Microorganisms

13 pages, 3295 KiB

Open AccessArticle

In Vivo Quantification of Surfactin Nonribosomal Peptide Synthetase Complexes in Bacillus subtilis

by Maliheh Vahidinasab, Lisa Thewes, Bahar Abrishamchi, Lars Lilge, Susanne Reiße, Elvio Henrique Benatto Perino and Rudolf Hausmann

Microorganisms 2024, 12(11), 2381; https://doi.org/10.3390/microorganisms12112381 - 20 Nov 2024

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Abstract

Surfactin, a potent biosurfactant produced by Bacillus subtilis, is synthesized using a non-ribosomal peptide synthetase (NRPS) encoded by the srfAA-AD operon. Despite its association with quorum sensing via the ComX pheromone, the dynamic behavior and in vivo quantification of the NRPS complex [...] Read more.

Surfactin, a potent biosurfactant produced by Bacillus subtilis, is synthesized using a non-ribosomal peptide synthetase (NRPS) encoded by the srfAA-AD operon. Despite its association with quorum sensing via the ComX pheromone, the dynamic behavior and in vivo quantification of the NRPS complex remain underexplored. This study established an in vivo quantification system using fluorescence labeling to monitor the availability of surfactin-forming NRPS subunits (SrfAA, SrfAB, SrfAC, and SrfAD) during bioprocesses. Four Bacillus subtilis sensor strains were constructed by fusing these subunits with the megfp gene, resulting in strains BMV25, BMV26, BMV27, and BMV28. These strains displayed growth and surfactin productivity similar to those of the parental strain, BMV9. Fluorescence signals indicated varying NRPS availability, with BMV27 showing the highest and BMV25 showing the lowest relative fluorescence units (RFUs). RFUs were converted to the relative number of NRPS molecules using open-source FPCountR package. During bioprocesses, NRPS availability peaked at the end of the exponential growth phase and declined in the stationary phase, suggesting reduced NRPS productivity under nutrient-limited conditions and potential post-translational regulation. This study provides a quantitative framework for monitoring NRPS dynamics in vivo, offering insights into optimizing surfactin production. The established sensor strains and quantification system enable the real-time monitoring of NRPS availability, aiding bioprocess optimization for industrial applications of surfactin and potentially other non-ribosomal peptides. Full article

(This article belongs to the Special Issue Advances in Microbial Surfactants: Production and Applications)

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13 pages, 2054 KiB

Open AccessArticle

The Rhizobacterium Bacillus amyloliquefaciens MHR24 Has Biocontrol Ability Against Fungal Phytopathogens and Promotes Growth in Arabidopsis thaliana

by Mónica Hernández-Rodríguez, Diana Jasso-de Rodríguez, Francisco Daniel Hernández-Castillo, Ivana Moggio, Eduardo Arias, José Humberto Valenzuela-Soto and Alberto Flores-Olivas

Microorganisms 2024, 12(11), 2380; https://doi.org/10.3390/microorganisms12112380 - 20 Nov 2024

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Abstract

A novel rhizobacteria Bacillus was isolated from rhizosphere of soil associated with tomato (Solanum lycopersicum L.) under open field conditions. The Bacillus amyloliquefaciens strain MHR24 (MHR24) is a promising biocontrol agent against several fungal phytopathogens. In this research, MHR24 was characterized by [...] Read more.

A novel rhizobacteria Bacillus was isolated from rhizosphere of soil associated with tomato (Solanum lycopersicum L.) under open field conditions. The Bacillus amyloliquefaciens strain MHR24 (MHR24) is a promising biocontrol agent against several fungal phytopathogens. In this research, MHR24 was characterized by an effective antagonistic ability against Alternaria alternata (Aa), Botrytis cinerea (Bc), Fusarium oxysporum F1 (F1), F. oxysporum F2 (F2), F. oxysporum R3 (F3), and Sclerotinia sclerotiorum (Sc). In particular, MHR24 showed a strong inhibition via airborne volatiles against Bc, F3, Aa, and F2 fungal strains. MHR24 also showed elevated saline stress tolerance at 1% and 25% to NaCl and KCl. The molecular sequence analysis of 16S rDNA confirmed the identity of the isolate as Bacillus amyloliquefaciens strain MHR24. Bioassays on Arabidopsis thaliana Col-0 inoculated with MHR24 showed in in vitro conditions that MHR24 significantly increases the foliar and root area, while in growth chamber conditions, it strongly increases the dry shoot biomass of A. thaliana. The observed results indicate that B. amyloliquefaciens MHR24 has a broad-spectrum biocontrol against fungal phytopathogens and can be used as a biofertilizer and biocontrol agent to improve horticultural crops. Full article

(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)

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17 pages, 3589 KiB

Open AccessArticle

Analysis of Microbial Community Heterogeneity and Carbon Fixation Capabilities in Oil-Contaminated Soils in Chinese Onshore Oilfields

by Jiayu Song, Yakui Chen, Yilei Han, Yunzhao Li, Zheng Liu, Xingchun Li, Diannan Lu and Chunmao Chen

Microorganisms 2024, 12(11), 2379; https://doi.org/10.3390/microorganisms12112379 - 20 Nov 2024

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Abstract

This study selected 27 soil samples from four representative horizontally distributed onshore oilfields in China to explore the diversity of soil microbial communities and their carbon fixation capacity, with a focus on the potential interaction between pollution and carbon fixation under oil pollution [...] Read more.

This study selected 27 soil samples from four representative horizontally distributed onshore oilfields in China to explore the diversity of soil microbial communities and their carbon fixation capacity, with a focus on the potential interaction between pollution and carbon fixation under oil pollution stress. The analysis of the soil physicochemical properties and microbial community structures from these oilfield samples confirmed a clear biogeographic isolation effect, indicating spatial heterogeneity in the microbial communities. Additionally, the key factors influencing microbial community composition differed across regions. The dominant bacterial phyla of soil microorganisms under soil pollution stress were Proteobacteria, Actinobacteriota, Chloroflexi, Acidobacteriota, Firmicutes, Bacteroidota, and Gemmatimonadota. A correlation network analysis identified Immundisolibacter, Acinetobacter, Blastococcus, Truepera, and Kocuria as key players in the microbial network, with most showing positive correlations. The results of the KEGG database functional annotation showed that degradation and carbon fixation metabolic pathways coexist in soil samples and maintain a balanced relative abundance. These metabolic pathways highlight the functional diversity of microorganisms. Among them, prokaryotic and eukaryotic carbon fixation pathways, along with benzoate degradation pathways, are predominant. These findings establish a theoretical basis for further exploration of the synergistic mechanisms underlying pollution reduction and carbon sequestration by microorganisms in petroleum-contaminated soils. Full article

(This article belongs to the Section Environmental Microbiology)

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22 pages, 12908 KiB

Open AccessArticle

Elevation Determines Fungal Diversity, and Land Use Governs Community Composition: A Dual Perspective from Gaoligong Mountains

by Zhuanfei Zeng, Ruilong Huang and Wei Li

Microorganisms 2024, 12(11), 2378; https://doi.org/10.3390/microorganisms12112378 - 20 Nov 2024

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Abstract

Soil fungi are closely tied to their surrounding environment. While numerous studies have reported the effects of land-use practices or elevations on soil fungi, our understanding of how their community structure and diversity vary with elevation across different land-use practices remains limited. In [...] Read more.

