Microorganisms

4 pages, 208 KiB

Open AccessEditorial

Plant Pathogenic Microorganisms: State-of-the-Art Research in Spain

by Elvira Fiallo-Olivé, Ana Palacio-Bielsa and Soledad Sacristán

Microorganisms 2023, 11(3), 816; https://doi.org/10.3390/microorganisms11030816 - 22 Mar 2023

Viewed by 1372

Pathogenic microorganisms, including fungi, oomycetes, bacteria, viruses, and viroids, constitute a serious threat to agriculture worldwide [...] Full article

(This article belongs to the Special Issue Plant Pathogenic Microorganisms: State-of-the-Art Research in Spain)

17 pages, 1242 KiB

Open AccessArticle

Screening of Native Trichoderma Species for Nickel and Copper Bioremediation Potential Determined by FTIR and XRF

by Gordana Racić, Igor Vukelić, Branko Kordić, Danka Radić, Milana Lazović, Ljiljana Nešić and Dejana Panković

Microorganisms 2023, 11(3), 815; https://doi.org/10.3390/microorganisms11030815 - 22 Mar 2023

Cited by 2 | Viewed by 1682

Abstract

Soil pollution with heavy metals is a serious threat to the environment. However, soils polluted with heavy metals are considered good sources of native metal-resistant Trichoderma strains. Trichoderma spp. are free-living fungi commonly isolated from different ecosystems, establishing endophytic associations with plants. They [...] Read more.

Soil pollution with heavy metals is a serious threat to the environment. However, soils polluted with heavy metals are considered good sources of native metal-resistant Trichoderma strains. Trichoderma spp. are free-living fungi commonly isolated from different ecosystems, establishing endophytic associations with plants. They have important ecological and biotechnological roles due to their production of a wide range of secondary metabolites, thus regulating plant growth and development or inducing resistance to plant pathogens. In this work we used indigenous Trichoderma strains that were previously isolated from different soil types to determine their tolerance to increased copper and nickel concentrations as well as mechanisms of metal removal. The concentrations of bioavailable metal concentrations were determined after extraction with diethylene-triamine pentaacetate (DTPA)-extractable metals (Cd, Cr, Co, Cu, Pb, Mn, Ni, and Zn) from the soil samples by inductively coupled plasma-optical emission spectrometry (ICP-OES). Two indigenous T. harzianum strains were selected for copper tolerance, and three indigenous T. longibrachiatum strains were selected for nickel tolerance tests. Strains were isolated from the soils with the highest and among the lowest DTPA-extractable metal concentrations to determine whether the adaptation to different concentrations of metals affects the mechanisms of remediation. Mechanisms of metal removal were determined using Fourier-transform infrared spectroscopy (FTIR) and X-ray fluorescence spectroscopy (XRF), non-destructive methods characterized by high measurement speed with little or no need for sample preparation and very low costs. Increased DTPA-extractable metal content for nickel and copper was detected in the soil samples above the target value (TV), and for nickel above the soil remediation intervention values (SRIVs), for total metal concentrations which were previously determined. The SRIV is a threshold of metal concentrations indicating a serious soil contamination, thus confirming the need for soil remediation. The use of FTIR and XRF methods revealed that the presence of both biosorption and accumulation of metals in the Trichoderma cells, providing good bioremediation potential for Ni and Cu. Full article

(This article belongs to the Special Issue Fungal Biodiversity for Bioremediation 2.0)

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16 pages, 3230 KiB

Open AccessArticle

The Impact of Early Life Experiences and Gut Microbiota on Neurobehavioral Development in Preterm Infants: A Longitudinal Cohort Study

by Jie Chen, Hongfei Li, Tingting Zhao, Kun Chen, Ming-Hui Chen, Zhe Sun, Wanli Xu, Kendra Maas, Barry M. Lester and Xiaomei S. Cong

Microorganisms 2023, 11(3), 814; https://doi.org/10.3390/microorganisms11030814 - 22 Mar 2023

Cited by 4 | Viewed by 1781

Abstract

Objectives: The objective of this study is to investigate the impact of early life experiences and gut microbiota on neurobehavioral development in preterm infants during neonatal intensive care unit (NICU) hospitalization. Methods: Preterm infants were followed from NICU admission until their 28th postnatal [...] Read more.

Objectives: The objective of this study is to investigate the impact of early life experiences and gut microbiota on neurobehavioral development in preterm infants during neonatal intensive care unit (NICU) hospitalization. Methods: Preterm infants were followed from NICU admission until their 28th postnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis. Results: Preterm infants who experienced a high level of pain/stress during the NICU hospitalization had higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs and taxa belonging to seven genera, i.e., Enterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1, and Streptococcus with five belonging to Firmicutes and two belonging to Proteobacteria phylum. The enriched abundance of Enterobacteriaceae_unclassified (OTU17) and Streptococcus (OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay. Conclusions: This study explored the dynamic impact of specific OTUs on neurobehavioral development in preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress and feeding in the NICU. The gut microbiota and acute pain/stressful experiences dynamically impact the neurobehavioral development in preterm infants during their NICU hospitalization. Full article

(This article belongs to the Section Gut Microbiota)

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14 pages, 4834 KiB

Open AccessArticle

Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater

by Sarah Schurig, Rea Kobialka, Andy Wende, Md Anik Ashfaq Khan, Phillip Lübcke, Elias Eger, Katharina Schaufler, Arwid Daugschies, Uwe Truyen and Ahmed Abd El Wahed

Microorganisms 2023, 11(3), 813; https://doi.org/10.3390/microorganisms11030813 - 22 Mar 2023

Cited by 1 | Viewed by 3450

Abstract

Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were [...] Read more.

Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels. Full article

(This article belongs to the Special Issue Microbial Ecosystems in Water and Wastewater Treatment)

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18 pages, 1500 KiB

Open AccessArticle

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

by José Q. García-Maldonado, Hever Latisnere-Barragán, Alejandra Escobar-Zepeda, Santiago Cadena, Patricia J. Ramírez-Arenas, Ricardo Vázquez-Juárez, Maurilia Rojas-Contreras and Alejandro López-Cortés

Microorganisms 2023, 11(3), 812; https://doi.org/10.3390/microorganisms11030812 - 22 Mar 2023

Cited by 3 | Viewed by 2174

Abstract

Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic [...] Read more.

Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments. Full article

(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)

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19 pages, 5444 KiB

Open AccessArticle

Histopathological, Immunohistochemical, Biochemical, and In Silico Molecular Docking Study of Fungal-Mediated Selenium Oxide Nanoparticles on Biomphalaria alexandrina (Ehrenberg, 1831) Snails

by Amina M. Ibrahim, Mahassen Ghazy, Heba El-Sayed, Rehab M. Abd El-Hameed, Rehab G. Khalil, Shereen M. Korany, Abeer S. Aloufi, Olfat A. Hammam and Mostafa Y. Morad

Microorganisms 2023, 11(3), 811; https://doi.org/10.3390/microorganisms11030811 - 22 Mar 2023

Cited by 1 | Viewed by 1633

Abstract

Daphnia magna and freshwater snails are used as delicate bioindicators of contaminated aquatic habitats. Due to their distinctive characteristics, selenium oxide nanoparticles (SeONPs) have received interest regarding their possible implications on aquatic environments. The current study attempted to investigate the probable mechanisms of [...] Read more.

Daphnia magna and freshwater snails are used as delicate bioindicators of contaminated aquatic habitats. Due to their distinctive characteristics, selenium oxide nanoparticles (SeONPs) have received interest regarding their possible implications on aquatic environments. The current study attempted to investigate the probable mechanisms of fungal-mediated selenium nanoparticles’ ecotoxicological effects on freshwater Biomphalaria alexandrina snails and Daphnia magna. SeONPs revealed a toxicological impact on D. magna, with a half-lethal concentration (LC₅₀) of 1.62 mg/L after 24 h and 1.08 mg/L after 48 h. Survival, fecundity, and reproductive rate were decreased in B. alexandrina snails exposed to SeONPs. Furthermore, the aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels were markedly elevated, while albumin and total protein levels decreased. Histopathological damage in the hermaphrodite and digestive glands was detected by light, electron microscopy, and immunohistochemistry studies. The molecular docking study revealed interactions of selenium oxide with the ALT and AST. In conclusion, B. alexandrina snails and D. magna could be employed as bioindicators of selenium nanomaterial pollution in aquatic ecosystems. This study emphasizes the possible ecological effects of releasing SeONPs into aquatic habitats, which could serve as motivation for regulatory organizations to monitor and control the use and disposal of SeONPs in industry. Full article

(This article belongs to the Special Issue Microbial Nanotechnology)

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18 pages, 1072 KiB

Open AccessArticle

The Impact of Mineral and Energy Supplementation and Phytogenic Compounds on Rumen Microbial Diversity and Nitrogen Utilization in Grazing Beef Cattle

by Ronyatta Weich Teobaldo, Yury Tatiana Granja-Salcedo, Abmael da Silva Cardoso, Milena Tavares Lima Constancio, Thais Ribeiro Brito, Eliéder Prates Romanzini and Ricardo Andrade Reis

Microorganisms 2023, 11(3), 810; https://doi.org/10.3390/microorganisms11030810 - 22 Mar 2023

Cited by 2 | Viewed by 1580

Abstract

The objective of this study was to evaluate the effect of the addition of a phytogenic compound blend (PHA) containing hydrolyzable tannins, carvacrol, and cinnamaldehyde oil to mineral salt or energy supplementation on the rumen microbiota and nitrogen metabolism of grazing Nellore cattle. [...] Read more.

The objective of this study was to evaluate the effect of the addition of a phytogenic compound blend (PHA) containing hydrolyzable tannins, carvacrol, and cinnamaldehyde oil to mineral salt or energy supplementation on the rumen microbiota and nitrogen metabolism of grazing Nellore cattle. Eight castrated Nellore steers were distributed in a double-Latin-square 4 × 4 design, with a 2 × 2 factorial arrangement (two types of supplements with or without the addition of the PHA), as follows: energy supplement without the PHA addition (EW); energy supplement with the PHA addition (EPHA); mineral supplement without the addition of the PHA (MW); mineral supplement with the PHA addition (MPHA). Steers that received supplements with the PHA have a lower ruminal proportion of valerate (with the PHA, 1.06%; without the PHA, 1.15%), a lower ruminal abundance of Verrucomicrobia, and a tendency for lower DM digestibility (with the PHA, 62.8%; without the PHA, 64.8%). Energy supplements allowed for higher ammonia concentrations (+2.28 mg of NH₃-N/dL), increased the propionate proportion (+0.29% of total VFA), and had a higher ruminal abundance of Proteobacteria and Spirochaetae phyla in the rumen. The PHA addition in the supplement did not improve nitrogen retention, reduced the ruminal proportion of valerate, and had a negative impact on both the total dry-matter digestibility and the abundance of several ruminal bacterial groups belonging to the Firmicutes and Verrucomicrobia phyla. Full article

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

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12 pages, 1683 KiB

Open AccessArticle

Long-Term Monitoring of Bioaerosols in an Environment without UV and Desiccation Stress, an Example from the Cave Postojnska Jama, Slovenia

by Janez Mulec, Sara Skok, Rok Tomazin, Jasmina Letić, Tadej Pliberšek, Sanja Stopinšek and Saša Simčič

Microorganisms 2023, 11(3), 809; https://doi.org/10.3390/microorganisms11030809 - 22 Mar 2023

Cited by 2 | Viewed by 1538

Abstract

A natural cave environment subject to regular human visitation was selected for aerobiological study to minimize the effects of severe temperature fluctuations, UV radiation, and desiccation stress on the aerobiome. The longer sampling period of bioaerosols, up to 22 months, was generally not [...] Read more.

