Microorganisms

33 pages, 5235 KB

Open AccessReview

Colletotrichum Species Associated with Alfalfa Anthracnose: An Overview and Historical Perspective

by Vojislav Trkulja, Tanja Vasić, Ranka Milašin, Nenad Trkulja, Slavica Matić, Milan Stević, Sanja Živković and Tatjana Popović Milovanović

Microorganisms 2026, 14(1), 261; https://doi.org/10.3390/microorganisms14010261 - 22 Jan 2026

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Abstract

Alfalfa anthracnose is an economically significant disease that leads to substantial biomass losses due to stem rot, reduced stand longevity, and a decline in forage nutritional quality. The disease is caused by multiple species within the genus Colletotrichum, including the 14 described [...] Read more.

Alfalfa anthracnose is an economically significant disease that leads to substantial biomass losses due to stem rot, reduced stand longevity, and a decline in forage nutritional quality. The disease is caused by multiple species within the genus Colletotrichum, including the 14 described species: C. gloeosporioides, C. truncatum, C. lindemuthianum, C. destructivum, C. dematium, C. trifolii, C. medicaginis, C. graminicola, C. coccodes, C. sojae, C. spinaciae, C. lini, C. americae-borealis, and C. tofieldiae. A thorough understanding of key aspects of the pathogen’s biology, along with its epidemiology, infection cycle, and accurate disease diagnosis, is essential for the development of sustainable management strategies. Knowledge of these factors allows us to anticipate disease outbreaks, implement timely interventions, and design integrated control measures that reduce reliance on chemical fungicides while maintaining crop productivity and forage quality. Although anthracnose management has traditionally relied on synthetic fungicides, this review synthesizes alternative control strategies to clarify the current state of knowledge and to provide new insights into the development of effective and sustainable approaches for managing Colletotrichum species. Full article

(This article belongs to the Special Issue Diversity of Plant Pathogens)

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17 pages, 3175 KB

Open AccessArticle

Flavonoid-Rich Cyperus esculentus Extracts Disrupt Cellular and Metabolic Functions in Staphylococcus aureus

by Yaning Zhang, Zhengdong Ma, Xuzhe Wang, Qilong Jiang, Xue Kang and Hongmei Gao

Microorganisms 2026, 14(1), 260; https://doi.org/10.3390/microorganisms14010260 - 22 Jan 2026

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Abstract

The escalating threat of antibiotic resistance, particularly from Staphylococcus aureus (S. aureus), has become a critical challenge in both public health and animal husbandry. The extensive use of conventional antibiotics in livestock production accelerates the emergence of resistant strains, heightening risks [...] Read more.

The escalating threat of antibiotic resistance, particularly from Staphylococcus aureus (S. aureus), has become a critical challenge in both public health and animal husbandry. The extensive use of conventional antibiotics in livestock production accelerates the emergence of resistant strains, heightening risks to food safety and human health. Although plant-derived bioactive compounds are increasingly recognized as promising alternatives to synthetic antimicrobials, the mechanisms underlying their efficacy—and the potential for synergistic action among different plant parts—remain poorly understood. In particular, the antibacterial interactions among extracts from different tissues of Cyperus esculentus L. (C. esculentus), a plant rich in flavonoids and phenolics, have yet to be systematically evaluated. Here, we investigated the antibacterial properties and mechanisms of ethanol extracts from the tubers, stems–leaves and their mixture of C. esculentus against S. aureus. Using Oxford cup diffusion assays, scanning electron microscopy (SEM), bacterial growth kinetics, and untargeted metabolomics, we assessed both phenotypic inhibition and metabolic disruption. The mixed extract exhibited the strongest antibacterial effect, producing a 26.15 mm inhibition zone—approximately 7% greater than that of single-part extracts—and induced cell wall rupture and disintegration as observed by SEM. Growth curve analyses revealed time-dependent bacterial suppression, while metabolomic profiling identified 845 differential metabolites, indicating disturbances in amino acid, lipid, and nucleotide metabolism. Flavonoids such as acacetin, diosmetin, naringenin, and silybin A were identified as principal active compounds contributing to these effects. Full article

(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)

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18 pages, 3393 KB

Open AccessArticle

Diversity Analysis of Fecal Microbiota in Goats Driven by White Blood Cell Count

by Meng Zeng, Hanlin Zhou, Qun Wu, Ke Wang, Hu Liu, Yuanting Yang, Weishi Peng, Anmiao Chen, Xiaoyan Deng, Chihai Ji, Xiaosong Zhang and Jiancheng Han

Microorganisms 2026, 14(1), 259; https://doi.org/10.3390/microorganisms14010259 - 22 Jan 2026

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Abstract

The Leizhou goat is a vital indigenous breed, yet its disease resilience can complicate early health monitoring. The white blood cell (WBC) count is a key indicator of immune status, but its relationship with the gut microbiota remains uncharacterized in this breed. This [...] Read more.

The Leizhou goat is a vital indigenous breed, yet its disease resilience can complicate early health monitoring. The white blood cell (WBC) count is a key indicator of immune status, but its relationship with the gut microbiota remains uncharacterized in this breed. This study aimed to characterize the fecal microbiota of Hainan black goats stratified based on their WBC counts. The goats were stratified into Lower, Middle, and High WBC groups based on peripheral WBC counts to compare their fecal microbiota and identify potential associations with systemic immunity. Significant differences in microbial alpha- and be-ta-diversity were observed among the groups, with the High WBC group showing the greatest richness. The microbiota was dominated by Bacillota and Bacteroidota at the phylum level. Linear discriminant analysis Effect Size (LEfSe) identified specific taxa en-riched in each group, such as Ruminococcusin the High WBC group. Critically, Spearman correlation analysis demonstrated significant positive correlations between WBC counts and the relative abundance of genera like unclassified_f_Oscillospiraceae and unclassi-fied_c_Clostridia. These findings demonstrate that WBC counts are significantly associated with distinct shifts in the gut microbial community structure of Hainan black goats. The identified WBC-associated microbial biomarkers suggest a link between the gut microbi-ome and host immune regulation, providing a foundation for future research on microbi-ota-mediated health assessment in goats. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 3108 KB

Open AccessArticle

Analysis of Intestinal Microbiota Differences and Functional Prediction Between Sichuan-Tibetan Black Pigs and Landrace Pigs

by Lichun Jiang, Yi Qing, Kaiyuan Huang, Huiling Huang, Chengmin Li and Yanci Li

Microorganisms 2026, 14(1), 258; https://doi.org/10.3390/microorganisms14010258 - 22 Jan 2026

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Abstract

This study aimed to investigate the structural differences and functional potential of the gut microbiota between Sichuan-Tibetan black pigs (n = 5) and Landrace pigs (n = 5) under identical rearing conditions. Fecal samples were collected and subjected to 16S rRNA [...] Read more.

