Microorganisms

25 pages, 5106 KiB

Open AccessArticle

Effects of Inulin-Based Prebiotics Alone or in Combination with Probiotics on Human Gut Microbiota and Markers of Immune System: A Randomized, Double-Blind, Placebo-Controlled Study in Healthy Subjects

by Alessandra De Giani, Anna Sandionigi, Jessica Zampolli, Angela Michelotti, Francesco Tursi, Massimo Labra and Patrizia Di Gennaro

Microorganisms 2022, 10(6), 1256; https://doi.org/10.3390/microorganisms10061256 - 20 Jun 2022

Cited by 11 | Viewed by 3318

Abstract

The gut microbiota is implicated in diverse interactions affecting human health. The present study reports a randomized, double-blind, placebo-controlled clinical study conducted by administering a new synbiotic formulation composed of two Lactobacillus strains (L. plantarum and L. acidophilus) and [...] Read more.

The gut microbiota is implicated in diverse interactions affecting human health. The present study reports a randomized, double-blind, placebo-controlled clinical study conducted by administering a new synbiotic formulation composed of two Lactobacillus strains (L. plantarum and L. acidophilus) and one Bifidobacterium strain (B. animalis subsp. lactis) and two types of fructans (fructo-oligosaccharides with a degree of polymerization of 3–5 and inulin-type fructans with 10 DP). The effects of this synbiotic were evaluated on healthy subjects for 28 days and the maintenance of its efficacy was evaluated at the end of a follow-up period of 28 days. The synbiotic treatment contributes to higher biodiversity of the gut microbiota, increasing the community richness with respect to the group with the prebiotics alone and the placebo group. Its positive effect is also reflected in the variation of microbial community structure favoring the beneficial short-chain fatty acids bacterial producers. The amelioration of the health status of the subjects was also established by the reduction of common infectious disease symptom incidence, the stimulation of the gut immune system showing a noteworthy variation of fecal β-defensin2 and calprotectin levels, and the modulation of the response of the respiratory tract’s immune system by salivary IgA as well as total antioxidant capacity biomarkers. Full article

(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota)

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16 pages, 1249 KiB

Open AccessEditor’s ChoiceArticle

Ingenious Action of Vibrio cholerae Neuraminidase Recruiting Additional GM1 Cholera Toxin Receptors for Primary Human Colon Epithelial Cells

by Johanna Detzner, Charlotte Püttmann, Gottfried Pohlentz and Johannes Müthing

Microorganisms 2022, 10(6), 1255; https://doi.org/10.3390/microorganisms10061255 - 20 Jun 2022

Cited by 1 | Viewed by 1620

Abstract

For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II³Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary [...] Read more.

For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II³Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary human colon epithelial cells (pHCoEpiCs) have not yet been described in detail. The same holds true for generating further GM1 receptor molecules from higher sialylated gangliosides with a GM1 core through the neuraminidase of V. cholerae. To avoid the artificial incorporation of exogenous gangliosides from animal serum harboring GM1 and higher sialylated ganglio-series gangliosides, pHCoEpiCs were cultured in serum-free medium. Thin-layer chromatography overlay binding assays using a choleragenoid combined with electrospray ionization mass spectrometry revealed GM1 lipoforms with sphingosine (d18:1) as the sole sphingoid base linked to C14:0, C16:0, C18:0 or C20:0 fatty acyl chains forming the ceramide (Cer) moieties of the main choleragenoid-binding GM1 species. Desialylation of GD1a (IV³Neu5Ac,II³Neu5Ac-Gg4Cer) and GT1b (IV³Neu5Ac,II³(Neu5Ac)₂-Gg4Cer) of pHCoEpiCs by V. cholerae neuraminidase was observed. GD1a-derived GM1 species with stable sphingosine (d18:1) and saturated fatty acyl chains varying in chain length from C16:0 up to C22:0 could be identified, indicating the ingenious interplay between CT and the neuraminidase of V. cholerae recruiting additional GM1 receptors of pHCoEpiCs. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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9 pages, 436 KiB

Open AccessCommunication

Comparison of DNA Extraction and Amplification Techniques for Use with Engorged Hard-Bodied Ticks

by Gretchen C. Reifenberger, Bryce A. Thomas and DeLacy V. L. Rhodes

Microorganisms 2022, 10(6), 1254; https://doi.org/10.3390/microorganisms10061254 - 20 Jun 2022

Cited by 5 | Viewed by 3554

Abstract

Tick-borne infections are a serious threat to humans, livestock, and companion animals in many parts of the world, often leading to high morbidity and mortality rates, along with decreased production values and/or costly treatments. The prevalence of the microbes responsible for these infections [...] Read more.

Tick-borne infections are a serious threat to humans, livestock, and companion animals in many parts of the world, often leading to high morbidity and mortality rates, along with decreased production values and/or costly treatments. The prevalence of the microbes responsible for these infections is typically assessed by the molecular identification of pathogens within the tick vectors. Ticks sampled from animals are often engorged with animal blood, presenting difficulties in the amplification of nucleic acids due to the inhibitory effects of mammalian blood on the enzymes used in polymerase chain reactions (PCRs). This study tested two tick preparation methods, three methods of DNA extraction, and four commercially available DNA polymerases to determine the most reliable method of extracting and amplifying DNA from engorged ticks. Our study found that the phenol–chloroform extraction method yielded the highest concentration of DNA, yet DNA extracted by this method was amplified the least successfully. Thermo Scientific’s Phusion Plus PCR Master Mix was the best at amplifying the tick 16s rRNA gene, regardless of extraction method. Finally, our study identified that using the Qiagen DNeasy Blood & Tissues kit for DNA extraction coupled with either Phusion Plus PCR Master Mix or GoTaq DNA polymerase Master Mix is the best combination for the optimized amplification of DNA extracted from engorged ticks. Full article

(This article belongs to the Special Issue Research on Ticks and Tick-Borne Pathogens)

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18 pages, 2969 KiB

Open AccessArticle

Enhancing Red Yeast Biomass Yield and Lipid Biosynthesis by Using Waste Nitrogen Source by Glucose Fed-Batch at Low Temperature

by Iwona Gientka, Magdalena Wirkowska-Wojdyła, Ewa Ostrowska-Ligęza, Monika Janowicz, Lidia Reczek, Alicja Synowiec and Stanisław Błażejak

Microorganisms 2022, 10(6), 1253; https://doi.org/10.3390/microorganisms10061253 - 20 Jun 2022

Cited by 6 | Viewed by 2092

Abstract

This work reports the effect of simple feeding strategies and temperature to obtain high-cell-density cultures of Rhodotorula glutinis var. rubescens LOCKR13 maximizing the de novo lipid productivity using deproteinated potato wastewater (DPW) as a basic medium. Feeding DPW with glucose enables a high [...] Read more.

