Microorganisms

24 pages, 3488 KB

Open AccessArticle

Colletotrichum scovillei and Prospective Biocontrol Agents Isolated from Asymptomatic Olive Trees

by Kallimachos Nifakos, Polina C. Tsalgatidou, Athanasios Tsafouros, Christina Angeli, Epaminondas Kartsonas, Costas Delis, Ioannis Charalampopoulos, Anastasia Venieraki and Panagiotis Katinakis

Microorganisms 2025, 13(12), 2838; https://doi.org/10.3390/microorganisms13122838 (registering DOI) - 13 Dec 2025

Abstract

Olive anthracnose is a major disease worldwide; although once chiefly attributed to Colletotrichum acutatum, it is now clear that the predominant pathogen varies among regions. In this study, we identified Colletotrichum scovillei for the first time as a latent pathogen in olive [...] Read more.

Olive anthracnose is a major disease worldwide; although once chiefly attributed to Colletotrichum acutatum, it is now clear that the predominant pathogen varies among regions. In this study, we identified Colletotrichum scovillei for the first time as a latent pathogen in olive fruits from groves in the Peloponnese, Greece, expanding the known diversity of Colletotrichum species associated with olive anthracnose. To better understand the ecological context of this finding, we examined the role of endophytic microorganisms in olive tissues and their interactions with phytopathogens. Endophytic fungi isolated from asymptomatic ripe olive fruits and leaves were characterized for phylogeny and potential pathogenicity, while competitive interactions between Colletotrichum species and other endophytes were assessed to identify potential biological control agents. In parallel, meteorological variability among sampling sites was analyzed to explore possible links with pathogen distribution. Our results indicate that naturally occurring endophytes sharing the Colletotrichum niche can suppress the necrotrophic phase of Colletotrichum spp., supporting the potential of such endophytes as sustainable tools for disease management. We detected C. scovillei in asymptomatic olives in one sampling year and confirmed its virulence via inoculation assays. This temporally limited yet virulent occurrence, alongside the activity of resident endophytes, supports an integrated, ecology-informed approach to anthracnose management. Full article

(This article belongs to the Special Issue Bio-Convergence: Microorganism Usage for Sustainability Applications)

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15 pages, 699 KB

Open AccessArticle

Operative Risk Factors and Microbiologic Profiles of Deep Infection Following Pilon Fracture Fixation

by Jackson M. Cathey, Crystal Jing, Julia E. Ralph, Kathleen Chang, Alexandra Krez, Joshua Helmkamp, Anna Bryniarski, Conor O'Neill, Samuel Adams and Albert T. Anastasio

Microorganisms 2025, 13(12), 2837; https://doi.org/10.3390/microorganisms13122837 (registering DOI) - 13 Dec 2025

Abstract

Deep tissue infection is a serious complication following operative fixation of pilon fractures, yet the influence of intraoperative factors and microbial characteristics remains underexplored. In this retrospective review of 123 patients treated with open reduction and internal fixation, we evaluated demographic, injury-related, operative, [...] Read more.

Deep tissue infection is a serious complication following operative fixation of pilon fractures, yet the influence of intraoperative factors and microbial characteristics remains underexplored. In this retrospective review of 123 patients treated with open reduction and internal fixation, we evaluated demographic, injury-related, operative, and microbiologic variables associated with deep infection. Patients who developed infection had longer operative times than those who did not. This modestly powered study found that operative duration was not independently associated with infection risk after adjustment for key covariates. Larger studies are needed to confirm this finding. Deep infection rates did not differ by surgical approach or time to fixation. Nine patients (7.3%) developed deep infection, with cultures demonstrating a heterogeneous microbial profile most commonly including Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, and Enterobacter cloacae. Deep infections resulted in nonunion in 67% (6/9), PTOA in 44% (4/9), and amputation in 33% (3/9) of cases. Full article

(This article belongs to the Section Medical Microbiology)

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28 pages, 3519 KB

Open AccessArticle

Impact of Grape Harvest Time on Wild Yeast Biodiversity and Its Influence on Wine Fermentation

by Mercè Sunyer-Figueres, Daniel Fernández-Vázquez, Cristina Cuesta-Martí, Inés Horcajo-Abal, Carlos Sánchez-Mateos, Alba Domènech, Enric Nart, Victoria A. Castillo-Olaya, Immaculada Andorrà and Miquel Puxeu

Microorganisms 2025, 13(12), 2836; https://doi.org/10.3390/microorganisms13122836 (registering DOI) - 13 Dec 2025

Abstract

Grape harvest time influences the berry composition, which impacts the organoleptic wine characteristics. Winemakers monitor technological, phenolic, and aromatic grape maturity to decide the harvest date. Little is known about the evolution of yeast ecology of grapes during the maturation period. The microbiota [...] Read more.

