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Microorganisms

Microorganisms is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with Microorganisms, and their members receive a discount on the article processing charges.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q1 (Microbiology (medical))
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.2 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Testimonials: See what our editors and authors say about Microorganisms.
Companion journal for Microorganisms include: Applied Microbiology and Bacteria.

Impact Factor: 4.2 (2024); 5-Year Impact Factor: 4.6 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2076-2607

Latest Articles

28 pages, 3573 KB

Open AccessArticle

Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot

by Xingxun Dai, Yuqin He, Yu Su, Huishu Mo, Weichun Li, Wanting Li, Shuhui Zi, Lufeng Liu and Yining Di

Microorganisms 2025, 13(9), 2202; https://doi.org/10.3390/microorganisms13092202 - 19 Sep 2025

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile [...] Read more.

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

(This article belongs to the Section Plant Microbe Interactions)

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21 pages, 3200 KB

Open AccessArticle

Probiotic Potential of Lactic Acid Bacteria Isolated from Moroccan Traditional Food Products

by Ange Olivier Parfait Yao, Majid Mounir, Hary Razafindralambo and Philippe Jacques

Microorganisms 2025, 13(9), 2201; https://doi.org/10.3390/microorganisms13092201 - 19 Sep 2025

This study assessed the performance and potential use of lactic acid bacteria (LAB) from Moroccan traditional foods as probiotics in animal feed. Five LAB strains Lactiplantibacillus plantarum from whey sourdough, Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides from goat cheese, Enterococcus durans and Lacticaseibacillus casei [...] Read more.

This study assessed the performance and potential use of lactic acid bacteria (LAB) from Moroccan traditional foods as probiotics in animal feed. Five LAB strains Lactiplantibacillus plantarum from whey sourdough, Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides from goat cheese, Enterococcus durans and Lacticaseibacillus casei from fermented milk were isolated and identified by 16S rRNA gene sequencing and MALDI-TOF mass spectrometry. Probiotic traits were evaluated by measuring acid/bile tolerance, cell surface hydrophobicity, emulsifying properties, antimicrobial activity and organic acid production, and safety checked through hemolysis and antibiotic sensitivity tests. L. plantarum, L. casei, and E. durans showed high survival rates after 24 h of culture under acid/bile stress conditions. The surface hydrophobicity of all strains ranged from 14.4 to 39.2%. L. plantarum showed the highest emulsifying capacity (81.4%) and stability (20%) after 24 h. Most strains inhibited pathogenic Staphylococcus epidermidis, Bacillus cereus, and Escherichia coli. Metabolite profiling revealed L. pseudomesenteroides as an interesting butyric acid-producing bacterium and L. plantarum as a remarkable strain releasing high content of organic acids. Their antibiotic susceptibility and non-hemolytic nature support their safety and potential use as feed additives. Full article

(This article belongs to the Section Microbial Biotechnology)

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22 pages, 1640 KB

Open AccessArticle

Proteomic Research of the Stress Response of Saccharomyces cerevisiae W303 Yeast to Metal Ions Eluted from Orthodontic Appliances

by Lara Dežulović, Božena Ćurko-Cofek and Gordana Čanadi Jurešić

Microorganisms 2025, 13(9), 2200; https://doi.org/10.3390/microorganisms13092200 - 19 Sep 2025

Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as [...] Read more.

Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as a model organism was investigated. Experimental yeast media in which metal ions (iron, aluminum, nickel, chromium, copper, and manganese) were eluted for 3, 7, 14, and 28 days were prepared and then used for yeast cultivation (up to the early stationary growth phase). The growth, increase, and viability of the cells were tested. The mitochondria were isolated from the spheroplasts, and the mitochondrial proteins were obtained and analyzed by liquid chromatography/mass spectrometry. Fortythree significantly altered proteins were identified. They showed significantly reduced expression in all metal-treated groups compared to the control. The metabolic processes for energy supply (glycolysis, gluconeogenesis, tricarboxylic acid cycle, and adenosine triphosphate synthesis) dominated with 50% of the total amount of significantly altered proteins in all samples, but their proportions changed at different time points. The downregulation of mitochondrial proteins such as Atp1, Atp2, and Pet9 under conditions of metal overload suggests a broader impairment of mitochondrial function. Three levels of response to stress can be observed—at relatively low metal ion concentrations in the medium (3 days of elution, approx. 3 mg/L), at medium concentrations (7 days of elution, approx. 5.5 mg/L), and at high concentrations (>8 mg/L, 14 and 28 days of elution), each affecting a specific group of proteins. The results show that mixtures of metal ions in experimental media led to a specific response (in terms of the amount and type of proteins) in each sample type to combat the provoked stress. Full article

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research, 2nd Edition)

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25 pages, 1882 KB

Open AccessReview

Neutralizing Antibodies vs. Viruses: Interacting Mechanisms and Escape Tactics

by Hao Lu, Yichen Liu, Yue Song, Longxin Chen, Limeng Zhang, Runting Li, Xiaoning Nie, Guoqiang Zhu, Xueyan Ding and Linqing Wang

Microorganisms 2025, 13(9), 2199; https://doi.org/10.3390/microorganisms13092199 - 19 Sep 2025

Virus-neutralizing antibodies (VNAs) serve as critical components of host immune defense, countering viral infections by specifically recognizing epitopes on viral surface antigens to block viral entry and replication. This review elucidates the functional mechanisms of VNAs, with a focus on the dynamic interactions [...] Read more.