This work reports the effect of simple feeding strategies and temperature to obtain high-cell-density cultures of Rhodotorula glutinis var. rubescens LOCKR13 maximizing the de novo lipid productivity using deproteinated potato wastewater (DPW) as a basic medium. Feeding DPW with glucose enables a high yield of Rhodotorula glutinis var. rubescens LOCKR13 biomass (52 g _d.w. L⁻¹) to be obtained. The highest values of lipid accumulation (34.15%, w/w), production (14.68 g L⁻¹) and yield coefficients (Y_L/S: 0.242 g g⁻¹), and volumetric productivity (P_L: 0.1 g L⁻¹ h⁻¹) were reached by the strain in the two-stage fed-batch process at 20 °C. The lipid of yeast biomass was rich in oleic acid (^Δ9C18:1) and palmitic acid (C16:0), and the lower temperature of incubation significantly increased the MUFA (especially oleic acid) content. For the first time, a unique set of thermal analyses of the microbial oil was performed. The isotherms of the oxidation kinetics (PDSC) showed that lipids extracted from the biomass of red yeast had high oxidative stability. This feature of the yeast oil can be useful for long-shelf-life food products and can be promising for the production of biodiesel. Full article

(This article belongs to the Special Issue Advances in Microbial Biosynthesis)

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15 pages, 2232 KiB

Open AccessArticle

Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere

by Qi Li, Chunxiang Hu and Haijian Yang

Microorganisms 2022, 10(6), 1252; https://doi.org/10.3390/microorganisms10061252 - 19 Jun 2022

Cited by 1 | Viewed by 1645

Abstract

How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at [...] Read more.

How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities. Full article

(This article belongs to the Section Environmental Microbiology)

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10 pages, 302 KiB

Open AccessEditor’s ChoiceArticle

Mating Interactions between Schistosoma bovis and S. mansoni and Compatibility of Their F1 Progeny with Biomphalaria glabrata and Bulinus truncatus

by Amos Mathias Onyekwere, Alejandra De Elias-Escribano, Julien Kincaid-Smith, Sarah Dametto, Jean-François Allienne, Anne Rognon, Maria Dolores Bargues and Jérôme Boissier

Microorganisms 2022, 10(6), 1251; https://doi.org/10.3390/microorganisms10061251 - 19 Jun 2022

Cited by 1 | Viewed by 1849

Abstract

Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the [...] Read more.

Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the pairing behavior between Schistosoma bovis and S. mansoni in mixed infections in mice. We used six mate choice experiments to assess mating interactions between the two schistosome species. We show that mating between the two Schistosoma species is not random and that S. mansoni exhibits greater mate recognition compared to S. bovis. We also performed reciprocal crosses (male S. mansoni × female S. bovis) and (female S. mansoni × male S. bovis) that produce active swimming miracidia. These miracidia were genotyped by ITS2 sequencing and proposed for mollusc infection. Molecular analyses show that all the miracidia are parthenogenetically produced (i.e., their harbor the mother ITS2 genotype) and as a consequence can only infect the mollusc of the maternal species. Offspring produced by male S. mansoni × female S. bovis pairing can only infect Bulinus truncatus whereas offspring produced by female S. mansoni × male S. bovis can only infect Biomphalaria glabrata snails. Evolutionary and epidemiological consequences are discussed. Full article

(This article belongs to the Section Parasitology)

11 pages, 968 KiB

Open AccessArticle

mRNA BNT162b Vaccine Elicited Higher Antibody and CD4⁺ T-Cell Responses than Patients with Mild COVID-19

by Federica Zavaglio, Irene Cassaniti, Josè Camilla Sammartino, Stelvio Tonello, Pier Paolo Sainaghi, Viola Novelli, Federica Meloni, Daniele Lilleri and Fausto Baldanti

Microorganisms 2022, 10(6), 1250; https://doi.org/10.3390/microorganisms10061250 - 18 Jun 2022

Cited by 2 | Viewed by 1780

Abstract

We compared the development and persistence of antibody and T-cell responses elicited by the mRNA BNT162b2 vaccine or SARS-CoV-2 infection. We analysed 37 post-COVID-19 patients (15 with pneumonia and 22 with mild symptoms) and 20 vaccinated subjects. Anti-Spike IgG and neutralising antibodies were [...] Read more.

We compared the development and persistence of antibody and T-cell responses elicited by the mRNA BNT162b2 vaccine or SARS-CoV-2 infection. We analysed 37 post-COVID-19 patients (15 with pneumonia and 22 with mild symptoms) and 20 vaccinated subjects. Anti-Spike IgG and neutralising antibodies were higher in vaccinated subjects and in patients with pneumonia than in patients with mild COVID-19, and persisted at higher levels in patients with pneumonia while declining in vaccinated subjects. However, the booster dose restored the initial antibody levels. The proliferative CD4⁺ T-cell response was similar in vaccinated subjects and patients with pneumonia, but was lower in mild COVID-19 patients and persisted in both vaccinated subjects and post-COVID patients. Instead, the proliferative CD8⁺ T-cell response was lower in vaccinated subjects than in patients with pneumonia, decreased six months after vaccination, and was not restored after the booster dose. The cytokine profile was mainly T_H1 in both vaccinated subjects and post-COVID-19 patients. The mRNA BNT162b2 vaccine elicited higher levels of antibody and CD4⁺ T-cell responses than those observed in mild COVID-19 patients. While the antibody response declined after six months and required a booster dose to be restored at the initial levels, the proliferative CD4⁺ T-cell response persisted over time. Full article

(This article belongs to the Section Virology)

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21 pages, 4624 KiB

Open AccessArticle

Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms

by Óscar Velasco-Rodríguez, Mariana Fil, Tonje M. B. Heggeset, Kristin F. Degnes, David Becerro-Recio, Katarina Kolsaková, Tone Haugen, Malene Jønsson, Macarena Toral-Martínez, Carlos García-Estrada, Alberto Sola-Landa, Kjell D. Josefsen, Håvard Sletta and Carlos Barreiro

Microorganisms 2022, 10(6), 1249; https://doi.org/10.3390/microorganisms10061249 - 18 Jun 2022

Cited by 6 | Viewed by 2113

Abstract

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a [...] Read more.

