrobials act as eco-friendly pesticides, eliminating phytopathogenic microbes responsible for causing plant diseases. In medicine and pharmacology, they are being explored as potential therapeutic agents. This review article is based on current studies conducted in the last four years, evaluating the effectiveness of food-based natural antimicrobials in food, agriculture, medicine, and pharmacology. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 4220 KiB

Open AccessReview

Toxic Algal Bloom Recurrence in the Era of Global Change: Lessons from the Chilean Patagonian Fjords

by Patricio A. Díaz and Rosa I. Figueroa

Microorganisms 2023, 11(8), 1874; https://doi.org/10.3390/microorganisms11081874 - 25 Jul 2023

Cited by 4 | Viewed by 1593

Abstract

Toxic and harmful algal blooms (HABs) are a global problem affecting human health, marine ecosystems, and coastal economies, the latter through their impact on aquaculture, fisheries, and tourism. As our knowledge and the techniques to study HABs advance, so do international monitoring efforts, [...] Read more.

Toxic and harmful algal blooms (HABs) are a global problem affecting human health, marine ecosystems, and coastal economies, the latter through their impact on aquaculture, fisheries, and tourism. As our knowledge and the techniques to study HABs advance, so do international monitoring efforts, which have led to a large increase in the total number of reported cases. However, in addition to increased detections, environmental factors associated with global change, mainly high nutrient levels and warming temperatures, are responsible for the increased occurrence, persistence, and geographical expansion of HABs. The Chilean Patagonian fjords provide an “open-air laboratory” for the study of climate change, including its impact on the blooms of several toxic microalgal species, which, in recent years, have undergone increases in their geographical range as well as their virulence and recurrence (the species Alexandrium catenella, Pseudochattonella verruculosa, and Heterosigma akashiwo, and others of the genera Dinophysis and Pseudo-nitzschia). Here, we review the evolution of HABs in the Chilean Patagonian fjords, with a focus on the established connections between key features of HABs (expansion, recurrence, and persistence) and their interaction with current and predicted global climate-change-related factors. We conclude that large-scale climatic anomalies such as the lack of rain and heat waves, events intensified by climate change, promote the massive proliferation of these species by creating ideal conditions for their growth and persistence, as they affect water-column stratification, nutrient inputs, and reproductive rates. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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26 pages, 1795 KiB

Open AccessReview

Regulatory Functions of Hypoxia in Host–Parasite Interactions: A Focus on Enteric, Tissue, and Blood Protozoa

by Emily DeMichele, Olivia Sosnowski, Andre G. Buret and Thibault Allain

Microorganisms 2023, 11(6), 1598; https://doi.org/10.3390/microorganisms11061598 - 16 Jun 2023

Cited by 3 | Viewed by 2152

Abstract

Body tissues are subjected to various oxygenic gradients and fluctuations and hence can become transiently hypoxic. Hypoxia-inducible factor (HIF) is the master transcriptional regulator of the cellular hypoxic response and is capable of modulating cellular metabolism, immune responses, epithelial barrier integrity, and local [...] Read more.

Body tissues are subjected to various oxygenic gradients and fluctuations and hence can become transiently hypoxic. Hypoxia-inducible factor (HIF) is the master transcriptional regulator of the cellular hypoxic response and is capable of modulating cellular metabolism, immune responses, epithelial barrier integrity, and local microbiota. Recent reports have characterized the hypoxic response to various infections. However, little is known about the role of HIF activation in the context of protozoan parasitic infections. Growing evidence suggests that tissue and blood protozoa can activate HIF and subsequent HIF target genes in the host, helping or hindering their pathogenicity. In the gut, enteric protozoa are adapted to steep longitudinal and radial oxygen gradients to complete their life cycle, yet the role of HIF during these protozoan infections remains unclear. This review focuses on the hypoxic response to protozoa and its role in the pathophysiology of parasitic infections. We also discuss how hypoxia modulates host immune responses in the context of protozoan infections. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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16 pages, 1523 KiB