Virus-neutralizing antibodies (VNAs) serve as critical components of host immune defense, countering viral infections by specifically recognizing epitopes on viral surface antigens to block viral entry and replication. This review elucidates the functional mechanisms of VNAs, with a focus on the dynamic interactions between the Fab region and viral epitopes, including steric hindrance and conformational locking, as well as the effector functions mediated by the Fc segment. Furthermore, we dissect diverse viral evasion strategies against neutralization that have emerged in recent studies, encompassing antigenic drift/shift, glycan shielding, epitope occlusion, antibody-dependent enhancement, and mutation accumulation under population immune pressure. Integrating structural biology insights with clinical evidence, we analyze challenges in developing broadly neutralizing antibodies and highlight innovative technological approaches. Our synthesis aims to establish a theoretical framework for the rational design and clinical translation of next-generation VNAs, thereby advancing novel strategies for antiviral therapeutics development. Full article

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

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20 pages, 2671 KB

Open AccessArticle

Role of NaCl and Glutamine on Biofilm Production from Pseudomonas aeruginosa

by Laura Maria De Plano, Antonella Iaconis, Salvatore Papasergi, Francesco Mediati, Daniele Caruso, Salvatore Pietro Paolo Guglielmino and Domenico Franco

Microorganisms 2025, 13(9), 2198; https://doi.org/10.3390/microorganisms13092198 - 19 Sep 2025

Pseudomonas aeruginosa is an opportunistic pathogen capable of forming antibiotic-resistant biofilms, contributing to persistent infections and treatment failure. Environmental factors such as osmolarity and nutrient availability are known to influence biofilm formation and virulence. In this study, we investigated the effects of NaCl [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen capable of forming antibiotic-resistant biofilms, contributing to persistent infections and treatment failure. Environmental factors such as osmolarity and nutrient availability are known to influence biofilm formation and virulence. In this study, we investigated the effects of NaCl depletion and glutamine supplementation on biofilm production in three P. aeruginosa strains: the laboratory strain ATCC 27853 and two clinical isolates with distinct antibiotic resistance profiles and phenazine production patterns (P. aeruginosa Pr, pyorubrin-producing, and P. aeruginosa Pc, pyocyanin-producing). Bacteria were cultured in standard Luria–Bertani (LB) medium, LB without NaCl, and LB in which yeast extract was replaced by glutamine. For each strain and condition, we assessed growth kinetics, phenazine production, and biofilm formation. Biofilm development was quantified via XTT assays and compared to secondary metabolite profiles. NaCl removal did not substantially affect growth, whereas glutamine supplementation reduced growth, especially in the laboratory strain. Both conditions modulated secondary metabolite production and biofilm formation in a strain-specific manner. In P. aeruginosa ATCC 27853, NaCl depletion significantly increased pyoverdine, pyocyanin, and QS gene expression, while biofilm formation showed significant differences only at 72 h; in contrast, glutamine supplementation affected only pyoverdine. A similar trend was observed in the clinical strain P. aeruginosa Pc, although NaCl depletion did not significantly impact pyoverdine production but already enhanced biofilm formation at 48 h. In P. aeruginosa Pr, only glutamine appeared to alter the considered parameters, increasing pyoverdine production while reducing pyocyanin and biofilm levels, although the absence of NaCl also negatively impacted biofilm formation. These findings highlight the impact of osmotic and nutritional signals on P. aeruginosa virulence traits. Full article

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

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15 pages, 401 KB

Open AccessArticle

Targeted Screening with the Use of Clinical Risk Factors for Detecting Congenital Cytomegalovirus Infection in Newborns: A Prospective Multicenter Cohort Study

by Soromon Kataoka, Masatoki Kaneko, Li Yang, Hajime Ota, Moeka Seki, Aya Kobamatsu, Daiki Nakayama, Yu Furuta, Fumie Tanuma, Yoshiyuki Fukushi, Shinichiro Wada, Keiji Haseyama and Hideto Yamada

Microorganisms 2025, 13(9), 2197; https://doi.org/10.3390/microorganisms13092197 - 19 Sep 2025

Congenital cytomegalovirus infection (cCMV) is one of the most common congenital infections. This study aimed to evaluate the diagnostic performance of targeted screening with the use of clinical risk factors for cCMV. A total of 3063 pregnant women and their 3139 newborns were [...] Read more.