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms. Full article

(This article belongs to the Special Issue Secondary Metabolism of Microorganisms)

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12 pages, 1704 KiB

Open AccessArticle

Method for Stress Assessment of Endosymbiotic Algae in Paramecium bursaria as a Model System for Endosymbiosis

by Toshiyuki Takahashi

Microorganisms 2022, 10(6), 1248; https://doi.org/10.3390/microorganisms10061248 - 18 Jun 2022

Cited by 1 | Viewed by 1681

Abstract

Endosymbiosis between heterotrophic host and microalga often breaks down because of environmental conditions, such as temperature change and exposure to toxic substances. By the time of the apparent breakdown of endosymbiosis, it is often too late for the endosymbiotic system to recover. In [...] Read more.

Endosymbiosis between heterotrophic host and microalga often breaks down because of environmental conditions, such as temperature change and exposure to toxic substances. By the time of the apparent breakdown of endosymbiosis, it is often too late for the endosymbiotic system to recover. In this study, I developed a technique for the stress assessment of endosymbiotic algae using Paramecium bursaria as an endosymbiosis model, after treatment with the herbicide paraquat, an endosymbiotic collapse inducer. Microcapillary flow cytometry was employed to evaluate a large number of cells in an approach that is more rapid than microscopy evaluation. In the assay, red fluorescence of the chlorophyll reflected the number of endosymbionts within the host cell, while yellow fluorescence fluctuated in response to the deteriorating viability of the endosymbiont under stress. Hence, the yellow/red fluorescence intensity ratio can be used as an algal stress index independent of the algal number. An optical evaluation revealed that the viability of the endosymbiotic algae within the host cell decreased after treatment with paraquat and that the remaining endosymbionts were exposed to high stress. The devised assay is a potential environmental monitoring method, applicable not only to P. bursaria but also to multicellular symbiotic units, such as corals. Full article

(This article belongs to the Special Issue Paramecium as Modern Model System)

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30 pages, 1985 KiB

Open AccessReview

Resistance Is Not Futile: The Role of Quorum Sensing Plasticity in Pseudomonas aeruginosa Infections and Its Link to Intrinsic Mechanisms of Antibiotic Resistance

by Kayla A. Simanek and Jon E. Paczkowski

Microorganisms 2022, 10(6), 1247; https://doi.org/10.3390/microorganisms10061247 - 18 Jun 2022

Cited by 12 | Viewed by 2931

Abstract

Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of extracellular signal molecules called autoinducers (AI). Quorum sensing is required for virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. [...] Read more.

Bacteria use a cell-cell communication process called quorum sensing (QS) to orchestrate collective behaviors. QS relies on the group-wide detection of extracellular signal molecules called autoinducers (AI). Quorum sensing is required for virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. In P. aeruginosa, LasR and RhlR are homologous LuxR-type soluble transcription factor receptors that bind their cognate AIs and activate the expression of genes encoding functions required for virulence and biofilm formation. While some bacterial signal transduction pathways follow a linear circuit, as phosphoryl groups are passed from one carrier protein to another ultimately resulting in up- or down-regulation of target genes, the QS system in P. aeruginosa is a dense network of receptors and regulators with interconnecting regulatory systems and outputs. Once activated, it is not understood how LasR and RhlR establish their signaling hierarchy, nor is it clear how these pathway connections are regulated, resulting in chronic infection. Here, we reviewed the mechanisms of QS progression as it relates to bacterial pathogenesis and antimicrobial resistance and tolerance. Full article

(This article belongs to the Special Issue How Does Pseudomonas aeruginosa Adapt to Its Environment?)

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16 pages, 836 KiB

Open AccessReview

Current Progress and Future Perspectives on the Use of Bacillus clausii

by Emilia Ghelardi, Ana Teresa Abreu y Abreu, Christian Boggio Marzet, Guillermo Álvarez Calatayud, Marcos Perez III and Ana Paula Moschione Castro

Microorganisms 2022, 10(6), 1246; https://doi.org/10.3390/microorganisms10061246 - 17 Jun 2022

Cited by 20 | Viewed by 7776

Abstract

Bacillus clausii is a probiotic that benefits human health. Its key characteristics include the ability to form spores; the resulting tolerance to heat, acid, and salt ensures safe passage through the human gastrointestinal tract with no loss of cells. Although B. [...] Read more.

Bacillus clausii is a probiotic that benefits human health. Its key characteristics include the ability to form spores; the resulting tolerance to heat, acid, and salt ensures safe passage through the human gastrointestinal tract with no loss of cells. Although B. clausii has been widely used for many decades, the beneficial properties of other probiotics, such as Lactobacillus spp. and Bifidobacterium spp., are better disseminated in the literature. In this review, we summarize the physiological, antimicrobial, and immunomodulatory properties of probiotic B. clausii strains. We also describe findings from studies that have investigated B. clausii probiotics from the perspective of quality and safety. We highlight innovative properties based on biochemical investigations of non-probiotic strains of B. clausii, revealing that B. clausii may have further health benefits in other therapeutic areas. Full article

(This article belongs to the Section Gut Microbiota)

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8 pages, 1495 KiB

Open AccessArticle

Genomic Characterization of Escherichia coli O8 Strains Producing Shiga Toxin 2l Subtype

by Xi Yang, Qian Liu, Hui Sun, Yanwen Xiong, Andreas Matussek and Xiangning Bai

Microorganisms 2022, 10(6), 1245; https://doi.org/10.3390/microorganisms10061245 - 17 Jun 2022

Cited by 5 | Viewed by 1756

Abstract

Shiga toxin-producing Escherichia coli (STEC) can cause diseases ranging from mild diarrhea to fatal extra-intestinal hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC, two Stx types (Stx1 and Stx2) and several subtypes varying in sequences, toxicity, and [...] Read more.

