Microorganisms

20 pages, 3665 KB

Open AccessArticle

Aircraft Wastewater as a Sentinel for Transboundary Antimicrobial Resistance: An Integrated Genomic Approach

by Abiola Senok, Rashed Alghafri, Douha Shouqair, Subham Verma, Lobna Mohammed, Mohammed Naji, Abdulla Albastaki, Rania Nassar, Dean Everett, Richard Goering and Mushtaq Khan

Microorganisms 2026, 14(9), 1988; https://doi.org/10.3390/microorganisms14091988 - 8 Sep 2026

Abstract

Background: Aircraft wastewater (AWW) provides a composite environmental matrix reflecting passengers from diverse geographic origins and may serve as a surveillance tool for AMR monitoring. Objectives: To characterize microbial community composition, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and genome-resolved features of [...] Read more.

Background: Aircraft wastewater (AWW) provides a composite environmental matrix reflecting passengers from diverse geographic origins and may serve as a surveillance tool for AMR monitoring. Objectives: To characterize microbial community composition, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and genome-resolved features of AWW. Methods: Samples (N = 10) were collected from long-haul flights arriving in the UAE between October 2024 and February 2025. Shotgun metagenomic sequencing and high-throughput quantitative PCR (HT-qPCR) were performed. Metagenome-assembled genomes (MAGs) were reconstructed. Results: Shotgun metagenomics identified 752 bacterial species dominated by gut-associated families, including Lachnospiraceae and Ruminococcaceae. A total of 345 ARGs were detected, with tetracycline resistance genes being most abundant. Regional variation in resistome composition was supported by permutational multivariate analysis of variance (PERMANOVA, p = 0.010), and principal coordinate analysis indicated separation by flight-origin region. MAG reconstruction recovered 1012 genomes, with 85.4% resolved to species level. MAG-based annotation identified 280 VFGs corresponding to 116 non-redundant virulence genes. HT-qPCR confirmed the widespread presence of key ARG classes and mobile genetic elements across samples, in keeping with metagenomic findings. Conclusions: AWW contains diverse microbial communities and AMR determinants. Genome-resolved analysis provided organism-level context for resistome and virulome characterization, confirming AWW as an environmental matrix for monitoring transboundary AMR dynamics. Full article

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12 pages, 1209 KB

Open AccessArticle

Targeting the 3C Protease of Hepatitis A Virus Subgenotype IB: Virtual Screening and Identification of Potent Lead Candidates

by Tatsuo Kanda, Reina Sasaki-Tanaka, Hiroaki Okamoto, Shuji Terai, Cole D. Cwiklowski and Kalyan C. Nagulapalli Venkata

Microorganisms 2026, 14(9), 1987; https://doi.org/10.3390/microorganisms14091987 (registering DOI) - 8 Sep 2026

Abstract

Hepatitis A virus (HAV) infection remains a global public health concern in both developing and developed countries. In the present study, we identified anti-HAV drugs, using AutoDock Vina Modeling software, and evaluated the compounds in vitro. Following cytotoxicity for Huh7 cells, 5 out [...] Read more.

Hepatitis A virus (HAV) infection remains a global public health concern in both developing and developed countries. In the present study, we identified anti-HAV drugs, using AutoDock Vina Modeling software, and evaluated the compounds in vitro. Following cytotoxicity for Huh7 cells, 5 out of 10 compounds were selected. We evaluated effective HAV 3C protease inhibitors with activity against both HAV genotype IB HM175/18f and HAV genotype IIIA HA11-1299-infected human hepatoma cells. Among the five compounds, we identified only one (KCN-A-12), which had an inhibitory effect on both HAV genotype IB HM175/18f and HAV genotype IIIA HA11-1299 replication in human hepatoma Huh7 cells. KCN-A-12 has more effective inhibitory effects on the replication of HAV genotype IB HM175/18f than that of HAV genotype IIIA HA11-1299. This difference may be attributable to the fact that our discovery system depends on crystal structures from HAV 3C protease based on the HAV genotype IB HM175 strain. In conclusion, we observed that KCN-A-12 was able to inhibit HAV replication. In silico screening for HAV 3C protease inhibitors may be useful for further discovery of anti-HAV drugs. Full article

(This article belongs to the Special Issue Infective Liver Diseases)

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17 pages, 2309 KB

Open AccessArticle

Gamma Irradiation Effects on Fatty Acid Profiles, Adhesion, Plasmid Stability, and Secreted Proteins in Shigella: In Silico Insights into Post-Irradiation Virulence

by Ali Ellafi, Najla Haddaji, Mabrouk Horchani, Karima Bekir, Rihab Lagha, Amina Bakhrouf, Eduardo Alberto López-Maldonado and Sonia Ben Younes

Microorganisms 2026, 14(9), 1986; https://doi.org/10.3390/microorganisms14091986 - 8 Sep 2026

Abstract

This study investigated the adaptive mechanisms of Shigella sonnei ATCC25931 in response to gamma irradiation stress (0.5 and 1 kGy), with a specific focus on the involvement of fatty acids (FAs) in membrane lipid composition remodeling, adherence, and extracellular proteins. The results demonstrated [...] Read more.