Soil fungi are closely tied to their surrounding environment. While numerous studies have reported the effects of land-use practices or elevations on soil fungi, our understanding of how their community structure and diversity vary with elevation across different land-use practices remains limited. In the present study, by collecting soil samples from four different land uses in the Gaoligong Mountain area, namely shrublands (SLs), coffee plantations (CPs), cornfields (CFs), and citrus orchards (COs), and combining them with the changes in altitude gradients (low: 900 m, medium: 1200 m, high: 1500 m), high-throughput sequencing technology was used to analyze the composition and diversity of soil fungal communities based on the collected soil samples. The results showed that the interaction between land-use types and elevation significantly influenced the structure and diversity of fungal communities, although their relative importance in shaping fungal diversity or community structure varied. Specifically, elevation posed a stronger effect on fungal community alpha-diversity and functional guilds, whereas land-use types had a greater influence over fungal community composition. Our study reveals the individual and combined effects of land-use practices and elevation on the structure and diversity of soil fungal communities in the Gaoligong Mountain region, enhancing our understanding of the distribution patterns and driving mechanisms of soil fungal communities in this biodiversity-rich region. Full article

(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions, 2nd Edition)

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22 pages, 6076 KiB

Open AccessArticle

Genomic Insights of Wheat Root-Associated Lysinibacillus fusiformis Reveal Its Related Functional Traits for Bioremediation of Soil Contaminated with Petroleum Products

by Roderic Gilles Claret Diabankana, Akerke Altaikyzy Zhamalbekova, Aigerim Erbolkyzy Shakirova, Valeriia Igorevna Vasiuk, Maria Nikolaevna Filimonova, Shamil Zavdatovich Validov, Radik Ilyasovich Safin and Daniel Mawuena Afordanyi

Microorganisms 2024, 12(11), 2377; https://doi.org/10.3390/microorganisms12112377 - 20 Nov 2024

Viewed by 318

Abstract

The negative ecological impact of industrialization, which involves the use of petroleum products and dyes in the environment, has prompted research into effective, sustainable, and economically beneficial green technologies. For green remediation primarily based on active microbial metabolites, these microbes are typically from [...] Read more.

The negative ecological impact of industrialization, which involves the use of petroleum products and dyes in the environment, has prompted research into effective, sustainable, and economically beneficial green technologies. For green remediation primarily based on active microbial metabolites, these microbes are typically from relevant sources. Active microbial metabolite production and genetic systems involved in xenobiotic degradation provide these microbes with the advantage of survival and proliferation in polluted ecological niches. In this study, we evaluated the ability of wheat root-associated L. fusiformis MGMM7 to degrade xenobiotic contaminants such as crude oil, phenol, and azo dyes. We sequenced the whole genome of MGMM7 and provided insights into the genomic structure of related strains isolated from contaminated sources. The results revealed that influenced by its isolation source, L. fusiformis MGMM7 demonstrated remediation and plant growth-promoting abilities in soil polluted with crude oil. Lysinibacillus fusiformis MGMM7 degraded up to 44.55 ± 5.47% crude oil and reduced its toxicity in contaminated soil experiments with garden cress (Lepidium sativum L.). Additionally, L. fusiformis MGMM7 demonstrated a significant ability to degrade Congo Red azo dye (200 mg/L), reducing its concentration by over 60% under both static and shaking cultivation conditions. However, the highest degradation efficiency was observed under shaking conditions. Genomic comparison among L. fusiformis strains revealed almost identical genomic profiles associated with xenobiotic assimilation. Genomic relatedness using Average Nucleotide Identity (ANI) and digital DNA–DNA hybridization (DDH) revealed that MGMM7 is distantly related to TZA38, Cu-15, and HJ.T1. Furthermore, subsystem distribution and pangenome analysis emphasized the distinctive features of MGMM7, including functional genes in its chromosome and plasmid, as well as the presence of unique genes involved in PAH assimilation, such as phnC/T/E, which is involved in phosphonate biodegradation, and nemA, which is involved in benzoate degradation and reductive degradation of N-ethylmaleimide. These findings highlight the potential properties of petroleum-degrading microorganisms isolated from non-contaminated rhizospheres and offer genomic insights into their functional diversity for xenobiotic remediation. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 1331 KiB

Open AccessArticle

Anthocyanin-Rich Extract Mitigates the Contribution of the Pathobiont Genus Haemophilus in Mild-to-Moderate Ulcerative Colitis Patients

by Yannik Zobrist, Michael Doulberis, Luc Biedermann, Gabriel E. Leventhal and Gerhard Rogler

Microorganisms 2024, 12(11), 2376; https://doi.org/10.3390/microorganisms12112376 - 20 Nov 2024

Viewed by 365

Abstract

Anthocyanins (ACs) have been shown to elicit anti-inflammatory and antioxidant effects in animal models of ulcerative colitis (UC). Furthermore, we previously observed in a double-blind randomized trial in UC patients that biochemical disease activity tended to be lower in patients that were exposed [...] Read more.

Anthocyanins (ACs) have been shown to elicit anti-inflammatory and antioxidant effects in animal models of ulcerative colitis (UC). Furthermore, we previously observed in a double-blind randomized trial in UC patients that biochemical disease activity tended to be lower in patients that were exposed to AC. Here, we report on the changes in the fecal microbiome composition in these patients upon AC exposure. UC patients received a 3 g daily dose of an AC-rich bilberry extract (ACRE) for eight weeks. We determined the microbiome composition in longitudinal stool samples from 24 patients and quantified the degree of change over time. We also correlated the relative abundances of individual microbial taxa at different timepoints to fecal concentrations of calprotectin, a proxy for inflammation. Microbiome composition did not change over time as a result of the intervention, in terms of both alpha and beta diversity. However, before the intervention, the abundance of Haemophilus parainfluenzae was positively correlated with fecal calprotectin concentrations, and this correlation persisted in placebo-treated subjects throughout the study. In contrast, the correlation between H. parainfluenzae and calprotectin vanished in ACRE-treated subjects, while the relative abundance of H. parainfluenzae did not change. Our results suggest that ACRE treatment mitigates the contribution of H. parainfluenzae to inflammation. Further research is warranted to better comprehend the role of microbial composition in response to medical therapy including AC-rich extract in UC patients. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 2nd Edition)

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21 pages, 7388 KiB

Open AccessArticle

Genomic Insight into Zoonotic and Environmental Vibrio vulnificus: Strains with T3SS2 as a Novel Threat to Public Health

by Ling-Chao Ma, Min Li, Yi-Ming Chen, Wei-Ye Chen, Yi-Wen Chen, Zi-Le Cheng, Yong-Zhang Zhu, Yan Zhang, Xiao-Kui Guo and Chang Liu

Microorganisms 2024, 12(11), 2375; https://doi.org/10.3390/microorganisms12112375 - 20 Nov 2024

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Abstract

Vibrio vulnificus is a significant opportunistic pathogen with the highest fatality rate among foodborne microbes. However, due to a lack of comprehensive surveillance, the characteristics of isolates in China remain poorly understood. This study analyzed 60 strains of V. vulnificus isolated from diverse [...] Read more.

Vibrio vulnificus is a significant opportunistic pathogen with the highest fatality rate among foodborne microbes. However, due to a lack of comprehensive surveillance, the characteristics of isolates in China remain poorly understood. This study analyzed 60 strains of V. vulnificus isolated from diverse sources in Shanghai, including shellfish, crabs, shrimps, throat swabs of migratory birds, as well as seafood farming water and seawater. Identification of the genotypes was performed using PCR, and cytotoxicity was determined using an LDH assay. DNA was sequenced using Illumina NovaSeq followed by a bioinformatic analysis. The results demonstrated that a majority of the strains belonged to the 16S rRNA B-vcgC genotype. All strains carried five antibiotic resistance genes (ARGs), with some strains carrying over ten ARGs, mediating resistance to multiple antibiotics. Five strains possessed a highly abundant effector delivery system, which further investigations revealed to be a type III secretion system II (T3SS2), marking the first description of T3SS2 in V. vulnificus. Phylogenetic analysis indicated that it belonged to a different genetic lineage from T3SS2α and T3SS2β of V. parahaemolyticus. Bacteria with T3SS2 sequences were concentrated in coastal areas and mostly within the genus Vibrio in the global prevalence survey. Our study provides essential baseline information for non-clinical V. vulnificus and discovers the existence of T3SS2 in several strains which may be more virulent, thereby posing a new threat to human health. Full article

(This article belongs to the Section Public Health Microbiology)

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15 pages, 8460 KiB

Open AccessArticle

Alginate-Degrading Modes, Oligosaccharide-Yielding Properties, and Potential Applications of a Novel Bacterial Multifunctional Enzyme, Aly16-1

by Lianghuan Zeng, Junge Li, Jingyan Gu, Wei Hu, Wenjun Han and Yuezhong Li

Microorganisms 2024, 12(11), 2374; https://doi.org/10.3390/microorganisms12112374 - 20 Nov 2024

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Abstract

Relatively little is known about enzymes with broad substrate spectra, leading to limited applications and progress. Herein, we elucidate Aly16-1 of Streptomyces sp. strain CB16 as a novel multifunctional member of the eighth polysaccharide lyase (PL8) family, although it shared few sequence identities [...] Read more.