This study aimed to investigate the structural differences and functional potential of the gut microbiota between Sichuan-Tibetan black pigs (n = 5) and Landrace pigs (n = 5) under identical rearing conditions. Fecal samples were collected and subjected to 16S rRNA gene sequencing followed by comprehensive bioinformatics analysis. The results revealed 963 and 910 operational taxonomic units (OTUs) in Sichuan-Tibetan black pigs and Landrace pigs, respectively, with 808 OTUs shared between the two breeds. While both breeds shared Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla, significant compositional differences were observed at the genus level. Sichuan-Tibetan black pigs exhibited higher abundance of Escherichia-Shigella, Streptococcus, Prevotella, Parabacteroides, and Collinsella, whereas Landrace pigs were enriched in Bacteroides. Alpha diversity analysis showed no significant differences in Shannon, Simpson, or ACE indices, though the Chao index differed markedly between the two groups. Beta diversity analysis (PCoA and NMDS) confirmed distinct microbial community structures between the breeds. Functional prediction analysis demonstrated that metabolic pathways dominated in both groups, but with notable functional differentiation: the microbiota of Sichuan-Tibetan black pigs showed significant enrichment in biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and amino acid biosynthesis; whereas, Landrace pigs were characterized by enhanced carbon and energy metabolism pathways. Additionally, BugBase phenotype prediction revealed significant differences in stress tolerance, cell wall properties, and oxygen utilization capabilities between the two groups. These findings provide valuable insights into the breed-specific characteristics of gut microbiota in swine and establish a foundation for further research on host-microbe interactions and their implications for animal health and nutrition. Full article

(This article belongs to the Special Issue Gut Microbes and Probiotics)

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13 pages, 35569 KB

Open AccessArticle

Genetic Diversity and Emerging Trends of Mycoplasma synoviae in China: Insights from a 2024 Nationwide MLST Study

by Lu Tu, Xuesong Li, Yiming Liu, Xin Jin, Lijuan Yin, Xiaoling Wang, Qingfeng Zhou, Kai Wang and Youzhi Tang

Microorganisms 2026, 14(1), 257; https://doi.org/10.3390/microorganisms14010257 - 22 Jan 2026

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Abstract

Mycoplasma synoviae (MS) is a major pathogen threatening China’s poultry industry, causing severe economic losses, and clarifying its epidemiology is pivotal for disease control and flock purification. In this study, a total of 3215 chicken samples collected from 643 broiler farms across 15 [...] Read more.

Mycoplasma synoviae (MS) is a major pathogen threatening China’s poultry industry, causing severe economic losses, and clarifying its epidemiology is pivotal for disease control and flock purification. In this study, a total of 3215 chicken samples collected from 643 broiler farms across 15 provinces in China in 2024 were analyzed. PCR detected 14% positivity (450 samples), and 18 isolates obtained from these positive samples (4.0% isolation rate). Multilocus sequence typing (MLST, 7 housekeeping genes) and neighbor-joining phylogenetic analysis (integrating 425 reference sequences from public databases) identified 13 distinct sequence types (STs), demonstrating considerable genetic diversity among circulating MS strains. Pathogenicity assessment of the five isolates revealed that the infected chickens exhibited varying degrees of infectious synovitis, while no respiratory signs were observed. In addition, antimicrobial susceptibility testing against 10 commonly used antibiotics was conducted on the 18 strains, providing urgently needed guidance for rational drug use in the clinical treatment of both breeder and broiler flocks. This large-scale epidemiological study yields crucial insights into the current prevalence and genetic diversity of MS in China and lays a scientific foundation for formulating targeted prevention strategies and optimizing management practices. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 3rd Edition)

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14 pages, 460 KB

Open AccessArticle

First Isolation of Klebsiella pneumoniae from Septicaemic Piglets in Poland

by Piotr Cybulski, Ines Spiekermeier, Radosław Kondratiuk, Artur Jabłoński, Patryk Tarka and Grzegorz Woźniakowski

Microorganisms 2026, 14(1), 256; https://doi.org/10.3390/microorganisms14010256 - 22 Jan 2026

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Abstract

Klebsiella pneumoniae is commonly known to cause a vast range of community-acquired or nosocomial infections. The isolation of K. pneumoniae has also been noted in diseased food-producing animals, including swine. The main goals of this study were to document clinical manifestation of a [...] Read more.

Klebsiella pneumoniae is commonly known to cause a vast range of community-acquired or nosocomial infections. The isolation of K. pneumoniae has also been noted in diseased food-producing animals, including swine. The main goals of this study were to document clinical manifestation of a septicaemia outbreak in suckling piglets due to K. pneumoniae ST25 and provide molecular characterisation of the isolates. For the purpose of this investigation, 13 dead suckling piglets with cyanosis were selected. All the isolates obtained from affected lungs were susceptible to apramycin, ceftiofur, gentamycin, neomycin, and spectinomycin, presented intermediate susceptibility to florfenicol, and were resistant to other tested antibiotics. Histopathological examination of lungs, kidneys, and livers revealed lesions typical of septicaemia. MLST analysis of the isolates demonstrated a complex metabolic profile of the bacteria with genes attributable to the hypervirulent phenotype. To the best of our knowledge, we documented the first outbreak of K. pneumoniae septicaemia in suckling piglets reared in Poland. Full article

(This article belongs to the Special Issue The Diagnosis, Treatment, Prevention, and Epidemiology of Infectious Diseases in Livestock: A One Health Approach)

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17 pages, 2470 KB

Open AccessArticle

The Tumor Cell Proliferation Inhibitory Activity of the Human Herpes Virus Type 6 U94 Protein Relies on a Stable Tridimensional Conformation

by Anna Bertelli, Matteo Uggeri, Federica Filippini, Melissa Duheric, Francesca Caccuri and Arnaldo Caruso

Microorganisms 2026, 14(1), 255; https://doi.org/10.3390/microorganisms14010255 - 22 Jan 2026

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Abstract

The U94 protein of Human Herpesvirus 6 exerts antiproliferative effects through downregulation of the Src proto-oncogene. We aimed to define the shortest U94 fragment that preserves antiproliferative activity and to explore its structural properties. U94 was truncated into shorter fragments, which were subjected [...] Read more.

The U94 protein of Human Herpesvirus 6 exerts antiproliferative effects through downregulation of the Src proto-oncogene. We aimed to define the shortest U94 fragment that preserves antiproliferative activity and to explore its structural properties. U94 was truncated into shorter fragments, which were subjected to computational analyses and proliferation assays on MDA-MB-468, BT-549 breast cancer cells. Src phosphorylation levels were scrutinized by Western blot analysis. Data obtained demonstrated that the U94 antiproliferative activity resides in its N-terminal region. Specifically, MT153 (aa 1–153) and MT117 (aa 1–117) fragments exhibited antiproliferative activity, whereas MV85 (aa 1–85) fragment did not. Computational analyses identified MG112 (aa 1–112) and MI108 (aa 1–108) as biologically active and suggested that the β-sheet of the structure is critical. The shortest KI95 fragment (aa 14–108), maintaining a stable β-sheet, demonstrated antiproliferative effects and Src downregulation. The antiproliferative activity of U94 and its active fragments relies on stable tridimensional conformation rather than on linear peptide sequence. KI95 represents the shortest active U94 fragment that preserves biological function, with critical residues likely located within the β-sheet region. These findings highlight the importance of structural integrity in U94 functionality and suggest KI95 as a potential therapeutic agent for cancer treatment. Full article

(This article belongs to the Special Issue State-of-the-Art Advances of Medical Virology in Italy)

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11 pages, 961 KB

Open AccessArticle

A Retrospective Study on the Aetiology of Clinical Bovine Mastitis and Its Antibiotic Resistance Profiles in Western Australia Dairy Farms

by Hilary Chok, Michael Laurence and Joshua W. Aleri

Microorganisms 2026, 14(1), 254; https://doi.org/10.3390/microorganisms14010254 - 21 Jan 2026

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Abstract

Clinical data on antimicrobial profiles are useful for dairy udder health treatment programmes and represents a component of antimicrobial stewardship. The study aimed to determine the bacterial aetiology of clinical mastitis in dairy herds in Western Australia and to evaluate their antibiotic resistance [...] Read more.