Shiga toxin-producing Escherichia coli (STEC) can cause diseases ranging from mild diarrhea to fatal extra-intestinal hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC, two Stx types (Stx1 and Stx2) and several subtypes varying in sequences, toxicity, and host specificity have been identified. Stx2l is a newly-designated subtype related to human disease but lacks thorough characterization. Here, we identified Stx2l from five STEC strains (Stx2l-STECs) recovered from raw mutton and beef in China. Whole-genome sequencing (WGS) was used to characterize the Stx2l-STECs in this study together with Stx2l-STECs retrieved from public databases. Our study revealed that all the analyzed Stx2l-STEC strains belonged to the same serogroup O8. Multilocus sequencing typing (MLST) showed two sequence types (ST88 and ST23) among these strains. Stx2l-converting prophages from different sources shared a highly similar structure and sequence. Single-nucleotide polymorphism (SNP)-based analysis revealed genetic relatedness between the human-derived and food-derived strains belonging to ST23. To conclude, our study supported the designation of Stx2l and demonstrated diverse host range and geographical distribution of Stx2l-STECs.Stx2l-STEC strains from different sources showed a high genetic similarity with an identical O8 serogroup. Further studies are needed to investigate the epidemiological trait and pathogenic potential of Stx2l-STEC strains. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Detection Methods, Food Safety, and Public Health)

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14 pages, 549 KiB

Open AccessArticle

Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium from Poultry

by Sohyun Cho, Elizabeth A. McMillan, John B. Barrett, Lari M. Hiott, Tiffanie A. Woodley, Sandra L. House, Jonathan G. Frye and Charlene R. Jackson

Microorganisms 2022, 10(6), 1244; https://doi.org/10.3390/microorganisms10061244 - 17 Jun 2022

Cited by 4 | Viewed by 1997

Abstract

The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the [...] Read more.

The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the diversity and prevalence of plasmid families from multidrug-resistant (MDR; resistance to three or more antimicrobials) enterococci from poultry carcasses were determined. Plasmid-positive MDR enterococci were also tested for the ability to transfer plasmids to other enterococci using conjugation. MDR Enterococcus faecalis (n = 98) and Enterococcus faecium (n = 696) that were isolated from poultry carcass rinsates between 2004 and 2011 were tested for the presence of 21 plasmid replicon (rep) families using multiplex PCR. Approximately 48% of E. faecalis (47/98) and 16% of E. faecium (110/696) were positive for at least one rep-family. Fourteen rep-families were detected overall, and ten rep-families were shared between E. faecalis and E. faecium. The rep₇ and rep₁₇ families were unique to E. faecalis, while the rep₅ and rep₈ families were unique to E. faecium. The rep₉ family was predominant in both E. faecalis and E. faecium for all the years tested. The greatest number of rep-families detected was in 2005 (n = 10), and the least was in 2009 (n = 1). Eight rep-families were transferred from E. faecalis donors to the E. faecalis JH2-2 recipient using conjugation. Results from this study showed that E. faecalis and E. faecium from poultry carcasses contain numerous and diverse rep-families that are capable of conjugal transfer. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Genetic Elements in Bacteria)

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16 pages, 2777 KiB

Open AccessArticle

Leishmania infantum Infection of Primary Human Myeloid Cells

by Morgane Picard, Calaiselvy Soundaramourty, Ricardo Silvestre, Jérôme Estaquier and Sónia André

Microorganisms 2022, 10(6), 1243; https://doi.org/10.3390/microorganisms10061243 - 17 Jun 2022

Cited by 2 | Viewed by 1791

Abstract

Circulating phagocytic cells often serve as cellular targets for a large number of pathogens such as Leishmania parasites. Studying primary human cells in an infectious context requires lengthy procedures for cell isolation that may affect the analysis performed. Using whole blood and a [...] Read more.

Circulating phagocytic cells often serve as cellular targets for a large number of pathogens such as Leishmania parasites. Studying primary human cells in an infectious context requires lengthy procedures for cell isolation that may affect the analysis performed. Using whole blood and a no-lyse and no-wash flow cytometric assay (NoNo assay), we monitored the Leishmania infantum infection of primary human cells. We demonstrated, using fluorescent parasites, that among monocyte cell populations, L. infantum preferentially infects classical (CD14⁺CD16⁻) and intermediate (CD14⁺CD16⁺) primary human monocytes in whole blood. Because classical monocytes are the preponderant population, they represent the larger L. infantum reservoir. Moreover, we also found that, concomitantly to monocyte infection, a subset of PMNs is infected early in whole blood. Of interest, in whole blood, PMNs are less infected compared to classical monocytes. Overall, by using this NoNo assay, we provided a novel avenue in our understanding of host–leishmania interactions. Full article

(This article belongs to the Special Issue Advances in Leishmania Research: From Basic Parasite Biology to Disease Control)

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15 pages, 1134 KiB

Open AccessArticle

Effect of Caging on Cryptosporidium parvum Proliferation in Mice

by Hannah N. Creasey, Wen Zhang and Giovanni Widmer

Microorganisms 2022, 10(6), 1242; https://doi.org/10.3390/microorganisms10061242 - 17 Jun 2022

Cited by 2 | Viewed by 1567

Abstract

Cryptosporidiosis is an enteric infection caused by several protozoan species in the genus Cryptosporidium (phylum Apicomplexa). Immunosuppressed mice are commonly used to model this infection. Surprisingly, for a pathogen like Cryptosporidium parvum, which is readily transmitted fecal-orally, mice housed in the same [...] Read more.