Relatively little is known about enzymes with broad substrate spectra, leading to limited applications and progress. Herein, we elucidate Aly16-1 of Streptomyces sp. strain CB16 as a novel multifunctional member of the eighth polysaccharide lyase (PL8) family, although it shared few sequence identities with the characterized enzymes. The recombinant enzyme rAly16-1 showed lyase activities against several acidic polysaccharides, including many glycosaminoglycan types, xanthan, and alginate. It was mannuronate (M)-preferred, endolytic, and optimal at 50 °C and pH 6.0. The smallest substrate was an ∆M-terminal (∆: unsaturated monosaccharide) trisaccharide, and the minimal product was ∆. In the final alginate digestions by rAly16-1, the fractions larger than disaccharides were ∆G-terminal (G: guluronate), while the disaccharides were mainly ∆M, showing an oligosaccharide-yielding property under the succession law. However, when degrading various oligosaccharides, rAly16-1 continued producing ∆M from the non-reducing end even when the substrates increased their sizes, quite different from the elucidated alginate lyases with variable alginate-degrading modes. Thus, co-determined by its M-preference, Aly16-1 is novel for its ∆M-yielding property in oligosaccharide preparations. Additionally, rAly16-1 can be applied in sequencing unsaturated trisaccharides, whether ∆M- or ∆G-terminal. This study provides novel insights into the characteristics and applications of a multifunctional enzyme within the PL8 family for resource explorations. Full article

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

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24 pages, 639 KiB

Open AccessReview

RNA Modifications in Pathogenic Viruses: Existence, Mechanism, and Impacts

by Yingying Zou, Zhoule Guo, Xing-Yi Ge and Ye Qiu

Microorganisms 2024, 12(11), 2373; https://doi.org/10.3390/microorganisms12112373 - 20 Nov 2024

Viewed by 447

Abstract

RNA modification is a key posttranscriptional process playing various biological roles, and one which has been reported to exist extensively in cellular RNAs. Interestingly, recent studies have shown that viral RNAs also contain a variety of RNA modifications, which are regulated dynamically by [...] Read more.

RNA modification is a key posttranscriptional process playing various biological roles, and one which has been reported to exist extensively in cellular RNAs. Interestingly, recent studies have shown that viral RNAs also contain a variety of RNA modifications, which are regulated dynamically by host modification machinery and play critical roles in different stages of the viral life cycle. In this review, we summarize the reports of four typical modifications reported on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), and N1-methyladenosine (m1A), describe the molecular mechanisms of these modification processes, and illustrate their impacts on viral replication, pathogenicity, and innate immune responses. Notably, we find that RNA modifications in different viruses share some common features and mechanisms in their generation, regulation, and function, highlighting the potential for viral RNA modifications and the related host machinery to serve as the targets or bases for the development of antiviral therapeutics and vaccines. Full article

(This article belongs to the Special Issue Viral Infection and Immunity)

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14 pages, 4998 KiB

Open AccessArticle

Organic Farming Enhances Diversity and Recruits Beneficial Soil Fungal Groups in Traditional Banana Plantations

by Maria Cristina O. Oliveira, Artur Alves, Carla Ragonezi, José G. R. de Freitas and Miguel A. A. Pinheiro De Carvalho

Microorganisms 2024, 12(11), 2372; https://doi.org/10.3390/microorganisms12112372 - 20 Nov 2024

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Abstract

This study investigates the impact of organic (OF) and conventional farming (CF) on soil fungal communities in banana monoculture plantations on Madeira Island. We hypothesized that OF promotes beneficial fungal groups over harmful ones, sustaining soil health. Soil samples were collected from six [...] Read more.

This study investigates the impact of organic (OF) and conventional farming (CF) on soil fungal communities in banana monoculture plantations on Madeira Island. We hypothesized that OF promotes beneficial fungal groups over harmful ones, sustaining soil health. Soil samples were collected from six plantations (three OF and three CF) for ITS amplicon sequencing to assess fungal diversity. Results showed that OF significantly enhanced fungal alpha-diversity (Shannon–Wiener index) and Evenness. The phylum Ascomycota dominated OF systems, while Basidiomycota prevailed in CF. Mortierella, a beneficial genus, was abundant in OF and is observed in CF but was less evident, being the genus Trechispora the most well represented in CF agrosystems. Additionally, OF was associated with higher soil pH and Mg levels, which correlated positively with beneficial fungal groups. Functional analysis revealed that OF promoted saprotrophic fungi, crucial for the decomposition of organic matter and nutrient cycling. However, both systems exhibited low levels of arbuscular mycorrhizal fungi, likely due to high phosphorus levels. These findings suggest that organic practices can enhance soil fungal diversity and health, although attention to nutrient management is critical to further improving soil–plant–fungi interactions. Full article

(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)

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18 pages, 6181 KiB

Open AccessArticle

The Colonization of Synthetic Microbial Communities Carried by Bio-Organic Fertilizers in Continuous Cropping Soil for Potato Plants

by Wenming Zhang, Shiqing Li, Pingliang Zhang, Xuyan Han, Yanhong Xing and Chenxu Yu

Microorganisms 2024, 12(11), 2371; https://doi.org/10.3390/microorganisms12112371 - 20 Nov 2024

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Abstract

Synthetic microbial communities (SynComs) play significant roles in soil health and sustainable agriculture. In this study, bacterial SynComs (SCBs) and fungal SynComs (SCFs) were constructed by selecting microbial species that could degrade the potato root exudates associated with continuous cropping obstacles. SCBs, SCFs, [...] Read more.

Synthetic microbial communities (SynComs) play significant roles in soil health and sustainable agriculture. In this study, bacterial SynComs (SCBs) and fungal SynComs (SCFs) were constructed by selecting microbial species that could degrade the potato root exudates associated with continuous cropping obstacles. SCBs, SCFs, and SCB + SCF combinations were then inoculated into organic fertilizers (OFs, made from sheep manure) to produce three bio-organic fertilizers (BOFs), denoted by SBFs (BOFs of inoculated SCBs), SFFs (BOFs of inoculated SCFs), and SBFFs (BOFs of inoculated SCB + SCF combinations), respectively. The OF and three BOFs, with a chemical fertilizer (CK) as the control, were then used in pot experiments involving potato growth with soil from a 4-year continuous cropping field. Microbial diversity sequencing was used to investigate the colonization of SCBs and SCFs into the rhizosphere soil and the bulk soil, and their effects on soil microbial diversity were evaluated. Source Tracker analysis showed that SCBs increased bacterial colonization from the SBFs into the rhizosphere soil, but at a relatively low level of 1% of the total soil bacteria, while SCFs increased fungi colonization from the SFF into the bulk soil at a much higher level of 5–18% of the total soil fungi. In combination, SCB + SCF significantly increased fungi colonization from the SBFF into both the bulk soil and the rhizosphere soil. Overall, the soil fungi were more susceptible to the influence of the BOFs than the bacteria. In general, the application of BOFs did not significantly change the soil microbial alpha diversity. Correlation network analysis showed that key species of bacteria were stable in the soils of the different groups, especially in the rhizosphere soil, while the key species of fungi significantly changed among the different groups. LEfSe analysis showed that the application of BOFs activated some rare species, which were correlated with improvements in the function categories of the tolerance of stress, nitrogen fixation, and saprotroph functions. Mantel test analysis showed that the BOFs significantly affected soil physicochemical properties, influencing bacterial key species, and core bacteria, promoting potato growth. It was also noted that the presence of SynCom-inoculated BOFs may lead to a slight increase in plant pathogens, which needs to be considered in the optimization of SynCom applications to overcome continuous cropping obstacles in potato production. Full article