This study investigated the adaptive mechanisms of Shigella sonnei ATCC25931 in response to gamma irradiation stress (0.5 and 1 kGy), with a specific focus on the involvement of fatty acids (FAs) in membrane lipid composition remodeling, adherence, and extracellular proteins. The results demonstrated a notable enhancement in cell hydrophobicity and adherence to KB cells following irradiation, although the invasion rate exhibited a decline from 14% to 2.35% at 1 kGy. Furthermore, gamma irradiation induced notable alterations in fatty acid (FA) composition, characterized by a pronounced reduction in the unsaturated/saturated FA ratio. Additionally, the plasmid profiles revealed the loss of several original plasmids after gamma irradiation. The alterations in extracellular proteins were observed through SDS-PAGE, which demonstrated a reduction in expression at 1 kGy. Furthermore, a molecular docking analysis indicated that fatty acids play a role in inhibiting VirF, a key regulator of Shigella virulence. The least effective inhibitor was capric acid, while linoleic and gamma-linolenic acids formed the most stable inhibitory complexes, which prevented VirF from activating the virulence system. These alterations in fatty acids, plasmids, and extracellular proteins constitute adaptive responses to irradiation-induced stress. Full article

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

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22 pages, 1504 KB

Open AccessReview

Intestinal–Bone Axis Mediated by Bifidobacterium: Mechanistic Analysis and Therapeutic Potential in Osteoporosis

by Fadong Li, Haoze Zhang, Boran Zhang, Xingwen Xie and Ning Li

Microorganisms 2026, 14(9), 1985; https://doi.org/10.3390/microorganisms14091985 - 8 Sep 2026

Abstract

Osteoporosis is one of the most prevalent metabolic bone diseases worldwide, and current pharmacological options are limited by adverse effects and are poorly suited to long-term use, underscoring the need for novel therapeutic targets. Bifidobacterium, one of the most representative beneficial bacterial [...] Read more.

Osteoporosis is one of the most prevalent metabolic bone diseases worldwide, and current pharmacological options are limited by adverse effects and are poorly suited to long-term use, underscoring the need for novel therapeutic targets. Bifidobacterium, one of the most representative beneficial bacterial genera in the human gut, has been linked to bone mineral density, and supplementation with specific strains improves bone metabolic parameters in animal models of osteoporosis. This narrative review examines the molecular mechanisms through which Bifidobacterium may protect bone via the gut–bone axis, encompassing four interconnected dimensions: reinforcement of the intestinal barrier, modulation of the immune network, remodeling of the gut microbiota, and production of bone-protective metabolites. The review makes three principal contributions. First, it establishes a four-tier mechanistic framework of Bifidobacterium-mediated regulation of osteoporosis in which the evidence is stratified into three categories—direct evidence from Bifidobacterium-specific studies, indirect evidence from other probiotics, and general mechanisms of gut microbiota-regulated bone metabolism—thereby strengthening the rigor of each argument and explicitly distinguishing evidence derived from Bifidobacterium-specific studies from that based on other probiotics or general gut-microbiota mechanisms throughout the review. Second, it systematically compares the osteoprotective efficacy of different Bifidobacterium strains (Bifidobacterium longum, Bifidobacterium lactis, Bifidobacterium adolescentis, etc.), highlighting the central importance of strain specificity. Third, it evaluates the strength of the evidence and identifies knowledge gaps for each mechanistic pathway. Most current evidence derives from cross-sectional studies and animal models; causal relationships await validation in large-scale prospective cohort studies and randomized controlled trials. In addition, functional disparities among strains and heterogeneity across clinical studies remain the core bottleneck in translating these fundamental findings into clinical practice. Full article

(This article belongs to the Special Issue Advances in Gut Microbiota–Host Interactions: Microbial Mechanisms, Modulators, and Translational Perspectives)

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18 pages, 893 KB

Open AccessArticle

Risk Factors of COVID-19 Severity and Related Death in Children in the Post-Pandemic Era

by Laura G. Coelho, Lilian M. Diniz, Stella C. Galante, Cristiane S. Dias, Maria Christina L. Oliveira, Enrico A. Colosimo, Ana Cristina Simões e Silva, Fernanda N. Duelis, Maria Eduarda T. Bernardes, Julia O. Zavitoski, Daniella R. B. Martelli, Fabrício Emanuel S. Oliveira, Hercílio Martelli-Júnior, Adriano L. Santos, Robert H. Mak and Eduardo A. Oliveira

Microorganisms 2026, 14(9), 1984; https://doi.org/10.3390/microorganisms14091984 - 8 Sep 2026

Abstract

In the post-pandemic era, identifying children who are most susceptible to severe illness and COVID-19-related mortality is essential for guiding public health policies. This study examined the risk factors for COVID-19-related severe illness and mortality from 2023 to mid-2025. We conducted a population-based [...] Read more.

In the post-pandemic era, identifying children who are most susceptible to severe illness and COVID-19-related mortality is essential for guiding public health policies. This study examined the risk factors for COVID-19-related severe illness and mortality from 2023 to mid-2025. We conducted a population-based cohort study using nationwide Brazilian data from patients aged <18 years with laboratory-confirmed SARS-CoV-2 infection between January 2023 and June 2025. The primary outcomes were COVID-19-related severity and death. Separate binary multivariable logistic regression models were developed for each of the outcomes. Among 465,689 children, 1.3% (n = 5963) developed severe illness, and 0.18% (n = 847) died. Factors associated with an increased risk of severe illness included age < 2 years, presence of comorbidities, Indigenous ethnicity, and lack of vaccination. Neurological disorders conferred the highest risk among the clinical conditions (adjusted odds ratio [aOR] = 34.1; 95% CI: 27.9–41.8). Regional differences were also observed; the North and Northeast regions showed higher mortality (aOR = 2.3; 95% CI: 1.8–3.0) than the Central-West region. Compared with White ethnicity, non-White ethnicities had higher mortality: Indigenous (aOR = 23.5; 95% CI: 13.5–39.3), Black (aOR = 1.95; 95% CI: 1.29–2.92), and Brown (aOR = 1.43; 95% CI: 1.18–1.73) ethnicities. Lack of any vaccine dose was associated with a significantly increased risk of severe illness (aOR = 1.39; 95% CI: 1.15–1.67. p < 0.001) and death (aOR = 2.1; 95% CI: 1.3–3.5; p < 0.001). In the post-pandemic era, younger age, comorbidities, sociodemographic disparities, and lack of vaccination were associated with an increased risk of severe illness and COVID-19-related death in the pediatric population. Full article

