Microorganisms

15 pages, 8813 KB

Open AccessArticle

Hepatincolaceae (Alphaproteobacteria) Symbionts of Snapping Shrimp Alpheus brevicristatus: Genomic Capacity for Functions Beyond Nutrient Scavenging

by Fang-Chao Zhu, Yan-Bin Yang, Pei-Pei Liu, Xin Liu, Qun-Jian Yin, Xu-Yang Chen and Shuo Yu

Microorganisms 2026, 14(8), 1864; https://doi.org/10.3390/microorganisms14081864 - 21 Aug 2026

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Abstract

Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb [...] Read more.

Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb in size) were recovered from the gut of the snapping shrimp Alpheus brevicristatus via metagenomic sequencing. Phylogenetic and whole-genome similarity analyses confirm that these two MAGs represent two novel, undescribed genera within the family Ca. Hepatincolaceae. Metabolic reconstruction reveals that they not only retain the canonical nutrient-scavenging pathways conserved across all Hepatincolaceae members, but also encode previously undocumented functional modules for antioxidant defense, vitamin B₁ and B₂ biosynthesis, and short-chain fatty acid production. They maintain a high oxygen-affinity cytochrome bd terminal oxidase to thrive in the anoxic gut microenvironment. Consistent with their symbiotic lifestyle, their genomes exhibit typical signatures of reductive evolution, such as reduced genome size, low GC content, and gene loss in amino acid and nucleotide de novo biosynthesis pathways. This study presents the first reported high-quality genomes of marine Ca. Hepatincolaceae symbionts, which are predicted to possess multiple metabolic functions extending beyond nutritional mutualism. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 1359 KB

Open AccessArticle

Evaluation of the Collection Efficiency of a Wet-Type Electrostatic Precipitator for Aerosolized Influenza A Virus

by Kazuya Nakamura, Takeshi Nagai, Hitoshi Ishiguro, Keiichi Kobayashi, Kazuhisa Nakagawa, Masahiro Okanojo and Akira Nukazuka

Microorganisms 2026, 14(8), 1863; https://doi.org/10.3390/microorganisms14081863 - 21 Aug 2026

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Abstract

Airborne viruses are a key driver of infectious disease transmission, highlighting the importance of reliable detection in public health surveillance. As atmospheric viral concentrations are very low, a sampler with a high viral collection efficiency is essential. Although multiple approaches for evaluating collection [...] Read more.

Airborne viruses are a key driver of infectious disease transmission, highlighting the importance of reliable detection in public health surveillance. As atmospheric viral concentrations are very low, a sampler with a high viral collection efficiency is essential. Although multiple approaches for evaluating collection efficiency have been applied using various samplers, no standardized sampler has yet been developed. We previously developed a wet-type electrostatic precipitator (WT-ESP) and successfully collected severe acute respiratory syndrome coronavirus 2 from the public environment. However, its efficiency for quantitative collection of airborne viruses remains unclear. This study aimed to clarify the collection efficiency of the WT-ESP. We evaluated collection efficiency via two different approaches: direct spray, where virus-containing aerosols were sprayed directly into the WT-ESP inlet, and indirect spray, where aerosols were dispersed into a closed space and then collected using the sampler. The direct spray tests achieved 20.1–50.2% collection efficiency, whereas the indirect spray test achieved an efficiency <12%. These findings highlight that electrostatic precipitation has an advantage of enhancing collection efficiency compared with values reported for impingers in previous studies and provide preliminary insights into the collection efficiencies under direct and indirect spray conditions, providing foundational data that bridge the gap between both methods. Full article

(This article belongs to the Special Issue Advances in Airborne Microbial Communities)

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14 pages, 4234 KB

Open AccessArticle

Salmonella Infection Induces Orchitis and Disrupts the Blood–Testis Barrier, Leading to Spermatogenic Disorders in Mice

by Yingchao Li, Qian Ma, Chenyang Shi, Qirui Zang, Yaolong Song, Mingshuai Chen, Binhuan Ma, Panpan Tong, Zhanqiang Su, Yi Zhang, Shicheng Wan, Aili Aierken and Mengfei Zhang

Microorganisms 2026, 14(8), 1862; https://doi.org/10.3390/microorganisms14081862 - 21 Aug 2026

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Abstract

This study investigated the pathological processes by which two Salmonella strains induce orchitis and impair spermatogenesis in mice, with emphasis on inflammation and blood–testis barrier (BTB) integrity. Thirty male Kunming mice were randomly assigned to the human-derived Salmonella enterica serovar Enteritidis H71 group, [...] Read more.