Grape harvest time influences the berry composition, which impacts the organoleptic wine characteristics. Winemakers monitor technological, phenolic, and aromatic grape maturity to decide the harvest date. Little is known about the evolution of yeast ecology of grapes during the maturation period. The microbiota involved in the fermentation impacts the wine composition and characteristics; therefore, changes in grape biodiversity could have an impact in fermentation kinetics and aroma compound formation. In this study, the yeast biodiversity of Grenache Noir and Carignan grapes from Montsant DO (Denomination of Origin) were analyzed at different ripening stages to assess how harvest time influences microbiota. The fermentation performance of the yeasts obtained was studied at both laboratory and pilot scales to evaluate the impact of these yeasts, both in pure and mixed cultures, on the wine’s chemical and aromatic composition as well as its sensory impact. The results indicated that early harvest favored a higher diversity of non-Saccharomyces species, whereas in more mature grapes, Saccharomyces cerevisiae species was dominant. The isolated strains of Saccharomyces differed in their fermentation performances, as well as ethanol content and acidity of wine. In general, they produced higher concentration of fermentative volatile compounds than a commercial strain. The non-Saccharomyces yeasts in mixed fermentations with the S. cerevisiae strains also impacted wine composition and characteristics, leading lower ethanol content or enhancing aromatic balance and sensory equilibrium. The results highlight that grape harvest timing influences microbial diversity and fermentative performance and thus should be considered to better determine the optimum harvest date and ensure consistent wine characteristics. Full article

(This article belongs to the Special Issue Wine Fermentation Microorganisms)

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15 pages, 834 KB

Open AccessArticle

Biofilm Formation in Arcobacter butzleri and Arcobacter cryaerophilus: Phenotypic and Genotypic Characterization of Food and Environmental Isolates

by Irena Musilová, Kateřina Kozlová and David Šilha

Microorganisms 2025, 13(12), 2835; https://doi.org/10.3390/microorganisms13122835 (registering DOI) - 13 Dec 2025

Abstract

Arcobacter butzleri and Arcobacter cryaerophilus are emerging foodborne and waterborne pathogens associated with enteritis and extraintestinal infections in humans. Their persistence in the environment and resistance to antimicrobial treatment are closely related to their ability to form biofilms, which provide protection against adverse [...] Read more.

Arcobacter butzleri and Arcobacter cryaerophilus are emerging foodborne and waterborne pathogens associated with enteritis and extraintestinal infections in humans. Their persistence in the environment and resistance to antimicrobial treatment are closely related to their ability to form biofilms, which provide protection against adverse conditions and support survival on food contact surfaces. This study evaluated both the genotypic and phenotypic aspects of biofilm formation among A. butzleri and A. cryaerophilus isolates from food and environmental sources. Six biofilm-associated genes (flaA, flaB, fliS, luxS, pta, and spoT) were detected by multiplex PCR, and biofilm production was assessed using the Christensen microtiter plate assay and Congo Red Agar (CRA) test. All A. cryaerophilus isolates carried the same gene set as A. butzleri, suggesting conserved genetic determinants of motility and Quorum sensing. However, phenotypic assays revealed interspecific variability: while most A. butzleri isolates formed strong biofilms, 70% of A. cryaerophilus strains showed moderate to strong formation despite all being CRA-negative. No direct correlation between gene presence and biofilm intensity was observed, indicating complex regulation of biofilm development. This study provides a comparative overview of biofilm formation in A. butzleri and A. cryaerophilus and highlights their adaptive potential and persistence in food-related environments. Full article

(This article belongs to the Special Issue Novel Antimicrobial Approaches in Biofilm Control in the Food Industry: Future Perspectives)

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36 pages, 8096 KB

Open AccessArticle

Enhancing Sheep Rumen Function, and Growth Performance Through Yeast Culture and Oxalic Acid Supplementation in a Hemicellulose-Based Diet

by Natnael D. Aschalew, Jialei Liu, Yuetong Liu, Wuwen Sun, Guopei Yin, Long Cheng, He Wang, Wanzhu Zhao, Longyu Zhang, Ziyuan Wang, Huaizhi Jiang, Tao Wang, Guixin Qin, Yuguo Zhen and Zhe Sun

Microorganisms 2025, 13(12), 2834; https://doi.org/10.3390/microorganisms13122834 - 12 Dec 2025

Abstract

Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects [...] Read more.

Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects of YC, OA, and their combination (YO) on rumen function, growth, and fattening in sheep. Twenty lambs were divided into 4 groups (ctrl, YC, OA, and YO; n = 5 each) and fed a diet supplemented with 2 levels of YC and 2 doses of OA for 60 days in a 2 × 2 factorial design. Growth and fattening performance, rumen microbiome analysis, serum indices and anti-oxidant levels, and metabolomic profiling were performed. Individual supplementation with YC and OA significantly increased the digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) (p < 0.001); neutral detergent fiber (NDF) (p < 0.05); and acid detergent fiber (ADF) (p < 0.001) and their interaction significantly increased dry matter intake (DMI) (p = 0.05). Serum IgA and IgM levels were higher in the supplemented groups (p < 0.05). Serum calcium levels were higher in the OA and YO groups (p < 0.001). The supplemented groups showed significantly higher growth hormone and superoxide dismutase levels (p < 0.05). The longissimus dorsi muscle had higher levels of iron in the OA and YO groups; zinc in the OA, YO, and YC groups (p < 0.01); and selenium in the YC group (p < 0.05). The OA group had a higher total antioxidant capacity. All supplemented groups showed higher bacterial richness and diversity. Ruminococcus, Succinivibrio, and Fibrobacter were positively correlated with the fermentation and digestibility parameters. The supplementation also altered metabolite levels and types in key physiological pathways. In conclusion, this supplementation improved bacterial composition, nutrient digestibility, weight gain, carcass weight and quality, serum indices, antioxidant levels and metabolomic profiles. This suggests potential for the development of dietary supplements for ruminants. Full article

(This article belongs to the Special Issue Rumen Microorganisms)

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19 pages, 1555 KB

Open AccessArticle

Screening of Lactic Acid Bacteria Tolerant to Antimicrobial Substances and Their Effects on the Quality of Cyperus esculentus Silage

by Hui Wang, Weiqi Liu, Shengyi Li, Shuan Jia and Xuzhe Wang

Microorganisms 2025, 13(12), 2833; https://doi.org/10.3390/microorganisms13122833 - 12 Dec 2025

Abstract

This study investigated the inhibitory effects of endogenous compounds from Cyperus esculentus on lactic acid bacteria and examined whether inoculation with selected strains could enhance silage fermentation quality. Lactic acid bacteria were isolated and identified from C. esculentus silage, and antibacterial assays were [...] Read more.

This study investigated the inhibitory effects of endogenous compounds from Cyperus esculentus on lactic acid bacteria and examined whether inoculation with selected strains could enhance silage fermentation quality. Lactic acid bacteria were isolated and identified from C. esculentus silage, and antibacterial assays were performed to screen strains suitable for inoculation. Results indicated that the endogenous compounds inhibited lactic acid bacteria, with sensitivity ranked as Lentilactobacillus buchneri > Lactiplantibacillus plantarum > Lacticaseibacillus rhamnosus. Scanning electron microscopy revealed no significant structural damage to bacterial cells caused by the inhibitory compounds. Metabolomic analysis suggested that these compounds may alter lactic acid bacterial metabolism by modulating key pathways, including amino acid and energy metabolism. Among the tested strains, Lcb. rhamnosus exhibited the highest tolerance to the endogenous compounds. Inoculation experiments demonstrated that the addition of Lcb. rhamnosus significantly enhanced the fermentation quality of C. esculentus silage. Full article

(This article belongs to the Special Issue Microorganisms in Silage)

26 pages, 5844 KB

Open AccessArticle

Unravelling the Genomic and Virulence Diversity of Legionella pneumophila Strains Isolated from Anthropogenic Water Systems

by Sofia Barigelli, Piotr Koper, Maya Petricciuolo, Andrea Firrincieli, Marta Palusińska-Szysz and Ermanno Federici

Microorganisms 2025, 13(12), 2832; https://doi.org/10.3390/microorganisms13122832 - 12 Dec 2025

Abstract

Legionella pneumophila, a waterborne pathogen naturally present in freshwater and capable of colonizing artificial water systems, is responsible for Legionnaires’ disease (LD), a severe form of pneumonia transmitted through inhalation of contaminated aerosols. Virulence of Legionella strains is affected by [...] Read more.