Open AccessReview

Relationship between Human Papillomavirus Status and the Cervicovaginal Microbiome in Cervical Cancer

by Hong Duc Thi Nguyen, Tan Minh Le, Eunmi Lee, Donghyeon Lee, Yeseul Choi, Junghwan Cho, Nora Jee-Young Park, Gun Oh Chong, Incheol Seo and Hyung Soo Han

Microorganisms 2023, 11(6), 1417; https://doi.org/10.3390/microorganisms11061417 - 27 May 2023

Cited by 2 | Viewed by 3495

Abstract

Uterine cervical cancer (CC) is a complex, multistep disease primarily linked to persistent infection with high-risk human papillomavirus (HR-HPV). However, it is widely acknowledged that HR-HPV infection alone cannot account for the formation and progression of CC. Emerging evidence suggests that the cervicovaginal [...] Read more.

Uterine cervical cancer (CC) is a complex, multistep disease primarily linked to persistent infection with high-risk human papillomavirus (HR-HPV). However, it is widely acknowledged that HR-HPV infection alone cannot account for the formation and progression of CC. Emerging evidence suggests that the cervicovaginal microbiome (CVM) also plays a significant role in HPV-related CC. Certain bacteria, such as Fusobacterium spp., Porphyromonas, Prevotella, and Campylobacter, are currently being considered as potential microbiomarkers for HPV-positive CC. However, the composition of the CVM in CC is inconsistent; thus, further studies are needed. This review comprehensively discusses the complex interplay between HPV and the CVM in cervical carcinogenesis. It is postulated that the dynamic interaction between HPV and the CVM creates an imbalanced cervicovaginal microenvironment that triggers dysbiosis, enhances HPV persistence, and promotes cervical carcinogenesis. Moreover, this review aims to provide updated evidence on the potential role of bacteriotherapy, particularly probiotics, in the treatment of CC. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 671 KiB

Open AccessReview

Human Bocavirus in Childhood: A True Respiratory Pathogen or a “Passenger” Virus? A Comprehensive Review

by Sandra Trapani, Alice Caporizzi, Silvia Ricci and Giuseppe Indolfi

Microorganisms 2023, 11(5), 1243; https://doi.org/10.3390/microorganisms11051243 - 09 May 2023

Cited by 1 | Viewed by 3724

Abstract

Recently, human bocavirus (HBoV) has appeared as an emerging pathogen, with an increasing number of cases reported worldwide. HBoV is mainly associated with upper and lower respiratory tract infections in adults and children. However, its role as a respiratory pathogen is still not [...] Read more.

Recently, human bocavirus (HBoV) has appeared as an emerging pathogen, with an increasing number of cases reported worldwide. HBoV is mainly associated with upper and lower respiratory tract infections in adults and children. However, its role as a respiratory pathogen is still not fully understood. It has been reported both as a co-infectious agent (predominantly with respiratory syncytial virus, rhinovirus, parainfluenza viruses, and adenovirus), and as an isolated viral pathogen during respiratory tract infections. It has also been found in asymptomatic subjects. The authors review the available literature on the epidemiology of HBoV, the underlying risk factors associated with infection, the virus’s transmission, and its pathogenicity as a single pathogen and in co-infections, as well as the current hypothesis about the host’s immune response. An update on different HBoV detection methods is provided, including the use of quantitative single or multiplex molecular methods (screening panels) on nasopharyngeal swabs or respiratory secretions, tissue biopsies, serum tests, and metagenomic next-generations sequencing in serum and respiratory secretions. The clinical features of infection, mainly regarding the respiratory tract but also, though rarely, the gastrointestinal one, are extensively described. Furthermore, a specific focus is dedicated to severe HBoV infections requiring hospitalization, oxygen therapy, and/or intensive care in the pediatric age; rare fatal cases have also been reported. Data on tissue viral persistence, reactivation, and reinfection are evaluated. A comparison of the clinical characteristics of single infection and viral or bacterial co-infections with high or low HBoV rates is carried out to establish the real burden of HBoV disease in the pediatric population. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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21 pages, 1242 KiB