A natural cave environment subject to regular human visitation was selected for aerobiological study to minimize the effects of severe temperature fluctuations, UV radiation, and desiccation stress on the aerobiome. The longer sampling period of bioaerosols, up to 22 months, was generally not associated with a proportionally incremental and cumulative increase of microbial biomass. The culture-independent biomass indicator ATP enabled quick and reliable determination of the total microbial biomass. Total airborne microbial biomass was influenced by human visitation to the cave, as confirmed by significantly higher concentrations being observed along tourist footpaths (p < 0.05). Airborne beta-glucans (BG) and lipopolysaccharide (LPS) are present in cave air, but their impact on the cave remains to be evaluated. Staphylococcus spp., as an indicator of human presence, was detected at all sites studied. Their long-term survival decrease is likely due to high relative humidity, low temperature, the material to which they adhere, and potentially natural elevated radon concentration. The most commonly recorded species were: S. saprophyticus, which was identified in 52% of the studied sites, S. equorum in 29%, and S. warneri in 24% of the studied sites. Only a few isolates were assigned to Risk group 2: S. aureus, S. epidermidis, S. haemolyticus, S. pasteuri, and S. saprophyticus. Full article

(This article belongs to the Collection Microbial Life in Extreme Environments)

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2 pages, 201 KiB

Open AccessEditorial

Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth

by Chatragadda Ramesh and Laurent Dufossé

Microorganisms 2023, 11(3), 808; https://doi.org/10.3390/microorganisms11030808 - 22 Mar 2023

Viewed by 1107

Abstract

The exploration of the microbial world in research continues to be fascinating and unending in several aspects of taxonomy, genomics, evolution, and industrial applications [...] Full article

(This article belongs to the Special Issue Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth)

13 pages, 3791 KiB

Open AccessArticle

Antimicrobial Activity of Green Synthesized Silver Nanoparticles Using Waste Leaves of Hyphaene thebaica (Doum Palm)

by Nadiyah M. Alabdallah and Essam Kotb

Microorganisms 2023, 11(3), 807; https://doi.org/10.3390/microorganisms11030807 - 22 Mar 2023

Cited by 1 | Viewed by 1413

Abstract

Silver nanoparticles (AgNPs) were biosynthesized for the first time from waste leaves extract of local doum palms in Tabuk, Saudi Arabia. The transmission electron microscope (TEM) revealed a spherical shape with a particle size from 18 to 33 nm. The d-spacing is about [...] Read more.

Silver nanoparticles (AgNPs) were biosynthesized for the first time from waste leaves extract of local doum palms in Tabuk, Saudi Arabia. The transmission electron microscope (TEM) revealed a spherical shape with a particle size from 18 to 33 nm. The d-spacing is about 2.6 Å, which confirms a face-centered cubic crystalline building. The biosynthesized AgNPs were evaluated as an antimicrobial agent against several pathogenic bacteria, including Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, and Pseudomonas aeruginosa ATCC 27853. The highest action was exerted against S. aureus ATCC 29213 (MIC = 1.5 µg/mL). Interestingly, AgNPs also showed anticandidal activity against the pathogenic yeasts Candida albicans ATCC 14053 (MIC = 24 µg/mL) and Candida tropicalis ATCC 13803 (MIC = 96 µg/mL). Scanning electron microscope (SEM) revealed deep morphological changes in Candida spp. due to the treatment of the AgNPs. Scarce pseudohyphae, perforation, exterior roughness, irregularly shaped cells, and production of protective exopolysaccharide (EPS) were the main features. In conclusion, the process of biosynthesis of AgNPs from the aqueous leaf extract of Hyphaene thebaica is environmentally compatible and induces the biosynthesis of tiny AgNPs that could be a promising candidate in biomedical applications, including antimicrobials against some pathogenic bacteria and yeasts. Full article

(This article belongs to the Special Issue Microbial Nanotechnology)

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11 pages, 1114 KiB

Open AccessSystematic Review

Efficacy of Fecal Microbiota Transplant on Behavioral and Gastrointestinal Symptoms in Pediatric Autism: A Systematic Review

by Zahra Dossaji, Adam Khattak, Kyaw Min Tun, Mark Hsu, Kavita Batra and Annie S. Hong

Microorganisms 2023, 11(3), 806; https://doi.org/10.3390/microorganisms11030806 - 22 Mar 2023

Viewed by 4074

Abstract

Background and Aims: There is a high prevalence of gastrointestinal-related (GI) symptoms among children with autism spectrum disorder (ASD), which is associated with the severity of behavioral symptoms. Fecal microbiota transplantation (FMT) is a proposed therapeutic strategy that aims to address the dysregulation [...] Read more.

Background and Aims: There is a high prevalence of gastrointestinal-related (GI) symptoms among children with autism spectrum disorder (ASD), which is associated with the severity of behavioral symptoms. Fecal microbiota transplantation (FMT) is a proposed therapeutic strategy that aims to address the dysregulation of the gut microbiome among children with ASD. Our study performed the first systematic review aimed to evaluate the benefits of FMT on the behavioral and gastrointestinal symptoms of pediatric patients with autism. Methods: A literature search was performed using variations of the keywords “pediatrics” and “fecal microbiota transplantation” in PubMed, EMBASE, CINAHL, Cochrane, and Web of Science from inception to 30 June 2022. Four studies that met the eligibility criteria were included in the systematic review. The efficacy of FMT on behavioral symptoms was measured by the difference in Aberrant Behavior Checklist (ABC) and Child Autism Rating Scale (CARS) scores before and after FMT. Results: We found a statistically significant improvement (p < 0.05) in ABC and CARS scores following FMT, with a statistically significant decrease in scores observed across all studies. In addition, substantial improvements in gastrointestinal symptoms were observed across all studies. Conclusion: Our findings suggest that FMT may offer a promising intervention for treating both behavioral and gastrointestinal symptoms in pediatric patients with autism. Full article

(This article belongs to the Special Issue Gut Microbiota and Host Diseases)

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2 pages, 172 KiB

Open AccessEditorial

A Special Issue on Marek’s Disease Virus—The Editors’ View

by Benedikt B. Kaufer, Mark S. Parcells and Luca D. Bertzbach

Microorganisms 2023, 11(3), 805; https://doi.org/10.3390/microorganisms11030805 - 21 Mar 2023

Viewed by 1215

Abstract

Marek’s disease virus (MDV), an Alphaherpesvirus belonging to the genus Mardivirus, causes T cell lymphomas in chickens and remains one of the greatest threats to poultry production worldwide [...] Full article

(This article belongs to the Special Issue Marek’s Disease Virus)

16 pages, 878 KiB

Open AccessArticle

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required

by Márton Szoboszlay, Laetitia Schramm, David Pinzauti, Jeanesse Scerri, Anna Sandionigi and Manuele Biazzo

Microorganisms 2023, 11(3), 804; https://doi.org/10.3390/microorganisms11030804 - 21 Mar 2023

Cited by 12 | Viewed by 6467

Abstract

Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the [...] Read more.

Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants. Full article

(This article belongs to the Special Issue Microbiome-Based Medicinal Products: The Next Frontier in Medicine)

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15 pages, 2031 KiB

Open AccessArticle

16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs

by Vesselin Baev, Elena Apostolova, Velitchka Gotcheva, Miglena Koprinarova, Maria Papageorgiou, João Miguel Rocha, Galina Yahubyan and Angel Angelov

Microorganisms 2023, 11(3), 803; https://doi.org/10.3390/microorganisms11030803 - 21 Mar 2023

Cited by 2 | Viewed by 1699

Abstract

Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, [...] Read more.

Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0–78.9%). Weissella (0.9–42.8%), Herbaspirillum (1.6–3.8%), Serratia (0.1–11.7%), Pediococcus (0.2–7.5%), Bacteroides (0.1–1.3%), and Sphingomonas (0.1–0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species’ relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters—one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)—may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study. Full article

(This article belongs to the Special Issue Screening and Characterization of the Diversity of Food Microorganisms and Their Metabolites 2022)

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15 pages, 1187 KiB

Open AccessArticle

Promising Probiotic Properties of the Yeasts Isolated from Rabilé, a Traditionally Fermented Beer Produced in Burkina Faso

by Iliassou Mogmenga, Marius Kounbèsiounè Somda, Cheik Amadou Tidiane Ouattara, Ibrahim Keita, Yérobessor Dabiré, Camelia Filofteia Diguță, Radu Cristian Toma, Lewis I. Ezeogu, Jerry O. Ugwuanyi, Aboubakar S. Ouattara and Florentina Matei

Microorganisms 2023, 11(3), 802; https://doi.org/10.3390/microorganisms11030802 - 21 Mar 2023

Cited by 2 | Viewed by 1580

Abstract

In recent years, research on yeasts as probiotics has gained more and more interest, which will allow the development of “new” products in the probiotics market. In this context, seventeen yeast strains isolated from Rabilé, a traditional beer produced in Burkina Faso, [...] Read more.

In recent years, research on yeasts as probiotics has gained more and more interest, which will allow the development of “new” products in the probiotics market. In this context, seventeen yeast strains isolated from Rabilé, a traditional beer produced in Burkina Faso, were assessed for their probiotic attributes. The yeast identification was performed by molecular methods, including PCR-RFLP and 5.8S-ITS region sequencing. Saccharomyces cerevisiae (14 strains) was the predominantly identified species, followed by Pichia kudriavzevii (2 strains) and Rhodotorula mucilaginosa (1 strain). Except for R. mucilaginosa, all yeast strains grew well at human temperature. The yeast strains showed high resistance when they were exposed to simulated gastrointestinal conditions. Auto-aggregation ability was between 70.20 ± 10.53% and 91.82 ± 1.96%, while co-aggregation with E. coli ranged from 24.92 ± 3.96% to 80.68 ± 9.53% and with S. enterica serovar Typhimurium from 40.89 ± 8.18% to 74.06 ± 7.94%. Furthermore, the hydrophobicity of isolated strains toward n-hexane was in the range from 43.17 ± 5.07% to 70.73 ± 2.42%. All yeast strains displayed high antioxidant capabilities, and the strains did not show hemolysis halos, such that they can be considered safe. Additionally, S. cerevisiae strains strongly inhibited the growth of foodborne pathogens. This is the first preliminary study to identify and characterize the yeast strains isolated from Rabilé with interesting probiotic properties. Full article

(This article belongs to the Special Issue Bacteria and Fungi Probiotics)

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13 pages, 2381 KiB

Open AccessArticle

Six-Month Synbio^® Administration Affects Nutritional and Inflammatory Parameters of Older Adults Included in the PROBIOSENIOR Project

by Chiara Salvesi, Stefania Silvi, Dennis Fiorini, Laura Alessandroni, Gianni Sagratini, Francesco Alessandro Palermo, Renato De Leone, Nadaniela Egidi, Carlo Cifani, Maria Vittoria Micioni Di Bonaventura, Amedeo Amedei, Elena Niccolai, Francesca Scocchera, Fausto Mannucci, Valerio Valeriani, Marco Malavasi, Sara Servili, Andrea Casula, Andrea Cresci, Ivano Corradetti, Maria Magdalena Coman and M. Cristina Verdenelli Show full author list Hide full author list

Microorganisms 2023, 11(3), 801; https://doi.org/10.3390/microorganisms11030801 - 21 Mar 2023

Cited by 1 | Viewed by 1556

Abstract

The physiological changes associated with ageing contribute to the incidence of diseases, morbidity, and mortality. For modern society, it is essential to find solutions to improve elderly people’s health and quality of life. Among promising strategies, the PROBIOSENIOR project proposed a daily six-month [...] Read more.

The physiological changes associated with ageing contribute to the incidence of diseases, morbidity, and mortality. For modern society, it is essential to find solutions to improve elderly people’s health and quality of life. Among promising strategies, the PROBIOSENIOR project proposed a daily six-month supplementation with new probiotic functional foods and nutraceuticals. The aim of this work was to evaluate the modulating effects of the probiotic diet on inflammatory markers and nutritional status. Ninety-seven elderly volunteers were randomly assigned to either a placebo-diet group or a probiotic-diet group (SYNBIO^®). Faeces, urine, and blood samples were collected before and after the supplementation to determine serum cytokines, biogenic amines, and inflammation markers. Comparing the results obtained before and after the intervention, probiotic supplementations significantly decreased the TNF-α circulating levels and significantly increased those of IGF-1. Biogenic-amine levels showed high variability, with significant variation only for histamine that decreased after the probiotic supplementation. The supplementation influenced the serum concentration of some crucial cytokines (IL-6, IL-8, and MIP-1α) that significantly decreased in the probiotic group. In addition, the Mini Nutritional Assessment questionnaire revealed that the probiotic-supplemented group had a significant improvement in nutritional status. In conclusion, the PROBIOSENIOR project demonstrated how SYNBIO^® supplementation may positively influence some nutritional and inflammatory parameters in the elderly. Full article

(This article belongs to the Section Food Microbiology)

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13 pages, 826 KiB

Open AccessArticle

Assessing Continuity of Adherence to Precautionary Measures for COVID-19 among Vaccinated People in Jazan, Saudi Arabia

by Anwar Alameer, Yahya Maslamani, Ibrahim M. Gosadi, Mohammed Y. Elamin, Mohammed A. Muaddi, Ahmad Y. Alqassim, Abrar Doweri, Ibrahim Namis, Fatimah Busayli, Hussam Ahmadini, Yehya Hejri and Abdu Dahlan

Microorganisms 2023, 11(3), 800; https://doi.org/10.3390/microorganisms11030800 - 21 Mar 2023

Cited by 3 | Viewed by 1442

Abstract

Background: Adherence to behavioral respiratory hygiene practices is essential in preventing the transmission of COVID-19, especially given the appearance of new variants of the COVID-19 virus. This study estimated the pre- and post-vaccination levels of adherence to COVID-19 preventive behavioral measures among vaccinated [...] Read more.