Cryptosporidiosis is an enteric infection caused by several protozoan species in the genus Cryptosporidium (phylum Apicomplexa). Immunosuppressed mice are commonly used to model this infection. Surprisingly, for a pathogen like Cryptosporidium parvum, which is readily transmitted fecal-orally, mice housed in the same cage can develop vastly different levels of infection, ranging from undetectable to lethal. The motivation for this study was to investigate this phenomenon and assess the association between the severity of cryptosporidiosis and the fecal microbiota. To this aim, the association between severity of cryptosporidiosis and caging (group caged vs. individually caged) and between the microbiota taxonomy and the course of the infection was examined. In contrast to mice caged in groups of four, a majority of mice caged individually did not excrete a detectable level of oocysts. Microbiota α diversity in samples collected between three days prior to infection and one day post-infection was negatively correlated with the severity of cryptosporidiosis, suggesting a causal negative relationship between microbiota diversity and susceptibility to C. parvum. Full article

(This article belongs to the Section Parasitology)

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10 pages, 1345 KiB

Open AccessArticle

Plant Growth-Promoting Microorganism Pseudarthrobacter sp. NIBRBAC000502770 Enhances the Growth and Flavonoid Content of Geum aleppicum

by Seung Hee Ham, A Ra Yoon, Hyun Eui Oh and Yoo Gyeong Park

Microorganisms 2022, 10(6), 1241; https://doi.org/10.3390/microorganisms10061241 - 17 Jun 2022

Cited by 18 | Viewed by 1973

Abstract

Plant growth-promoting rhizobacteria are known to enhance the growth and antioxidant activity of several plants. However, the effects of such rhizobacteria on Geum aleppicum, a plant with pharmacological potential in Korea are unknown. In this study, we investigated the effects of Pseudarthrobacter [...] Read more.

Plant growth-promoting rhizobacteria are known to enhance the growth and antioxidant activity of several plants. However, the effects of such rhizobacteria on Geum aleppicum, a plant with pharmacological potential in Korea are unknown. In this study, we investigated the effects of Pseudarthrobacter sp. NIBRBAC000502770 treatment (100 mL/pot, every two weeks for 55 days), in the form of culture medium, 100−fold diluted culture, culture supernatant, and pelleted cells resuspended in water, on the growth, antibacterial activity and flavonoid content of G. aleppicum. The NIBRBAC000502770 strain showed high indole-3-acetic acid (IAA) content of 461.81 μg∙mL⁻¹. The dry weight of the roots was significantly higher in the supernatant, diluted culture, and pellet-treated plants compared to that in the control plants. Additionally, the plant height, root length, leaf length, leaf width, chlorophyll content, biomass, and dry weight of the shoot were highest in the pellet-treated plants. Further, methanol extracts of pellet-treated plants showed significantly high flavonoid content compared to that in the control plants (28 mg∙g⁻¹ vs. 7.5 mg∙g⁻¹) and exhibited strong antibacterial activity against Gram-positive and negative bacteria. These results demonstrate the beneficial effects of Pseudarthrobacter sp. NIBRBAC000502770 on the growth and flavonoid content of G. aleppicum. Full article

(This article belongs to the Special Issue Plant-Bacteria Interactions)

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15 pages, 2385 KiB

Open AccessArticle

Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus

by Haiyan Ren, Anqi Yin, Pingping Wu, Huanyu Zhou, Jungang Zhou, Yao Yu and Hong Lu

Microorganisms 2022, 10(6), 1240; https://doi.org/10.3390/microorganisms10061240 - 17 Jun 2022

Cited by 1 | Viewed by 2349

Abstract

The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for [...] Read more.

The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for the first time. Next, a Cre-loxP system was established in K. marxianus. In this system, the Cre recombinase was expressed from a leaky LAC4 promoter in a plasmid to alleviate the cytotoxicity of Cre, and the unstable plasmid contained a panARS element to facilitate the clearance of the plasmid from the cells. By using LAC4 as a reporter gene, the recombination frequencies between loxP sites or loxPsym sites were 99% and 73%, respectively. A K. marxianus strain containing 16 loxPsym sites in the genome was constructed. The recombination frequency of large-scale chromosomal rearrangements between 16 loxPsym sites was up to 38.9%. Our study provides valuable information and tools for studying chromosomal structures and functions in K. marxianus. Full article

(This article belongs to the Special Issue Biotechnological Applications of Yeasts)

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116 pages, 4657 KiB

Open AccessReview

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

by Ronit Vogt Sionov and Doron Steinberg

Microorganisms 2022, 10(6), 1239; https://doi.org/10.3390/microorganisms10061239 - 16 Jun 2022

Cited by 50 | Viewed by 8836

Abstract

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated [...] Read more.

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections. Full article

(This article belongs to the Special Issue Targeting Quorum Sensing to Combat Biofilm-Associated Infectious Diseases)

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13 pages, 1130 KiB

Open AccessArticle

A Calculator for COVID-19 Severity Prediction Based on Patient Risk Factors and Number of Vaccines Received

by Ariel Israel, Alejandro A. Schäffer, Eugene Merzon, Ilan Green, Eli Magen, Avivit Golan-Cohen, Shlomo Vinker and Eytan Ruppin

Microorganisms 2022, 10(6), 1238; https://doi.org/10.3390/microorganisms10061238 - 16 Jun 2022

Cited by 3 | Viewed by 2381

Abstract

Vaccines have allowed for a significant decrease in COVID-19 risk, and new antiviral medications can prevent disease progression if given early in the course of the disease. The rapid and accurate estimation of the risk of severe disease in new patients is needed [...] Read more.

Vaccines have allowed for a significant decrease in COVID-19 risk, and new antiviral medications can prevent disease progression if given early in the course of the disease. The rapid and accurate estimation of the risk of severe disease in new patients is needed to prioritize the treatment of high-risk patients and maximize lives saved. We used electronic health records from 101,039 individuals infected with SARS-CoV-2, since the beginning of the pandemic and until 30 November 2021, in a national healthcare organization in Israel to build logistic models estimating the probability of subsequent hospitalization and death of newly infected patients based on a few major risk factors (age, sex, body mass index, hemoglobin A1C, kidney function, and the presence of hypertension, pulmonary disease, and malignancy) and the number of BNT162b2 mRNA vaccine doses received. The model’s performance was assessed by 10-fold cross-validation: the area under the curve was 0.889 for predicting hospitalization and 0.967 for predicting mortality. A total of 50%, 80%, and 90% of death events could be predicted with respective specificities of 98.6%, 95.2%, and 91.2%. These models enable the rapid identification of individuals at high risk for hospitalization and death when infected, and they can be used to prioritize patients to receive scarce medications or booster vaccination. The calculator is available online. Full article

(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines)

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8 pages, 547 KiB

Open AccessArticle

Evaluation of Commercial Concentration Methods for Microscopic Diagnosis of Protozoa and Helminths in Human Stool Samples in a Non-Endemic Area

by Brice Autier, Jean-Pierre Gangneux and Florence Robert-Gangneux

Microorganisms 2022, 10(6), 1237; https://doi.org/10.3390/microorganisms10061237 - 16 Jun 2022

Viewed by 1804

Abstract

The diagnosis of intestinal parasitic infections still widely relies on microscopic examination of stools and requires reliable reagents and staff expertise. The ParaFlo^® assays (Eurobio Ingen) are ready-to-use concentration methods for parasite egg detection, and they could improve reagent traceability and ease [...] Read more.