Clinical data on antimicrobial profiles are useful for dairy udder health treatment programmes and represents a component of antimicrobial stewardship. The study aimed to determine the bacterial aetiology of clinical mastitis in dairy herds in Western Australia and to evaluate their antibiotic resistance profiles. This retrospective study utilised clinical antimicrobial profile data from two referral diagnostic centres within the region of Western Australia. A total of 545 mastitic samples were submitted for antimicrobial culture and testing over a period of 10 years (2008–2018). Of these, 406 showed bacterial growth and 139 no bacterial growth was observed. The most common isolates were Streptococcus uberis (25.3%), Staphylococcus aureus (17.2%), and Escherichia coli (9.4%). No growth was identified in 25.5% of the mastitis milk samples. The antimicrobial profiles revealed high susceptibilities towards cefuroxime (95.7%), clavulox (89.4%), and oxytetracycline (89%), whilst showing high resistance towards novobiovin (70%). From this study, it is concluded that there was a decline in the resistance trends towards the isolates of both S. uberis and S. aureus over the 10-year period and contagious mastitis had a higher occurrence. There is a need to consider surveillance programmes that determine the patterns of on-farm antimicrobial usage and further characterise the pathogens based on the presence of resistance antimicrobial genes. Data on antimicrobial surveillance represent an important component of antimicrobial stewardship. Full article

(This article belongs to the Section Veterinary Microbiology)

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17 pages, 650 KB

Open AccessReview

Resolving the “Thick-Wall Challenge” in Haematococcus pluvialis: From Metabolic Reprogramming to Clinical Translation

by Tao Chen, Xun Zhu and Qiang Liao

Microorganisms 2026, 14(1), 253; https://doi.org/10.3390/microorganisms14010253 - 21 Jan 2026

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Abstract

Astaxanthin, derived from Haematococcus pluvialis, is a potent antioxidant with significant therapeutic potential. However, its large-scale commercialization is hindered by the “thick-wall challenge”, a phenomenon where the stress conditions required for astaxanthin accumulation also trigger the formation of resistant secondary cell walls. [...] Read more.

Astaxanthin, derived from Haematococcus pluvialis, is a potent antioxidant with significant therapeutic potential. However, its large-scale commercialization is hindered by the “thick-wall challenge”, a phenomenon where the stress conditions required for astaxanthin accumulation also trigger the formation of resistant secondary cell walls. This challenge complicates extraction and reduces bioaccessibility, thereby increasing production costs. Recent advancements have focused on uncoupling astaxanthin biosynthesis from cell wall reinforcement, utilizing metabolic engineering and strain selection to reduce wall formation while maintaining high yields. Furthermore, green extraction techniques, such as electrotechnologies and ionic liquids, are being explored to improve efficiency and environmental sustainability. This review synthesizes these innovations, including biorefinery systems that maximize biomass valorization, and discusses emerging clinical applications. We highlight the challenges in bridging the gap between laboratory successes and clinical translation, and suggest future directions for resolving the thick-wall challenge, advancing astaxanthin production, and expanding its therapeutic uses in nutraceuticals and pharmaceuticals. Full article

(This article belongs to the Topic Microalgae: Current Trends in Basic Research and Applications)

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16 pages, 3603 KB

Open AccessArticle

Bovine Parainfluenza Virus Type 3 Infection Reprograms the Bovine Serum Lipidome Associated with Phosphatidylinositol Depletion and Sphingolipid Axis Activation

by Shubo Wen, Jiongjie Zhang, Na Lu, Deqing Tian, Lingpin Meng, Zheng Gao and Yang Song

Microorganisms 2026, 14(1), 252; https://doi.org/10.3390/microorganisms14010252 - 21 Jan 2026

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Abstract

Bovine Parainfluenza Virus Type 3 (BPIV3) is a critical pathogen in the Bovine Respiratory Disease Complex (BRDC), leading to significant economic losses in the cattle industry. However, the metabolic reprogramming induced by BPIV3 in cattle remains poorly understood. This study aimed to investigate [...] Read more.

Bovine Parainfluenza Virus Type 3 (BPIV3) is a critical pathogen in the Bovine Respiratory Disease Complex (BRDC), leading to significant economic losses in the cattle industry. However, the metabolic reprogramming induced by BPIV3 in cattle remains poorly understood. This study aimed to investigate the impact of BPIV3 infection on the serum metabolome of Simmental cattle using untargeted metabolomics and ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS). The results revealed significant alterations in the lipidome, including the upregulation of phosphatidylcholine (PC) and phosphatidylglycerol (PG), and the downregulation of phosphatidylinositol (PI). Sphingolipid metabolism also showed considerable changes, with increased levels of Trihexosylceramide and D-erythro-Sphingosine C-17. Furthermore, metabolic pathway analysis identified enriched pathways related to lipid metabolism, amino acid metabolism, and energy sensing. These findings suggest that BPIV3 infection induces substantial shifts in lipid metabolism, which may facilitate viral replication and immune evasion. Our results provide a deeper understanding of the metabolic changes in BPIV3-infected cattle and propose potential targets for therapeutic intervention. Full article

(This article belongs to the Special Issue Microbial Infections in Ruminants)

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18 pages, 3124 KB

Open AccessArticle

Diet–Microbiome Relationships in Prostate-Cancer Survivors with Prior Androgen Deprivation-Therapy Exposure and Previous Exercise Intervention Enrollment

by Jacob Raber, Abigail O’Niel, Kristin D. Kasschau, Alexandra Pederson, Naomi Robinson, Carolyn Guidarelli, Christopher Chalmers, Kerri Winters-Stone and Thomas J. Sharpton

Microorganisms 2026, 14(1), 251; https://doi.org/10.3390/microorganisms14010251 - 21 Jan 2026

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Abstract

The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet–microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet–microbiome associations in 79 prostate-cancer survivors (ages [...] Read more.

The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet–microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet–microbiome associations in 79 prostate-cancer survivors (ages 62–81) enrolled in a randomized exercise intervention trial, 59.5% of whom still have active metastatic disease. Dietary intake was assessed using the Diet History Questionnaire (201 variables) and analyzed using three validated dietary pattern scores: Mediterranean Diet Adherence Score (MEDAS), Healthy Eating Index-2015 (HEI-2015), and the Mediterranean-Dash Intervention for Neurodegenerative Delay (MIND) diet score. Gut microbiome composition was characterized via 16S rRNA sequencing. Dimensionality reduction strategies, including theory-driven diet scores and data-driven machine learning (Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO)), were used. Statistical analyses included beta regression for alpha diversity, Permutational Multivariate Analysis of Variance (PERMANOVA) for beta diversity (both Bray–Curtis and Sørensen metrics), and Microbiome Multivariable Associations with Linear Models (MaAsLin2) with negative binomial regression for taxa-level associations. All models tested interactions with exercise intervention, APOLIPOPROTEIN E (APOE) genotype, and testosterone levels. There was an interaction between MEDAS and exercise type on gut alpha diversity (Shannon: p = 0.0022), with stronger diet–diversity associations in strength training and Tai Chi groups than flexibility controls. All three diet-quality scores predicted beta diversity (HEI p = 0.002; MIND p = 0.025; MEDAS p = 0.034) but not Bray–Curtis (abundance-weighted) distance, suggesting diet shapes community membership rather than relative abundances. Taxa-level analysis revealed 129 genera with diet associations or diet × host factor interactions. Among 297 dietary variables tested for cognitive outcomes, only caffeine significantly predicted Montreal Cognitive Assessment (MoCA) scores after False Discovery Rate (FDR) correction (p = 0.0009, q = 0.014) through direct pathways beneficial to cognitive performance without notable gut microbiome modulation. In cancer survivors, dietary recommendations should be tailored to exercise habits, genetic background, and hormonal status. Full article

(This article belongs to the Special Issue The Interactions Between Nutrients and Microbiota)

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24 pages, 2819 KB

Open AccessArticle

Long-Term Organic Fertilization Enhances Soil Fertility and Reshapes Microbial Community Structure with Decreasing Effects Across Soil Depth

by Suyao Li, Yulin Li, Xu Yan, Zhengyang Gu, Dong Xue, Kaihua Wang, Yuting Yang, Min Lv, Yujie Han, Jinbiao Li, Yanyan Lv and Anyong Hu

Microorganisms 2026, 14(1), 250; https://doi.org/10.3390/microorganisms14010250 - 21 Jan 2026

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Abstract

Sustaining agricultural productivity and soil health under intensive cultivation requires a comprehensive understanding of fertilization effects, particularly on deeper soil layers, which has received limited attention compared to surface soils. This study investigated how different fertilization regimes (inorganic, organic, and combined organic–inorganic fertilizers) [...] Read more.