Background: Adherence to behavioral respiratory hygiene practices is essential in preventing the transmission of COVID-19, especially given the appearance of new variants of the COVID-19 virus. This study estimated the pre- and post-vaccination levels of adherence to COVID-19 preventive behavioral measures among vaccinated people. Methods: This cross-sectional study assessed the sociodemographics and preventive behavioral measures, and pre- and post-vaccination data, via a questionnaire. Paired t-tests and Chi-squared tests were used to assess the variation in adherence levels. Results: Of the 480 participants, 57.9% were male, and 30.4% were aged between 30 and 39 years of age. After vaccination, there was a statistically significant decline in adherence to all the assessed behavioral protective measures (p < 0.05). Being 50 years old or older, female, a healthcare worker, and a smoker were associated with higher adherence levels compared with other groups in the same categories. Conclusions: A change in the behavior of the community members regarding COVID-19 after receiving the vaccination and a reduction in adherence to respiratory hygiene practices was observed. This indicates the importance of raising awareness about the possibility of reinfection with COVID-19 despite the vaccination, and the importance of behavioral respiratory hygiene for the prevention and control of COVID-19. Full article

(This article belongs to the Special Issue Coronaviruses: Past, Present, and Future)

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18 pages, 6916 KiB

Open AccessArticle

HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut

by Lu Li, Xiaojie Zhao and Johnny J. He

Microorganisms 2023, 11(3), 799; https://doi.org/10.3390/microorganisms11030799 - 21 Mar 2023

Cited by 1 | Viewed by 1379

Abstract

The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial [...] Read more.

The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial barrier integrity, which contribute to inflammation and immune activation. Our recent study shows that Tat expression and cocaine exposure result in changes of genome-wide DNA methylation and gene expression and lead to worsen the learning and memory impairments. In the current study, we extended the study to determine effects of Tat and cocaine on the gut microbiota composition. We found that both Tat expression and cocaine exposure increased Alteromonadaceae in 6-month-old female/male mice. In addition, we found that Tat, cocaine, or both increased Alteromonadaceae, Bacteroidaceae, Cyanobiaceae, Erysipelotrichaceae, and Muribaculaceae but decreased Clostridiales_vadinBB60_group, Desulfovibrionaceae, Helicobacteraceae, Lachnospiraceae, and Ruminococcaceae in 12-month-old female mice. Lastly, we analyzed changes of metabolic pathways and found that Tat decreased energy metabolism and nucleotide metabolism, and increased lipid metabolism and metabolism of other amino acids while cocaine increased lipid metabolism in 12-month-old female mice. These results demonstrated that Tat expression and cocaine exposure resulted in significant changes of the gut microbiota in an age- and sex-dependent manner and provide additional evidence to support the bidirectional gut–brain axis hypothesis. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems 2.0)

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12 pages, 1866 KiB

Open AccessCommunication

Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation

by Sicong Li, Jiahua Wang, Jie Liu, Hongcai Zhang, Tianqiang Bao, Chengwen Sun, Jiasong Fang and Junwei Cao

Microorganisms 2023, 11(3), 798; https://doi.org/10.3390/microorganisms11030798 - 21 Mar 2023

Cited by 1 | Viewed by 1732

Abstract

Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the [...] Read more.

Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments. Full article

(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)

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21 pages, 3548 KiB

Open AccessArticle

Characterization of the Bacterial Microbiome in Natural Populations of Barley Stem Gall Midge, Mayetiola hordei, in Morocco

by Imane Remmal, Naima Bel Mokhtar, Amal Maurady, Mohammed Reda Britel, Karim El Fakhouri, Elias Asimakis, George Tsiamis and Panagiota Stathopoulou

Microorganisms 2023, 11(3), 797; https://doi.org/10.3390/microorganisms11030797 - 21 Mar 2023

Viewed by 1993

Abstract

Mayetiola hordei (Kieffer), known as barley stem gall midge, is one of the most destructive barley pests in many areas around the world, inflicting significant qualitative and quantitative damage to crop production. In this study, we investigate the presence of reproductive symbionts, the [...] Read more.

Mayetiola hordei (Kieffer), known as barley stem gall midge, is one of the most destructive barley pests in many areas around the world, inflicting significant qualitative and quantitative damage to crop production. In this study, we investigate the presence of reproductive symbionts, the effect of geographical origin on the bacterial microbiome’s structure, and the diversity associated with natural populations of M. hordei located in four barley-producing areas in Morocco. Wolbachia infection was discovered in 9% of the natural populations using a precise 16S rDNA PCR assay. High-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene indicated that the native environments of samples had a substantial environmental impact on the microbiota taxonomic assortment. Briefly, 5 phyla, 7 classes, and 42 genera were identified across all the samples. To our knowledge, this is the first report on the bacterial composition of M. hordei natural populations. The presence of Wolbachia infection may assist in the diagnosis of ideal natural populations, providing a new insight into the employment of Wolbachia in the control of barley midge populations, in the context of the sterile insect technique or other biological control methods. Full article

(This article belongs to the Special Issue Odi Et Amo: Diversity of Insect–Microbe Interactions, from Antagonism to Mutualism, and Their Manipulation for Pest Control)

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14 pages, 6331 KiB

Open AccessArticle

Knocking Down Gm16685 Decreases Liver Granuloma in Murine Schistosomiasis Japonica

by Ruyu Zhao, Xiaoxue Tang, Huiyao Lin, Chen Xing, Na Xu, Bingxin Dai, Pingping Wang, Wei Shao, Miao Liu, Jijia Shen, Shengqun Deng and Cuiping Ren

Microorganisms 2023, 11(3), 796; https://doi.org/10.3390/microorganisms11030796 - 21 Mar 2023

Cited by 1 | Viewed by 1415

Abstract

Long noncoding RNAs (lncRNAs) can regulate key genes and pathways in liver disease development. Moreover, macrophages are speculated to play an important role in regulating granulomatous inflammation during schistosomiasis. However, the role of lncRNAs in the formation of liver granulomas by influencing the [...] Read more.