(This article belongs to the Topic Interactions between Plants and Soil Microbes in Natural Ecosystem)

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12 pages, 1824 KiB

Open AccessArticle

Differential Cytotoxic Effects of Cell-Free Supernatants of Emerging Pathogens Escherichia albertii and Escherichia fergusonii on Four Cell Lines Reveal Vero Cells as a Putative Candidate for Cytotoxicity Analysis

by Kandhan Srinivas, Sandeep Ghatak, Kekungu-u Puro, Zakir Hussain, Mosuri Chendu Bharat Prasad, Arockiasamy Arun Prince Milton, Careen Liza Pakyntein, Dadimi Bhargavi, Samir Das, Madesh Angappan, Vanita Lyngdoh, Sabia Khan, Nur Abdul Kader and Umjerksiar Ramshon

Microorganisms 2024, 12(11), 2370; https://doi.org/10.3390/microorganisms12112370 - 20 Nov 2024

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Abstract

Escherichia albertii and Escherichia fergusonii are recognized as emerging pathogens with zoonotic potential. Despite their increasing importance, there is a paucity of data on the cytotoxicity of these two pathogens. Therefore, in the present study, we investigated the cytotoxic potentials of the cell-free [...] Read more.

Escherichia albertii and Escherichia fergusonii are recognized as emerging pathogens with zoonotic potential. Despite their increasing importance, there is a paucity of data on the cytotoxicity of these two pathogens. Therefore, in the present study, we investigated the cytotoxic potentials of the cell-free supernatants from 10 E. albertii and 15 E. fergusonii isolates for their cytotoxic effects on four different cell lines (CHO, Vero, HeLa, and MDCK). All E. albertii isolates (100%) and all but one E. fergusonii (93.33%) were cytotoxic. E. albertii isolates produced similar cytotoxicity titres across the cell lines, whereas the Vero cell was found to be the most sensitive to toxins produced by E. fergusonii (p < 0.05), followed by HeLa and CHO cells. MDCK was the least sensitive cell line to E. fergusonii toxins (p < 0.05). PCR detection of cytotoxicity-associated genes (cdtB, stx1, and stx2) indicated uniform possession of cdtB gene by all E. albertii isolates, while stx1 and stx2 genes were harboured neither by E. albertii, nor E. fergusonii. Taken together, our results provided experimental evidence of the cytotoxic effects of these two emerging pathogens, and Vero cells were identified as an optimal candidate to study the cytotoxic effects of E. albertii and E. fergusonii. Full article

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

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15 pages, 3220 KiB

Open AccessArticle

Regulatory Standard for Determining Preoperative Skin Preparation Efficacy Underreports True Dermal Bioburden in a Porcine Model

by Hannah R. Duffy, Nicholas N. Ashton, Abbey Blair, Nathanael Hooper, Porter Stulce and Dustin L. Williams

Microorganisms 2024, 12(11), 2369; https://doi.org/10.3390/microorganisms12112369 - 20 Nov 2024

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Abstract

Medical device companies and regulatory bodies rely on a nondestructive bacterial sampling technique specified by the American Society for Testing and Materials (ASTM E1173-15) to test preoperative skin preparations (PSPs). Despite the widespread use of PSPs, opportunistic skin-flora pathogens remain the most significant [...] Read more.

Medical device companies and regulatory bodies rely on a nondestructive bacterial sampling technique specified by the American Society for Testing and Materials (ASTM E1173-15) to test preoperative skin preparations (PSPs). Despite the widespread use of PSPs, opportunistic skin-flora pathogens remain the most significant contributor to surgical site infections, suggesting that the ASTM testing standard may be underreporting true dermal bioburden. We hypothesized that ASTM E1173-15 may fail to capture deep skin-dwelling flora. To test this hypothesis, we applied ASTM E1173-15 and a full-thickness skin sampling technique, which we established previously through application to the backs of seven pigs (Yorkshire/Landrace hybrid) following a clinically used PSP (4% chlorhexidine gluconate). The results showed that samples quantified using the full-thickness skin method consistently cultured more bacteria than the ASTM standard, which principally targeted surface-dwelling bacteria. Following PSP, the ASTM standard yielded 1.05 ± 0.24 log₁₀ CFU/cm², while the full-thickness tissue method resulted in 3.24 ± 0.24 log₁₀ CFU/cm², more than a 2 log₁₀ difference (p < 0.001). Immunofluorescence images corroborated the data, showing that Staphylococcus epidermidis was present in deep skin regions with or without PSP treatment. Outcomes suggested that a full-thickness sampling technique may better evaluate PSP technologies as it resolves bioburdens dwelling in deeper skin regions. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT), Third Edition)

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17 pages, 5148 KiB

Open AccessArticle

Eukaryotic Microalgae Communities from Tropical Karstic Freshwater Lagoons in an Anthropic Disturbance Gradient Microscopic and Metagenomic Analysis

by Vanessa Rosaldo-Benitez, Gerardo A. Ayil-Chan, Natalia Labrín-Sotomayor, Ruby Valdéz-Ojeda and Yuri J. Peña-Ramírez

Microorganisms 2024, 12(11), 2368; https://doi.org/10.3390/microorganisms12112368 - 20 Nov 2024

Viewed by 388

Abstract

The Yucatan aquifer sustains the people living in the Mayan forest and its associated fauna. Human activities threaten water quality and the environmental services associated with it. To assess the eukaryotic microalgae community structure as a bioindicator of water quality, we employed a [...] Read more.

The Yucatan aquifer sustains the people living in the Mayan forest and its associated fauna. Human activities threaten water quality and the environmental services associated with it. To assess the eukaryotic microalgae community structure as a bioindicator of water quality, we employed a combined approach of microscopic and shotgun metagenomics to identify specific genera associated with shifts in physicochemical parameters in three permanent lagoons located in Campeche, Mexico. We could identify highly complex and diverse communities independent of human activity intensity, harboring an average of 362 genera at each lagoon. Of those, 85 were affected by alkalinity, carbonates, water hardness, and cyanuric acid levels. Some genera, like Nannochloropsis and Thraustotheca, showed significant negative correlations with lead concentration. The functional annotation of genes revealed these communities’ highly diverse metabolic capabilities and the pending work for extensive genomic characterization of rare clades. Full article

(This article belongs to the Special Issue Molecular Ecology of Microalgae and Cyanobacteria)

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15 pages, 300 KiB

Open AccessArticle

Survey on the Occurrence of Zoonotic Bacterial Pathogens in the Feces of Wolves (Canis lupus italicus) Collected in a Protected Area in Central Italy

by Fabrizio Bertelloni, Giulia Cagnoli and Valentina Virginia Ebani

Microorganisms 2024, 12(11), 2367; https://doi.org/10.3390/microorganisms12112367 - 20 Nov 2024

Viewed by 401

Abstract

Previous investigations have explored the involvement of wolves in parasitic and viral diseases, but data on the zoonotic bacteria are limited. The aim of this study was to assess the occurrence of bacterial zoonotic agents in 16 wolf (Canis lupus italicus) [...] Read more.