(This article belongs to the Special Issue Post-COVID Era: Epidemiology and Vaccine Research)

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17 pages, 1023 KB

Open AccessArticle

Physicochemical and Functional Characterization of a Novel Extremophilic Exopolysaccharide Produced by Janibacter limosus

by Chaima Farhat, Patrícia Concórdio Reis, Besma Ettoumi, Kleyde Ramos, Ameur Cherif, Filomena Freitas and Habib Chouchane

Microorganisms 2026, 14(9), 1983; https://doi.org/10.3390/microorganisms14091983 - 8 Sep 2026

Abstract

Extremophilic exopolysaccharides (EPSs) from extreme-environment microorganisms exhibit multifunctional and specific properties relevant to food, pharmaceutical, and environmental applications. This study reports the physicochemical characteristics of a novel EPS secreted by the marine actinobacterium Janibacter limosus (JlEPS) isolated from the Tyrrhenian Sea. The biopolymer [...] Read more.

Extremophilic exopolysaccharides (EPSs) from extreme-environment microorganisms exhibit multifunctional and specific properties relevant to food, pharmaceutical, and environmental applications. This study reports the physicochemical characteristics of a novel EPS secreted by the marine actinobacterium Janibacter limosus (JlEPS) isolated from the Tyrrhenian Sea. The biopolymer was characterized for its molecular mass, monosaccharide composition, functional groups, rheological, and thermal behavior. JlEPS was found as an acidic heteropolysaccharide composed of eight sugar monomers. Neutral and acidic sugars predominate, with glucose (36.60 ± 0.46 mol%), rhamnose (23.62 ± 0.15 mol%), and galacturonic acid (16.54 ± 0.18 mol%). Amino sugars were also detected, including galactosamine (8.70 ± 0.01 mol%) and glucosamine (4.00 ± 0.10 mol%). Arabinose (7.8 ± 0.76 mol%), galactose (1.35 ± 0.01 mol%), and fucose (1.42 ± 0.06 mol%) were present in minor amounts. The average molecular weight (M_w) of the biopolymer was 1.60 × 10⁶ Da, with a polydispersity index of 1.022, indicating a relatively homogeneous population. FT-IR indicated uronic acids and glycosidic linkages, while TGA demonstrated stability up to 250 °C. JlEPS solutions behaved as pseudoplastic fluids, and the flow curves were fitted with the Carreau model (R² = 0.96–0.99). The zero-shear viscosity increased from 0.542 ± 0.187 Pa·s (0.5%) to (5.01 ± 0.91) × 10⁴ Pa·s, while the flow index decreased from 0.368 ± 0.032 to 0.100 ± 0.028, confirming strong pseudoplasticity and extensive molecular entanglements. JlEPS is a complex with a defined composition and high viscosity, supporting its potential for multiple applications. Full article

(This article belongs to the Special Issue Microbiota Dynamics in Environmental and Host Systems: From Ecology to Applications)

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21 pages, 10063 KB

Open AccessArticle

Effects of a Combined Antimicrobial Peptide and Candida utilis Supplementation on Rumen Development and Microecology of Weaned Hu Lambs

by Qing Lin, Jinjuan Zhao, Xiangdong Huo, Kai Lou, Qidong Zhu, Ruoyu Mao and Min Hou

Microorganisms 2026, 14(9), 1982; https://doi.org/10.3390/microorganisms14091982 - 8 Sep 2026

Abstract

Rumen development and microecological homeostasis are critical for post-weaning health in lambs; however, effective nutritional strategies combining probiotics and antimicrobial peptides remain underexplored. This study investigated the effects of graded doses of a combined additive (Candida utilis + antimicrobial peptide (AMP)) on [...] Read more.

Rumen development and microecological homeostasis are critical for post-weaning health in lambs; however, effective nutritional strategies combining probiotics and antimicrobial peptides remain underexplored. This study investigated the effects of graded doses of a combined additive (Candida utilis + antimicrobial peptide (AMP)) on rumen development and microecology in weaned Hu lambs. Forty healthy pre-weaning male lambs (initial body weight: 15.77 ± 1.25 kg; age: 42.98 ± 1.80 d) were randomly assigned to four groups (n = 10): a control group (CK, fed milk/basal diet), and three treatment groups receiving the same milk/basal diet supplemented with graded doses of the combined additive, based on feed intake (LCB: AMP 0.05 g/kg + C. utilis 0.1 g/kg, MCB: AMP 0.05 g/kg + C. utilis 0.8 g/kg, HCB: AMP 0.05 g/kg + C. utilis 1.5 g/kg) over a 40-day period starting from day 6. At the end of the trial, six lambs per group were randomly selected for sampling for analyses of rumen morphology, fermentation parameters, 16S rRNA amplicon sequencing, and untargeted metabolomics. Results showed that, compared with CK, (1) MCB and HCB increased papilla height, and HCB also increased papilla width (p < 0.05); papilla width and muscular layer thickness showed significant linear increases with increasing additive dose (p < 0.05). (2) All treatments linearly reduced ruminal pH (p < 0.05), although all values remained within the normal physiological range; meanwhile, all treatment groups showed elevated levels of microbial protein (MCP), butyrate, valerate, and isovalerate; MCP also increased linearly with dose (p < 0.05); LCB decreased the acetate-to-propionate ratio(A:P), and this ratio exhibited a significant quadratic trend across treatment groups (p < 0.05). (3) HCB increased the α-diversity indices and reduced Methanobacteriota abundance; LCB elevated Bacillota; and all treatments decreased Spirochaetota, Synergistota, and Cyanobacteriota but increased Actinomycetota, Verrucomicrobiota, and Thermodesulfobacteriota (p < 0.05). (4) The number of differential metabolites and KEGG pathway enrichments gradually increased with increasing doses of the combined additive, with HCB exerting the most extensive modulatory effects on signaling and neural pathways. (5) Volatile fatty acids, Bacteroidota, and Xylanibacter were positively correlated with rumen development parameters (p < 0.05). Collectively, dietary supplementation with the combined additive improved rumen fermentation, microbial community structure, and metabolic profiles, with the high-dose (HCB) regimen showing the most effects on select parameters, whereas the low-dose (LCB) regimen exhibited advantages in specific fermentation traits. These findings provide preliminary evidence for the potential application of this combined additive in post-weaning lamb diets. Full article