This study investigated the pathological processes by which two Salmonella strains induce orchitis and impair spermatogenesis in mice, with emphasis on inflammation and blood–testis barrier (BTB) integrity. Thirty male Kunming mice were randomly assigned to the human-derived Salmonella enterica serovar Enteritidis H71 group, the sheep-derived Salmonella enterica serovar Agona W42 group, or the phosphate-buffered saline control group (n = 10 per group). An acute orchitis model was established by intrascrotal injection. Histopathological examination revealed marked testicular and epididymal lesions, disruption of the spermatogenic epithelium, and reduced sperm abundance in infected mice. Transcriptomic analysis identified 4546 differentially expressed genes shared by the two infected groups and showed enrichment of the Toll-like receptor (TLR), nuclear factor kappa B (NF-κB), and mitogen-activated protein kinase (MAPK) signaling pathways. Real-time quantitative PCR further showed increased expression of interleukin 6 (Il6), interleukin 1 beta (Il1b), and tumor necrosis factor (Tnf), accompanied by reduced expression of tight junction protein 1 (Tjp1), occludin (Ocln), and synaptonemal complex protein 3 (Sycp3) in infected mice (p < 0.05), except for Tjp1 in the W42 group. These findings indicate that Salmonella-induced inflammatory activation is associated with BTB disruption and impaired spermatogenesis, providing a basis for further investigation of bacterial orchitis and zoonotic reproductive risks. Full article

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

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21 pages, 2786 KB

Open AccessReview

Fungal Infections Associated with Sphingosine 1-Phosphate Receptor Modulators: Immunological Mechanisms, Clinical Patterns, and Management Considerations

by Kian Michael Yazdan, Sai Tapasvi Madam and Shirisha Pasula

Microorganisms 2026, 14(8), 1861; https://doi.org/10.3390/microorganisms14081861 - 21 Aug 2026

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Abstract

Fungal infections constitute a large portion of serious infections worldwide and are increasing, partially due to new immunomodulatory therapies, such as Sphingosine-1-Phosphate (S1P) receptor modulators, including fingolimod for the treatment of multiple sclerosis (MS). Fingolimod antagonizes multiple S1P receptors, including S1PR₁, [...] Read more.

Fungal infections constitute a large portion of serious infections worldwide and are increasing, partially due to new immunomodulatory therapies, such as Sphingosine-1-Phosphate (S1P) receptor modulators, including fingolimod for the treatment of multiple sclerosis (MS). Fingolimod antagonizes multiple S1P receptors, including S1PR₁, S1PR₃, S1PR₄, and S1PR₅, resulting in immunological alterations that may increase susceptibility to invasive fungal infections (IFIs). Our PubMed-based literature search identified 43 published cases and a 60-patient case series describing invasive fungal infections in patients receiving S1P receptor modulators. Of these, cryptococcosis was the most frequently documented infection, followed by histoplasmosis and coccidioidomycosis. Most published cases involved patients on fingolimod, whereas evidence for the other medications in this class is extremely limited. Currently, there are no standardized fungal screening protocols. A baseline complete blood count with differentials should be obtained before the initiation of S1P receptor modulator therapy. Patients should also be monitored clinically for signs and symptoms of fungal infection. Primary antifungal prophylaxis and routine serum cryptococcal antigen testing are not currently recommended. Management of suspected IFIs should focus on diagnostic workup to identify the causative organism and extent of organ involvement to determine the appropriate antifungal therapy. Decisions regarding interruption or discontinuation of MS therapy should be individualized according to the clinical syndrome, infection severity, and risk of MS rebound. This narrative review synthesizes the available mechanistic and clinical evidence on invasive fungal infections in patients with multiple sclerosis receiving S1P receptor modulator therapy. Full article