Congenital cytomegalovirus infection (cCMV) is one of the most common congenital infections. This study aimed to evaluate the diagnostic performance of targeted screening with the use of clinical risk factors for cCMV. A total of 3063 pregnant women and their 3139 newborns were enrolled. Six clinical findings consisting of maternal fever or flu-like symptoms during pregnancy (fever/flu-like symptoms), hospitalization for threatened miscarriage or preterm labor before 34 weeks of gestation, preterm delivery before 34 weeks of gestation, fetal ultrasound abnormalities, small for gestational age (SGA), and refer results of automated auditory brainstem response screening (AABR refer) were defined as cCMV risk factors before participant registration. All newborns underwent urine cytomegalovirus polymerase chain reaction tests within one week of birth. The predictive accuracy of these six risk factors was analyzed. Nine (0.29%) of the three thousand one hundred and thirty-nine newborns were diagnosed with cCMV, having at least one of the six risk factors. Logistic regression analysis identified fever/flu-like symptoms (odds ratio (OR), 7.5; 95% CI, 1.9–30.3), fetal ultrasound abnormalities (OR, 17.9; 95% CI, 4.4–72.8), SGA (OR, 6.8; 95% CI, 1.8–25.6), and AABR refer (OR, 75.5; 95% CI, 19.7–289) as significant risk factors. The predictive accuracy of the targeted screening for cCMV, when at least one of the six risk factors was present, yielded 100% sensitivity (95% CI, 55.5–100) and 70.7% specificity (95% CI, 69.1–72.3), with a Youden index of 0.707. When at least one of the four significant risk factors was present, 100% sensitivity (95% CI, 55.5–100) and 81.2% specificity (95% CI, 79.8–82.6) with the maximum Youden index of 0.812 were achieved. In conclusion, targeted screening with the use of clinical risk factors in mothers and their newborns could effectively identify cCMV. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Infections in the Immunocompromised Host)

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31 pages, 2380 KB

Open AccessArticle

Metabarcoding Unveils Seasonal Soil Microbiota Shifts and Their Influence on Boletus edulis and Boletus reticulatus Mycelium in Quercus robur Stands

by Serena Santolamazza-Carbone, Laura Iglesias-Bernabé, Elena Benito-Rueda, Esther Barreal and Pedro Pablo Gallego

Microorganisms 2025, 13(9), 2196; https://doi.org/10.3390/microorganisms13092196 - 19 Sep 2025

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in [...] Read more.

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in Galicia (NW Spain) and their relationship with Boletus edulis and Boletus reticulatus mycelium prevalence and concentration. Soil microbiota richness, diversity, and composition, as well as seasonal variation in Boletus mycelium, were assessed using DNA metabarcoding and qPCR, respectively. Sampling was conducted in autumn at two 30–40-year-old Q. robur stands. Bacterial communities were dominated by Acidobacteria (34%) and Proteobacteria (33%), with Acidobacterium (12%), Paludibaculum (9%), and Edaphobacter (7%) identified as most abundant. Fungal communities were primarily Basidiomycota (93%), led by Russula (46%). For both bacteria and fungi, the highest OTU richness was observed in September, followed by a significant decrease in October and a partial recovery in November. Boletus species were found to exhibit positive correlations with specific bacteria (e.g., Massilia, Rhizobium) and fungi (e.g., Amanita, Clavaria, Inocybe, Scleroderma, Suillus and Mortierella), suggesting a potential influence of these microbes on mycelium development. This study provides novel insights into the seasonal dynamics of soil microbiota and their potential role in Boletus ecology, thereby advancing understanding of host–microbe interactions in temperate forests. Full article

(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture, 2nd Edition)

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13 pages, 946 KB

Open AccessArticle

Acanthospermum australe Extract Inhibits the Chaperone Activity of Plasmodium falciparum Heat Shock Protein 70-1

by Ntombikhona Appear Koza, Ntokozo Nkosinathi Myeza, Heinrich Hoppe, Rebamang Anthony Mosa, Abidemi Paul Kappo, Mthokozisi Blessing Cedric Simelane and Andrew Rowland Opoku

Microorganisms 2025, 13(9), 2195; https://doi.org/10.3390/microorganisms13092195 - 19 Sep 2025

The resistance of malaria parasites towards the current antimalarial therapies continues to fuel the search for new antimalarial drugs, preferably from natural sources. This study aimed to investigate the potential of the dichloromethane extract of Acanthospermum australe to inhibit Plasmodium falciparum heat shock [...] Read more.

The resistance of malaria parasites towards the current antimalarial therapies continues to fuel the search for new antimalarial drugs, preferably from natural sources. This study aimed to investigate the potential of the dichloromethane extract of Acanthospermum australe to inhibit Plasmodium falciparum heat shock protein 70-1 (PfHsp70-1). The plasmodium lactate dehydrogenase (pLDH) assay was used to determine the antiplasmodial activity of the crude extract against the chloroquine-sensitive P. falciparum strain 3D7. The inhibitory effect of the plant extract on the chaperone activity of P. falciparum heat shock protein 70-1 (PfHsp70-1) was determined using the ATPase, thermally induced luciferase and malate dehydrogenase (MDH) assays. The extract showed a significantly high activity against P. falciparum strain 3D7 with an IC₅₀ value of 1.3 µg/mL. A decrease in thermally induced aggregation of MDH and luciferase was observed when each of the proteins was incubated with PfHsp70-1 only. However, an increased protein aggregation was observed when the proteins were incubated with PfHsp70-1 in the presence of the plant extract. The extract also exhibited inhibitory activity on the ATPase activity of PfHsp70-1. The results obtained from this study suggest that A. australe extract contains compounds that could target malaria parasite Hsp70 functions. Full article