Open AccessReview

The Skin Microbiome: Current Techniques, Challenges, and Future Directions

by Tasha M. Santiago-Rodriguez, Brice Le François, Jean M. Macklaim, Evgueni Doukhanine and Emily B. Hollister

Microorganisms 2023, 11(5), 1222; https://doi.org/10.3390/microorganisms11051222 - 06 May 2023

Cited by 3 | Viewed by 6303

Abstract

Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the [...] Read more.

Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host’s immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome’s role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 1875 KiB

Open AccessReview

Challenges for Plant Growth Promoting Microorganism Transfer from Science to Industry: A Case Study from Chile

by Eduardo Muñoz-Carvajal, Juan Pablo Araya-Angel, Nicolás Garrido-Sáez, Máximo González and Alexandra Stoll

Microorganisms 2023, 11(4), 1061; https://doi.org/10.3390/microorganisms11041061 - 19 Apr 2023

Cited by 2 | Viewed by 1518

Abstract

Research on the plant growth promoting microorganisms (PGPM) is increasing strongly due to the biotechnological potential for the agricultural, forestry, and food industry. The benefits of using PGPM in crop production are well proven; however, their incorporation in agricultural management is still limited. [...] Read more.

Research on the plant growth promoting microorganisms (PGPM) is increasing strongly due to the biotechnological potential for the agricultural, forestry, and food industry. The benefits of using PGPM in crop production are well proven; however, their incorporation in agricultural management is still limited. Therefore, we wanted to explore the gaps and challenges for the transfer of biotechnological innovations based on PGPM to the agricultural sector. Our systematic review of the state of the art of PGPM research and knowledge transfer takes Chile as an example. Several transfer limiting aspects are identified and discussed. Our two main conclusions are: neither academia nor industry can meet unfounded expectations during technology transfer, but mutually clarifying their needs, capabilities, and limitations is the starting point for successful collaborations; the generation of a collaborative innovation environment, where academia as well as public and private stakeholders (including the local community) take part, is crucial to enhance the acceptance and integration of PGPM on the way to sustainable agriculture. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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27 pages, 1086 KiB

Open AccessReview

Next-Generation Leishmanization: Revisiting Molecular Targets for Selecting Genetically Engineered Live-Attenuated Leishmania

by Paulo O. L. Moreira, Paula M. Nogueira and Rubens L. Monte-Neto

Microorganisms 2023, 11(4), 1043; https://doi.org/10.3390/microorganisms11041043 - 16 Apr 2023

Cited by 3 | Viewed by 1685

Abstract

Despite decades of research devoted to finding a vaccine against leishmaniasis, we are still lacking a safe and effective vaccine for humans. Given this scenario, the search for a new prophylaxis alternative for controlling leishmaniasis should be a global priority. Inspired by leishmanization—a [...] Read more.

Despite decades of research devoted to finding a vaccine against leishmaniasis, we are still lacking a safe and effective vaccine for humans. Given this scenario, the search for a new prophylaxis alternative for controlling leishmaniasis should be a global priority. Inspired by leishmanization—a first generation vaccine strategy where live L. major parasites are inoculated in the skin to protect against reinfection—live-attenuated Leishmania vaccine candidates are promising alternatives due to their robust elicited protective immune response. In addition, they do not cause disease and could provide long-term protection upon challenge with a virulent strain. The discovery of a precise and easy way to perform CRISPR/Cas-based gene editing allowed the selection of safer null mutant live-attenuated Leishmania parasites obtained by gene disruption. Here, we revisited molecular targets associated with the selection of live-attenuated vaccinal strains, discussing their function, their limiting factors and the ideal candidate for the next generation of genetically engineered live-attenuated Leishmania vaccines to control leishmaniasis. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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19 pages, 1011 KiB