(This article belongs to the Special Issue Clinical Research on Fungal Infections)

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16 pages, 429 KB

Open AccessArticle

Molecular Detection of Blastocystis ST2 and ST4 and Exploratory 16S rRNA Gene Community Profiles in a 12-Week Dairy-Intervention Pilot Study

by Panayiota Tsokkou, Chad Schou, Catherine O’Dowd Phanis, Kyriacos A. Hasapis, Stella A. Nicolaou, Eleni P. Andreou and Evelina Charidemou

Microorganisms 2026, 14(8), 1860; https://doi.org/10.3390/microorganisms14081860 - 21 Aug 2026

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Abstract

Blastocystis is a common intestinal protist whose clinical and ecological significance remains uncertain. This secondary exploratory analysis examined Blastocystis PCR detection in paired baseline and Week 12 stool samples collected during a randomized pilot intervention comparing daily goat-milk and cow-milk consumption. Nineteen healthy [...] Read more.

Blastocystis is a common intestinal protist whose clinical and ecological significance remains uncertain. This secondary exploratory analysis examined Blastocystis PCR detection in paired baseline and Week 12 stool samples collected during a randomized pilot intervention comparing daily goat-milk and cow-milk consumption. Nineteen healthy Greek Cypriot adults provided 38 stool samples. Stool DNA was screened by PCR targeting a partial 18S rRNA gene fragment, and positive amplicons were Sanger sequenced for subtype assignment. Blastocystis was detected at both time points in 3 of 19 participants (15.8%); ST2 was identified in two participants and ST4 in one. No Cryptosporidium spp. or Giardia duodenalis PCR-positive samples were identified. In exploratory 16S rRNA gene analyses, median Shannon diversity index was 6.10 versus 4.85 at baseline (p = 0.171) and 5.67 versus 4.17 at Week 12 (p = 0.085) in repeat-detection and no-detection groups, respectively. Bray–Curtis PERMANOVA was non-significant at baseline (R² = 0.0946, p = 0.0815) and Week 12 (R² = 0.0597, p = 0.8576); Aitchison-distance sensitivity analyses were likewise non-significant (p = 0.0547 and p = 0.3232, respectively). No selected genus-level comparison met the false-discovery-rate-adjusted threshold. The three-participant repeat-detection subgroup precluded reliable analysis of dairy-arm effects, subtype-specific differences, cardiometabolic outcomes, or bacterial-community associations. In this small pilot cohort, ST2 and ST4 were identified in paired baseline and Week 12 stool samples from three healthy adults, providing molecular evidence of repeat detection over the sampled interval. Larger studies with more frequent sampling, quantitative assays, and adequately powered, prespecified analyses are needed to investigate the temporal dynamics and host-associated correlates of Blastocystis detection. Full article

(This article belongs to the Section Gut Microbiota)

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17 pages, 9938 KB

Open AccessArticle

Extraction and Purification of a Melanin from Aureobasidium melanogenum with Evaluation of Its Stability and In Vitro Antitumor Activity

by Yu Lin, Wei Liang, Bo Yu, Lan Ma, Lin Shu, Zhiqun Liang and Wei Zeng

Microorganisms 2026, 14(8), 1859; https://doi.org/10.3390/microorganisms14081859 - 20 Aug 2026

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Abstract

Microbial melanins are natural pigments with broad application potential, and Aureobasidium melanogenum is a promising strain for industrial production of melanin. However, the separation, purification, and biological activities of melanin derived from this strain remain largely unexplored. In this study, an efficient extraction [...] Read more.