The diagnosis of intestinal parasitic infections still widely relies on microscopic examination of stools and requires reliable reagents and staff expertise. The ParaFlo^® assays (Eurobio Ingen) are ready-to-use concentration methods for parasite egg detection, and they could improve reagent traceability and ease of manipulation. Ninety-three stool samples were analyzed with the ParaFlo^® concentration methods and then compared with routine microscopic methods for protozoa and helminth detection: seventy-eight were analyzed with ParaFlo^® Bailenger and in-house Thebault or Bailenger concentrations, and fifty-five were analyzed with ParaFlo^®DC and the in-house merthiolate-formalin diphasic concentration (DC) method. Fully concordant results were obtained for 75%, 70%, and 69% of samples when comparing ParaFlo^® DC and in-house DC, ParaFlo^® Bailenger and in-house Bailenger, and ParaFlo^® Bailenger and Thebault, respectively. The performances of the ParaFlo^® assays did not differ statistically from that obtained with their in-house counterparts (Bailenger and DC) for the detection of protozoa, but ParaFlo^® Bailenger performed significantly poorer than the Thebault method (p < 0.001). No statistical differences were observed between the commercial and in-house methods for helminth detection. These marketed concentration methods could be used in routine if combined with other techniques for protozoa detection. Full article

(This article belongs to the Section Parasitology)

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40 pages, 2080 KiB

Open AccessArticle

Distribution of Tick-Borne Pathogens in Domestic Animals and Their Ticks in the Countries of the Mediterranean Basin between 2000 and 2021: A Systematic Review

by Baptiste Defaye, Sara Moutailler, Vanina Pasqualini and Yann Quilichini

Microorganisms 2022, 10(6), 1236; https://doi.org/10.3390/microorganisms10061236 - 16 Jun 2022

Cited by 6 | Viewed by 2955

Abstract

Tick-borne pathogens (TBPs) include a wide range of bacteria, parasites and viruses that cause a large spectrum of animal, human and zoonotic tick-borne diseases (TBDs). The object of this review was to establish an inventory and an analysis of TBPs found in domestic [...] Read more.

Tick-borne pathogens (TBPs) include a wide range of bacteria, parasites and viruses that cause a large spectrum of animal, human and zoonotic tick-borne diseases (TBDs). The object of this review was to establish an inventory and an analysis of TBPs found in domestic animals in the countries of the Mediterranean Basin. This geographic area occupies a central position between several continents and is an area of movement for animals, humans and pathogens of interest and their vectors, which is important in terms of animal and human health. In this systematic review, we included a total of 271 publications produced between 2000–2021 concerning TBPs in domestic animals. Among this literature, we found a total of 90 pathogen species (known as TBPs) reported in the 20 countries of the area; these were detected in tick species from domestic animals and were also directly detected in domestic animals. In all, 31 tick species were recorded and 12 domestic animal species, the latter comprising nine livestock and three pet species. More than 50% of the publications were from Western Europe. Island data were extracted and assessed, as islands of the Mediterranean Basin were represented in 16% of the publications and 77.8% of the TBPs reported. Our results show the importance of islands in the monitoring of TBPs, despite the low percentage of publications. Full article

(This article belongs to the Special Issue Research on Ticks and Tick-Borne Pathogens)

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17 pages, 3912 KiB

Open AccessArticle

Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum Isolates

by Emily J. Davenport and Arpita Bose

Microorganisms 2022, 10(6), 1235; https://doi.org/10.3390/microorganisms10061235 - 16 Jun 2022

Cited by 1 | Viewed by 2075

Abstract

Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were [...] Read more.

Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were isolated from a marine estuary to observe these metabolisms in marine phototrophs. One representative strain, Rhodovulum sulfidophilum strain AB26, can perform phototrophic iron oxidation (photoferrotrophy) and couples carbon dioxide fixation to pEEU. Here, we reclassify two R. sulfidophilum isolates, strainAB26 and strain AB19, as Rhodovulum visakhapatnamense using taxonomic re-evaluation based on 16S and pufM phylogenetic analyses. The strain AB26 genome consists of 4,380,746 base-pairs, including two plasmids, and encodes 4296 predicted protein-coding genes. Strain AB26 contains 22 histidine kinases, 20 response regulators, and dedicates ~16% of its genome to transport. Transcriptomic data under aerobic, photoheterotrophy, photoautotrophy, and pEEU reveals how gene expression varies between metabolisms in a novel R. visakhapatnamense strain. Genome comparison led by transcriptomic data under pEEU reveals potential pEEU-relevant genes both unique to R. visakhapatnamense strains and shared within the R. sulfidophilum genomes. With these data we identify potential pEEU-important transcripts and how speciation may affect molecular mechanisms of pEEU in Rhodovulum species from the same environment. Full article

(This article belongs to the Special Issue Phototrophic Bacteria)

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15 pages, 1069 KiB

Open AccessReview

Diversity and Functional Roles of the Gut Microbiota in Lepidopteran Insects

by Xiancui Zhang, Fan Zhang and Xingmeng Lu

Microorganisms 2022, 10(6), 1234; https://doi.org/10.3390/microorganisms10061234 - 16 Jun 2022

Cited by 31 | Viewed by 4712

Abstract

Lepidopteran insects are one of the most widespread and speciose lineages on Earth, with many common pests and beneficial insect species. The evolutionary success of their diversification depends on the essential functions of gut microorganisms. This diverse gut microbiota of lepidopteran insects provides [...] Read more.