Open AccessReview

Mechanisms and Applications of Bacterial Inoculants in Plant Drought Stress Tolerance

by Priscila Pires Bittencourt, Alice Ferreira Alves, Mariana Barduco Ferreira, Luiz Eduardo Souza da Silva Irineu, Vitor Batista Pinto and Fabio Lopes Olivares

Microorganisms 2023, 11(2), 502; https://doi.org/10.3390/microorganisms11020502 - 17 Feb 2023

Cited by 15 | Viewed by 3752

Abstract

Agricultural systems are highly affected by climatic factors such as temperature, rain, humidity, wind, and solar radiation, so the climate and its changes are major risk factors for agricultural activities. A small portion of the agricultural areas of Brazil is irrigated, while the [...] Read more.

Agricultural systems are highly affected by climatic factors such as temperature, rain, humidity, wind, and solar radiation, so the climate and its changes are major risk factors for agricultural activities. A small portion of the agricultural areas of Brazil is irrigated, while the vast majority directly depends on the natural variations of the rains. The increase in temperatures due to climate change will lead to increased water consumption by farmers and a reduction in water availability, putting production capacity at risk. Drought is a limiting environmental factor for plant growth and one of the natural phenomena that most affects agricultural productivity. The response of plants to water stress is complex and involves coordination between gene expression and its integration with hormones. Studies suggest that bacteria have mechanisms to mitigate the effects of water stress and promote more significant growth in these plant species. The underlined mechanism involves root-to-shoot phenotypic changes in growth rate, architecture, hydraulic conductivity, water conservation, plant cell protection, and damage restoration through integrating phytohormones modulation, stress-induced enzymatic apparatus, and metabolites. Thus, this review aims to demonstrate how plant growth-promoting bacteria could mitigate negative responses in plants exposed to water stress and provide examples of technological conversion applied to agroecosystems. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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20 pages, 790 KiB

Open AccessReview

The Vaginal Microbiome in Health and Disease—What Role Do Common Intimate Hygiene Practices Play?

by Alexandra M. Holdcroft, Demelza J. Ireland and Matthew S. Payne

Microorganisms 2023, 11(2), 298; https://doi.org/10.3390/microorganisms11020298 - 23 Jan 2023

Cited by 16 | Viewed by 7665

Abstract

The vaginal microbiome is a dynamic, sensitive microenvironment. The hallmark of a ‘healthy’ vaginal microbiome is currently believed to be one dominated by Lactobacillus spp., which acidifies the vaginal environment and help to protect against invading pathogens. However, a ‘normal’ microbiome is often [...] Read more.

The vaginal microbiome is a dynamic, sensitive microenvironment. The hallmark of a ‘healthy’ vaginal microbiome is currently believed to be one dominated by Lactobacillus spp., which acidifies the vaginal environment and help to protect against invading pathogens. However, a ‘normal’ microbiome is often difficult, if not impossible, to characterise given that it varies in response to numerous variables, including pregnancy, the menstrual cycle, contraceptive use, diet, ethnicity, and stress. A Lactobacillus-depleted microbiome has been linked to a variety of adverse vaginal health outcomes, including preterm birth (PTB), bacterial vaginosis (BV), and increased risk of sexually transmitted infections. The latter two of these have also been associated with feminine intimate hygiene practices, many of which are practised without any evidence of health benefits. The most extensively studied practice is vaginal douching, which is known to cause vaginal dysbiosis, predisposing women to BV, pelvic inflammatory disease, and PTB. However, little is known of the impact that intimate hygiene practices and associated products have on the vaginal microbiome. This review aims to outline the major factors influencing the vaginal microbiome and common vaginal infections, as well as to summarise current research surrounding the impact of hygiene products and practices on the vaginal microbiome. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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17 pages, 1293 KiB