(This article belongs to the Special Issue Advances in Rumen Microbiome Science: Emerging Technologies for Sustainable Livestock Production)

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21 pages, 15312 KB

Open AccessArticle

Integrated Analysis of Paired Crude Oil and Produced Water Reveals Stress-Tolerant Hydrocarbon-Degrading Bacteria with Bioremediation Potential

by Ning Mao, Tingli Yang, Ying Niu, Jingjing Zhang, Guike Yang, Xin Zhang, Xiaying Wang and Xiaobin Ou

Microorganisms 2026, 14(9), 1981; https://doi.org/10.3390/microorganisms14091981 - 8 Sep 2026

Abstract

Oilfield microbiome studies have extensively characterized microbial community composition or isolated individual hydrocarbon degraders, but integrated exploration of cultivable functional bacteria from paired crude-oil and produced-water environments remains limited, particularly for strains combining hydrocarbon utilization with stress-tolerance and biosurfactant-related traits. In this study, [...] Read more.

Oilfield microbiome studies have extensively characterized microbial community composition or isolated individual hydrocarbon degraders, but integrated exploration of cultivable functional bacteria from paired crude-oil and produced-water environments remains limited, particularly for strains combining hydrocarbon utilization with stress-tolerance and biosurfactant-related traits. In this study, paired crude-oil and produced-water samples from the Huoshaoshan Oilfield were investigated by combining 16S rRNA amplicon sequencing with culture-dependent isolation and functional screening. A total of 135 bacterial isolates representing 22 genera were recovered, of which 70 showed hydrocarbon-utilizing potential in primary screening. The collection also included isolates capable of growth at 10% NaCl and up to 55 °C. Comparison of sequencing and cultivation revealed marked differences between environmental abundance and recoverable functional resources. Representative isolates showed distinct removal profiles toward n-tetracosane (C₂₄), naphthalene, phenanthrene, and fluoranthene under saline conditions, with Halomonas nitritophilus Ff1 and Halomonas sp. Fc15 showing particularly strong performance. Sequence-confirmed alkB and PAH-RHDα fragments provided additional molecular support for the observed hydrocarbon-removal phenotypes. A three-strain consortium composed of Sphingomonas sp. Fa24, Halomonas nitritophilus Ff1, and Stutzerimonas stutzeri Ff2 achieved 87.4% C₂₄ removal, exceeding the corresponding monocultures. These findings link oilfield microbial community profiling with cultivable functional resource mining and provide candidate strains for saline petroleum bioremediation. Full article

(This article belongs to the Collection Biodegradation and Environmental Microbiomes)

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14 pages, 440 KB

Open AccessArticle

Multi-Laboratory Evaluation of Modified BAM Chapter 19b and Long-Term Detection of Cyclospora cayetanensis in Fresh Salsa/Pico de Gallo

by Sonia Almeria, Ellie Lauren Rogers and Jeremi Mullins

Microorganisms 2026, 14(9), 1980; https://doi.org/10.3390/microorganisms14091980 - 8 Sep 2026

Abstract

Cyclospora cayetanensis is a foodborne parasite that causes the human diarrheal disease cyclosporiasis. Multiple outbreaks of C. cayetanensis have been linked to Mexican-style dishes containing uncooked cilantro. The Bacteriological Analytical Manual (BAM) Chapter 19b method for the detection of C. cayetanensis has been [...] Read more.

Cyclospora cayetanensis is a foodborne parasite that causes the human diarrheal disease cyclosporiasis. Multiple outbreaks of C. cayetanensis have been linked to Mexican-style dishes containing uncooked cilantro. The Bacteriological Analytical Manual (BAM) Chapter 19b method for the detection of C. cayetanensis has been validated in cilantro, but not in complex foods containing cilantro, such as fresh salsa/pico de gallo. In a previous study, specific modifications of the BAM method were performed in fresh salsa/pico de gallo for optimal detection of C. cayetanensis. In the present study, further evaluation of those modifications in fresh salsa/pico de gallo were performed using the updated BAM Chapter 19b mitochondrial-based qPCR (Mit1C qPCR). Six FDA laboratories analyzed six blind-coded salsa/pico de gallo test samples each. These samples included two unseeded samples, three samples seeded with five oocysts, and one sample seeded with 200 oocysts. All laboratories performed the updated washing and DNA extraction modification steps. The overall C. cayetanensis detection rates across laboratories for fresh salsa/pico de gallo samples inoculated with 200 oocysts, five oocysts, and un-inoculated samples were 100% (6/6), 100% (18/18), and 0% (0/12), respectively. The method showed extremely high sensitivity and high reproducibility across all laboratories. Un-inoculated samples were all negative for each laboratory, indicative of high C. cayetanensis specificity. This is the first evaluation of the performance of detection of C. cayetanensis using the updated BAM Chapter 19b (Mit1C qPCR) in a complex matrix, e.g., fresh salsa/pico de gallo. A second study evaluated the presence of the parasite in a long-term study in fresh salsa/pico de gallo samples inoculated with C. cayetanensis and analyzed up to three weeks after inoculation. Samples were positive for the detection of the parasite at each time-point of the study, indicating that the method could be used to detect the parasite in leftovers of fresh salsa/pico de gallo up to three weeks old in outbreak investigations. Evaluation and deploying effective methods to detect C. cayetanensis in high-risk fresh produce and prepared dishes are critical to monitor and respond to active outbreaks. Full article