Lepidopteran insects are one of the most widespread and speciose lineages on Earth, with many common pests and beneficial insect species. The evolutionary success of their diversification depends on the essential functions of gut microorganisms. This diverse gut microbiota of lepidopteran insects provides benefits in nutrition and reproductive regulation and plays an important role in the defence against pathogens, enhancing host immune homeostasis. In addition, gut symbionts have shown promising applications in the development of novel tools for biological control, biodegradation of waste, and blocking the transmission of insect-borne diseases. Even though most microbial symbionts are unculturable, the rapidly expanding catalogue of microbial genomes and the application of modern genetic techniques offer a viable alternative for studying these microbes. Here, we discuss the gut structure and microbial diversity of lepidopteran insects, as well as advances in the understanding of symbiotic relationships and interactions between hosts and symbionts. Furthermore, we provide an overview of the function of the gut microbiota, including in host nutrition and metabolism, immune defence, and potential mechanisms of detoxification. Due to the relevance of lepidopteran pests in agricultural production, it can be expected that the research on the interactions between lepidopteran insects and their gut microbiota will be used for biological pest control and protection of beneficial insects in the future. Full article

(This article belongs to the Special Issue Feature Reviews in Gut Microbiota)

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7 pages, 496 KiB

Open AccessCommunication

Distinguishing Kingella kingae from Pyogenic Acute Septic Arthritis in Young Portuguese Children

by Catarina Gouveia, Ana Subtil, Susana Norte, Joana Arcangelo, Madalena Almeida Santos, Rita Corte-Real, Maria João Simões, Helena Canhão and Delfin Tavares

Microorganisms 2022, 10(6), 1233; https://doi.org/10.3390/microorganisms10061233 - 16 Jun 2022

Cited by 5 | Viewed by 1323

Abstract

(1) Background: We aim to identify clinical and laboratorial parameters to distinguish Kingella kingae from pyogenic septic arthritis (SA). (2) Methods: A longitudinal, observational, single-centre study of children < 5 years old with microbiological positive SA admitted to a paediatric hospital [...] Read more.

(1) Background: We aim to identify clinical and laboratorial parameters to distinguish Kingella kingae from pyogenic septic arthritis (SA). (2) Methods: A longitudinal, observational, single-centre study of children < 5 years old with microbiological positive SA admitted to a paediatric hospital from 2013–2020 was performed. Clinical and laboratorial data at admission and at 48 h, as well as on treatment and evolution, were obtained. (3) Results: We found a total of 75 children, 44 with K. kingae and 31 with pyogenic infections (mostly MSSA, S. pneumoniae and S. pyogenes). K. kingae affected younger children with low or absent fever, low inflammatory markers and a favourable prognosis. In the univariate analyses, fever, septic look, CRP and ESR at admission and CRP at 48 h were significantly lower in K. kingae SA. In the multivariate analyses, age > 6 months ≤ 2 years, apyrexy and CRP ≤ 100 mg/L were significative, with an overall predictive positive value of 86.5%, and 88.4% for K. kingae. For this model, ROC curves were capable of differentiating (AUC 0.861, 95% CI 0.767–0.955) K. kingae SA from typical pathogens. (4) Conclusions: Age > 6 months ≤ 2 years, apyrexy and PCR ≤ 100 mg/L were the main predictive factors to distinguish K. kingae from pyogenic SA < 5 years. These data need to be validated in a larger study. Full article

(This article belongs to the Special Issue Kingella kingae: Virulence Factors, Clinical Disease, and Diagnostics)

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19 pages, 726 KiB

Open AccessArticle

The Main Bacterial Communities Identified in the Sites Affected by Periimplantitis: A Systematic Review

by Simina Angela Lăcrimioara Iușan, Ondine Patricia Lucaciu, Nausica Bianca Petrescu, Ioana Codruța Mirică, Dan-Alexandru Toc, Silviu Albu and Carmen Costache

Microorganisms 2022, 10(6), 1232; https://doi.org/10.3390/microorganisms10061232 - 16 Jun 2022

Cited by 8 | Viewed by 1999

Abstract

(1) Background: Periimplantitis is an infectious condition that affects the periimplant tissue and is of bacterial etiology. However, to date, the exact bacterial flora involved in its occurrence is not known. The aim of this literature review was to summarize the articles published [...] Read more.

(1) Background: Periimplantitis is an infectious condition that affects the periimplant tissue and is of bacterial etiology. However, to date, the exact bacterial flora involved in its occurrence is not known. The aim of this literature review was to summarize the articles published on this topic and to identify the main bacterial species isolated in periimplantitis. (2) Methods: The articles published in three databases were researched: Pubmed, Embase and Web of Science using Prisma guides and combinations of MeSH terms. We selected 25 items from the 980 found by applying the inclusion and exclusion criteria. (3) Results: We quantified the results of the 25 studies included in this review. In general, the most commonly identified bacterial species were Gram-negative anaerobic species, as Prevotella, Streptococcus, Fusobacterium and Treponema. (4) Conclusion: The most frequent bacteria in the periimplantitis sites identified in this review are Gram-negative anaerobic species, also involved in the pathogenesis of the periodontal disease. Full article

(This article belongs to the Special Issue Implant and Prosthetic Infections)

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16 pages, 2107 KiB

Open AccessArticle

Escherichia/Shigella, SCFAs, and Metabolic Pathways—The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico

by Tonatiuh Abimael Baltazar-Díaz, Luz Alicia González-Hernández, Juan Manuel Aldana-Ledesma, Marcela Peña-Rodríguez, Alejandra Natali Vega-Magaña, Adelaida Sara Minia Zepeda-Morales, Rocío Ivette López-Roa, Susana del Toro-Arreola, Erika Martínez-López, Adriana María Salazar-Montes and Miriam Ruth Bueno-Topete

Microorganisms 2022, 10(6), 1231; https://doi.org/10.3390/microorganisms10061231 - 16 Jun 2022

Cited by 26 | Viewed by 4014

Abstract

Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples [...] Read more.

Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease 2.0)

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20 pages, 717 KiB

Open AccessReview

Viral Hyperparasitism in Bat Ectoparasites: Implications for Pathogen Maintenance and Transmission

by Alexander Tendu, Alice Catherine Hughes, Nicolas Berthet and Gary Wong

Microorganisms 2022, 10(6), 1230; https://doi.org/10.3390/microorganisms10061230 - 16 Jun 2022

Cited by 4 | Viewed by 2836

Abstract

Humans continue to encroach on the habitats of wild animals, potentially bringing different species into contact that would not typically encounter each other under natural circumstances, and forcing them into stressful, suboptimal conditions. Stressors from unsustainable human land use changes are suspected to [...] Read more.