(This article belongs to the Special Issue Research on Mosquito-Borne Pathogens)

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16 pages, 599 KB

Open AccessReview

An Overview of the Epidemiology of Multidrug Resistance and Bacterial Resistance Mechanisms: What Solutions Are Available? A Comprehensive Review

by Victoria Birlutiu and Rares-Mircea Birlutiu

Microorganisms 2025, 13(9), 2194; https://doi.org/10.3390/microorganisms13092194 - 19 Sep 2025

Antimicrobial resistance has emerged as one of the most critical public health challenges of the 21st century, threatening to undermine the foundations of modern medicine. In 2019, bacterial infections accounted for 13.6% of all global deaths, with more than 7.7 million fatalities directly [...] Read more.

Antimicrobial resistance has emerged as one of the most critical public health challenges of the 21st century, threatening to undermine the foundations of modern medicine. In 2019, bacterial infections accounted for 13.6% of all global deaths, with more than 7.7 million fatalities directly attributable to 33 bacterial pathogens, most prominently Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Resistance mechanisms are multifactorial, encompassing enzymatic degradation, target modification, efflux pump overexpression, reduced membrane permeability, and biofilm formation, often in combination, leading to multidrug-resistant, extensively drug-resistant, and pandrug-resistant phenotypes. Alarmingly, projections estimate that by 2050 AMR could result in over 10 million deaths annually. This comprehensive review synthesizes global epidemiological data, insights into bacterial resistance mechanisms, and emerging therapeutic solutions, including novel antibiotics such as lasso peptides and macrocyclic peptides (e.g., zosurabalpin), naturally derived compounds (e.g., corallopyronin, clovibactin, chlorotonil A), and targeted inhibitors (e.g., Debio 1453 for Neisseria gonorrhoeae). Addressing the AMR crisis requires coordinated international efforts, accelerated drug discovery, and the integration of innovative non-antibiotic approaches to preserve the efficacy of existing therapies and ensure preparedness against future bacterial threats. Full article

(This article belongs to the Special Issue The Epidemiology, Clinical Aspects, Treatment and Preventive Strategies for Infectious Diseases in the Era of Antimicrobial Resistance (AMR))

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20 pages, 1651 KB

Open AccessReview

Emerging Roles of the Gut Microbiome in Musculoskeletal Injury and Repair

by Joseph L. Roberts and Connor C. Park

Microorganisms 2025, 13(9), 2193; https://doi.org/10.3390/microorganisms13092193 - 19 Sep 2025

Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, [...] Read more.

Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, and inflammatory or autoimmune conditions. Recently, a growing body of evidence has revealed a compelling relationship between gut microbiota composition and musculoskeletal injury recovery, highlighting its potential as a novel therapeutic target. Musculoskeletal injuries, including fractures, post-traumatic osteoarthritis, and tendon or ligament injuries, commonly lead to changes in the community structure of the gut microbiota, intestinal permeability, and systemic inflammation, processes known to negatively influence tissue repair. Preclinical studies demonstrate that microbiota-targeted interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, effectively restore gut barrier integrity, modulate inflammation, and normalize gut-derived metabolite profiles. Despite these promising findings, critical gaps remain in translating these effects into clinical practice, particularly regarding the mechanisms linking specific microbiota changes to improved musculoskeletal healing outcomes. Future research incorporating rigorous clinical trials, multi-omics analyses, and advanced predictive tools, including artificial intelligence and microbiome-informed digital twins, is urgently needed to fully harness the therapeutic potential of microbiome-based interventions in musculoskeletal injury recovery. This narrative review provides insights into our evolving understanding of the relationship between the gut microbiota and musculoskeletal injury and explores the potential of gut microbiota-targeted therapies for improved healing outcomes. Full article

(This article belongs to the Special Issue Intestine as a Hub for Host-Microbe Interactions and Its Impact on Local and Systemic Health)

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19 pages, 3409 KB

Open AccessArticle

Unveiling Bacterial Diversity in Portuguese Red Wine Effluents Through a Metagenomic Approach

by Ana Gabriela Gomes, Ana Cláudia Sousa, João S. Carreira, Alberto Oliveira, Marta C. Justino and Carla Amarelo Santos

Microorganisms 2025, 13(9), 2192; https://doi.org/10.3390/microorganisms13092192 - 19 Sep 2025

The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard–winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples [...] Read more.