(This article belongs to the Section Food Microbiology)

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16 pages, 1762 KB

Open AccessArticle

Association Between Thiazolidinedione Therapy and Tuberculosis-Related Events in Type 2 Diabetes: A Population-Based Cohort Study

by Fu-Shun Yen, James Cheng-Chung Wei, Shao-Fan Yen, Chen-Yu Sung, Teng-Shun Yu, Fuu-Jen Tsai, Chih-Cheng Hsu and Chii-Min Hwu

Microorganisms 2026, 14(9), 1979; https://doi.org/10.3390/microorganisms14091979 - 8 Sep 2026

Abstract

Tuberculosis (TB) remains a major global health burden, and diabetes mellitus increases the risk of active TB. Thiazolidinediones (TZDs) have immunomodulatory effects, but their association with TB remains unclear. This study investigated the associations between TZD use and TB-related events in patients with [...] Read more.

Tuberculosis (TB) remains a major global health burden, and diabetes mellitus increases the risk of active TB. Thiazolidinediones (TZDs) have immunomodulatory effects, but their association with TB remains unclear. This study investigated the associations between TZD use and TB-related events in patients with type 2 diabetes (T2D), including TB requiring anti-TB treatment, pulmonary TB, and TB-related hospitalization. Using Taiwan’s National Health Insurance Research Database, adults with newly diagnosed T2D between 2000 and 2017 were identified. Propensity score matching and Cox proportional hazards models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for TB requiring anti-TB treatment, pulmonary TB, and TB-related hospitalization. After 1:1 matching, 44,095 TZD user–nonuser pairs and 9225 rosiglitazone user–nonuser pairs were identified. Overall, TZD use was not significantly associated with TB-related outcomes. However, rosiglitazone use was associated with lower risks of TB requiring anti-TB treatment (aHR, 0.56; 95% CI, 0.36–0.86), pulmonary TB (aHR, 0.79; 95% CI, 0.68–0.92), and TB-related hospitalization (aHR, 0.59; 95% CI, 0.43–0.81). Rosiglitazone use was associated with lower risks of TB-related outcomes in the primary Cox analyses; however, these associations were attenuated in time-dependent analyses and were no longer statistically significant after accounting for death as a competing event. These observational findings should therefore be considered hypothesis-generating rather than evidence of a causal or protective effect and require confirmation using more robust causal-inference approaches. Full article

(This article belongs to the Special Issue Mycobacterium tuberculosis: Diagnostics, Drug Resistance and Molecular Epidemiology)

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14 pages, 307 KB

Open AccessArticle

Causes of Bacterial Infections and Antibiotic Resistance Profiles in Patients with Chronic Wounds

by Meltem Yılmaz and Onur Ozturk

Microorganisms 2026, 14(9), 1978; https://doi.org/10.3390/microorganisms14091978 - 8 Sep 2026

Abstract

This retrospective, descriptive study examined the microbial distribution and antibiotic resistance profiles of predominant pathogens in chronic wounds among patients presenting to a regional hospital’s chronic wound outpatient clinic between July and November 2025, with the aim of informing empirical antibiotic therapy and [...] Read more.

This retrospective, descriptive study examined the microbial distribution and antibiotic resistance profiles of predominant pathogens in chronic wounds among patients presenting to a regional hospital’s chronic wound outpatient clinic between July and November 2025, with the aim of informing empirical antibiotic therapy and regional antibiotic stewardship programs. Among the 105 patients included (mean age 62.69 ± 17.14 years, 60% male), diabetic foot ulcer was the most common wound type (49.5%). Of the isolates obtained, 70.2% (n = 73) were Gram-negative and 29.8% (n = 31) were Gram-positive microorganisms, with Escherichia coli and Pseudomonas aeruginosa being the most frequently isolated pathogens (16.3% each), followed by Staphylococcus aureus (15.4%). S. aureus predominated in diabetic foot ulcers, whereas P. aeruginosa predominated in peripheral artery disease, though no statistically significant association was found between wound type and bacterial group (p = 0.055). A multidrug-resistant phenotype was detected in 16.3% (17/104) of isolates. No significant differences emerged between Gram-negative and Gram-positive groups regarding HbA1c, WBC, and CRP levels (p > 0.05), although WBC and CRP showed a moderate positive correlation (ρ = 0.396, p < 0.001). These findings highlight the predominance of Gram-negative microorganisms and considerable antibiotic resistance in chronic wound infections, emphasizing that culture-based diagnosis remains essential since laboratory parameters cannot reliably predict the causative microbial group, and that empirical therapy should be guided by local resistance patterns. Full article

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

8 pages, 234 KB

Open AccessCase Report

Isolation of Neisseria meningitidis Serogroup B from Urine in a 74-Day-Old Infant: A Case Report

by Argyro Siapika, Fevronia Kolonitsiou, Venetia Bellou, Despoina Gkentzi and Nikolaos Giormezis

Microorganisms 2026, 14(9), 1977; https://doi.org/10.3390/microorganisms14091977 - 7 Sep 2026

Abstract

Neisseria meningitidis is a major cause of invasive bacterial disease in infancy, usually presenting as meningitis and/or septicemia. Initial isolation of this organism from urine is exceptionally rare, particularly in young infants. We report a 74-day-old previously healthy infant who presented with fever [...] Read more.