Open AccessReview

Endotoxemia and Gastrointestinal Cancers: Insight into the Mechanisms Underlying a Dangerous Relationship

by Vittoria Manilla, Natalia Di Tommaso, Francesco Santopaolo, Antonio Gasbarrini and Francesca Romana Ponziani

Microorganisms 2023, 11(2), 267; https://doi.org/10.3390/microorganisms11020267 - 19 Jan 2023

Cited by 5 | Viewed by 3711

Abstract

Lipopolysaccharide (LPS), also known as endotoxin, is a component of the membrane of gram-negative bacteria and a well-recognized marker of sepsis. In case of disruption of the intestinal barrier, as occurs with unhealthy diets, alcohol consumption, or during chronic diseases, the microbiota residing [...] Read more.

Lipopolysaccharide (LPS), also known as endotoxin, is a component of the membrane of gram-negative bacteria and a well-recognized marker of sepsis. In case of disruption of the intestinal barrier, as occurs with unhealthy diets, alcohol consumption, or during chronic diseases, the microbiota residing in the gastrointestinal tract becomes a crucial factor in amplifying the systemic inflammatory response. Indeed, the translocation of LPS into the bloodstream and its interaction with toll-like receptors (TLRs) triggers molecular pathways involved in cytokine release and immune dysregulation. This is a critical step in the exacerbation of many diseases, including metabolic disorders and cancer. Indeed, the role of LPS in cancer development is widely recognized, and examples include gastric tumor related to Helicobacter pylori infection and hepatocellular carcinoma, both of which are preceded by a prolonged inflammatory injury; in addition, the risk of recurrence and development of metastasis appears to be associated with endotoxemia. Here, we review the mechanisms that link the promotion and progression of tumorigenesis with endotoxemia, and the possible therapeutic interventions that can be deployed to counteract these events. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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21 pages, 738 KiB

Open AccessReview

The Use of Probiotics during Rearing of Hermetia illucens: Potential, Caveats, and Knowledge Gaps

by Ellen Gorrens, Antoine Lecocq and Jeroen De Smet

Microorganisms 2023, 11(2), 245; https://doi.org/10.3390/microorganisms11020245 - 18 Jan 2023

Cited by 2 | Viewed by 2957

Abstract

Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to optimize yield and quality. However [...] Read more.

Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to optimize yield and quality. However recently, research has started to focus more on the associated microbes in the larval digestive system and their substrates and the effect of manipulating the composition of these communities on insect performance as a form of microbiome engineering. Here we present an overview of the existing literature on the use of microorganisms during rearing of the BSFL to optimize the productivity of this insect. These studies have had variable outcomes and potential explanations for this variation are offered to inspire future research that might lead to a better success rate for microbiome engineering in BSFL. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 1061 KiB

Open AccessReview

TORC1 Signaling in Fungi: From Yeasts to Filamentous Fungi

by Yuhua Wang, Xi Zheng, Guohong Li and Xin Wang

Microorganisms 2023, 11(1), 218; https://doi.org/10.3390/microorganisms11010218 - 15 Jan 2023

Cited by 4 | Viewed by 3180

Abstract

Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been [...] Read more.

Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been reported that TORC1 is of great significance in regulating cytotoxicity, morphology, protein synthesis and degradation, nutrient absorption, and metabolism. In this review, we mainly discuss the upstream and downstream signaling pathways of TORC1 to reveal its role in fungi. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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22 pages, 2404 KiB

Open AccessReview

Exploiting the Native Microorganisms from Different Food Matrices to Formulate Starter Cultures for Sourdough Bread Production

by Natali Hernández-Parada, Oscar González-Ríos, Mirna Leonor Suárez-Quiroz, Zorba Josué Hernández-Estrada, Claudia Yuritzi Figueroa-Hernández, Juan de Dios Figueroa-Cárdenas, Patricia Rayas-Duarte and María Cruz Figueroa-Espinoza