Legionella pneumophila, a waterborne pathogen naturally present in freshwater and capable of colonizing artificial water systems, is responsible for Legionnaires’ disease (LD), a severe form of pneumonia transmitted through inhalation of contaminated aerosols. Virulence of Legionella strains is affected by the plasticity of their genome, shaped by horizontal gene transfer and recombination events. Thus, contaminated water systems can host diverse Legionella populations with a distinct virulence potential. Here, we compare the genomic diversity of Legionella pneumophila strains isolated in water systems of academic buildings, together with their cytotoxicity and intracellular replication in THP-1-like macrophages. A six-year environmental surveillance revealed Legionella pneumophila contamination in 20 out of the 50 monitored sites, identifying five serogroups (sg) and 13 Sequence Types (STs). Phylogenetic investigations based on core genome multilocus sequence typing (cgMLST) and comparative genomics of representative isolates of each ST showed a broad diversity and a heterogeneous virulence repertoire, especially within the Dot/Icm and Lvh secretion systems. Following macrophage infection, a strain-dependent cytotoxicity and intracellular replication was observed, underlying significant pathogenic diversity within the same species and stage-dependent infection dynamics. Together, these results showed strain-specific genetic and phenotypic virulence traits to be considered during risk assessment in environmental surveillance. Full article

(This article belongs to the Special Issue Legionella pneumophila: A Microorganism with Thousand Faces, 2nd Edition)

30 pages, 951 KB

Open AccessReview

A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation

by Nombulelo Mntambo, Thilona Arumugam, Ashiq Pramchand, Kamlen Pillay and Veron Ramsuran

Microorganisms 2025, 13(12), 2831; https://doi.org/10.3390/microorganisms13122831 - 12 Dec 2025

Abstract

The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of [...] Read more.

The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of global microbial diversity. This bias is evident in Africa, where populations, including those in South Africa, show unique combinations of genetic variation, dietary patterns and environmental exposures that are insufficiently captured in current datasets but offer opportunities to uncover novel insights into microbial evolution and its influences on health across diverse settings. In response to this gap, this review synthesises global patterns in gut microbiota composition and diversity while situating South African findings within this broader context. We examine evidence across microbial domains, including bacteria, fungi, viruses, archaea, protozoa and helminths, and highlight the impact of dietary transitions and environmental exposures on microbial community structure. Although still emerging, research on the gut microbiome of South African populations consistently reports contrasts between rural and urban populations, with rural groups enriched in fibre-fermenting and anti-inflammatory taxa, whereas urban communities often exhibit reduced diversity and features of dysbiosis linked to Westernisation. However, limited sample sizes, heterogeneous methodologies and absence of multi-omic approaches constrain robust interpretation. These lacunae in current knowledge emphasise the urgent need for large-scale, longitudinal studies that reflect South Africa’s demographic and geographic diversity. Strengthening this evidence will not only help identify microbial signatures linked to modifiable lifestyle factors but will also guide nutrition, prevention and screening programmes to improve health in African populations. Full article

(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)

21 pages, 2928 KB

Open AccessArticle

Taxonomic and Metagenomic Survey of a Peat-Based Straw Degrading Biofertilizer

by Grigory V. Gladkov, Anastasiia K. Kimeklis, Olga V. Orlova, Tatiana O. Lisina, Tatiana S. Aksenova, Arina A. Kichko, Alexander G. Pinaev and Evgeny E. Andronov

Microorganisms 2025, 13(12), 2830; https://doi.org/10.3390/microorganisms13122830 - 12 Dec 2025

Abstract

The mobilization of complex microbial communities from natural resources can be a valuable alternative to the use of single-species biofertilizers when it comes to the decomposition of plant residues. However, the functioning and interaction of microorganisms within these communities remain largely unexplored. Our [...] Read more.

The mobilization of complex microbial communities from natural resources can be a valuable alternative to the use of single-species biofertilizers when it comes to the decomposition of plant residues. However, the functioning and interaction of microorganisms within these communities remain largely unexplored. Our task was to investigate the cellulose-degrading community using the biofertilizer BAGS (peat-based compost with straw) as an example and define its active component. For this, we monitored the succession of the biofertilizer’s taxonomic composition during two consecutive rounds of its six-month composting process, varying in the applied mineral fertilization. The amount of added nitrogen significantly affected the performance of the biofertilizer, contributing to its high cellulolytic activity. Based on the network analysis, the biofertilizer’s mature phase was determined, and its characteristic ASVs (amplicon sequence variants) were described. Metagenomic analysis of this phase revealed MAGs (metagenome-assembled genomes) corresponding to these ASVs, which contained genes for cellulose and aromatics degradation, as well as genes for nitrogen and sulfur pathways, including anaerobic nitrate reduction and thiosulfate oxidation. Thus, we propose that the cellulose-decomposing bacterial component of BAGS, associated with the mature phase, occupied different trophic niches, not limited to cellulose degradation, which should be considered when designing natural or artificial microbial systems for the decomposition of plant residues. Full article

(This article belongs to the Section Microbial Biotechnology)

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15 pages, 2041 KB

Open AccessArticle

Gut Microbiome and Metabolome Signatures Associated with Heat Tolerance in Dairy Cows

by Mingxun Li, Peng Chen, Can Liu, Shimeng Wang, Hao Zhang, Jiaxi Li, Niel A. Karrow, Yongjiang Mao and Zhangping Yang

Microorganisms 2025, 13(12), 2829; https://doi.org/10.3390/microorganisms13122829 - 12 Dec 2025

Abstract

Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome–metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 [...] Read more.

Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome–metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial–metabolite networks, exemplified by the Faecalimonas–LysoPS (16:0/0:0) and UBA737–Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial–metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle. Full article

(This article belongs to the Section Veterinary Microbiology)

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19 pages, 2566 KB

Open AccessArticle

Occurrence and Distribution of Antibiotics and Antibiotic Resistance Genes in the Water and Sediments of Reservoir-Based Drinking Water Sources in Henan, China

by Wei Yuan, Yijun Shang, Meng Bai, Mingwang Sun, Ziqiang Su, Xi Yang, Luqman Riaz, Yiping Guo and Jianhong Lu

Microorganisms 2025, 13(12), 2828; https://doi.org/10.3390/microorganisms13122828 - 12 Dec 2025

Abstract

The improper use of antibiotics accelerates the emergence of resistance via environmental selection pressures, jeopardizing public health and ecosystems by promoting the worldwide dissemination of antibiotic resistance genes (ARGs). Reservoirs, as crucial water supplies, have been recognized as primary reservoirs of ARGs, particularly [...] Read more.

The improper use of antibiotics accelerates the emergence of resistance via environmental selection pressures, jeopardizing public health and ecosystems by promoting the worldwide dissemination of antibiotic resistance genes (ARGs). Reservoirs, as crucial water supplies, have been recognized as primary reservoirs of ARGs, particularly those that originate from the Yellow River, necessitating further investigation. This study analyzed 9 ARGs, 3 mobile genetic elements (MGEs), 16 antibiotics, and 10 heavy metals in water/sediments from three reservoirs originating from the Yellow River in Henan Province, China. The findings indicated that antibiotic concentrations in water exceeded those in sediment, with quinolones detected at 100% frequency (5.47–116.03 ng/L) and enrofloxacin predominating (3.36–107.71 ng/L). Redundancy analysis revealed that MGEs exert greater control over ARG dissemination than antibiotics, with intI1 showing strong positive correlations with sul1 (p < 0.05). Conversely, heavy metals (Zn, As, Cd) suppress ARG proliferation through negative selection pressures. A network study indicated Mycobacterium, Pseudarthrobacter, and Massilia as critical hosts for ermB, tetA, and qnrA, respectively. Of the three reservoirs, Jian’gang Reservoir, driven by synergistic effects of unique microbial ecology, water self-purification capacity, and flow dynamics, exhibited the best removal effectiveness of ARGs from input to outflow, with 71.75% in the water and 97.91% in the sediment. These findings provide critical insights into the prevalence, migration, and self-purification processes of ARGs in reservoirs originating from the Yellow River, integrating environmental factors and microbial data to clarify the complex dynamics affecting ARG behavior and inform targeted pollution control strategies. Full article

(This article belongs to the Special Issue Microbiological Approaches to Water Pollution Control and Water Ecological Restoration)

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19 pages, 489 KB

Open AccessReview

Efficacy of Antimicrobials Against Enveloped and Non-Enveloped Viruses on Porous Materials: A Review

by Jinge Huang, Breanna Kimbrell, Runan Yan, Angela M. Fraser and Xiuping Jiang

Microorganisms 2025, 13(12), 2827; https://doi.org/10.3390/microorganisms13122827 - 12 Dec 2025

Abstract

Fomites are common vehicles for viral transmission. Most studies on virus disinfection have focused on non-porous, hard surfaces, with few investigating porous materials. This review addresses two research questions: (1) What affects viral viability on reusable porous materials? (2) Which antimicrobials effectively target [...] Read more.

Fomites are common vehicles for viral transmission. Most studies on virus disinfection have focused on non-porous, hard surfaces, with few investigating porous materials. This review addresses two research questions: (1) What affects viral viability on reusable porous materials? (2) Which antimicrobials effectively target viruses on these materials? Among existing studies, viral persistence on reusable porous surfaces was influenced by several factors, including viral envelope status, virus subtype, material type and structure, temperature, relative humidity, deposition method, and transmission medium. Disinfectants evaluated included ultraviolet irradiation, steam, chlorine, quaternary ammonium compounds, alcohols, glutaraldehyde, silver, and peroxide-based agents. Chlorine and steam were most effective; glutaraldehyde and peroxides showed limited action against non-enveloped viruses. Viral persistence and disinfection efficacy on reusable porous materials are influenced by multiple factors, highlighting the need for robust environmental management and infection control practices. Lack of standard tests and long-term disinfection effects on material integrity remain key challenges needing further study. Full article

(This article belongs to the Special Issue New Developments in Virus Detection and Disinfection in the Environment)

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16 pages, 1156 KB

Open AccessReview

Advances in Lignocellulose-Degrading Enzyme Discovery from Anaerobic Rumen Fungi

by Rajan Dhakal, Wei Guo, Ricardo Augusto M. Vieira, Leluo Guan and André Luis Alves Neves

Microorganisms 2025, 13(12), 2826; https://doi.org/10.3390/microorganisms13122826 - 12 Dec 2025

Abstract

Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further [...] Read more.

Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further characterization. Anaerobic rumen fungi play a pivotal role in lignocellulose degradation due to their unique enzymatic capabilities. This review explores the enzymatic systems of rumen anaerobic fungi, highlighting their ability to produce a diverse array of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. These enzymes facilitate the breakdown of complex plant polymers, making anaerobic fungi essential contributors to fiber degradation in the rumen ecosystem and valuable resources for biotechnological applications. This review summarizes the structural and functional diversity of fungal CAZymes, and the mechanical disruption of plant cell walls by fungal rhizoidal networks is discussed, showcasing the ability of fungi to enhance substrate accessibility and facilitate microbial colonization. Recent studies using genomic, transcriptomic, and biochemical approaches have uncovered several novel CAZymes in anaerobic fungi, including multifunctional xylanases, β-glucosidases, and esterases. These findings highlight the continued expansion of fungal enzyme repertoires and their potential for biotechnology and feed applications. Continued research in this field will enhance our understanding of microbial ecology and enzyme function, paving the way for applications that address global challenges in energy, food security, and environmental sustainability. Full article

(This article belongs to the Section Microbial Biotechnology)

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14 pages, 2223 KB

Open AccessArticle

Genetic Diversity of Siberian Isolates of Borrelia burgdorferi Sensu Lato by the ospA Gene

by Yana Igolkina, Vera Rar, Valeriy Yakimenko, Alevtina Bardasheva, Valeria Fedorets, Alfrid Karimov, Gavril Rubtsov, Tamara Epikhina and Nina Tikunova

Microorganisms 2025, 13(12), 2825; https://doi.org/10.3390/microorganisms13122825 - 11 Dec 2025

Abstract

The genetic diversity of the ospA gene of the Borrelia burgdorferi sensu lato species complex encoding outer surface protein A has been widely investigated. However, the information on the genetic variability of Borrelia isolates from Siberia for this gene is limited. In [...] Read more.

The genetic diversity of the ospA gene of the Borrelia burgdorferi sensu lato species complex encoding outer surface protein A has been widely investigated. However, the information on the genetic variability of Borrelia isolates from Siberia for this gene is limited. In this study, we analyzed complete ospA gene sequences from 36 Borrelia isolates from Western Siberia, comprising 6 Borrelia afzelii, 16 Borrelia bavariensis, 1 Borrelia garinii, and 13 “Candidatus Borrelia sibirica” isolates. The obtained ospA gene sequences of B. afzelii were conserved and formed a single clade. In contrast, B. bavariensis sequences were highly variable, segregating into two distinct clades consistent with the phylogeography of Asian isolates. Notably, the B. bavariensis samples identified in molted Ixodes trianguliceps and Ixodes apronophorus were first characterized for the ospA gene; the obtained sequences corresponded to those from I. persulcatus. This study provides the first characterization of the ospA gene in “Candidatus B. sibirica”, revealing highly conserved sequences (99.8–100% intraspecific identity). The ospA gene sequences of “Candidatus B. sibirica” shared less than 88.7% identity with those of other Borrelia genospecies. Phylogenetic analysis placed “Candidatus B. sibirica” in a unique, well-supported clade, confirming its distinct phylogenetic status and suggesting potential ecological specialization in nidicolous Ixodes species. Full article

(This article belongs to the Special Issue One Health Research on Zoonotic Tick-Borne Pathogens)

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12 pages, 1496 KB

Open AccessCommunication

Genomic Insights into bla_NDM-5-Producing Escherichia coli ST648 Isolates from Human and Wildlife Sources in Lebanon

by Zahraa F. Samadi, Ziad C. Jabbour, Zeinab R. Hodroj, Hadi M. Hussein, Abdallah Kurdi, Lama Hamadeh, Rami Mahfouz, Mahmoud I. Khalil, Rana El Hajj, Ghassan M. Matar and Antoine G. Abou Fayad

Microorganisms 2025, 13(12), 2824; https://doi.org/10.3390/microorganisms13122824 - 11 Dec 2025

Abstract

Escherichia coli sequence type 648 (ST648), a lineage within the clinically important phylogroup F, has disseminated worldwide in humans and animals. In this study, we performed whole-genome sequencing and comparative genomic analysis for two New Delhi metallo-beta-lactamase (bla_NDM-5) carrying E. [...] Read more.