The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard–winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples collected at a winery in the Setúbal Peninsula, Portugal. Metagenomic analysis targeting the 16S rRNA gene was used to characterise microbial diversity and identify taxa with potential relevance for biotechnology and environmental applications. The effluents exhibited a diverse microbiome, including Prevotella paludivivens, species from the Lactobacillus genus, and members of the Clostridiaceae family, the latter representing about 5% of the total community. Functional profiling of lactic acid bacteria revealed the predominance of Oenococcus and Lactobacillus genera, highlighting adaptive traits that may be beneficial under stress conditions. These results suggest that winery effluents, often considered waste, harbour microbial communities with functional potential that extends beyond fermentation, contributing to a broader grape–wine microbial system. The findings emphasise the value of studying winemaking byproducts as reservoirs of microbial diversity and as resources for developing innovative and sustainable applications in biotechnology and environmental management within the wine industry. Full article

(This article belongs to the Special Issue Microbiology of the Grape-Wine System)

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14 pages, 4266 KB

Open AccessArticle

Detection of Aeromonas hydrophila by Basic and Fluorescent MIRA Assays

by Qiuya Huang, Fa Dai, Lujia Su, Miaomiao Zhang, Xinjie Miao, Yujie Ding, Cheng Xu and Jiehao Xu

Microorganisms 2025, 13(9), 2191; https://doi.org/10.3390/microorganisms13092191 - 19 Sep 2025

Aeromonas hydrophila is a prevalent opportunistic pathogen in aquaculture. To establish a rapid, convenient, and accurate detection method for A. hydrophila, this study developed and evaluated Multi-Enzyme Isothermal Rapid Amplification (MIRA) assays, which could complete amplification within 20 min at a constant [...] Read more.

Aeromonas hydrophila is a prevalent opportunistic pathogen in aquaculture. To establish a rapid, convenient, and accurate detection method for A. hydrophila, this study developed and evaluated Multi-Enzyme Isothermal Rapid Amplification (MIRA) assays, which could complete amplification within 20 min at a constant temperature of 39 °C. The basic MIRA assay targeting the aerolysin (aerA) gene demonstrated high specificity, showing no cross-reactivity with six related bacterial species including Aeromonas veronii, Vibrio harveyi, Pseudomonas fluorescens, Bacillus subtilis, Bacillus cereus, and Lactiplantibacillus plantarum. The fluorescent MIRA assay achieved a detection limit of 1 fg/μL (3.1 × 10² copies/μL) when using the pUC57-aerA standard plasmid, while real-time quantitative PCR achieved a detection limit of 0.1 fg/μL (31 copies/μL). Thus, the MIRA assay exhibited 10-fold lower sensitivity than qPCR but shortened the reaction time from several hours (nearly two hours) to within one hour. Both the specificity and sensitivity of the MIRA reactions were evaluated with three independent experiments. These findings suggested that the developed MIRA assays provide a rapid, specific, and practical diagnostic tool for A. hydrophila detection in aquaculture environments, particularly suitable for resource-limited field applications. Full article

(This article belongs to the Section Microbial Biotechnology)

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30 pages, 500 KB

Open AccessSystematic Review

Role of Lipidomics in Respiratory Tract Infections: A Systematic Review of Emerging Evidence

by Vasiliki E. Georgakopoulou, Konstantinos Dodos and Vassiliki C. Pitiriga

Microorganisms 2025, 13(9), 2190; https://doi.org/10.3390/microorganisms13092190 - 19 Sep 2025

Lower respiratory tract infections (LRTIs) remain a major cause of global morbidity and mortality, yet accurate pathogen identification and risk stratification continue to pose clinical challenges. Lipidomics—the comprehensive analysis of lipid species within biological systems—has emerged as a promising tool to unravel host–pathogen [...] Read more.

Lower respiratory tract infections (LRTIs) remain a major cause of global morbidity and mortality, yet accurate pathogen identification and risk stratification continue to pose clinical challenges. Lipidomics—the comprehensive analysis of lipid species within biological systems—has emerged as a promising tool to unravel host–pathogen interactions and reveal novel diagnostic and prognostic biomarkers. This systematic review synthesizes evidence from nine original studies applying mass spectrometry-based lipidomic profiling in human LRTIs, including community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), and coronavirus disease 2019 (COVID-19). Across diverse study designs, sample types, and analytical platforms, consistent alterations in lipid metabolism were observed. Perturbations in phospholipid classes, particularly phosphatidylcholines (PCs) and lysophosphatidylcholines (LPCs), were frequently associated with disease severity and immune activation. The ratios of PC to LPC and phosphatidylethanolamine (PE) to lysophosphatidylethanolamine (LPE) emerged as markers of inflammatory remodeling. Sphingolipids—including sphingomyelins (SMs) and sphingosine-1-phosphate (S1P)—were identified as key modulators of monocyte and neutrophil activation. Fatty acid–derived lipid mediators such as oxylipins (e.g., 12,13-epoxyoctadecenoic acid and 15-hydroxyeicosatetraenoic acid) and acylcarnitines reflected pathogen-specific immune responses and mitochondrial dysfunction. Several lipid-based classifiers demonstrated superior diagnostic and prognostic performance compared to conventional clinical scores, including the CURB-65 and pneumonia severity index. However, significant heterogeneity in experimental design, lipid identification workflows, and reporting standards limits inter-study comparability. While preliminary findings support the integration of lipidomics into infectious disease research, larger multi-omic and longitudinal studies are required. This review provides the first comprehensive synthesis of lipidomic alterations in human LRTIs and highlights their emerging translational relevance. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