Previous investigations have explored the involvement of wolves in parasitic and viral diseases, but data on the zoonotic bacteria are limited. The aim of this study was to assess the occurrence of bacterial zoonotic agents in 16 wolf (Canis lupus italicus) fecal samples collected in a protected area in Central Italy. Campylobacter spp., Salmonella spp., Yersinia spp., Listeria monocytogenes, and Shiga Toxin-Producing Escherichia coli (STEC) were investigated by culture, while polymerase chain reaction (PCR) was employed to detect Coxiella burnetii, Mycobacterium spp., Brucella spp., and Francisella tularensis. The presence of Extended Spectrum β-Lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae was also evaluated, using selective isolation media and detection of antimicrobial resistance genes. All samples were negative for Campylobacter spp., Salmonella spp., C. burnetii, Mycobacterium spp., Brucella spp., F. tularensis, and carbapenemase-producing Enterobacteriaceae. One sample tested positive for Yersinia aldovae and three for Yersinia enterocolitica BT1A. One L. monocytogenes (serogroup IIa) and one STEC, carrying the stx1 gene, were isolated. Two ESBL isolates were detected: one Serratia fonticola, carrying bla_FONA-3/6 gene, and one Escherichia coli, carrying bla_CTX-M-1 gene. Both ESBL isolates were resistant to different antimicrobials and therefore classified as multi-drug-resistant. Our data suggest that wolves are potential carriers of zoonotic bacteria and may contribute to the environmental contamination through their feces. Full article

(This article belongs to the Special Issue Advances in Veterinary Microbiology)

17 pages, 10663 KiB

Open AccessArticle

Recombinant SAG2A Protein from Toxoplasma gondii Modulates Immune Profile and Induces Metabolic Changes Associated with Reduced Tachyzoite Infection in Peritoneal Exudate Cells from Susceptible C57BL/6 Mice

by Thaíse Anne Rocha dos Santos, Mário Cézar de Oliveira, Edson Mario de Andrade Silva, Uener Ribeiro dos Santos, Monaliza Macêdo Ferreira, Ana Luísa Corrêa Soares, Neide Maria Silva, Tiago Antônio de Oliveira Mendes, Jamilly Azevedo Leal-Sena, Jair Pereira da Cunha-Júnior, Tiago Wilson Patriarca Mineo, José Roberto Mineo, Érica Araújo Mendes, Jane Lima-Santos and Carlos Priminho Pirovani

Microorganisms 2024, 12(11), 2366; https://doi.org/10.3390/microorganisms12112366 - 20 Nov 2024

Viewed by 292

Abstract

Toxoplasmosis is a neglected disease that represents a significant public health problem. The antigenic profile of T. gondii is complex, and the immune response can lead to either susceptibility or resistance. Some antigens, such as surface antigen glycoprotein (SAG), are expressed on the [...] Read more.

Toxoplasmosis is a neglected disease that represents a significant public health problem. The antigenic profile of T. gondii is complex, and the immune response can lead to either susceptibility or resistance. Some antigens, such as surface antigen glycoprotein (SAG), are expressed on the surface of tachyzoite stages and interact with the host immune cells. In this study, we investigated the potential of the recombinant SAG2A protein of T. gondii to control parasitism and modulate the immune response in the peritoneal exudate cells (PECs) of both susceptible (C57BL/6) and resistant (BALB/c) mice using an in vitro infection model, gene expression, proteomic analysis, and bioinformatic tools. Our results showed that rSAG2A-treated PECs presented a lower parasitism in C57BL/6 mice but not in the PECs from BALB/c mice, and induced a pro-inflammatory cytokine profile in C57BL/6 mice (iNOS, TNF-α, and IL-6). rSAG2A modulated different exclusive proteins in each mouse lineage, with PECs from the C57BL/6 mice being more sensitive to modulation by rSAG2A. Additionally, biological processes crucial to parasite survival and immune response were modulated by rSAG2A in the C57BL/6 PECs, including fatty acid beta-oxidation, reactive oxygen species metabolism, interferon production, and cytokine-mediated signaling pathways. Together, our study indicates that rSAG2A controls T. gondii parasitism in susceptible C57BL/6 PECs through the modulation of pro-inflammatory cytokines and enhanced expression of proteins involved in the cytotoxic response. Full article

(This article belongs to the Special Issue Parasites and Infection: Strategies to Control, Diagnose, and Treat Parasitic Diseases)

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14 pages, 754 KiB

Open AccessArticle

A Quick Sequential Organ Failure Assessment (qSOFA) Score Greater than 1 and Shortened Ampicillin Use Predict Death and One-Year Mortality in Hospitalized Patients with Non-Perinatal Invasive Listeriosis: A Retrospective Analysis of 118 Consecutive Cases

by Shuh-Kuan Liau, Cheng-Chieh Hung, Chao-Yu Chen, Yi-Chun Liu, Yueh-An Lu, Yu-Jr Lin, Yung-Chang Chen, Ya-Chung Tian, Fan-Gang Tseng and Hsiang-Hao Hsu

Microorganisms 2024, 12(11), 2365; https://doi.org/10.3390/microorganisms12112365 - 19 Nov 2024

Viewed by 324

Abstract

Listeria monocytogenes causes listeriosis, a serious foodborne illness with a high mortality rate, especially in vulnerable populations. It accounts for 19% of foodborne deaths, with invasive cases having a mortality rate of up to 44%, leading to conditions like meningitis, bacteremia, and meningoencephalitis. [...] Read more.

Listeria monocytogenes causes listeriosis, a serious foodborne illness with a high mortality rate, especially in vulnerable populations. It accounts for 19% of foodborne deaths, with invasive cases having a mortality rate of up to 44%, leading to conditions like meningitis, bacteremia, and meningoencephalitis. However, the prognostic factors remain unclear. This study examines the hospital outcomes of invasive listeriosis and identifies risk factors for in-hospital and one-year mortality. We analyzed the electronic medical records of 118 hospitalized patients with non-perinatal, culture-proven invasive listeriosis collected over a 21-year period. The in-hospital mortality rate was 36.4%, with only 33.1% surviving one year and 22.0% surviving two years. The key findings indicate that a quick Sequential Organ Failure Assessment (qSOFA) score of ≥2 (OR 106.59, p < 0.001), respiratory failure (OR 7.58, p = 0.031), and shorter ampicillin duration (OR 0.53, p = 0.012) independently predicted poorer in-hospital outcomes. Additionally, a qSOFA score of ≥2 (OR 8.46, p < 0.001) and shorter ampicillin duration (OR 0.65, p < 0.001) were linked to higher one-year mortality. This study is the first to identify a qSOFA score of ≥2 as a significant marker for high-risk invasive listeriosis patients, with poorer outcomes linked to a qSOFA score of ≥2, respiratory failure, and shorter ampicillin use. Full article

(This article belongs to the Section Medical Microbiology)

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12 pages, 936 KiB

Open AccessReview

Hepatitis C Diagnosis and Treatment Among Indigenous People in a Canadian Context: Challenges and Community-Led Solutions

by Kate P. R. Dunn, Mia J. Biondi and Samuel S. Lee

Microorganisms 2024, 12(11), 2364; https://doi.org/10.3390/microorganisms12112364 - 19 Nov 2024

Viewed by 491

Abstract

The historical and ongoing impacts of the influence of colonization are experienced by Indigenous people in systemic racism, inequity in healthcare access, and intergenerational trauma; originating in the disruption of a way of life and seen in a grief response, with links to [...] Read more.