Humans continue to encroach on the habitats of wild animals, potentially bringing different species into contact that would not typically encounter each other under natural circumstances, and forcing them into stressful, suboptimal conditions. Stressors from unsustainable human land use changes are suspected to dramatically exacerbate the probability of zoonotic spillover of pathogens from their natural reservoir hosts to humans, both by increasing viral load (and shedding) and the interface between wildlife with livestock, pets and humans. Given their known role as reservoir hosts, bats continue to be investigated for their possible role as the origins of many viral outbreaks. However, the participation of bat-associated ectoparasites in the spread of potential pathogens requires further work to establish. Here, we conducted a comprehensive review of viruses, viral genes and other viral sequences obtained from bat ectoparasites from studies over the last four decades. This review summarizes research findings of the seven virus families in which these studies have been performed, including Paramyxoviridae, Reoviridae, Flaviviridae, Peribunyaviridae, Nairoviridae, Rhabdoviridae and Filoviridae. We highlight that bat ectoparasites, including dipterans and ticks, are often found to have medically important viruses and may have a role in the maintenance of these pathogens within bat populations. Full article

(This article belongs to the Special Issue Discovery and Characterization of Novel/Emerging Viruses)

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19 pages, 5374 KiB

Open AccessArticle

SARS-CoV-2: Two Years in the Pandemic: What Have We Observed from Genome Sequencing Results in Lithuania?

by Lukas Zemaitis, Gediminas Alzbutas, Emilija Gecyte, Dovydas Gecys and Vaiva Lesauskaite

Microorganisms 2022, 10(6), 1229; https://doi.org/10.3390/microorganisms10061229 - 16 Jun 2022

Viewed by 2435

Abstract

SARS-CoV-2 has spread vastly throughout the word. In this study, we focus on the patterns of spread in Lithuania. By analysing the genetically sequenced data of different lineages and their first appearances, we were able to compare the dynamics of spreading of the [...] Read more.

SARS-CoV-2 has spread vastly throughout the word. In this study, we focus on the patterns of spread in Lithuania. By analysing the genetically sequenced data of different lineages and their first appearances, we were able to compare the dynamics of spreading of the lineages and recognize the main possible cause. The impact of emigration patterns and international travel on the variety of lineages was also assessed. Results showed different patterns of spread, and while a vast variety of different lineages were brought in by international travel, many of the viral outbreaks were caused by local lineages. It can be concluded that international travel had the most impact on the spread of SARS-CoV-2. Full article

(This article belongs to the Section Virology)

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13 pages, 2809 KiB

Open AccessArticle

Effects of Fermented Herbal Tea Residue on Serum Indices and Fecal Microorganisms of Chuanzhong Black Goats

by Chongya Gao, Longfei Wu, Weiran Zhao, Yiye Chen, Ming Deng, Guangbin Liu, Yongqing Guo and Baoli Sun

Microorganisms 2022, 10(6), 1228; https://doi.org/10.3390/microorganisms10061228 - 16 Jun 2022

Cited by 3 | Viewed by 1657

Abstract

Herbal tea residues (HTRs) are a by−product of herbal tea processing that contains many nutrients and active substances but are often discarded as waste. The main aim of the present study was to determine the food safety of HTRs and lay the foundation [...] Read more.

Herbal tea residues (HTRs) are a by−product of herbal tea processing that contains many nutrients and active substances but are often discarded as waste. The main aim of the present study was to determine the food safety of HTRs and lay the foundation for its use as a novel feed resource for goats. In this study, discarded HTRs were fermented and then fed to 33 female Chuanzhong black goats (121 ± 4.00 days) with similar weight (9.33 ± 0.95 kg) and genetic background, which were divided into three groups (fermented herbal tea residue (FHTR) replacement of 0%, 15% and 30% of the forage component of the diet). The feeding experiment lasted for 35 days. On day 35, our findings indicated that the concentrations of hydroxyl radicals and urea increased linearly, and the concentrations of glutathione peroxidase increased quadratically with the increase in FHTR. In addition, we investigated the fecal microbiota composition of eight Chuanzhong black goats in the control, 15% and 30% FHTR replacement groups and found that FHTR had no remarkable effect on the fecal microbiota composition. Results indicated that goat physiological functions remained stable after FHTR was added to the diet. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 3595 KiB

Open AccessArticle

Enhancing Biocide Efficacy: Targeting Extracellular DNA for Marine Biofilm Disruption

by Benjamin Tuck, Elizabeth Watkin, Anthony Somers, Maria Forsyth and Laura L. Machuca

Microorganisms 2022, 10(6), 1227; https://doi.org/10.3390/microorganisms10061227 - 15 Jun 2022

Cited by 2 | Viewed by 1583

Abstract

Biofilm formation is a global health, safety and economic concern. The extracellular composition of deleterious multispecies biofilms remains uncanvassed, leading to an absence of targeted biofilm mitigation strategies. Besides economic incentives, drive also exists from industry and research to develop and apply environmentally [...] Read more.

Biofilm formation is a global health, safety and economic concern. The extracellular composition of deleterious multispecies biofilms remains uncanvassed, leading to an absence of targeted biofilm mitigation strategies. Besides economic incentives, drive also exists from industry and research to develop and apply environmentally sustainable chemical treatments (biocides); especially in engineered systems associated with the marine environment. Recently, extracellular DNA (eDNA) was implicated as a critical structural polymer in marine biofilms. Additionally, an environmentally sustainable, multi-functional biocide was also introduced to manage corrosion and biofilm formation. To anticipate biofilm tolerance acquisition to chemical treatments and reduce biocide application quantities, the present research investigated eDNA as a target for biofilm dispersal and potential enhancement of biocide function. Results indicate that mature biofilm viability can be reduced by two-fold using reduced concentrations of the biocide alone (1 mM instead of the recommended 10 mM). Importantly, through the incorporation of an eDNA degradation stage, biocide function could be enhanced by a further ~90% (one further log reduction in viability). Biofilm architecture analysis post-treatment revealed that endonuclease targeting of the matrix allowed greater biocide penetration, leading to the observed viability reduction. Biofilm matrix eDNA is a promising target for biofilm dispersal and antimicrobial enhancement in clinical and engineered systems. Full article

(This article belongs to the Special Issue Biofilms and Microbiologically Influenced Corrosion: Recent Advances in Analysis, Detection and Mitigation)

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