Neisseria meningitidis is a major cause of invasive bacterial disease in infancy, usually presenting as meningitis and/or septicemia. Initial isolation of this organism from urine is exceptionally rare, particularly in young infants. We report a 74-day-old previously healthy infant who presented with fever without an apparent source. Urine obtained by sterile suprapubic aspiration unexpectedly grew N. meningitidis serogroup B. Blood culture subsequently confirmed invasive meningococcal disease, whereas cerebrospinal fluid (CSF) culture and multiplex PCR were negative despite pathologic CSF findings. The urinary isolate was therefore interpreted as probable secondary hematogenous seeding rather than primary urinary tract infection. The patient received ceftriaxone, with temporary escalation to meropenem because of persistent fever; neuroimaging excluded intracranial complications. Complement screening (50% hemolytic complement, CH50) was normal, and the infant recovered fully. This case illustrates an unusual microbiological presentation of probable invasive meningococcal disease, and highlights the importance of promptly interpreting unexpected culture results in febrile young infants. Full article

(This article belongs to the Section Medical Microbiology)

23 pages, 2013 KB

Open AccessArticle

Dual Engines of Adsorption and Biodegradation: Ammonium Nitrogen Removal and Mechanism Analysis by EM-Modified Corn Straw Biochar in Aqueous Solution

by Penghui Wu, Zijie Sang and Ge Zhang

Microorganisms 2026, 14(9), 1976; https://doi.org/10.3390/microorganisms14091976 - 7 Sep 2026

Abstract

Agricultural ammonium pollution from farmland drainage and low-value crop straw utilization are two critical rural environmental problems that cannot be solved by single remediation approaches. Herein, a novel composite was prepared by immobilizing effective microorganisms (EM) on corn straw biochar to construct a [...] Read more.

Agricultural ammonium pollution from farmland drainage and low-value crop straw utilization are two critical rural environmental problems that cannot be solved by single remediation approaches. Herein, a novel composite was prepared by immobilizing effective microorganisms (EM) on corn straw biochar to construct a synergistic adsorption–biodegradation system, and its nitrogen removal mechanism was systematically investigated at structural and molecular levels. Metagenomic analysis detected a complete set of heterotrophic nitrification–aerobic denitrification (HN-AD) functional genes (amoA, hao, napA, nirK, norB, nosZ) in the isolated strain Bacillus thuringiensis A1, revealing the genetic potential of this strain for ammonium biodegradation. EM modification optimized biochar pore structure and increased the equilibrium adsorption capacity to 1.215 mg/g, which was 66.4% higher than that of pristine biochar (0.73 mg/g). Sterilization control tests indicated that physicochemical adsorption occupied the dominant position in ammonium removal, while microbial biodegradation acted as an auxiliary removal pathway. Importantly, the synergistic relationship between the two pathways should be interpreted cautiously, since autoclaving may subtly alter biochar physicochemical properties, and direct paired characterization of viable composites before and after sterilization is technically unavailable. Kinetic and thermodynamic results further validated the improved adsorption performance after modification. Overall, EM immobilization promoted ammonium adsorption via pore optimization, while pore-confined microbes achieved sustainable HN-AD biotransformation, jointly realizing synergistic nitrogen removal. This study provides a mechanistic reference for the optimized design and application of biochar–microbe composites in agricultural nitrogen pollution control. Full article

(This article belongs to the Special Issue Microbes in Wastewater Treatment)

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21 pages, 1757 KB

Open AccessArticle

Temporal Dynamics of Airborne Bacterial and Fungal Communities in Megacity Shanghai: Diel Asynchrony, Environmental Drivers, and Cold Front Perturbations

by Jiaxin Wang, Ling Li, Yanyu Wang, Wenwen Sun and Tiantao Cheng

Microorganisms 2026, 14(9), 1975; https://doi.org/10.3390/microorganisms14091975 - 7 Sep 2026

Abstract

Atmospheric bacteria and fungi are key components of urban bioaerosols, and their community structures are closely related to urban air quality, bioaerosol concentration, and environmental driving factors. However, the temporal dynamics and environmental drivers of bacterial and fungal community structures remain poorly characterized [...] Read more.

Atmospheric bacteria and fungi are key components of urban bioaerosols, and their community structures are closely related to urban air quality, bioaerosol concentration, and environmental driving factors. However, the temporal dynamics and environmental drivers of bacterial and fungal community structures remain poorly characterized in megacities such as Shanghai, China. From November 2024 to November 2025, we conducted a year-long, cross-seasonal bioaerosol sampling and high-throughput DNA sequencing campaign to investigate the seasonal and diel variations, environmental covariation, and meteorological responses of atmospheric bacteria and fungi in Shanghai. The results show that seasonal transitions cannot significantly alter the α-diversity of bacterial or fungal communities, but significantly shift their community compositions, exhibiting a stronger differentiation for fungi than bacteria (PERMANOVA R² = 0.133 vs. 0.054, p = 0.001). At the diel scale, bacterial communities exhibit weak diurnal variation, whereas fungal communities display significantly higher nocturnal Chao1 richness and Shannon diversity, along with distinct compositional separation. Cladosporium and Alternaria are enriched during the day, while saprotrophic basidiomycetes such as Irpex and Trametes are more abundant at night. Fungal composition covaries most strongly with meteorological gradients governed by boundary layer height, clear-sky surface downward solar radiation, temperature, relative humidity, atmospheric pressure and visibility, whereas bacterial–environment associations are weaker. The Relative Exposure-Relevant Proportion (RERP), dominated by Cladosporium and Alternaria, is higher during daytime and negatively associated with relative humidity (β = −0.23, q = 0.001). During a strong cold-air event, bacterial communities shifted rapidly following immediate air mass replacement and high wind shear before stabilizing, whereas fungal communities underwent a more gradual and cumulative turnover. The RERP also elevated during this event, accompanied by a greater contribution from Talaromyces. These findings reveal contrasting dynamics between airborne bacteria and fungi under both background and transient synoptic disturbances, providing crucial observational insights for bioaerosol modeling and risk prediction in urban environments. Full article