The historical and ongoing impacts of the influence of colonization are experienced by Indigenous people in systemic racism, inequity in healthcare access, and intergenerational trauma; originating in the disruption of a way of life and seen in a grief response, with links to disparate hepatitis C virus (HCV) prevalence. Despite this, the focus often remains on the increased incidence without a strengths-based lens. Although HCV is a global concern that can result in cirrhosis, liver failure, or cancer, diagnosing and linking people to care and treatment early can prevent advanced liver disease. Efforts to engage certain priority populations are occurring; however, historical context and current practices are often forgotten or overlooked. This is especially true with respect to Indigenous people in Canada. This review considers the published literature to elucidate the context of historical and ongoing colonizing impacts seen in the current HCV treatment gaps experienced by Indigenous people in Canada. In addition, we highlight strengths-based and Indigenous-led initiatives and programming that inspire hopefulness and steps toward community-engaged solutions to meet the World Health Organization Goals of eliminating HCV as a public health threat. Full article

(This article belongs to the Special Issue Control and Elimination of Viral Hepatitis)

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11 pages, 1327 KiB

Open AccessArticle

Antigenic Divergence from the Seasonal Vaccine of the Influenza Virus Strains Circulating in Romania During Three Successive Seasons (2021–2024)

by Ovidiu Vlaicu, Leontina Banica, Robert Hohan, Marius Surleac, Dragoş Florea, Victor Daniel Miron, Andreea Tudor, Oana Săndulescu, Anca Cristina Drăgănescu, Dan Oțelea and Simona Paraschiv

Microorganisms 2024, 12(11), 2363; https://doi.org/10.3390/microorganisms12112363 - 19 Nov 2024

Viewed by 441

Abstract

Influenza viruses continue to be an important public health threat. Vaccination is the most effective measure to control the influenza virus circulation. However, these viruses are continuously evolving through antigenic drift/shift, and thus the vaccine efficiency is affected. The aim of this study [...] Read more.

Influenza viruses continue to be an important public health threat. Vaccination is the most effective measure to control the influenza virus circulation. However, these viruses are continuously evolving through antigenic drift/shift, and thus the vaccine efficiency is affected. The aim of this study was to characterize the viral strains circulating in Romania, in a population with declining vaccination coverage, during the last three cold seasons by evaluating the hemagglutinin antigenic relatedness to the vaccine strains. All the available sequences collected between August 2021 and June 2024 were analyzed by using phylogenetic analysis and the P_epitope model to predict vaccine efficacy. The results showed that the 2021/2022 influenza season was dominated by the circulation of highly diverse clades of A(H3N2) viruses with high mutational divergence as compared to the vaccine strain, which might contribute to the reduction in vaccine efficacy. During the 2022/2023 influenza season, both influenza A and B viruses were reported, with few antigenic site mutations. The 2023/2024 influenza season was dominated by the circulation of influenza A viruses: A/H1N1pdm09 clade 6B.1A.5a.2a and A/H3N2 clade 2a.3a.1. The clade 2a.3a.1 also showed high variability when compared to the vaccine strain, presumably leading to reduced vaccine efficacy. This study illustrates the high diversity of influenza viruses circulating in a population with low vaccination coverage during the previous cold seasons. The viral diversity impacted vaccine efficacy, hence the need for public health programs to increase vaccine uptake and improve vaccine formulation in order to limit viral transmission. Full article

(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)

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12 pages, 1398 KiB

Open AccessArticle

Wound Gel Formulations Containing Poloxamer 407 and Polyhexanide Have In Vitro Antimicrobial and Antibiofilm Activity Against Wound-Associated Microbial Pathogens

by Jeyachchandran Visvalingam, Nandadeva Yakandawala, Suresh Regmi, Adetola Adeniji, Parveen Sharma and Miloslav Sailer

Microorganisms 2024, 12(11), 2362; https://doi.org/10.3390/microorganisms12112362 - 19 Nov 2024

Viewed by 582

Abstract

Chronic wounds are often caused or exacerbated by microbial biofilms that are highly resistant to antimicrobial treatments and that prevent healing. This study compared the antimicrobial and antibiofilm activity of nine topical wound treatments, comprising gels with different concentrations of poloxamer 407 (20–26%) [...] Read more.

Chronic wounds are often caused or exacerbated by microbial biofilms that are highly resistant to antimicrobial treatments and that prevent healing. This study compared the antimicrobial and antibiofilm activity of nine topical wound treatments, comprising gels with different concentrations of poloxamer 407 (20–26%) and different pH levels (4–6) and containing polyhexanide (PHMB) as an antimicrobial agent; the effects of pH on wound gels containing this agent have not been previously reported. The wound gel formulations were tested against six common wound-associated microbial pathogens: Staphylococcus aureus, S. epidermidis, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, and Candida albicans. Time-kill assays were used to assess antimicrobial activity against planktonic forms of each species, and a colony biofilm model was used to assess antibiofilm activity against existing biofilms as well as inhibition of new biofilm formation. Biofilm inhibition activity was also assessed in the presence of common wound dressing materials. Wound gels with higher pH levels exhibited stronger antimicrobial activity, while poloxamer 407 concentrations >20% negatively impacted antimicrobial activity. Wound gel formulations were identified that had antimicrobial, antibiofilm, and biofilm inhibition activity against all tested species in vitro. Biofilm inhibition activity was not affected by contact with common wound dressings. Further development of these wound gels may provide a valuable new option for the treatment and prevention of chronic wounds. Full article

(This article belongs to the Special Issue Pathogenic Biofilms: Physiology, Molecular Mechanisms and Counter Strategies)

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25 pages, 3870 KiB

Open AccessArticle

Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses

by Roland Zell, Marco Groth, Lukas Selinka and Hans-Christoph Selinka

Microorganisms 2024, 12(11), 2361; https://doi.org/10.3390/microorganisms12112361 - 19 Nov 2024

Viewed by 356

Abstract

In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete [...] Read more.

In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains. Full article

(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)

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14 pages, 978 KiB

Open AccessArticle

CMV Infection Risk Factors and Viral Dynamics After Valganciclovir Prophylaxis: 10 Years of Experience in Lung Transplant Recipients

by Sarela García-Masedo Fernández, Rosalía Laporta, Christian García Fadul, Myriam Aguilar Pérez, Jorge Anel Pedroche, Raquel Sanabrias Fernández de Sevilla, Ana Royuela, Isabel Sánchez Romero and María Piedad Ussetti Gil

Microorganisms 2024, 12(11), 2360; https://doi.org/10.3390/microorganisms12112360 - 19 Nov 2024

Viewed by 384

Abstract

(1) The prevention of cytomegalovirus (CMV) in lung transplant recipients (LTx) is based on the administration of VGC for a period of 6–12 months, but there is little information on the premature discontinuation of the drug. Our objective was to evaluate the reasons [...] Read more.

(1) The prevention of cytomegalovirus (CMV) in lung transplant recipients (LTx) is based on the administration of VGC for a period of 6–12 months, but there is little information on the premature discontinuation of the drug. Our objective was to evaluate the reasons for early cessation of VGC and the dynamics of CMV replication after discontinuation. (2) We carried out a retrospective study of LTx on VGC prophylaxis according to guidelines, with an outpatient follow-up period of >90 days. The detection of any level of CMV-DNA in the plasma (Cobas, Roche Diagnostics^®) during a period of 18 months after the discontinuation of VGC was considered positive. (3) We included 312 patients (64% male, mean age 53.50 ± 12.27; 71% D+R+, 15% D−R+, and 14% D+R−) in our study. The prescribed prophylaxis was completed by 179 patients (57.05%). The mean duration of prophylaxis was 7.17 ± 1.08 months. The recorded reasons for VGC discontinuation in 133 patients (43%) were myelotoxicity (n = 55), impaired renal function (n = 32), and gastrointestinal disturbances (n = 11). The reason for discontinuation was not recorded for 29 patients. CMV-DNA was detected in 79% (n = 246) of cases, and D+R+ and D+R− recipients showed a high risk of detection (p < 0.001). The median times to onset of CMV-DNA detection were 35 days in D+R−, 73 days in D+R+, and 96 days in D−R+ (p < 0.001). (4) Adverse effects of VGC are frequent in LTx. CMV-DNA detection is very common after the discontinuation of VGC and is related to the CMV donor and recipient serostatus. Full article

(This article belongs to the Collection Feature Papers in Medical Microbiology)

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12 pages, 1382 KiB

Open AccessArticle

Salinarimonas chemoclinalis, an Aerobic Anoxygenic Phototroph Isolated from a Saline, Sulfate-Rich Meromictic Lake

by Katia Messner, John A. Kyndt and Vladimir Yurkov

Microorganisms 2024, 12(11), 2359; https://doi.org/10.3390/microorganisms12112359 - 19 Nov 2024

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Abstract

A pink-pigmented, ovoid-rod-shaped, Gram-negative bacterial strain ML10^T was previously isolated in a study of a meromictic lake in British Columbia, Canada. It produces bacteriochlorophyll a, which is incorporated into the reaction center and light harvesting I complexes. This alongside no anaerobic [...] Read more.