Sustaining agricultural productivity and soil health under intensive cultivation requires a comprehensive understanding of fertilization effects, particularly on deeper soil layers, which has received limited attention compared to surface soils. This study investigated how different fertilization regimes (inorganic, organic, and combined organic–inorganic fertilizers) influence soil physicochemical properties, microbial diversity, community structure, and functional gene abundances at three soil depths (0–20 cm, 20–40 cm, and 40–60 cm) in a 40-year fertilization experiment. Organic fertilization significantly improved topsoil fertility indicators such as soil organic matter (56.6–109.2%), total nitrogen (66.7–122.0%), total phosphorus (198.6–413.2%), and available phosphorus (984.8–1622.1%) and potassium (35.3–438.1%). Compared with the unfertilized control and nitrogen-only treatment, rice yield increased by 97.1–130.5% under NPK and sole organic fertilization, and further increased by 184.1–255.9% under combined organic–inorganic fertilization. However, fertilization effects diminished with soil depth due to limited nutrient mobility. Microbial diversity significantly decreased with depth and was minimally influenced by fertilization treatments. Microbial community structure varied notably among fertilization treatments at the surface layer, mainly driven by soil nutrients, whereas soil depth had a dominant effect on microbial community structure and compositions. Co-occurrence networks showed the highest complexity in surface soil microbial communities, which declined with soil depth, reflecting potential synergistic and mutualistic relationships in topsoil and the adaptation of microbial communities to nutrient-limited conditions in subsoil. Microbial functional gene analyses highlighted clear depth-dependent distributions, with surface layers enriched in decomposition-related genes, while deeper layers favored anaerobic processes. Overall, long-term fertilization exerted strong depth-dependent effects on soil fertility, microbial community structure, and functional potential in paddy soils. Full article

(This article belongs to the Special Issue Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition)

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20 pages, 825 KB

Open AccessArticle

A Probiotic Bacillus velezensis Consortium Exhibits Superior Efficacy over Two Alternative Probiotics in Suppressing Swine Pathogens and Modulating Intestinal Barrier Function and Immune Responses In Vitro

by Josh Walker, Katrine Bie Larsen, Steffen Yde Bak, Niels Cristensen, Nicolas Chubbs, Weiqing Zeng, Adrian Schwarzenberg and Chong Shen

Microorganisms 2026, 14(1), 249; https://doi.org/10.3390/microorganisms14010249 - 21 Jan 2026

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Abstract

Despite increasing interest in probiotics as antibiotic alternatives in swine production, few studies have directly compared the functional efficacy of different commercial probiotic formulations under controlled conditions. We conducted an in vitro study using porcine intestinal epithelial (IPEC-J2) and macrophage-like (3D4/21) cell models [...] Read more.

Despite increasing interest in probiotics as antibiotic alternatives in swine production, few studies have directly compared the functional efficacy of different commercial probiotic formulations under controlled conditions. We conducted an in vitro study using porcine intestinal epithelial (IPEC-J2) and macrophage-like (3D4/21) cell models to compare the efficacy of three commercial probiotic consortia (C1: three strains of Bacillus velezensis; C2: B. licheniformis + B. subtilis; C3: Clostridium butyricum). Treatments were evaluated for their ability to inhibit pathogenic Escherichia coli, Clostridium perfringens, and Salmonella spp., enhance epithelial barrier integrity, and modulate immune responses. Experimental endpoints included pathogen inhibition assays, adhesion to IPEC-J2 cells, transepithelial electrical resistance (TEER), tight junction protein expression, and cytokine profiling via RT-qPCR and proteomics. Data were analyzed using the Kruskal–Wallis test with false discovery rate (FDR) control at 5%. C1 cell-free supernatant (CFS) strongly inhibited pathogen growth (84.8 ± 5.3% inhibition of ETEC F4⁺F18⁻ vs. medium control; p < 0.05), whereas C2 had no effect, and C3 inhibited only one isolate. The coculture of IPEC-J2 cells with C1 CFS increased the expression of TJ proteins ZO-1, MUC13, and MUC20 (+12.9–46.6% vs. control; p < 0.001) and anti-inflammatory TGF-β; reduced pro-inflammatory IL-6 in LPS-stimulated 3D4/21 cells. In comparison, C2 and C3 showed minimal impact on epithelial barrier integrity and immune modulation, as indicated by negligible changes in TEER values, tight junction protein expression (ZO-1, MUC13, MUC20), and cytokine profiles relative to the control. In conclusion, C1 demonstrated greater in vitro efficacy than C2 (B. licheniformis + B. subtilis) and C3 (Clostridium butyricum), including pathogen inhibition assays, epithelial adhesion, TEER measurements, and cytokine modulation, suggesting its potential as a leading candidate for functional probiotic applications. Full article

(This article belongs to the Special Issue The Role of Probiotics in Animal Health)

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22 pages, 844 KB

Open AccessArticle

Genetic Characteristics Associated with Probiotic Functions in Four Indonesian Skin Microbiome-Derived Bacterial Strains

by Ahmad Husein Alkaff, Amarila Malik, Patricia Arabela Situmeang and Nicholas C. K. Heng

Microorganisms 2026, 14(1), 248; https://doi.org/10.3390/microorganisms14010248 - 21 Jan 2026

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Abstract

The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their “generally recognized as safe” (GRAS) status remains challenging. Here, [...] Read more.

The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their “generally recognized as safe” (GRAS) status remains challenging. Here, we have subjected the annotated draft genome sequences of four human skin-derived bacterial strains, namely Bacillus subtilis MBF10-19J, Micrococcus luteus MBF05-19J, Staphylococcus hominis MBF12-19J, and Staphylococcus warneri MBF02-19J, to bioinformatic analyses to detect the genes associated with important probiotic traits, as well as undesirable characteristics such as antibiotic resistance, virulence factors, and toxic metabolites. Each bacterium harbors at least one type of adhesin-encoding gene, while only S. hominis MBF12-19J and S. warneri MBF02-19J contain the putative genes encoding enzymes for metabolism improvement. In vitro assays, including antibiotic susceptibility and antimicrobial activity testing, revealed strain-specific safety characteristics that complement the genomic findings. With regard to antibiotic resistance determinants, S. hominis MBF12-19J showed the most favorable profile, S. warneri MBF02-19J and M. luteus MBF05-19J appeared suitable when used with appropriate caution, and B. subtilis MBF10-19J exhibited amoxicillin resistance, i.e., warrants careful evaluation. Further in vivo validation is needed to determine whether these strains do indeed comply with GRAS evaluation frameworks. Full article

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

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20 pages, 6092 KB

Open AccessArticle

Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Egyptian Children with Diarrhoea

by Radwa Abdelwahab, Munirah M. Alhammadi, Muhammad Yasir, Ehsan A. Hassan, Entsar H. Ahmed, Nagla H. Abu-Faddan, Enas A. Daef, Stephen J. W. Busby and Douglas F. Browning

Microorganisms 2026, 14(1), 247; https://doi.org/10.3390/microorganisms14010247 - 21 Jan 2026

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Abstract

Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is [...] Read more.

Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third-generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug-resistant (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children who presented with diarrhoea at the Outpatients Clinic of Assiut University Children’s Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum β-lactamase genes, as well as bla_NDM and bla_OXA carbapenemase genes, likely encoded on IncX3 and IncF plasmids. Many of these strains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones belonging to sequence types ST167, ST410, and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world. Full article

(This article belongs to the Special Issue Bacterial Infections in Clinical Settings, 2nd Edition)

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16 pages, 2886 KB

Open AccessArticle

Surfactin–Bacillaene Copathway Engineering Strategy Boosts Fengycin Production and Antifungal Activity in Bacillus velezensis HN-Q-8

by Yuzhu Gao, Liuhui Zhao, Dai Zhang, Dongmei Zhao, Qian Li, Haibin Jiang, Yang Pan, Jiehua Zhu and Zhihui Yang

Microorganisms 2026, 14(1), 246; https://doi.org/10.3390/microorganisms14010246 - 21 Jan 2026

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Abstract

Previous studies have demonstrated that Bacillus velezensis HN-Q-8 shows significant inhibitory effects against various plant pathogenic fungi causing potato diseases, primarily attributed to the production of fengycin. However, the low yield of fengycin in wild-type strains limits its practical application, and the influence [...] Read more.

Previous studies have demonstrated that Bacillus velezensis HN-Q-8 shows significant inhibitory effects against various plant pathogenic fungi causing potato diseases, primarily attributed to the production of fengycin. However, the low yield of fengycin in wild-type strains limits its practical application, and the influence of its biosynthesis pathway on volatile organic compound production remains unclear. In this study, to enhance fengycin production in Bacillus velezensis HN-Q-8, we applied metabolic engineering by targeting competitive pathways. Specifically, a double mutant (ΔsrfAAΔbaeBE) was constructed by knocking out the surfactin synthase gene srfAA and the bacillaene synthesis gene baeBE. The fengycin yield of the ΔsrfAAΔbaeBE mutant in the basal (sodium glutamate) fermentation medium reached 98.83 mg/L, representing a 2.39-fold increase over the wild-type strain. Subsequent medium optimization by supplementing peptone further boosted production to 155.61 mg/L, which was 3.77-fold higher than the wild-type level. The lipopeptide extract from the double mutant strain ΔsrfAAΔbaeBE demonstrated potentiated antifungal activity against four major potato fungal pathogens: Alternaria solani (early blight), Rhizoctonia solani (black scurf), Fusarium oxysporum (wilt), and Botrytis cinerea (gray mold). The active volatile compounds released by ΔsrfAAΔbaeBE, such as benzaldehyde and 2,5-dimethylpyrazine were significantly increased. The knockout of srfAA and baeBE also distinctly altered the physiology of the strain: the double mutant exhibited enhanced biofilm formation, an accelerated early growth rate followed by early decline, and a severely reduced sporulation capacity. These results confirmed the feasibility of molecularly modifying Bacillus velezensis HN-Q-8 to improve fengycin production and antifungal activity for further agricultural application. Full article

(This article belongs to the Section Microbial Biotechnology)

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2 pages, 759 KB

Open AccessCorrection

Correction: Askoura et al. Alteration of Salmonella enterica Virulence and Host Pathogenesis through Targeting sdiA by Using the CRISPR-Cas9 System. Microorganisms 2021, 9, 2564

by Momen Askoura, Ahmad J. Almalki, Amr S. Abu Lila, Khaled Almansour, Farhan Alshammari, El-Sayed Khafagy, Tarek S. Ibrahim and Wael A. H. Hegazy

Microorganisms 2026, 14(1), 245; https://doi.org/10.3390/microorganisms14010245 - 21 Jan 2026

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Abstract

In the original publication, there was a mistake in Figure 7B as published [...] Full article

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

19 pages, 2477 KB

Open AccessArticle

Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types

by Yaru Xiong, Zhihui Dai, Fangling He, Rongjiao Liu, Juan Wang, Zhifei Zhan, Huayun Jia, Shengbao Chen and Liang Cai

Microorganisms 2026, 14(1), 244; https://doi.org/10.3390/microorganisms14010244 - 21 Jan 2026

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Abstract

The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites [...] Read more.

The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host—Hantavirus pairings (HTNV—Apodemus agrarius and SEOV—Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis. Full article

(This article belongs to the Section Public Health Microbiology)

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18 pages, 4918 KB

Open AccessArticle

Synthetic Microbial Communities Enhance Artificial Cyanobacterial Crusts Formation via Spatiotemporal Synergy

by Qi Li, Pingting Zhu, Guoxia Tian, Qingliang Cui, Pengyu Zhang, Lingyan Dong, Chensi Min and Linchuan Fang

Microorganisms 2026, 14(1), 243; https://doi.org/10.3390/microorganisms14010243 - 21 Jan 2026

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Abstract

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic [...] Read more.

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic microbial communities (SynComs), each dominated by microorganisms specialized in exopolysaccharide (EPS) production (3 strains), siderophore production (3 strains), or nitrogen fixation (4 strains), on ACCs formation following inoculation with Microcoleus vaginatus. This study was carried out in a controlled laboratory setting with a 12 h light/dark cycle and a light intensity of 2400–2700 lux. Following a 24-day cultivation period, EPS-producing or nitrogen-fixing SynComs significantly increased the chlorophyll-a content by 16.0–16.3%. Except for the nitrogen-fixing bacteria treatment, other SynComs enhanced the soil organic matter content of ACCs by 9.1% to 27.3%. The content of EPS was significantly improved by all three SynComs by 14.1~19.2%. Urease activity rose by 6.7% when siderophore-producing bacteria were added. The impacts of SynComs on ammonium nitrogen (NH₄⁺-N) showed different temporal dynamics: nitrogen-fixing SynComs significantly increased NH₄⁺-N early (≤10 days), while EPS-producing and siderophore-producing SynComs enhanced accumulation later (17–24 days). SynComs inoculation markedly accelerated cyanobacterial and general microbial colonization and growth. In comparison to day 0, the 16S rRNA gene copy number of ACCs increased by 24.1% and 43.0%, respectively, in the EPS-producing and nitrogen-fixing SynComs. Additionally, correlation analysis showed that SynComs transformed the weak correlations in the control into a strong positive correlation between NH₄⁺-N and both Chl-a and microbial biomass. Our findings demonstrate SynComs, particularly the EPS-producing or nitrogen-fixing SynComs, enhance ACCs formation through elucidated mechanisms, providing a theoretical basis for optimizing ACCs-based desertification control strategies. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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16 pages, 4194 KB

Open AccessArticle

A Recombinant Porcine Epidemic Diarrhea Virus with Multiple S2 Subunit Mutations from China: Isolation, Genetic Characterization, and Pathogenicity Analysis

by Nana Yan, Jingru Xu, Yuqi Li, Sisi Fan, Shuqi Qiu, Linjie Huang, Xiaoziyi Xiao, Yuting Liao, Weiye Lin, Bo Dong, Ailing Dai and Kewei Fan

Microorganisms 2026, 14(1), 242; https://doi.org/10.3390/microorganisms14010242 - 21 Jan 2026

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Abstract

Porcine epidemic diarrhea virus (PEDV) is a major cause of fatal diarrhea in piglets. The continuous emergence of new variants, driven by recombination and mutation, poses a persistent global threat to the swine industry, resulting in significant economic losses. Therefore, ongoing surveillance of [...] Read more.