(This article belongs to the Special Issue Research on Airborne Microbial Communities)

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27 pages, 1490 KB

Open AccessReview

Metabolite-Resolved Validation of Bacterial Organophosphate Transformation in Soil: A Critical Review of Selected Organophosphate Case Studies

by Lazzat Asylbekkyzy, Meruyert O. Bauenova, Assemgul K. Sadvakasova, Dariga K. Kirbayeva, Bekzhan D. Kossalbayev, Fiaz Ahmad and Dilnaz E. Zaletova

Microorganisms 2026, 14(9), 1974; https://doi.org/10.3390/microorganisms14091974 - 7 Sep 2026

Abstract

This structured critical narrative review evaluates the bacterial transformation of six selected organophosphate pesticides—chlorpyrifos, methyl parathion, parathion, diazinon, malathion, and phosalone—in relation to chemical, mechanistic, and environmental evidence. Peer-reviewed literature was searched in Scopus and PubMed for the period from 1 January 2020 [...] Read more.

This structured critical narrative review evaluates the bacterial transformation of six selected organophosphate pesticides—chlorpyrifos, methyl parathion, parathion, diazinon, malathion, and phosalone—in relation to chemical, mechanistic, and environmental evidence. Peer-reviewed literature was searched in Scopus and PubMed for the period from 1 January 2020 to 26 August 2026 and was supplemented by backward-reference screening and forward citation tracking of foundational studies. Evidence was assessed across eight domains spanning association, tolerance, controlled dissipation, product-resolved transformation, mechanistic attribution, non-sterile-soil validation, detoxification or ecological recovery, and field readiness. The selected compounds reveal substantial differences in pathway resolution: chlorpyrifos has the most developed parent–product evidence base, methyl parathion and parathion are comparatively well characterized at the hydrolytic and enzyme levels, diazinon and malathion retain important downstream uncertainties, and phosalone remains an unresolved evidence-gap comparator. The synthesis shows that credible soil bioremediation requires convergence among parent–product kinetics, catalytic attribution, transformation-product turnover, performance beyond natural attenuation, toxicity reduction, and recovery of relevant soil or plant functions. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 5026 KB

Open AccessArticle

Enumeration Method for Pseudomonas aeruginosa in Water with High Bacterial Background Flora

by Elfy Ly, Tess M. Hiemink, Sharona de Rijk, Karola Waar, Franciska M. Schets, Lucía Hernández Leal, Mark C. M. van Loosdrecht, Hetty Blaak and Heike Schmitt

Microorganisms 2026, 14(9), 1973; https://doi.org/10.3390/microorganisms14091973 - 7 Sep 2026

Abstract

Reliable detection of Pseudomonas aeruginosa (PA) in water is essential for public health water quality assessments, yet culture-based methods remain challenged by high background flora. This study compared the performance of mPA-C agar and the commercial RAPID’ P. aeruginosa (RAPID PA) agar in [...] Read more.

Reliable detection of Pseudomonas aeruginosa (PA) in water is essential for public health water quality assessments, yet culture-based methods remain challenged by high background flora. This study compared the performance of mPA-C agar and the commercial RAPID’ P. aeruginosa (RAPID PA) agar in (ozone-) treated wastewater effluent and (spiked) swimming pond water and evaluated how presumptive colony colour definitions and confirmation steps affected performance characteristics. mPA-C showed strong matrix dependence and high observer variability due to a broad colour colony variation (of both PA and non-PA). RAPID PA produced clearer and more consistent pigmentation with relatively limited background growth and performed more consistently across matrices. Expanding the presumptive colony colour definition significantly improved sensitivity of RAPID PA with minimal loss of specificity. A quick subculturing step on RAPID PA for visual confirmation further enhanced specificity and markedly reduced false-positive rates. Extended incubation to 48 h increased performance only for swimming ponds. RAPID PA performed more consistently across matrices. Overall, using RAPID PA with expanded colour criteria and subculturing as a low-effort confirmation step enabled effective culture-based detection of P. aeruginosa in high-background-flora water samples. This medium represents a practical and robust alternative for routine monitoring. Full article

(This article belongs to the Special Issue Surveillance of Pathogens in the Environment)

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12 pages, 965 KB

Open AccessReview

Emerging Roles of tRNA Modifications in Translational Adaptation of Human Fungal Pathogens

by Yuqi Zhu, Jiaqi Chen, Xinran Li, Ling Lu and Yuanwei Zhang

Microorganisms 2026, 14(9), 1972; https://doi.org/10.3390/microorganisms14091972 - 7 Sep 2026

Abstract

Invasive fungal infections can be life-threatening, particularly in patients with impaired immunity, yet treatment remains limited to a few antifungal drug classes. During infection, fungal pathogens encounter changes in temperature, nutrient availability, immune pressure and drug exposure that challenge their growth and survival. [...] Read more.