Escherichia coli sequence type 648 (ST648), a lineage within the clinically important phylogroup F, has disseminated worldwide in humans and animals. In this study, we performed whole-genome sequencing and comparative genomic analysis for two New Delhi metallo-beta-lactamase (bla_NDM-5) carrying E. coli strains: ECsOL198, recovered from a wild Eurasian otter in Northern Lebanon, and ECOL247, isolated from a hospitalized leukemia patient. Both isolates belonged to phylogroup F and serotype O9:H4, and exhibited IncFIA, IncFIB, and IncFII plasmids. They shared a similar antimicrobial resistance profile, including a carbapenemase gene (bla_NDM-5), β-lactamase genes (bla_TEM-1, bla_CTX-M-15, and bla_OXA-1), and other genes that confer resistance to aminoglycosides (acc(3)-Ile, aadA2), sulfonamides (sul1), tetracyclines (tet(A)), and fluoroquinolones (mutations in gyrA and parC). Both isolates also carried common virulence-associated genes related to adhesion, iron acquisition, environmental persistence, and immune evasion. Whole-genome multilocus sequence typing (wgMLST) revealed that both isolates formed a distinct subclade closely related to a bloodstream-derived ST648 isolate from India, indicating limited relatedness to global clones. These findings highlight the transmission of nearly clonal multidrug-resistant E. coli ST648 in both clinical and non-clinical settings, raising concerns about the threat to public health. Full article

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

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17 pages, 1387 KB

Open AccessReview

The Mechanisms of Bacillus subtilis as a Plant-Beneficial Rhizobacterium in Plant–Microbe Interactions

by Mark Owusu Adjei, Ruohan Yu, Xianming Cao and Ben Fan

Microorganisms 2025, 13(12), 2823; https://doi.org/10.3390/microorganisms13122823 - 11 Dec 2025

Abstract

The rhizosphere is a dynamic microenvironment where plants interact with diverse native microbial communities that significantly influence growth, health, and resilience. Among plant-growth-promoting rhizobacteria, Bacillus subtilis stands out as a multifunctional species with exceptional ability to colonize plant roots, form robust biofilm, and [...] Read more.

The rhizosphere is a dynamic microenvironment where plants interact with diverse native microbial communities that significantly influence growth, health, and resilience. Among plant-growth-promoting rhizobacteria, Bacillus subtilis stands out as a multifunctional species with exceptional ability to colonize plant roots, form robust biofilm, and confer protection against diseases. Its resilience as a spore-former, genetic ability to produce active compounds such as antibiotics, and phytohormones make it a valuable species for agriculture and forest sustainability. This review reveals the molecular and physiological mechanisms underlying B. subtilis interactions with plants, focusing on biofilm formation, root colonization, biocontrol and disease suppression, and promotion of plant growth. We further examine its role in root colonization, which triggers extensive reprogramming of plant gene expression, thereby integrating growth promotion with enhanced immune competence through a network that regulates plant-beneficial traits. Its genomic regulation supports colonization, stress tolerance, and immune support, while synergistic interactions with other microbes highlight its adaptability. As a versatile bio-fertilizer and biocontrol agent, further study of its strain-specific traits and rhizosphere interactions is key to maximizing its role in sustainable agriculture and forest control under environmental changes. Full article

(This article belongs to the Collection Feature Papers in Plant Microbe Interactions)

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14 pages, 1834 KB

Open AccessArticle

Effects of Adding Astragali Radix and Inulae Radix on Fermentation Quality, Nutrient Preservation, and Microbial Community in Barley Silage

by Ying Yun, Ying Ying, Juanjuan Sun, Jinmei Zhao, Wenxi Wang and Boyang Kang

Microorganisms 2025, 13(12), 2822; https://doi.org/10.3390/microorganisms13122822 - 11 Dec 2025

Abstract

Chinese herbal medicine (CHM) residues represent a promising and sustainable category of silage additives, with the potential to modulate fermentation and enhance nutrient preservation. This study investigated the effects of two CHMs, Astragalus membranaceus L. (Astragali Radix, AR) and Inula helenium L. (Inulae [...] Read more.