Porcine epidemic diarrhea virus (PEDV) is a major cause of fatal diarrhea in piglets. The continuous emergence of new variants, driven by recombination and mutation, poses a persistent global threat to the swine industry, resulting in significant economic losses. Therefore, ongoing surveillance of PEDV evolution is critical. In this study, we isolated a novel PEDV strain, designated PEDV/FJLY202201, from experimental intestinal samples collected from a diarrheal piglet in Fujian, China, and sequenced its complete genome. Complete genome analysis, phylogenetic analysis, and recombination analysis were conducted. Results showed that PEDV/FJLY202201 was a recombinant strain derived from two recombination events between G2a and G2b strains, with three breakpoints located in the ORF1b, Domain 0 (D0) and S2 subunit, respectively. Notably, multiple mutations were identified in the S2 subunit, a finding that has been rarely reported before. Furthermore, following challenge with the PEDV/FJLY202201 strain, 3-day-old piglets exhibited severe diarrhea, sustained a 30.35% weight loss, and reached 100% mortality, collectively demonstrating its high virulence. These data reveal the complex evolution of PEDV/FJLY202201 and provide a foundation for a better understanding of the genetic evolution and molecular pathogenesis of PEDV. Full article

(This article belongs to the Section Veterinary Microbiology)

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19 pages, 1505 KB

Open AccessArticle

Species Identification, Virulence Factors, and Antifungal Resistance in Clinical Candida Isolates from ICU Patients

by Paola Aparecida Alves Ferreira, Lucas Daniel Cibolli Roso, Daniel Almeida Freitas, Ana Paula Pereira Bressani, Paulo Henrique da Cruz Ferreira, Emerson Cotta Bodevan, Cristiane Rocha Fagundes Moura, Rosane Freitas Schwan, Vanessa Amaral Mendonça, Karina Teixeira Magalhães-Guedes and Cíntia Lacerda Ramos

Microorganisms 2026, 14(1), 241; https://doi.org/10.3390/microorganisms14010241 - 21 Jan 2026

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Abstract

Candida spp. are important opportunistic human fungal pathogens. This study aimed to identify and characterize Candida spp. obtained from patients admitted to an Intensive Care Unit (ICU), focusing on virulence attributes and susceptibility to antifungal agents. A total of 131 isolates from oral [...] Read more.

Candida spp. are important opportunistic human fungal pathogens. This study aimed to identify and characterize Candida spp. obtained from patients admitted to an Intensive Care Unit (ICU), focusing on virulence attributes and susceptibility to antifungal agents. A total of 131 isolates from oral and tracheobronchial secretions of adult ICU patients were evaluated. Phenotypic identification was performed using chromogenic culture media for Candida, followed by MALDI-TOF mass spectrometry, with representative isolates confirmed by ITS sequencing. Antifungal susceptibility to fluconazole, ketoconazole, and amphotericin B was determined only by the agar disk diffusion method, and virulence was assessed through esterase, DNase, protease, and hemolytic activity assays. C. albicans was the prevalent species, followed by C. tropicalis, C. krusei, C. glabrata, C. parapsilosis, C. dubliniensis, C. lusitaniae, and C. guilliermondii. Antifungal resistance rates reached 51.1% for fluconazole, 42.7% for ketoconazole, and 19.1% for amphotericin B, as determined by disk diffusion method. Overall, 64.9% of the isolates exhibited esterase activity, 18.3% DNase, 45.8% protease, and 67.2% exhibited hemolytic activity. Oral isolates were more frequent than tracheal isolates and demonstrated a higher prevalence of antifungal resistance and virulence traits. These findings underscore the epidemiological importance of characterizing Candida species in hospitals to better understand the yeast profile and to support adequate clinical management. Full article

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

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17 pages, 374 KB

Open AccessArticle

Detection of Pathogens by a Novel User-Developed Broad-Range BR 16S PCR rRNA Polymerase Chain Reaction/Gene Sequencing Assay: Multiyear Experience in a Large Canadian Healthcare Zone

by Thomas Griener, Barbara Chow and Deirdre Church

Microorganisms 2026, 14(1), 240; https://doi.org/10.3390/microorganisms14010240 - 20 Jan 2026

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Abstract

Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 [...] Read more.

Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 specimens were analyzed from 661 patients: 61% had negative cultures and BR 16S PCR tests; 35% had negative cultures but positive BR 16S PCR tests; and only 4% had negative cultures with indeterminate BR 16S PCR results. After resolution of indeterminate BR 16S PCR results (i.e., 29 negative, 1 false-positive, and 1 positive) the assay showed a sensitivity of 98.26% (95% CI = 96.00–99.43%), specificity of 99.79% (95% CI: 99.82–99.99%), positive predictive value of 99.65% (95% CI: 97.56–99.95%), negative predictive value of 98.94% (95% CI: 97.51–99.55%), and accuracy of 99.21% (95% CI: 98.28–99.71%) for a disease prevalence of 38.10% (95% CI: 34.62–41.66%). Gram stain purulence predicted the BR 16S PCR result better (69.4%) than organisms (24.6%), but the latter had a higher PPV (78.5%). Increased peripheral WBC (86.1%) or CRP (71.8%) predicted positive BR 16S PCR results. Our DPO BR 16S PCR assay improved pathogen detection over culture and minimized contamination. Broad range 16S rDNA PCR/sequencing (BR 16S PCR) is an important diagnostic technique in cases with invasive infection due to fastidious or uncultivatable pathogens. However, appropriate case selection, the quality of clinical specimen, and the specific assay primers affect its performance. Our novel BR 16S PCR assay uses unique dual-priming oligonucleotides (DPO) primers and fast protocols for rapid, optimal detection of bacterial pathogens, while minimizing contamination. Fast BR 16S PCR assay reports occurred within 24–48 h. BR 16S PCR and culture analyzed a diverse range of clinical specimens from patients with invasive infections. BR 16S PCR demonstrated a high performance for accurately detecting pathogens, ruling out infections, and minimizing contamination. BR 16S PCR detection of a pathogen allowed the appropriate clinical management of one-third of patients in this cohort. BR 16S PCR is an essential tool for the clinical management of patients with invasive infection when primary cultures are negative or contaminated. Full article

(This article belongs to the Special Issue Clinical Microbiology and Related Diseases)

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20 pages, 1746 KB

Open AccessArticle

Antimycobacterial Mechanisms and Anti-Virulence Activities of Polyphenolic-Rich South African Medicinal Plants Against Mycobacterium smegmatis

by Matsilane L. Mashilo, Mashilo M. Matotoka and Peter Masoko

Microorganisms 2026, 14(1), 239; https://doi.org/10.3390/microorganisms14010239 - 20 Jan 2026

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Abstract

The rise of multidrug-resistant tuberculosis (TB) necessitates alternative therapeutic sources. This study investigated the polyphenolic content and the antioxidant, antimycobacterial, and anti-virulence activities of selected medicinal plants traditionally used to treat TB and related symptoms. Total phenolics, tannins, and flavonoids were quantified using [...] Read more.