Microorganisms 2023, 11(1), 109; https://doi.org/10.3390/microorganisms11010109 - 31 Dec 2022

Cited by 3 | Viewed by 3770

Abstract

The use of sourdough for bread production involves fermentation, which is dominated by lactic acid bacteria (LAB) and yeast. Sourdough can be inoculated with a starter culture or through a food matrix containing microorganisms to initiate sourdough fermentation. Sourdough is used as leavening [...] Read more.

The use of sourdough for bread production involves fermentation, which is dominated by lactic acid bacteria (LAB) and yeast. Sourdough can be inoculated with a starter culture or through a food matrix containing microorganisms to initiate sourdough fermentation. Sourdough is used as leavening agent for bread making, and metabolites produced by LAB and yeast confer a specific aroma and flavor profile to bread, thus improving its sensory attributes. However, few publications report the effect of microorganisms from different food products and by-products on sourdough fermentation. This review focuses on using different starter cultures from various food sources, from wheat flour to starter cultures. Additionally, included are the types of sourdough, the sourdough fermentation process, and the biochemical transformations that take place during the sourdough fermentation process. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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19 pages, 1886 KiB

Open AccessReview

microRNAs: Critical Players during Helminth Infections

by Maura Rojas-Pirela, Diego Andrade-Alviárez, Wilfredo Quiñones, Maria Verónica Rojas, Christian Castillo, Ana Liempi, Lisvaneth Medina, Jesus Guerrero-Muñoz, Alejandro Fernández-Moya, Yessica Andreina Ortega, Sebastián Araneda, Juan Diego Maya and Ulrike Kemmerling

Microorganisms 2023, 11(1), 61; https://doi.org/10.3390/microorganisms11010061 - 25 Dec 2022

Cited by 5 | Viewed by 2445

Abstract

microRNAs (miRNAs) are a group of small non-coding RNAs that regulate gene expression post-transcriptionally through their interaction with the 3′ untranslated regions (3′ UTR) of target mRNAs, affecting their stability and/or translation. Therefore, miRNAs regulate biological processes such as signal transduction, cell death, [...] Read more.

microRNAs (miRNAs) are a group of small non-coding RNAs that regulate gene expression post-transcriptionally through their interaction with the 3′ untranslated regions (3′ UTR) of target mRNAs, affecting their stability and/or translation. Therefore, miRNAs regulate biological processes such as signal transduction, cell death, autophagy, metabolism, development, cellular proliferation, and differentiation. Dysregulated expression of microRNAs is associated with infectious diseases, where miRNAs modulate important aspects of the parasite–host interaction. Helminths are parasitic worms that cause various neglected tropical diseases affecting millions worldwide. These parasites have sophisticated mechanisms that give them a surprising immunomodulatory capacity favoring parasite persistence and establishment of infection. In this review, we analyze miRNAs in infections caused by helminths, emphasizing their role in immune regulation and its implication in diagnosis, prognosis, and the development of therapeutic strategies. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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20 pages, 1177 KiB

Open AccessReview

Development of Microalgae Biodiesel: Current Status and Perspectives

by Livia Marques Casanova, Leonardo Brantes Bacellar Mendes, Thamiris de Souza Corrêa, Ronaldo Bernardo da Silva, Rafael Richard Joao, Andrew Macrae and Alane Beatriz Vermelho

Microorganisms 2023, 11(1), 34; https://doi.org/10.3390/microorganisms11010034 - 22 Dec 2022

Cited by 9 | Viewed by 3900

Abstract

Microalgae are regarded as a promising source of biodiesel. In contrast with conventional crops currently used to produce commercial biodiesel, microalgae can be cultivated on non-arable land, besides having a higher growth rate and productivity. However, microalgal biodiesel is not yet regarded as [...] Read more.