Invasive fungal infections can be life-threatening, particularly in patients with impaired immunity, yet treatment remains limited to a few antifungal drug classes. During infection, fungal pathogens encounter changes in temperature, nutrient availability, immune pressure and drug exposure that challenge their growth and survival. tRNA modifications may contribute to adaptation by supporting tRNA stability, aminoacylation and codon decoding. Studies in Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans have linked conserved tRNA-modification pathways to fungal development, host interaction, stress adaptation, virulence and the response to 5-fluorocytosine, with evidence ranging from genetic and infection phenotypes to biochemical characterization of modification reactions. In this Review, we examine how these studies connect modification chemistry and substrate tRNAs with translation, protein output and infection phenotypes. We also draw on mechanistic studies from model organisms and plant-pathogenic fungi to clarify translational links that remain unresolved in human fungal pathogens. We conclude by discussing when tRNA-modification pathways become functionally limiting under host-associated conditions and how they may alter antifungal responses. Full article

(This article belongs to the Special Issue An Update on Aspergillus fumigatus)

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31 pages, 2671 KB

Open AccessArticle

Comparative Population Genomics and Machine Learning Reveal a Distinct Regional Genomic Fingerprint of Middle Eastern Acinetobacter baumannii

by Blnd Azad Ismail, Areen Muhsin Abdulrahman and Shukur Wasman Smail

Microorganisms 2026, 14(9), 1971; https://doi.org/10.3390/microorganisms14091971 - 7 Sep 2026

Abstract

Acinetobacter baumannii is a major multidrug-resistant nosocomial pathogen, yet its population structure and evolutionary dynamics in the Middle East remain poorly understood. This study compared Middle Eastern and global isolates to identify regional genomic signatures. We analyzed 199 high-quality A. baumannii genomes (100 [...] Read more.

Acinetobacter baumannii is a major multidrug-resistant nosocomial pathogen, yet its population structure and evolutionary dynamics in the Middle East remain poorly understood. This study compared Middle Eastern and global isolates to identify regional genomic signatures. We analyzed 199 high-quality A. baumannii genomes (100 Middle Eastern and 99 global) using pangenome reconstruction, core-genome phylogenetics, resistome and virulome profiling, genome-wide association studies, and machine learning. The pangenome comprised 10,971 genes, including 1102 unique to Middle Eastern isolates. Compared with global isolates, Middle Eastern genomes carried fewer antimicrobial resistance genes but a higher abundance of mobility-associated genes. A distinct regional cluster was dominated by sequence type 2 (ST2), representing 66% of Middle Eastern isolates. Genome-wide association analysis identified region-associated markers, particularly ISAba1 variants and the tufB gene. A Random Forest classifier distinguished Middle Eastern from global isolates with 79.9% accuracy. Virulence gene repertoires were similar between groups, and resistance gene burdens remained stable over time. Middle Eastern A. baumannii isolates exhibit a distinct regional genomic signature characterized by accessory-genome conservation, reduced genomic heterogeneity, enrichment of ISAba1-associated markers, and increased mobility-associated gene content. These features differentiate the regional population from globally distributed isolates despite the similar prevalence of the ST2/IC2 lineage in both cohorts. Full article

(This article belongs to the Special Issue Advances in Clinical Infections and Antimicrobial Resistance)

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18 pages, 5726 KB

Open AccessArticle

Long-Term Organic Fertilization Drives Soil Organic Carbon Accumulation in Black Soil Through Microbial Necromass Carbon and CAZyme-Mediated Carbon Turnover

by Yang Liu, Haoyan Li, Xinxin Guo, Nan Wang, Ning Huang, Hongbin Wang, Jinhua Liu, Chenyu Zhao, Luze Yang, Biao Sui and Xingmin Zhao

Microorganisms 2026, 14(9), 1970; https://doi.org/10.3390/microorganisms14091970 - 7 Sep 2026

Abstract

Long-term organic inputs increase soil organic carbon (SOC) in black soil; however, it remains uncertain if straw and manure enhance SOC via separate microbial necromass carbon (MNC) routes. Therefore, a 12-year field experiment was conducted to explore this mechanism. Treatments included inorganic fertilizer, [...] Read more.

Long-term organic inputs increase soil organic carbon (SOC) in black soil; however, it remains uncertain if straw and manure enhance SOC via separate microbial necromass carbon (MNC) routes. Therefore, a 12-year field experiment was conducted to explore this mechanism. Treatments included inorganic fertilizer, partial substitution of inorganic fertilizer with straw, and partial substitution of inorganic fertilizer with manure, along with a no-fertilizer control. According to the results, compared with inorganic fertilizer alone, treatments involving both organic manure and straw returned markedly raised the levels of SOC, MNC, bacterial necromass carbon (BNC), and fungal necromass carbon (FNC). Notably, compared to the CK treatment, N75S showed a greater contribution of MNC to SOC (MNC/SOC), but in both N75M and M, the MNC/SOC was lower than in CK. The CAZyme genes related to hemicellulose, lignin, chitin, and peptidoglycan differed among treatments. Elevated gene abundances for plant-derived lignin and hemicellulose decomposition were observed under M and N75M, whereas they reduced the genes responsible for peptidoglycan and glucan. However, under N75S, there was a notable rise in the number of genes responsible for hemicellulose and lignin, as well as an increase in genes that degrade chitin and peptidoglycans. In conclusion, this finding demonstrates that long-term straw return tends to promote SOC stabilization primarily through the microbial necromass pathway, while the application of manure over the long term tends to increase the total SOC primarily through the input of exogenous organic carbon. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)

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