Long noncoding RNAs (lncRNAs) can regulate key genes and pathways in liver disease development. Moreover, macrophages are speculated to play an important role in regulating granulomatous inflammation during schistosomiasis. However, the role of lncRNAs in the formation of liver granulomas by influencing the polarization of macrophages in Schistosoma japonicum infection is unclear. Our study aimed to determine whether lncRNAs can play a role in S. japonicum-induced hepatic egg granulomas and elucidate their effect on macrophages. We established S. japonicum infection models and screened the target lncRNA Gm16685 highly expressed in schistosomiasis mice using high-throughput sequencing. Hematoxylin and eosin staining revealed that the knockdown of Gm16685 reduced the area of egg granulomas. Moreover, M1 macrophage factor genes were significantly downregulated in Gm16685 knockdown livers. Meanwhile, M2 macrophage factor genes were significantly upregulated, which was consistent with the protein detection results. Hepatocytes, hepatic stellate cells, and macrophages were isolated from mouse models infected with S. japonicum, with Gm16685 being significantly upregulated in macrophages. Moreover, the knockdown of Gm16685 in RAW264.7 cells revealed similar results to in liver tissue. RNA fluorescence in situ hybridization (FISH) and nucleocytoplasmic separation experiments revealed that Gm16685 was predominantly localized in the cytoplasm of cells. We found that miR-205-5p was upregulated after Gm16685 was knocked down. After overexpression of miR-205-5p, the expression of Gm16685 and inflammatory factors was significantly downregulated. These results indicate that Gm16685 can participate in the pathogenesis of hepatic disease in schistosomiasis and promote M1 macrophage polarization by regulating miR-205-5p. Thus, our study may provide a new target for schistosomiasis japonica treatment. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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11 pages, 1294 KiB

Open AccessArticle

Morphological and Molecular Characterization of Eimeria spp. Infecting Domestic Poultry Gallus gallus in Riyadh City, Saudi Arabia

by Mohammed M. Mares, Saleh Al-Quraishy, Rewaida Abdel-Gaber and Mutee Murshed

Microorganisms 2023, 11(3), 795; https://doi.org/10.3390/microorganisms11030795 - 21 Mar 2023

Cited by 4 | Viewed by 2546

Abstract

Coccidiosis in chickens is one of the major problems in the poultry industry, caused by protozoan parasites of the genus Eimeria. The current study used morphological and molecular characteristics to identify Eimeria spp. infecting domestic chickens (Gallus gallus) in the Riyadh [...] Read more.

Coccidiosis in chickens is one of the major problems in the poultry industry, caused by protozoan parasites of the genus Eimeria. The current study used morphological and molecular characteristics to identify Eimeria spp. infecting domestic chickens (Gallus gallus) in the Riyadh region of Saudi Arabia. In this study, 120 domestic poultry were examined and 30 were found to be infected with oocysts of Eimeria spp. (25%). According to the morphology of the recorded oocysts, five species were found. Eimeria necatrix was the first species discovered, and it was distinguished by oblong, ovoid-shaped oocysts with double-layered walls that measured 20 (23–23) and 17 (16–20) μm. The second species was Eimeria maxima, which had oval- to egg-shaped oocysts with double-layered walls and measurements of 28 (26–29) and 23 (20–24) μm. The third species was Eimeria tenella, characterized by oval-shaped oocysts with double-layered walls and measurements of 21 (20–24) × 17 (16–20) μm. Eimeria praecox was the fourth species that was characterized by spherical-shaped oocysts with single-layered walls and measurements of 21 (19–23) × 20 (19–20) μm. Eimeria acervulina was the last species to have oval-shaped oocysts with double-layered walls and measurements of 20 (18–25) and 17 (14–20) μm. The percentages of infection with Eimeria species were as follows: E. tenella, 10.84%; E. necatrix, 5.84%; E. acervulina, 4.16%; E. maxima, 2.5%; and E. praecox, 1.66%. Nested PCR based on the amplification of internal transcribed spacer I (ITS-I) regions confirmed the presence of the five Eimeria species in the examined fecal samples with their specific amplicon sizes: E. necatrix (383 bp), E. maxima (145 bp), E. tenella (278 bp), E. praecopx (116 bp), and E. acervulina (321 bp). Full article

(This article belongs to the Special Issue Parasitic Diseases in Livestock)

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14 pages, 9607 KiB

Open AccessArticle

Mucosa-Associated Oscillospira sp. Is Related to Intestinal Stricture and Post-Operative Disease Course in Crohn’s Disease

by Shukai Zhan, Caiguang Liu, Jixin Meng, Ren Mao, Tong Tu, Jianming Lin, Minhu Chen, Zhirong Zeng and Xiaojun Zhuang

Microorganisms 2023, 11(3), 794; https://doi.org/10.3390/microorganisms11030794 - 20 Mar 2023

Cited by 4 | Viewed by 1547

Abstract

Intestinal stricture remains one of the most intractable complications in Crohn’s disease (CD), and the involved mechanisms are poorly understood. Accumulating evidence suggests that the gut microbiota contributes to the pathogenesis of intestinal fibrosis. In this study, we investigated specific mucosa-associated microbiota related [...] Read more.

Intestinal stricture remains one of the most intractable complications in Crohn’s disease (CD), and the involved mechanisms are poorly understood. Accumulating evidence suggests that the gut microbiota contributes to the pathogenesis of intestinal fibrosis. In this study, we investigated specific mucosa-associated microbiota related to intestinal strictures and their role in predicting postoperative disease course. Twenty CD patients who had undergone operative treatments were enrolled and followed up. Intestinal mucosa and full-thickness sections from stenotic and non-stenotic sites were sterilely collected. DNA extraction and bacterial 16s rRNA gene sequencing were conducted. Radiological and histological evaluations were performed to assess fibrosis. Microbial alpha diversity was significantly decreased in stenotic sites (p = 0.009). At the genus level, Lactobacillus, Oscillospira, Subdoligranulum, Hydrogenophaga, Clostridium and Allobaculum were decreased in stenotic segments (p < 0.1). The difference in Oscillospira sp. (stenotic vs. non-stenotic) was negatively correlated with the erythrocyte sedimentation rate (correlation coefficient (CC) −0.432, p = 0.057) and white blood cell count (CC −0.392, p = 0.087) and positively correlated with serum free fatty acids (CC 0.575, p < 0.05). This difference was negatively associated with intestinal fibrosis evaluated by imagological and histological methods (CC −0.511 and −0.653, p < 0.05). Furthermore, CD patients with a higher abundance of Oscillospira sp. in the residual intestine might experience longer remission periods (p < 0.05). The mucosa-associated microbiota varied between stenotic and non-stenotic sites in CD. Most notably, Oscillospira sp. was negatively correlated with intestinal fibrosis and postoperative disease course. It could be a promising biomarker to predict post-operative disease recurrence and a microbial-based therapeutic target. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 343 KiB