Microalgae are regarded as a promising source of biodiesel. In contrast with conventional crops currently used to produce commercial biodiesel, microalgae can be cultivated on non-arable land, besides having a higher growth rate and productivity. However, microalgal biodiesel is not yet regarded as economically competitive, compared to fossil fuels and crop-based biodiesel; therefore, it is not commercially produced. This review provides an overall perspective on technologies with the potential to increase efficiency and reduce the general costs of biodiesel production from microalgae. Opportunities and challenges for large-scale production are discussed. We present the current scenario of Brazilian research in the field and show a successful case in the research and development of microalgal biodiesel in open ponds by Petrobras. This publicly held Brazilian corporation has been investing in research in this sector for over a decade. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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11 pages, 1188 KiB

Open AccessReview

Widespread but Poorly Understood Bacteria: Candidate Phyla Radiation

by Yanhan Ji, Ping Zhang, Sihan Zhou, Ping Gao, Baozhan Wang and Jiandong Jiang

Microorganisms 2022, 10(11), 2232; https://doi.org/10.3390/microorganisms10112232 - 11 Nov 2022

Cited by 9 | Viewed by 2691

Abstract

Candidate Phyla Radiation (CPR) bacteria is a bacterial division composed mainly of candidate phyla bacteria with ultra-small cell sizes, streamlined genomes, and limited metabolic capacity, which are generally considered to survive in a parasitic or symbiotic manner. Despite their wide distribution and rich [...] Read more.

Candidate Phyla Radiation (CPR) bacteria is a bacterial division composed mainly of candidate phyla bacteria with ultra-small cell sizes, streamlined genomes, and limited metabolic capacity, which are generally considered to survive in a parasitic or symbiotic manner. Despite their wide distribution and rich diversity, CPR bacteria have received little attention until recent years, and are therefore poorly understood. This review systematically summarizes the history of CPR research, the parasitic/symbiotic lifestyle, and the ecological distribution and unique metabolic features of CPR bacteria, hoping to provide guidance for future ecological and physiological research on CPR bacteria. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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28 pages, 11529 KiB

Open AccessReview

Unusual Cell Structures and Organelles in Giardia intestinalis and Trichomonas vaginalis Are Potential Drug Targets

by Marlene Benchimol, Ana Paula Gadelha and Wanderley de Souza

Microorganisms 2022, 10(11), 2176; https://doi.org/10.3390/microorganisms10112176 - 02 Nov 2022

Cited by 7 | Viewed by 5167

Abstract

This review presents the main cell organelles and structures of two important protist parasites, Giardia intestinalis, and Trichomonas vaginalis; many are unusual and are not found in other eukaryotic cells, thus could be good candidates for new drug targets aimed at improvement [...] Read more.

This review presents the main cell organelles and structures of two important protist parasites, Giardia intestinalis, and Trichomonas vaginalis; many are unusual and are not found in other eukaryotic cells, thus could be good candidates for new drug targets aimed at improvement of the chemotherapy of diseases caused by these eukaryotic protists. For example, in Giardia, the ventral disc is a specific structure to this parasite and is fundamental for the adhesion and pathogenicity to the host. In Trichomonas, the hydrogenosome, a double membrane-bounded organelle that produces ATP, also can be a good target. Other structures include mitosomes, ribosomes, and proteasomes. Metronidazole is the most frequent compound used to kill many anaerobic organisms, including Giardia and Trichomonas. It enters the cell by passive diffusion and needs to find a highly reductive environment to be reduced to the nitro radicals to be active. However, it provokes several side effects, and some strains present metronidazole resistance. Therefore, to improve the quality of the chemotherapy against parasitic protozoa is important to invest in the development of highly specific compounds that interfere with key steps of essential metabolic pathways or in the functional macromolecular complexes which are most often associated with cell structures and organelles. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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9 pages, 745 KiB