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25 pages, 6655 KB

Open AccessArticle

Posttranscriptional 3′-Terminal Modifications of Escherichia coli RNA Fragments Evolved for Diversity Boosting

by Nikita M. Kamoldinov, Valery V. Panyukov, Nikolay P. Kolzhetsov, Natalia Y. Markelova, Konstantin S. Shavkunov, Uliana S. Shvyreva, Olga V. Alikina, Olga A. Glazunova, Iuliia A. Praslova and Olga N. Ozoline

Microorganisms 2025, 13(9), 2189; https://doi.org/10.3390/microorganisms13092189 - 19 Sep 2025

An emerging area of microbial biology focuses on oligonucleotides excised from functional RNAs and subsequently fulfilling an independent cellular role. Some of these products are subjected to modifications that may expand their functional inventory. Here, we applied a differential analysis of intra- and [...] Read more.

An emerging area of microbial biology focuses on oligonucleotides excised from functional RNAs and subsequently fulfilling an independent cellular role. Some of these products are subjected to modifications that may expand their functional inventory. Here, we applied a differential analysis of intra- and extracellular RNA fragments produced by wild-type Escherichia coli and its dps-null mutant and discovered leucine tRNA fragments with random 3′-terminal extensions among oligonucleotides with Dps-dependent secretion. We observed an exclusive intracellular enrichment of modified LeuT(VPQ) tRNA fragments compared to secretomes, with abundance level dependent on growth medium and the presence of competing bacteria. To assess the pervasiveness of this phenomenon, we developed a custom computational pipeline for detecting variable RNA termini in RNA-seq data. Beyond LeuT(VPQ) tRNA fragments, several other genomic loci yielded oligos with highly heterogeneous ends, indicating that terminal elongation, most prevalent in LeuT(VPQ), is not exclusive to these fragments. Ex vivo testing using synthetic LeuT(VPQ) analogs revealed their stimulatory effect on the persistence of multiple taxa in an artificial microbiome, which was attenuated by 3′-end elongation. We propose that non-template extensions may serve to broaden the spectrum of target molecules for elimination of unused mRNAs by an interference-like mechanism or to generate sequences absent from the E. coli genome as part of a primitive defense system. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)

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13 pages, 1185 KB

Open AccessArticle

First Detection of Cytauxzoon spp. DNA in Questing Ixodes ricinus Ticks

by Marina L. Meli, Theres Meili, Benita Pineroli, Eva Boenzli, Ramon M. Eichenberger, Barbara Willi and Regina Hofmann-Lehmann

Microorganisms 2025, 13(9), 2188; https://doi.org/10.3390/microorganisms13092188 - 19 Sep 2025

Feline cytauxzoonosis is an emerging tick-borne disease in Europe. While infections have been reported in different European countries, the tick vector remains unknown. This study investigated 665 ticks collected in 2019 (n = 160), 2022 (n = 7), and 2024 (n = 498) [...] Read more.

Feline cytauxzoonosis is an emerging tick-borne disease in Europe. While infections have been reported in different European countries, the tick vector remains unknown. This study investigated 665 ticks collected in 2019 (n = 160), 2022 (n = 7), and 2024 (n = 498) in a Cytauxzoon spp. hotspot region in central Switzerland (62 ticks from cats; 603 ticks from vegetation). Ticks were morphologically characterized, pooled by origin and life-stage, and screened for Cytauxzoon spp. 18S rRNA by qPCR and conventional PCR, and positive samples confirmed by sequencing. All ticks belonged to Ixodes ricinus (50 males, 83 females, 532 nymphs). Four tick pools from 2019 tested Cytauxzoon spp. positive: one pool of 3 non-engorged male ticks from two cats and three pools of 5–6 nymphs each from vegetation. All ticks collected in 2022 and 2024 tested negative. Amplification of the almost full-length (1535 bp, one pool) or partial (140–219 bp, three pools) 18S rRNA gene revealed a sequence identity of 98.6–100% with Cytauxzoon spp. previously detected in cats from this area. The detection of Cytauxzoon spp. in questing I. ricinus nymphs suggests a potential role of this tick species in the parasites’ transmission cycle in Central Europe and raises the possibility of transstadial or potentially transovarial transmission. Mitochondrial gene sequencing was unsuccessful, but the detected Cytauxzoon spp. likely represent Cytauxzoon europaeus. Discrepancies between qPCR and conventional PCR results point to possible amplification of tick endosymbionts, highlighting the importance of confirmatory sequencing, particularly when testing tick-derived DNA. Thus, the 18S rRNA qPCR assay used appears suboptimal for screening tick samples, as its specificity in this matrix was limited. In conclusion, this is the first report of Cytauxzoon spp. in questing I. ricinus ticks in Europe. Our findings underscore the need for further research to confirm vector competence and clarify transmission dynamics. Full article

(This article belongs to the Section Public Health Microbiology)