The rise of multidrug-resistant tuberculosis (TB) necessitates alternative therapeutic sources. This study investigated the polyphenolic content and the antioxidant, antimycobacterial, and anti-virulence activities of selected medicinal plants traditionally used to treat TB and related symptoms. Total phenolics, tannins, and flavonoids were quantified using colorimetric assays. Antioxidant capacity was assessed via DPPH and ferric-reducing power assays. Antimycobacterial activity against Mycobacterium smegmatis was evaluated using broth microdilution, growth kinetics, cell constituent leakage, and respiratory chain dehydrogenase inhibition assays. Anti-virulence effects were examined using crystal violet biofilm and swarming motility assays. Tarchonanthus camphoratus showed the highest polyphenolic levels and, together with Combretum hereroense, strong antioxidant activity. Extracts of Senecio macroglossus, Nerium oleander, and Tetradenia riparia displayed potent antimycobacterial activity (MIC = 0.16 mg/mL), characterized by delayed exponential growth, membrane damage, and metabolic inhibition. Tabernaemontana elegans exhibited the weakest activity (MIC > 2.5 mg/mL). Most extracts also significantly impaired motility (12–100%) and early-stage biofilm formation. Polyphenolic-rich plant extracts demonstrated promising antimycobacterial and anti-virulence properties against M. smegmatis, highlighting their potential as leads for developing novel anti-TB agents. Full article

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

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21 pages, 1237 KB

Open AccessArticle

Unveiling the Hidden Reservoir: High Prevalence of Occult Hepatitis B and Associated Surface Gene Mutations in a Healthy Vietnamese Adult Cohort

by Huynh Hoang Khanh Thu, Yulia V. Ostankova, Alexander N. Shchemelev, Elena N. Serikova, Vladimir S. Davydenko, Tran Ton, Truong Thi Xuan Lien, Edward S. Ramsay and Areg A. Totolian

Microorganisms 2026, 14(1), 238; https://doi.org/10.3390/microorganisms14010238 - 20 Jan 2026

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Abstract

Vietnam faces a hyperendemic burden of hepatitis B virus (HBV) infection, but the prevalence of occult HBV infection (OBI) and its underlying molecular mechanisms in healthy populations remain poorly understood. This study aimed to characterize the serological and molecular HBV profile of a [...] Read more.

Vietnam faces a hyperendemic burden of hepatitis B virus (HBV) infection, but the prevalence of occult HBV infection (OBI) and its underlying molecular mechanisms in healthy populations remain poorly understood. This study aimed to characterize the serological and molecular HBV profile of a healthy Vietnamese adult cohort in Southern Vietnam. We assessed the prevalence of occult HBV infection (OBI) and HBsAg-positivity (serving as a proxy for probable chronic infection). In this cross-sectional study, 397 healthy adults from Southern Vietnam underwent serological screening for HBsAg, anti-HBs, and anti-HBc. All participants were screened for HBV DNA using a high-sensitivity PCR assay (LOD ≥ 5 IU/mL). For all viremic cases, the full Pre-S/S region was sequenced to determine genotype and characterize escape mutations. We uncovered a high prevalence of both HBsAg-positivity (17.6%) and OBI (9.3% HBsAg-negative, HBV DNA-positive). Serological analysis revealed a massive, age-dependent reservoir of past exposure (63.7% anti-HBc) characterized by a high and increasing prevalence of the anti-HBc only profile (31.5%), a key serological marker for OBI. This trend contrasted sharply with a steep age-related decline in protective anti-HBs. The viral landscape was dominated by genotypes B (73.8%) and C (26.2%), with sub-genotypes B4 and C1 being the most prevalent. Critically, individuals with OBI carried a significantly higher burden of S gene escape mutations compared to those with HBsAg-positivity (p < 0.001). Canonical escape variants, including sG145R (21.6%), sK141R/T/E/Q (24.3%), and sT116N/A/I/S (18.9%), were exclusively or highly enriched in the OBI group. A LASSO-logistic model based on this mutational profile successfully predicted occult infection with high accuracy (AUC = 0.83). A substantial hidden reservoir of occult HBV infection exists within the healthy adult population of Vietnam, driven by a high burden of S gene escape mutations. These findings highlight the significant limitations of conventional HBsAg-only screening. They also underscore the need for comprehensive molecular surveillance to address the true scope of HBV viremia, hopefully enabling a reduction in hidden transmission of clinically significant viral variants. Full article

(This article belongs to the Section Virology)

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17 pages, 1647 KB

Open AccessArticle

Novel Genetic Diversity and Geographic Structures of Aspergillus fumigatus (Order Eurotiales, Family Aspergillaceae) in the Karst Regions of Guizhou, China

by Duanyong Zhou, Yixian Liu, Qifeng Zhang, Ying Zhang and Jianping Xu

Microorganisms 2026, 14(1), 237; https://doi.org/10.3390/microorganisms14010237 - 20 Jan 2026

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Abstract

Aspergillus fumigatus is the primary pathogen causing aspergillosis. Recent molecular population genetic studies have demonstrated that A. fumigatus exhibits high local genetic diversity, with evidence for limited differentiation among geographic populations. However, research on the impacts of geomorphological factors on shaping the population [...] Read more.

Aspergillus fumigatus is the primary pathogen causing aspergillosis. Recent molecular population genetic studies have demonstrated that A. fumigatus exhibits high local genetic diversity, with evidence for limited differentiation among geographic populations. However, research on the impacts of geomorphological factors on shaping the population genetic diversity patterns of this species remains scarce. In this study, large-scale sampling and in-depth population genetic analysis were performed on soil-derived A. fumigatus from Guizhou Province, a representative karst landscape in southern China. This area is dominated by plateaus and mountains (accounting for 92.5% of the total area) and represents a classic example of conical karst landscapes. A total of 206 A. fumigatus strains were isolated from 9 sampling sites across Guizhou. Genetic diversity, genetic differentiation, and population structure of these strains were analyzed based on short tandem repeats (STRs) at 9 loci. The results revealed that A. fumigatus in the karst region of Guizhou harbors abundant novel alleles and genotypes, with high genetic diversity. Gene flow among geographical populations was infrequent, and significant genetic differentiation was detected between 30 of the 36 pairs of geographical populations where mountain ranges played a very important role, with the overall regional genetic differentiation reaching PhiPT = 0.061 (p = 0.001). Furthermore, the Guizhou populations showed significant differences from those reported in other regions worldwide. Surprisingly, only one of the 206 (0.49%) A. fumigatus isolates from this region exhibited resistance to the two medical triazoles commonly used for treating aspergillosis, and this resistance frequency was far lower than those reported in previous studies from other regions. We discuss the implications of our results for evolution and environmental antifungal resistance management in this important human fungal pathogen. Full article

(This article belongs to the Special Issue Ecology and Genetics of Medically Important Fungi)

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19 pages, 2136 KB

Open AccessArticle

Biosynthesis of Glycine from One-Carbon Resources Using an Engineered Escherichia coli Whole-Cell Catalyst

by Muran Fu, Hongling Shi, Xueyang Bai, Qian Gao, Fei Liu, Dandan Li, Yunchao Kan, Chuang Xue, Lunguang Yao and Cunduo Tang

Microorganisms 2026, 14(1), 236; https://doi.org/10.3390/microorganisms14010236 - 20 Jan 2026

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Abstract

Carbon dioxide (CO₂) is a cost-effective, abundant, and renewable carbon source, but its utilization technologies face several issues. The reductive glycine pathway (RGP) is recognized as one of the most efficient one-carbon (C1) assimilation routes in nature, with its core component—the [...] Read more.