Open AccessBrief Report

Heat-Killed Tobacco Mosaic Virus Mitigates Plant Abiotic Stress Symptoms

by Sruthy Maria Augustine, Stavros Tzigos and Rod Snowdon

Microorganisms 2023, 11(1), 87; https://doi.org/10.3390/microorganisms11010087 - 29 Dec 2022

Viewed by 2025

Abstract

Since the discovery of the tobacco mosaic virus in the 1890s, awareness has grown in regard to how viruses affect the environment. Viral infections are now known to cause various effects besides pathogenicity, with some viruses in fact having a beneficial impact on [...] Read more.

Since the discovery of the tobacco mosaic virus in the 1890s, awareness has grown in regard to how viruses affect the environment. Viral infections are now known to cause various effects besides pathogenicity, with some viruses in fact having a beneficial impact on plants. Although research has focused on disease-causing viruses that can infect plants, many wild plants are also infected with non-pathogenic viral agents. Traditionally, abiotic, and biotic stresses have been studied as isolated stimuli that trigger signaling pathways within the plant. However, both biotic and abiotic stress can trigger complex molecular interactions within plants, which in turn drive interconnected response pathways. Here, we demonstrate that heat-killed tobacco mosaic virus (TMV) can increase abiotic stress tolerance in plants, an effect that could potentially be implemented in challenging growth environments. To our knowledge, this is the first report of plant abiotic stress tolerance following treatment with heat-killed viral particles. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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26 pages, 1143 KiB

Open AccessSystematic Review

Gram-Negative Endogenous Endophthalmitis: A Systematic Review

by Giorgio Tiecco, Davide Laurenda, Alice Mulè, Stefania Arsuffi, Samuele Storti, Manuela Migliorati, Alessandro Boldini, Liana Signorini, Francesco Castelli and Eugenia Quiros-Roldan

Microorganisms 2023, 11(1), 80; https://doi.org/10.3390/microorganisms11010080 - 28 Dec 2022

Cited by 6 | Viewed by 2007

Abstract

Background: Gram-negative bacteria are causative agents of endogenous endophthalmitis (EBE). We aim to systematically review the current literature to assess the aetiologies, risk factors, and early ocular lesions in cases of Gram-negative EBE. Methods: All peer-reviewed articles between January 2002 and [...] Read more.

Background: Gram-negative bacteria are causative agents of endogenous endophthalmitis (EBE). We aim to systematically review the current literature to assess the aetiologies, risk factors, and early ocular lesions in cases of Gram-negative EBE. Methods: All peer-reviewed articles between January 2002 and August 2022 regarding Gram-negative EBE were included. We conducted a literature search on PubMed and Cochrane Controlled Trials. Results: A total of 115 studies and 591 patients were included, prevalently Asian (98; 81.7%) and male (302; 62.9%). The most common comorbidity was diabetes (231; 55%). The main aetiologies were Klebsiella pneumoniae (510; 66.1%), Pseudomonas aeruginosa (111; 14.4%), and Escherichia coli (60; 7.8%). Liver abscesses (266; 54.5%) were the predominant source of infection. The most frequent ocular lesions were vitreal opacity (134; 49.6%) and hypopyon (95; 35.2%). Ceftriaxone (76; 30.9%), fluoroquinolones (14; 14.4%), and ceftazidime (213; 78.0%) were the most widely used as systemic, topical, and intravitreal anti-Gram-negative agents, respectively. The most reported surgical approaches were vitrectomy (130; 24.1%) and evisceration/exenteration (60; 11.1%). Frequently, visual acuity at discharge was no light perception (301; 55.2%). Conclusions: Gram-negative EBEs are associated with poor outcomes. Our systematic review is mainly based on case reports and case series with significant heterogeneity. The main strength is the large sample spanning over 20 years. Our findings underscore the importance of considering ocular involvement in Gram-negative infections. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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