Open AccessReview

Anti-Quorum Sensing Activity of Probiotics: The Mechanism and Role in Food and Gut Health

by Mohammed Kamal Salman, Jumana Abuqwider and Gianluigi Mauriello

Microorganisms 2023, 11(3), 793; https://doi.org/10.3390/microorganisms11030793 - 20 Mar 2023

Cited by 8 | Viewed by 3277

Abstract

Background: Quorum sensing (QS) is a cell-to-cell communication mechanism that occurs between inter- and intra-bacterial species and is regulated by signaling molecules called autoinducers (AIs). It has been suggested that probiotics can exert a QS inhibitory effect through their metabolites. Purpose: To provide [...] Read more.

Background: Quorum sensing (QS) is a cell-to-cell communication mechanism that occurs between inter- and intra-bacterial species and is regulated by signaling molecules called autoinducers (AIs). It has been suggested that probiotics can exert a QS inhibitory effect through their metabolites. Purpose: To provide an overview of (1) the anti-QS activity of probiotics and its mechanism against foodborne pathogenic and spoilage bacteria; (2) the potential role of the QS of probiotics in gut health; and (3) the impact of microencapsulation on QS. Results: Lactobacillus species have been extensively studied for their anti-QS activity and have been found to effectively disrupt QS in vitro. However, their effectiveness in a food matrix is yet to be determined as they interfere with the AI receptor or its synthesis. QS plays an important role in both the biofilm formation of probiotics and pathogenic bacteria. Moreover, in vitro and animal studies have shown that QS molecules can modulate cytokine responses and gut dysbiosis and maintain intestinal barrier function. In this scenario, microencapsulation was found to enhance AI activity. However, its impact on the anti-QS activity of probiotics and its underlying mechanism remains unclear. Conclusions: Probiotics are potential candidates to block QS activity in foodborne pathogenic and food spoilage bacteria. Microencapsulation increases QS efficacy. However, more research is still needed for the identification of the QS inhibitory metabolites from probiotics and for the elucidation of the anti-QS mechanism of probiotics (microcapsules and free cells) in food and the human gut. Full article

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

22 pages, 3800 KiB

Open AccessArticle

Comparative Genomic Analysis of Virulent Vibrio (Listonella) anguillarum Serotypes Revealed Genetic Diversity and Genomic Signatures in the O-Antigen Biosynthesis Gene Cluster

by Vimbai Irene Machimbirike, Ignacio Vasquez, Trung Cao, Joy Chukwu-Osazuwa, Oluwatoyin Onireti, Cristopher Segovia, Pongsak Khunrae, Triwit Rattanarojpong, Marije Booman, Simon Jones, Manuel Soto-Davila, Brian Dixon and Javier Santander

Microorganisms 2023, 11(3), 792; https://doi.org/10.3390/microorganisms11030792 - 20 Mar 2023

Cited by 4 | Viewed by 2231

Abstract

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen [...] Read more.

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen are unknown. Here, we fully sequenced and characterized a strain of V. anguillarum O1 (J382) isolated from winter steelhead trout (Oncorhynchus mykiss irideus) in British Columbia, Canada. Koch’s postulates using the O1 strain were replicated in naïve lumpfish (Cyclopterus lumpus) and compared to O2. Phenotypic and genotypic comparisons were conducted for serotypes O1, O2, and O3, using biochemical tests and bioinformatic tools, respectively. The genome of V. anguillarum O1 (J382) contains two chromosomes (3.13 Mb and 1.03 Mb) and two typical pJM1-like plasmids (65,573 and 76,959 bp). Furthermore, V. anguillarum O1 (J382) displayed resistance to colistin sulphate, which differs from serotype O2 and could be attributed to the presence of the ugd gene. Comparative genomic analysis, among the serotypes, showed that intra-species evolution is driven by insertion sequences, bacteriophages, and a different repertoire of putative ncRNAs. Genetic heterogeneity in the O-antigen biosynthesis gene cluster is characterized by the absence or the presence of unique genes, which could result in differences in the immune evasion mechanisms employed by the respective serotypes. This study contributes to understanding the genetic differences among V. anguillarum serovars and their evolution. Full article

(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals)

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11 pages, 1350 KiB

Open AccessCommunication

Probiotic Bifidobacterium breve MCC1274 Protects against Oxidative Stress and Neuronal Lipid Droplet Formation via PLIN4 Gene Regulation

by François Bernier, Tatsuya Kuhara and Jinzhong Xiao

Microorganisms 2023, 11(3), 791; https://doi.org/10.3390/microorganisms11030791 - 20 Mar 2023

Cited by 4 | Viewed by 3691

Abstract

Consumption of Bifidobacterium breve MCC1274 has been shown to improve memory and prevent brain atrophy in populations with mild cognitive impairment (MCI). Preclinical in vivo studies using Alzheimer’s disease (AD) models indicate that this probiotic protects against brain inflammation. There is growing evidence [...] Read more.

Consumption of Bifidobacterium breve MCC1274 has been shown to improve memory and prevent brain atrophy in populations with mild cognitive impairment (MCI). Preclinical in vivo studies using Alzheimer’s disease (AD) models indicate that this probiotic protects against brain inflammation. There is growing evidence that lipid droplets are associated with brain inflammation, and lipid-associated proteins called perilipins could play an important role in neurodegenerative diseases such as dementia. In this study, we found that B. breve MCC1274 cell extracts significantly decreased the expression of perilipin 4 (PLIN4), which encodes a lipid droplet docking protein whose expression is known to be increased during inflammation in SH-SY5Y cells. Niacin, an MCC1274 cell extract component, increased PLIN4 expression by itself. Moreover, MCC1274 cell extracts and niacin blocked the PLIN4 induction caused by oxidative stress in SH-SY5Y cells, reduced lipid droplet formation, and prevented IL-6 cytokine production. These results offer a possible explanation for the effect of this strain on brain inflammation. Full article

(This article belongs to the Special Issue Effects of Probiotics on Health)

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14 pages, 2340 KiB

Open AccessArticle

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

by Effimia M. Papatheodorou, Spiros Papakostas and George P. Stamou

Microorganisms 2023, 11(3), 790; https://doi.org/10.3390/microorganisms11030790 - 19 Mar 2023

Cited by 2 | Viewed by 1255

Abstract

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present [...] Read more.