Carbon dioxide (CO₂) is a cost-effective, abundant, and renewable carbon source, but its utilization technologies face several issues. The reductive glycine pathway (RGP) is recognized as one of the most efficient one-carbon (C1) assimilation routes in nature, with its core component—the glycine cleavage system (GCS: GcvP, GcvH, GcvT, and GcvL)—playing an essential role in C1 metabolism. To develop efficient CO₂ conversion and utilization pathways, we identified NhFtfL and AmFchA-MtdA with high catalytic efficiency through gene mining and constructed a four-plasmid co-expression system in E. coli BL21(DE3) using Gibson Assembly. This system integrated GcvP-GcvH, GcvT-GcvL, NhFtfL-AmFchA-MtdA, and RsPPK2, thereby reconstituting the complete RGP while enhancing ATP supply. The engineered strain functioned as an efficient whole-cell biocatalyst, achieving a glycine space–time productivity of 0.125 mmol/L/h via one-pot conversion of formate. Furthermore, we expanded the application scope by developing a whole-cell electrocatalysis system that directly synthesized glycine from CO₂ and NH₄Cl, achieving a glycine space–time productivity of 0.135 mmol/L/h. This study demonstrates the potential of the engineered RGP system for upgrading C1 resources and supports the transition toward carbon neutrality. Full article

(This article belongs to the Section Microbial Biotechnology)

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14 pages, 966 KB

Open AccessArticle

SARS-CoV-2 Infection Associated with HHV-6A Reactivation and an Inhibitory KIR2DL2/HLA-C1 Immunogenetic Profile

by Sabrina Rizzo, Matteo Ferraresi, Giovanni Strazzabosco, Marcello Baroni, Juana Maria Sanz, Angelina Passaro, Daria Bortolotti, Roberta Rizzo and Giovanna Schiuma

Microorganisms 2026, 14(1), 235; https://doi.org/10.3390/microorganisms14010235 - 20 Jan 2026

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Abstract

Natural killer (NK) cells are central to antiviral immunity through a balance of activating and inhibitory receptors, including killer immunoglobulin-like receptors (KIRs). We have previously observed that an increased frequency of the inhibitory receptor KIR2DL2 and its ligand HLA-C1 is associated with heightened [...] Read more.

Natural killer (NK) cells are central to antiviral immunity through a balance of activating and inhibitory receptors, including killer immunoglobulin-like receptors (KIRs). We have previously observed that an increased frequency of the inhibitory receptor KIR2DL2 and its ligand HLA-C1 is associated with heightened susceptibility to human herpesvirus (HHV) infection, supporting a role for KIR-mediated NK cell regulation in host–virus interactions. We investigated whether the co-infection of SARS-CoV-2 and human herpesvirus 6 (HHV-6) might be connected to the expression of KIR2DL2/HLA-C1. We analyzed 110 SARS-CoV-2-positive subjects and 109 SARS-CoV-2-negative subjects for the KIR2DL2 and HLA-C1 genotype and for HHV-6A/B reactivation in plasma samples. SARS-CoV-2-positive subjects showed a significantly higher frequency of the KIR2DL2/HLA-C1 haplotype and increased reactivation of HHV-6A. Among deceased and comorbid patients, the co-occurrence of the KIR2DL2/HLA-C1 haplotype and HHV-6A DNAemia was more frequent, particularly in those with cardiovascular disorders. These findings suggest that the KIR2DL2/HLA-C1 haplotype might promote NK cell inhibition, facilitating HHV-6A persistence and contributing to immune dysregulation during SARS-CoV-2 infection. The combined presence of KIR2DL2/HLA-C1 and HHV-6A may, therefore, represent a molecular signature of COVID-19 outcomes. Full article

(This article belongs to the Collection Feature Papers in Virology)

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18 pages, 548 KB

Open AccessReview

Clinical and Immunological Perspectives on the Nasal Microbiome’s Role in Olfactory Function and Dysfunction

by Farwa Mukhtar, Antonio Guarnieri, Maria Di Naro, Daria Nicolosi, Natasha Brancazio, Attilio Varricchio, Antonio Varricchio, Muhammad Zubair, Tamar Didbaridze, Giulio Petronio Petronio and Roberto Di Marco

Microorganisms 2026, 14(1), 234; https://doi.org/10.3390/microorganisms14010234 - 20 Jan 2026

Cited by 1 | Viewed by 461

Abstract

The nasal microbiome represents a complex and dynamic microbial ecosystem that contributes to mucosal defense, epithelial homeostasis, immune regulation, and olfactory function. Increasing evidence indicates that this microbial community actively interacts with host physiology, while alterations in its composition are associated with chronic [...] Read more.

The nasal microbiome represents a complex and dynamic microbial ecosystem that contributes to mucosal defense, epithelial homeostasis, immune regulation, and olfactory function. Increasing evidence indicates that this microbial community actively interacts with host physiology, while alterations in its composition are associated with chronic inflammation, oxidative stress, and olfactory impairment. Such changes have been reported in conditions including chronic rhinosinusitis, allergic rhinitis, and post-viral anosmia. Beyond local effects, chronic nasal inflammation has been hypothesized to influence neuroinflammatory processes and protein aggregation pathways involving α-synuclein and tau, potentially linking nasal microbial imbalance to neurodegenerative mechanisms. However, current evidence remains largely indirect and does not support a causal relationship. This narrative review summarizes current clinical and immunological evidence on the role of the nasal microbiome in olfactory function and dysfunction, highlighting limitations of existing studies and outlining future research directions. Full article

(This article belongs to the Section Medical Microbiology)

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12 pages, 519 KB

Open AccessArticle

Comparative Analysis of Microbial Detection in Traditional Culture Versus Metagenomic Next-Generation Sequencing in Patients with Periprosthetic Joint Infection: A Prospective Observational Study

by Po-Yu Liu, Hung-Jen Tang, Susan Shin-Jung Lee, Chun-Hsing Liao, Chien-Hsien Huang, Han-Yueh Kuo, Wang-Huei Sheng and Taiwan Metagenomic Sequencing Microbiology Study Group

Microorganisms 2026, 14(1), 233; https://doi.org/10.3390/microorganisms14010233 - 20 Jan 2026

Viewed by 287

Abstract

Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve [...] Read more.

Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar’s test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods. Full article

(This article belongs to the Section Medical Microbiology)

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Open AccessArticle

Spatial and Vertical Stratification of Groundwater Microbial Communities Reveals Proteobacterial Dominance and Redox-Driven Ecological Transitions

by Rahaf S. Aljuaid, Sahar A. Alshareef, Basma T. Jamal, Ftoon H. Dhafeer, Alaa A. Alnahari and Ruba A. Ashy

Microorganisms 2026, 14(1), 232; https://doi.org/10.3390/microorganisms14010232 - 19 Jan 2026

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Abstract

Groundwater microbial communities exhibit pronounced vertical and spatial structuring driven by physicochemical gradients. Here, we investigated microbial assemblages across surface and subsurface layers of three groundwater wells distributed along a 1.26 km transect in the Wadi Awja aquifer system (Jeddah, Saudi Arabia) using [...] Read more.

Groundwater microbial communities exhibit pronounced vertical and spatial structuring driven by physicochemical gradients. Here, we investigated microbial assemblages across surface and subsurface layers of three groundwater wells distributed along a 1.26 km transect in the Wadi Awja aquifer system (Jeddah, Saudi Arabia) using high-throughput 16S rRNA gene amplicon sequencing. Across all samples, Pseudomonadota (Proteobacteria) dominated community composition, accounting for ~50–65% of surface assemblages and increasing to ~90% in deeper strata, indicating strong vertical selection. This depth-associated enrichment coincided with reduced community evenness and the prevalence of metabolically versatile, facultatively anaerobic taxa. Although Actinomycetota, Bacteroidota, and Planctomycetota contributed substantially to overall diversity, their relative abundances declined with depth, reinforcing the dominance of Proteobacteria under suboxic conditions. Notably, members of Enterobacteriaceae, particularly Escherichia spp., were consistently enriched in deeper layers, coinciding with simplified community structures. Collectively, these results demonstrate that groundwater microbial communities undergo sharp redox-associated ecological transitions over short spatial scales, emphasizing the role of localized hydrogeochemical heterogeneity in shaping subsurface microbial assemblages. Full article

(This article belongs to the Section Environmental Microbiology)

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Microorganisms, Volume 14, Issue 1 (January 2026) – 261 articles

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