A pink-pigmented, ovoid-rod-shaped, Gram-negative bacterial strain ML10^T was previously isolated in a study of a meromictic lake in British Columbia, Canada. It produces bacteriochlorophyll a, which is incorporated into the reaction center and light harvesting I complexes. This alongside no anaerobic or photoautotrophic growth supports the designation of the strain as an aerobic anoxygenic phototroph. The cells produce wavy polar flagellum and accumulate clear, refractive granules, presumed to be polyhydroxyalkanoate. Sequence of the 16S rRNA gene identified close relatedness to Salinarimonas rosea (97.85%), Salinarimonas ramus (97.92%) and Saliniramus fredricksonii (94.61%). The DNA G + C content was 72.06 mol %. Differences in cellular fatty acids and some physiological tests compared to Salinarimonadaceae members, as well as average nucleotide identity and digital DNA-DNA hybridization, define the strain as a new species in Salinarimonas. Therefore, we propose that ML10^T (=NCIMB 15586^T = DSM 118510^T) be classified as the type strain of a new species in the genus with the name Salinarimonas chemoclinalis sp. nov. Full article

(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)

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20 pages, 8040 KiB

Open AccessArticle

A Modified Novel Validated High-Throughput Hemagglutinin Inhibition Assay Using Recombinant Virus-like Particles and Human Red Blood Cells for the Objective Evaluation of Recombinant Hemagglutinin Nanoparticle Seasonal Influenza Vaccine

by Timothy S. Vincent, Mingzhu Zhu, Anand Parekh, Urvashi Patel, Shane Cloney-Clark, Andrew Klindworth, David Silva, Andrew Gorinson, Karlee Miranda, Mi Wang, Zachary Longacre, Bin Zhou, Iksung Cho, Rongman Cai, Raj Kalkeri, Louis Fries, Vivek Shinde and Joyce S. Plested

Microorganisms 2024, 12(11), 2358; https://doi.org/10.3390/microorganisms12112358 - 19 Nov 2024

Viewed by 361

Abstract

Currently available seasonal influenza vaccines confer variable protection due to antigenic changes resulting from the accumulation of diverse mutations. The analysis of new seasonal influenza vaccines is challenging in part due to the limitations of the traditional hemagglutination inhibition (HAI) assay with A/H3N2 [...] Read more.

Currently available seasonal influenza vaccines confer variable protection due to antigenic changes resulting from the accumulation of diverse mutations. The analysis of new seasonal influenza vaccines is challenging in part due to the limitations of the traditional hemagglutination inhibition (HAI) assay with A/H3N2 strains. An improved and objective novel HAI assay was developed with recombinant virus-like particles (VLPs) and an egg-derived virus as agglutinins, the oseltamivir treatment of VLPs, human red blood cells, and using an automated image reader-based analysis of hemagglutination. HAI validation was demonstrated using four VLPs and egg-derived strains, with 46–56 serum samples tested 12 times in duplicate per strain. The validated HAI assay was precise as indicated by the percent geometric coefficient of variation for intra-, inter-, and total assay precision, as well as accurate as evidenced by percent bias measurements. The assay exhibited linearity, specificity for homologous type/subtype strains, and sensitivity with a starting dilution of 1:10. Assay robustness and sample stability were demonstrated as a percentage difference compared to reference condition. Validated HAI results were equivalent for the single and duplicate sample testing and correlated well with a qualified live wild-type influenza microneutralization assay. These findings demonstrate the suitability of this high-throughput novel modified validated HAI assay for evaluating vaccine immunogenicity and efficacy. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 1252 KiB

Open AccessArticle

Prevalence, Antimicrobial Susceptibility, and Resistance Genes of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Broilers Sold in Open Markets of Dakar, Senegal

by Abdoulaye Cissé, Bissoume Sambe Ba, Ousmane Sow, Abdoul Aziz Wane, Issa Ndiaye, Cheikh Fall, Makhtar Camara and Yakhya Dieye

Microorganisms 2024, 12(11), 2357; https://doi.org/10.3390/microorganisms12112357 - 19 Nov 2024

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Abstract

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) poses a significant public health concern due to its widespread prevalence and resistance to multiple antibiotics. This study aimed to assess the prevalence, resistance profile, and carriage of ESBL-encoding genes in ESBL-Ec isolates from broilers [...] Read more.

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) poses a significant public health concern due to its widespread prevalence and resistance to multiple antibiotics. This study aimed to assess the prevalence, resistance profile, and carriage of ESBL-encoding genes in ESBL-Ec isolates from broilers in two markets of Dakar, Senegal. Sampling over a one-year period revealed that 61.7% of broilers carried ESBL-Ec in their cecum. Antibiotic susceptibility testing of 186 ESBL-Ec isolates showed high resistance to β-lactam antibiotics, including ampicillin, ticarcillin, and third-generation cephalosporins. Notably, all isolates were susceptible to imipenem. Multidrug resistance was frequent, with 91.4% of the isolates displaying this phenotype. Comparison between the two markets revealed variations in resistance to quinolones. PCR analysis detected bla_CTX-M genes in all isolates, with bla_CTX-M-1 being the most prevalent subgroup. Additionally, bla_TEM and bla_OXA genes were found in 26.3% and 2.7% of isolates, respectively, while no bla_SHV genes were detected. Combinations of ESBL genes were common, with bla_CTX-M15-bla_TEM being the most frequent. These findings highlight the widespread prevalence of ESBL-Ec in broilers from Dakar markets, indicating a potential risk of transmission to humans through the food chain. Effective surveillance and intervention strategies are crucial to mitigate the spread of antimicrobial resistance in humans and animals. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Infections and Pathogenesis of Microorganisms (Second Edition))

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1 pages, 161 KiB

Open AccessCorrection

Correction: Alvarado et al. Alginate–Bentonite Encapsulation of Extremophillic Bacterial Consortia Enhances Chenopodium quinoa Tolerance to Metal Stress. Microorganisms 2024, 12, 2066

by Roxana Alvarado, Cesar Arriagada-Escamilla, Javier Ortiz, Reinaldo Campos-Vargas and Pablo Cornejo

Microorganisms 2024, 12(11), 2356; https://doi.org/10.3390/microorganisms12112356 - 19 Nov 2024

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Abstract

In the original publication [...] Full article

(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)

17 pages, 5695 KiB

Open AccessArticle

Assembly Characteristics and Influencing Factors of the Soil Microbial Community in the Typical Forest of Funiu Mountain

by Kunrun He, Yiran Lai, Shurui Hu, Meiyi Song, Ye Su, Chunyang Li, Xinle Wu, Chunyue Zhang, Yuanhang Hua, Jinyong Huang, Shujuan Guo and Yadong Xu

Microorganisms 2024, 12(11), 2355; https://doi.org/10.3390/microorganisms12112355 - 18 Nov 2024

Viewed by 452

Abstract

Assessing the relationship between litter characteristics and soil microbial community traits across different forest types can enhance our understanding of the synergistic interactions among litter, soil, and microorganisms. This study focused on three representative forest types in the Funiu Mountains—Larix gmelinii (LG), [...] Read more.