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11 pages, 336 KB

Open AccessArticle

Prevalence and Clinical Characteristics of Visceral Involvement in HIV-Associated Kaposi Sarcoma: A Three-Year Retrospective Cohort Study at a Tertiary Care Center in Mexico

by Emily Itzel Pecero-García, Juan Carlos Domínguez-Hermosillo, Yessica Sara Pérez-González, Juan Pablo Sánchez-Navarro, Mauricio Alfredo Ambriz-Alarcón, Natalia Jaime-Gómez, Sol Ramírez-Ochoa, Gabino Cervantes-Guevara, Berenice Vicente-Hernández, Francisco Javier Hernández-Mora and Enrique Cervantes-Pérez

Microorganisms 2025, 13(9), 2187; https://doi.org/10.3390/microorganisms13092187 - 19 Sep 2025

Despite advances in the understanding of Kaposi sarcoma (KS), research from resource-limited settings remains limited. This study aimed to estimate the proportion of epidemic visceral KS among Mexican people living with HIV (PLHIV) and to describe their clinical and biochemical characteristics. We included [...] Read more.

Despite advances in the understanding of Kaposi sarcoma (KS), research from resource-limited settings remains limited. This study aimed to estimate the proportion of epidemic visceral KS among Mexican people living with HIV (PLHIV) and to describe their clinical and biochemical characteristics. We included PLHIV with histopathologically confirmed KS who received care at the National Medical Center La Raza between March 2020 and February 2023. We calculated the prevalence of epidemic KS and epidemic visceral KS and analyzed clinical and biochemical variables potentially associated with visceral involvement. The prevalence of epidemic KS was 5.6%. Among these cases, 51.4% had visceral involvement, yielding an overall prevalence of 2.8%. Patients with epidemic visceral KS exhibited significantly higher rates of oral mucosal involvement and lower hemoglobin levels compared with those without visceral disease. These findings highlight the substantial burden of epidemic visceral KS in this population and should be confirmed in future studies with larger cohorts and robust designs aimed at identifying clinical and biochemical predictors of visceral involvement. Full article

(This article belongs to the Special Issue Understanding the Interactions Between HIV and Other Infections and Their Impact on Immune Function)

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23 pages, 11105 KB

Open AccessArticle

Elucidation of Mechanism of Soil Degradation Caused by Continuous Cropping of Dictyophora rubrovalvata Using Metagenomic and Metabolomic Technologies

by Chengrui Lu, Guozheng Qian, Ludi Luo, Yunsong Peng, Hao Ren, Bo Yan and Yongyan Xu

Microorganisms 2025, 13(9), 2186; https://doi.org/10.3390/microorganisms13092186 - 19 Sep 2025

Dictyophora rubrovalvata is a soil-cultivated edible fungus with high economic and medicinal value, yet its continuous cultivation is frequently hindered by cropping obstacles. To elucidate the underlying ecological mechanisms, this study employed metagenomic sequencing and untargeted metabolomics (UHPLC–OE–MS) to analyze the changes in [...] Read more.

Dictyophora rubrovalvata is a soil-cultivated edible fungus with high economic and medicinal value, yet its continuous cultivation is frequently hindered by cropping obstacles. To elucidate the underlying ecological mechanisms, this study employed metagenomic sequencing and untargeted metabolomics (UHPLC–OE–MS) to analyze the changes in soil microbial communities and metabolite profiles under different continuous cropping treatments (CC0: Uncultivated; CC1: one cropping cycle; CC2: two cropping cycle; CC3: three cropping cycle.). Continuous cropping significantly decreased soil pH from 7.94 to 7.52 and available phosphorus (AP) from 213.69 mg/kg to 15.7 mg/kg, while increasing available nitrogen (AN) from 284.5 mg/kg to 886.33 mg/kg. The Shannon index of fungal communities rose from 3.15 to 4.55. Notably, the relative abundance of the beneficial bacterium Sphingomonas declined from 15.63% to 1.12%, whereas the pathogenic fungus Aspergillus increased from 0.06% to 3.06%. A total of 1408 secondary metabolites were detected, with 39 significantly upregulated and 416 downregulated in CC3 compared to CC0. Several autotoxic compounds, including ferulic acid, hydroxycinnamic acid derivatives, and jasmonic acid, were enriched and positively correlated with pathogenic fungi. These results suggest that continuous cropping may reshape the soil microecosystem by promoting autotoxic metabolite accumulation and pathogenic Microbial enrichment, thereby contributing to soil degradation and cropping obstacles. Full article

(This article belongs to the Section Microbiomes)

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11 pages, 248 KB

Open AccessArticle

Cutibacterium acnes Phylotyping and Antibiotic Resistance to Six Antibiotics: A Bulgarian Study

by Lyudmila Boyanova, Georgi Dimitrov, Vessela Raykova, Kircho Patrikov, Raina Gergova and Rumyana Markovska

Microorganisms 2025, 13(9), 2185; https://doi.org/10.3390/microorganisms13092185 - 19 Sep 2025

Cutibacterium acnes subspecies/phylotypes can cause infections requiring antibiotic therapy. Phylotyping of 73 (55 acneic and 18 non-acneic) C. acnes strains was performed, and antibiotic susceptibility was tested by E tests, breakpoint susceptibility test, or disk diffusion method. The dominant phylotype in both acneic [...] Read more.