Chinese herbal medicine (CHM) residues represent a promising and sustainable category of silage additives, with the potential to modulate fermentation and enhance nutrient preservation. This study investigated the effects of two CHMs, Astragalus membranaceus L. (Astragali Radix, AR) and Inula helenium L. (Inulae Radix, IR), on the fermentation profile, nutritional composition, and bacterial community structure in barley silage. The forage was ensiled without additive (control, CK), or with 1% or 2% (w/w) of AR or IR for 75 days. The results showed that all additive treatments significantly improved fermentation quality, as evidenced by lower pH and reduced ammonia-nitrogen (NH₃-N) content compared to CK. The 2% IR treatment was most effective in promoting homolactic fermentation, yielding the highest lactic acid content and lactic acid-to-acetic acid ratio. Nutritionally, additives significantly increased dry matter, starch, and water-soluble carbohydrates, while decreasing neutral and acid detergent fiber contents. High-throughput sequencing of the 16S rRNA gene revealed that both herbal additives profoundly reshaped the microbial community. They suppressed undesirable bacteria and significantly enriched beneficial Lactobacillus species. Principal component analysis confirmed a distinct separation in microbial community structure between control and treated silages. These findings underscore the potential of these herbal residues as natural modulators of the silage microbiome for improved forage conservation. Full article

(This article belongs to the Special Issue Microorganisms in Silage)

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13 pages, 495 KB

Open AccessReview

Advances in Novel Detection Technologies for Occult Hepatitis B Virus Infection: Building an Ultra-Sensitive Barrier for Transfusion Safety

by Meng Yi, Yuwei Hu, Bin Fan, Yiming Pan, Bo Pan, Jue Wang and Zhong Liu

Microorganisms 2025, 13(12), 2821; https://doi.org/10.3390/microorganisms13122821 - 11 Dec 2025

Abstract

Occult hepatitis B virus infection (OBI), characterized by extremely low viral loads and the persistent intrahepatic presence of cccDNA, poses a profound challenge to global public health security. With a prevalence ranging from 0.06% to over 15% in different donor populations, OBI maintains [...] Read more.

Occult hepatitis B virus infection (OBI), characterized by extremely low viral loads and the persistent intrahepatic presence of cccDNA, poses a profound challenge to global public health security. With a prevalence ranging from 0.06% to over 15% in different donor populations, OBI maintains a risk of transmission and can progress to hepatocellular carcinoma. Its prevention and control have long been limited by the sensitivity constraints of conventional detection methods, highlighting the urgent need for more sensitive diagnostic innovations. Emerging technologies offer distinct breakthroughs: ddPCR facilitates absolute quantification; CRISPR-Cas systems coupled with isothermal amplification enable rapid, point-of-care testing; third-generation sequencing resolves viral integration and mutations; and nanomaterials enhance the signal detection. This review synthesises advancements in OBI diagnostic technologies and provides a comparative overview of their strengths, limitations, and transfusion safety implications, as well as their potential applications in blood transfusion. Recommendations are also proposed to inform the advancement of OBI risk control in blood transfusion and to guide the development of novel diagnostic technologies, particularly relevant to regions with high HBV endemicity, such as China. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Hepatitis Viruses: Who They Are and Consequences)

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19 pages, 5804 KB

Open AccessArticle

Epstein–Barr Virus Promotes Gastric Cancer Progression by Modulating m6A-Dependent YTHDF1–TSC22D1 Axis

by Yea Rim An, Jaehun Jung, Kyeong Min Kwon, Jun Yeob Kim, Min-Hyeok Lee, Ju Yeon Lee, Minho Lee and Suk Kyeong Lee

Microorganisms 2025, 13(12), 2820; https://doi.org/10.3390/microorganisms13122820 - 11 Dec 2025

Abstract

Epstein–Barr virus (EBV) infection is closely associated with gastric cancer, yet its role in m6A-dependent gene regulation remains poorly understood. In this study, we investigated how EBV infection alters the m6A methylation pattern in gastric cancer cells and examined its impact on TSC22D1 [...] Read more.

Epstein–Barr virus (EBV) infection is closely associated with gastric cancer, yet its role in m6A-dependent gene regulation remains poorly understood. In this study, we investigated how EBV infection alters the m6A methylation pattern in gastric cancer cells and examined its impact on TSC22D1 mRNA stability through interaction with the m6A reader protein YTHDF1. m6A RNA immunoprecipitation sequencing (MeRIP-seq) revealed a significant reduction in m6A methylation of TSC22D1 in EBV-infected gastric cancer cells (AGS-EBV) compared with EBV-negative cells (AGS). Moreover, YTHDF1 knockdown increased both the stability and expression of TSC22D1. These findings demonstrate that YTHDF1 binds to TSC22D1 mRNA and promotes its m6A-dependent degradation. Collectively, our results suggest that EBV infection modulates m6A modification to regulate gene stability and identify the YTHDF1–TSC22D1 axis as a potential therapeutic target in EBV-associated gastric cancer. Full article

(This article belongs to the Section Virology)

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