Assessing the relationship between litter characteristics and soil microbial community traits across different forest types can enhance our understanding of the synergistic interactions among litter, soil, and microorganisms. This study focused on three representative forest types in the Funiu Mountains—Larix gmelinii (LG), Quercus aliena var. acutiserrata (QA), and Quercus aliena var. acutiserrata + Pinus armandii (QAPA). The findings indicated no significant differences in Chao1 among the three forests; however, the Shannon index exhibited an initial increase followed by a decline. NMDS and ANOSIM analyses revealed significant structural differences across these forest types. Network topological metrics (nodes, edges, average degree, and average path distance) for bacterial taxa were higher in LG and QA compared with QAPA. Additionally, LG and QA demonstrated significantly greater average niche breadth than QAPA. The results from the null models (the proportion occupied by dispersal limitation is 62.2%, 82.2%, and 64.4% in LG, QA, and QAPA), modified stochasticity ratio (LG: 0.708, QA: 0.664, and QAPA: 0.801), and neutral community models (LG: R² = 0.665, QA: R² = 0.630, and QAPA: R² = 0.665) suggested that stochastic processes predominantly govern the assembly of soil bacterial communities. Random forest analysis alongside Mantel tests highlighted LTP (litter total phosphorus), STN (soil total nitrogen), MCP (carbon-to-phosphorus ratio of microbial biomass), and SCN (soil carbon-to-nitrogen ratio) as critical factors affecting bacterial niche width; conversely LCN (litter carbon-to-nitrogen ratio), RCP (ratio of dissolved carbon to phosphorus), MCP, and SCN emerged as key determinants influencing community assembly processes. Furthermore, the PLS-SEM results underscored how both litter characteristics along with soil properties—and their associated alpha diversity—impact variations in niche breadth while also shaping community assembly dynamics overall. This research provides vital insights into understanding synergistic relationships between litter quality, soil characteristics, and microbial community across diverse forest ecosystems. Full article

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

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13 pages, 279 KiB

Open AccessArticle

Occurrence of Aggregatibacter actinomycetemcomitans and Its JP2 Genotype in a Cohort of 220 Western Australians with Unstable Periodontitis

by Nabil Khzam, Omar Kujan, Dorte Haubek and Leticia Algarves Miranda

Microorganisms 2024, 12(11), 2354; https://doi.org/10.3390/microorganisms12112354 - 18 Nov 2024

Viewed by 394

Abstract

Aim: The main purpose of the present study was to investigate the carrier rate of Aggregatibacter actinomycetemcomitans and its JP2 genotype in a cohort of 200 Western Australians diagnosed with periodontitis. Materials and Methods: In this descriptive cross-sectional study, 220 consecutive patients with [...] Read more.

Aim: The main purpose of the present study was to investigate the carrier rate of Aggregatibacter actinomycetemcomitans and its JP2 genotype in a cohort of 200 Western Australians diagnosed with periodontitis. Materials and Methods: In this descriptive cross-sectional study, 220 consecutive patients with periodontitis, aged 18 years and older, were recruited to a specialist periodontal practice in Perth City. Every patient included in this study contributed three different intra-oral samples. Periodontal, radiographical, and microbiological assessments were performed. The samples were analysed using a polymerase chain reaction for the detection of Aggregatibacter actinomycetemcomitans and its JP2 genotype using the primers and conditions described previously. A Chi-square test and logistic regression analysis were performed to evaluate the results. Results: The prevalence of Aggregatibacter actinomycetemcomitans was 28.18%. The carrier rates of A. actinomycetemcomitans in the unstimulated saliva, cheek swabs, and pooled subgingival plaque samples were 21.80%, 19.50%, and 17.70%, respectively. There was a significant correlation between the severe form of periodontitis (stage IV, grade C) and younger age (p = 0.004), positive family history of periodontitis (p < 0.001), oral hygiene method (p < 0.001), and irregular dental visit attendance (p < 0.001). The binary logistic regression analysis revealed that having severe periodontitis risk increased almost three times in those who were young (OR: 2.812) and came from a family with a history of periodontal disease (OR: 3.194). However, the risk of severe periodontitis was five times higher in those patients with tooth loss due to periodontal disease (OR: 5.071). The highly leukotoxic JP2 genotype of Aggregatibacter actinomycetemcomitans was not detected. Conclusions: This study of a Western Australian cohort confirmed the low presence of Aggregatibacter actinomycetemcomitans and the complete absence of its JP2 genotype. Young age, family history of periodontal disease, lack of flossing, irregular dental visits, and tooth loss due to periodontitis were identified as potential risk factors for periodontitis stage IV, grade C in this cohort. Full article

(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)

18 pages, 1726 KiB

Open AccessArticle

In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages

by Clarissa Reginato Taufer, Juliana da Silva and Pabulo Henrique Rampelotto

Microorganisms 2024, 12(11), 2353; https://doi.org/10.3390/microorganisms12112353 - 18 Nov 2024

Viewed by 359

Abstract

The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are [...] Read more.

The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3–V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. Bifidobacterium emerged as a potential biomarker of disease severity and a therapeutic target. Bacteroides presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. Lactobacillus showed significant changes in abundance across the COVID-19 stages. On the other hand, Akkermansia and Faecalibacterium did not show significant differences, while Oscillospira and Ruminococcus produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly Bifidobacterium and Bacteroides. Full article

(This article belongs to the Special Issue Feature Papers in Microbiomes 2025)

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18 pages, 4581 KiB

Open AccessArticle

Seasonal Characterization of the Aerobiome in Hematopoietic Stem Cell Transplant Rooms: Potential Risk for Immunosuppressed Patients

by Emilio Mariano Durán-Manuel, Edgar Fiscal-Baxin, Andres Emmanuel Nolasco-Rojas, Miguel Ángel Loyola-Cruz, Clemente Cruz-Cruz, Marianela Paredes-Mendoza, Adolfo López-Ornelas, Dulce Milagros Razo Blanco-Hernández, Nayeli Goreti Nieto-Velázquez, Aída Verónica Rodríguez-Tovar, Adrián Ramírez-Granillo, Enzo Vásquez-Jiménez, Verónica Fernández-Sánchez, Erika Gómez-Zamora, Mónica Alethia Cureño-Díaz, Andrea Milán-Salvatierra, Carlos Alberto Jiménez-Zamarripa, Claudia Camelia Calzada-Mendoza and Juan Manuel Bello-López

Microorganisms 2024, 12(11), 2352; https://doi.org/10.3390/microorganisms12112352 - 18 Nov 2024

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Abstract

Infections pose a risk for patients undergoing hematopoietic stem cell (HSC) transplants due to their immunosuppression, making them susceptible to opportunistic infections. Therefore, understanding the composition of the aerobiome in this area is vital. The aim of this study was to characterize the [...] Read more.

Infections pose a risk for patients undergoing hematopoietic stem cell (HSC) transplants due to their immunosuppression, making them susceptible to opportunistic infections. Therefore, understanding the composition of the aerobiome in this area is vital. The aim of this study was to characterize the aerobiome in an HSC transplant area, evaluating the impact of infrastructure and health personnel operations on air contamination. The environmental parameters and aerobiome of the HSC transplant area at Hospital Juárez de México were quantified over one year. Finally, a double-entry Vester matrix was constructed to classify problems according to their degree of causality. The abundance and taxonomic diversity of the aerobiome were dependent on seasonality, environmental factors, and high-efficiency filtration. Gram-positive bacteria predominated, followed by fungi and Gram-negative bacteria. ANOVA revealed significant differences in the bacterial aerobiome but not in the fungal aerobiome among the transplant rooms. Clinically, fungi such as Aspergillus fumigatus, Alternaria spp., Cladosporium spp., and Penicillium spp. were identified. ESKAPE bacteria typing revealed clonal dispersion. Finally, the Vester matrix highlighted critical problems associated with contamination due to the absence of HEPA filtration and non-adherence in patient management practices. HEPA filtration and positive pressure are essential to improve the air quality and reduce the microbiological load. However, the control areas will depend on patient management and routine activities, such as entry protocols in controlled areas. Full article

(This article belongs to the Section Public Health Microbiology)

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Microorganisms, Volume 12, Issue 11 (November 2024) – 270 articles

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