Cutibacterium acnes subspecies/phylotypes can cause infections requiring antibiotic therapy. Phylotyping of 73 (55 acneic and 18 non-acneic) C. acnes strains was performed, and antibiotic susceptibility was tested by E tests, breakpoint susceptibility test, or disk diffusion method. The dominant phylotype in both acneic and non-acneic strains was IA1 (56.2%). Phylotype II was >3-fold more frequent in non-acneic than acneic isolates. Resistance in acneic strains was >41% for clindamycin, 36.4% for tetracycline and 15.9% for levofloxacin, and that in non-acneic strains was >38% for clindamycin, 22.2% for tetracycline and 5.6% for levofloxacin. No strain was piperacillin/tazobactam or vancomycin resistant. Amoxicillin resistance was found in both acneic (5.4%) and non-acneic strains (11.1%), and was rare (1.8%) in phylotype I but higher (23.5%) in other strains. Double resistance was found in 32.6% of acneic and 22.2% of the non-acneic strains, and 9.3% of acneic strains displayed multidrug resistance. In conclusion, IA1 phylotype was dominant in both acneic and non-acneic strains, and type II was more frequent in non-acneic isolates. The detection (at >6%) of amoxicillin resistance represents a rare yet important finding. The presence of double/multidrug resistance strongly implies the need of susceptibility-guided therapy of the associated infections. Full article

(This article belongs to the Special Issue Healthcare-Associated Infections and Antimicrobial Therapy—2nd Edition)

25 pages, 9148 KB

Open AccessArticle

PCV2 Infection Represses the Differentiation of Light Zone Germinal Center B Cells by Inhibiting Their Interaction with Helper Cells

by Tengfei Shi, Qian Du, Jiasai Kang, Haoshu Zhang, Xinru Xu, Yang Wang, Dewen Tong and Yong Huang

Microorganisms 2025, 13(9), 2184; https://doi.org/10.3390/microorganisms13092184 - 18 Sep 2025

Porcine circovirus 2 (PCV2) is one of the most widespread immunosuppressive viruses, impairing the protective efficacy of vaccines in pig herds. Previous studies have shown that PCV2 infection reduces the generation of immune memory and antibody secretion induced by vaccination in hosts. In [...] Read more.

Porcine circovirus 2 (PCV2) is one of the most widespread immunosuppressive viruses, impairing the protective efficacy of vaccines in pig herds. Previous studies have shown that PCV2 infection reduces the generation of immune memory and antibody secretion induced by vaccination in hosts. In this study, we used single-cell mRNA sequencing of mice splenic cells to show that PCV2 infection decelerates the differentiation of light zone germinal center (GC) B cells into memory B cells and plasma cells. We found that, although PCV2 infection led to lymphocyte depletion in the spleens of mice, the remaining splenic B cells were activated by the infection. The percentage of naïve B cells in PCV2-infected mice decreased mainly due to differentiation rather than death. Meanwhile, the percentages of memory B cells and plasma cells increased without significant enhancement of functional gene expression. Focusing on the GC B cells, we found that PCV2 infection activated the proliferation of dark zone GC B cells, but not the differentiation of light zone GC B cells. Furthermore, the transcriptional level of Prdm1 was not significantly altered by PCV2 infection, and the level of Bach2 was dramatically reduced. Further analysis showed that the interactions between light zone GC B cells and dendritic cells, macrophages, and follicular helper T cells were weakened in the spleens of PCV2-infected mice. In conclusion, this study found that PCV2 infection impairs the differentiation of B cells into functional memory B cells and plasma cells. This may be an important and previously unrecognized reason why PCV2 infection impairs vaccine efficiency. Full article

(This article belongs to the Special Issue Animal Viral Infectious Diseases)

19 pages, 390 KB

Open AccessReview

Virulence Regulation in Borrelia burgdorferi

by Sierra George and Zhiming Ouyang

Microorganisms 2025, 13(9), 2183; https://doi.org/10.3390/microorganisms13092183 - 18 Sep 2025

Borrelia burgdorferi, the causative agent of Lyme disease, is the most common vector-borne disease in the United States. Compared with other bacterial pathogens, B. burgdorferi has many unique features. For instance, its highly segmented genome was predicted to encode very few proteins directly [...] Read more.

Borrelia burgdorferi, the causative agent of Lyme disease, is the most common vector-borne disease in the United States. Compared with other bacterial pathogens, B. burgdorferi has many unique features. For instance, its highly segmented genome was predicted to encode very few proteins directly dedicated to gene expression regulation. Yet, the spirochete continuously reprograms its transcriptome and proteome to promote survival and pathogenesis as spirochetes traverse the enzootic lifecycle between ticks and mammals. Signal sensing systems, a unique alternative sigma factor cascade, and multi-functional regulators work in concert to coordinate virulence gene expression under different tick and mammal environments. In this review, we have summarized recent advances in gene regulation in B. burgdorferi. Full article

(This article belongs to the Special Issue Ticks, Tick Microbiome and Tick-Borne Diseases)

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