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU. Full article

(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions)

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17 pages, 923 KiB

Open AccessReview

Bone Health in People Living with HIV/AIDS: An Update of Where We Are and Potential Future Strategies

by Musaab Ahmed, Dushyant Mital, Nuha Eljaili Abubaker, Maria Panourgia, Henry Owles, Ioanna Papadaki and Mohamed H. Ahmed

Microorganisms 2023, 11(3), 789; https://doi.org/10.3390/microorganisms11030789 - 19 Mar 2023

Cited by 5 | Viewed by 3820

Abstract

The developments in Human Immunodeficiency Virus (HIV) treatment and in the care of people living with HIV (PLWHIV) and Acquired Immunodeficiency Syndrome (AIDS) over the last three decades has led to a significant increase in life expectancy, on par with HIV-negative individuals. Aside [...] Read more.

The developments in Human Immunodeficiency Virus (HIV) treatment and in the care of people living with HIV (PLWHIV) and Acquired Immunodeficiency Syndrome (AIDS) over the last three decades has led to a significant increase in life expectancy, on par with HIV-negative individuals. Aside from the fact that bone fractures tend to occur 10 years earlier than in HIV-negative individuals, HIV is, per se, an independent risk factor for bone fractures. A few available antiretroviral therapies (ARVs) are also linked with osteoporosis, particularly those involving tenofovir disoproxil fumarate (TDF). HIV and hepatitis C (HCV) coinfection is associated with a greater risk of osteoporosis and fracture than HIV monoinfection. Both the Fracture Risk Assessment Tool (FRAX) and measurement of bone mineral density (BMD) via a DEXA scan are routinely used in the assessment of fracture risk in individuals living with HIV, as bone loss is thought to start between the ages of 40 and 50 years old. The main treatment for established osteoporosis involves bisphosphonates. Supplementation with calcium and vitamin D is part of clinical practice of most HIV centers globally. Further research is needed to assess (i) the cut-off age for assessment of osteoporosis, (ii) the utility of anti-osteoporotic agents in PLWHIV and (iii) how concomitant viral infections and COVID-19 in PLWHIV can increase risk of osteoporosis. Full article

(This article belongs to the Special Issue Viruses and Endocrine Diseases)

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15 pages, 1831 KiB

Open AccessArticle

Growth Dynamic and Threshold Values for Spermicidal Effects of Multidrug-Resistant Bacteria in Extended Boar Semen

by Anne-Marie Luther, Christina Beckermann, Thu Quynh Nguyen, Jutta Verspohl and Dagmar Waberski

Microorganisms 2023, 11(3), 788; https://doi.org/10.3390/microorganisms11030788 - 19 Mar 2023

Cited by 4 | Viewed by 1383

Abstract

The aim of this study was first to examine the prevalence of bacteria-associated loss of sperm quality in samples from insemination centers during a seven-year semen monitoring program and, second, to investigate the growth dynamic of four different multidrug-resistant bacterial species and their [...] Read more.

The aim of this study was first to examine the prevalence of bacteria-associated loss of sperm quality in samples from insemination centers during a seven-year semen monitoring program and, second, to investigate the growth dynamic of four different multidrug-resistant bacterial species and their impact on sperm quality during semen storage. A reduced sperm quality associated with bacterial contamination was found in 0.5% of 3219 of the samples from insemination centers. In samples spiked with Serratia marcescens and Klebsiella oxytoca, bacterial growth by six log levels was seen during storage at 17 °C, causing loss of sperm motility, membrane integrity, membrane fluidity, and mitochondrial membrane potential at >10⁷ CFU/mL (p < 0.05). Storage at 5 °C in the Androstar Premium extender efficiently inhibited their growth. Achromobacter xylosoxidans and Burkholderia cepacia showed limited growth up to two log levels at 17 °C and did not impair sperm quality. In conclusion, spermatozoa tolerate moderate loads of multidrug-resistant bacteria, and hypothermic, antibiotic-free semen storage effectively limits bacterial growth. The constant use of antibiotics in semen extenders should be reconsidered. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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15 pages, 665 KiB

Open AccessReview

Challenges and Recent Advancements in COVID-19 Vaccines

by Shao-Cheng Wang, Chung-I Rai and Yuan-Chuan Chen

Microorganisms 2023, 11(3), 787; https://doi.org/10.3390/microorganisms11030787 - 18 Mar 2023

Cited by 1 | Viewed by 3047

Abstract

Vaccination is the most effective method for the prevention of COVID-19 caused by SARS-CoV-2, which is still a global epidemic. However, the evolution of SARS-CoV-2 is so rapid that various variants, including the Alpha, Beta, Gamma, Delta, and Omicron variants, have emerged, lowering [...] Read more.

Vaccination is the most effective method for the prevention of COVID-19 caused by SARS-CoV-2, which is still a global epidemic. However, the evolution of SARS-CoV-2 is so rapid that various variants, including the Alpha, Beta, Gamma, Delta, and Omicron variants, have emerged, lowering the protection rate of vaccines and even resulting in breakthrough infections. Additionally, some rare but severe adverse reactions induced by COVID-19 vaccines may raise safety concerns and hinder vaccine promotion; however, clinical studies have shown that the benefits of vaccination outweigh the risks caused by adverse reactions. Current vaccines approved with emergency use authorization (EUA) were originally adaptive for adults only, and infants, children, and adolescents are not included. New-generation vaccines are needed to overcome the challenges of limited adaptive age population, breakthrough infection (mainly due to virus variant emergencies), and critical adverse reactions. Fortunately, some advances in COVID-19 vaccines have been obtained regarding enlarged adaptive populations for clinical applications, such as the Pfizer/BioNTech vaccine and the Moderna vaccine. In this article, we provide a review on the challenges and recent advancements in COVID-19 vaccines. The development of next-generation COVID-19 vaccines should lay emphasis on the expansion of adaptive age populations in all individuals, the induction of immune responses to viral variants, the avoidance or alleviation of rare but potentially critical adverse reactions, and the discovery of subunit vaccines with adjuvants encapsulated in nanoparticles. Full article

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

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