Microbial melanins are natural pigments with broad application potential, and Aureobasidium melanogenum is a promising strain for industrial production of melanin. However, the separation, purification, and biological activities of melanin derived from this strain remain largely unexplored. In this study, an efficient extraction and purification process for melanin from the fermentation broth of A. melanogenum GXZ-6 was established through single-factor optimization, and the final purity of the melanin reached 94.4%. Spectroscopic stability tests showed that the melanin was highly stable under dark, natural light, a wide pH range (2–12), and temperatures ≤ 37 °C. However, UV light, high temperature (>50 °C), ultrasonication, and certain metal ions (especially Cr³⁺) markedly altered its absorbance at 225 nm. More importantly, the purified melanin exhibited concentration-dependent antiproliferative activity against human cancer cell lines of A549, HCT116, MCF-7, and HepG2, with IC₅₀ values ranging from 25.50 to 72.33 μg/mL. HepG2 cells were the most sensitive (IC₅₀ = 25.50 μg/mL), and the melanin showed moderate selectivity toward normal hepatocytes (LO2). Mechanistic studies revealed that melanin effectively inhibited HepG2 cell migration, induced apoptosis, depolarized the mitochondrial membrane potential, and activated the caspase-3/PARP pathway. In summary, this study provides a simple, scalable, and environmentally friendly process for producing high-purity melanin with potential antitumor activity. Full article

(This article belongs to the Special Issue Microbial Synthesis of Natural Products and Their Potential Applications)

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23 pages, 1456 KB

Open AccessReview

Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments

by Badal Mavry, Sneha Lohar, Garima Awasthi, Kumud Kant Awasthi, Mahipal Singh Sankhla, Anuj Sharma, Rajeev Kumar, Yogesh Kumar, Ruchi Pathania and Theodoros Varzakas

Microorganisms 2026, 14(8), 1858; https://doi.org/10.3390/microorganisms14081858 - 20 Aug 2026

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Abstract

Microbial forensics has beneficial characteristics for investigating crimes. Law and order are fundamental to any nation and carry significant responsibilities. Failure in this domain may result in wrongful convictions or the guilty remaining free. Key duties include managing criminal cases and addressing threats [...] Read more.

Microbial forensics has beneficial characteristics for investigating crimes. Law and order are fundamental to any nation and carry significant responsibilities. Failure in this domain may result in wrongful convictions or the guilty remaining free. Key duties include managing criminal cases and addressing threats to public order. While identifying the culprit, establishing their connection to the crime is paramount. Since legal systems require evidence for conviction, law enforcement increasingly relies on advancing scientific methods to meet this need. For example, in this case, after applying conventional techniques like DNA analysis and fingerprinting, a new technique, such as microbial forensics or fingerprints, can be applied. Trace evidence can be in the form of microbial fingerprints, and this evidence can play an important role in solving the crime. Microbial communities are dense and active in living and non-living things and in the environment. The classification and roles of these bacterial populations could be used as markers. The distinction between forensic samples is achievable because there is a diversity of microbial communities found in the human body from one location to another, and even in identical twins. The specific microbiome, which can be found on the skin or in specific body areas, may precisely identify the suspect’s connection with the crime scene for the purposes of human identification. This paper discusses the objects and latest advancements in the science of microbial forensics and their significance within the law enforcement process. Full article

(This article belongs to the Section Environmental Microbiology)

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16 pages, 1933 KB

Open AccessArticle

Combined Plasmid Redesign and Transfection Optimization Significantly Increases Upstream AAV Titers While Maintaining Vector Quality and In Vivo Potency

by Shiliang Hu, Yinxing Chen, Carmen Wu, Wilhad Hans Reuter, June Deng, Nannan Jia, Noel Walsh, Amy Bastille, Thomas M. Edwards, Matthias Hebben, Nelson Chau and Jing Liao

Microorganisms 2026, 14(8), 1857; https://doi.org/10.3390/microorganisms14081857 - 20 Aug 2026

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Abstract

A high manufacturing cost of goods (CoG) remains a critical barrier to the broad clinical adoption of gene therapies and is driven in part by limited productivity in adeno-associated virus (AAV) manufacturing. Here, we report an optimized AAV production process developed to markedly [...] Read more.

A high manufacturing cost of goods (CoG) remains a critical barrier to the broad clinical adoption of gene therapies and is driven in part by limited productivity in adeno-associated virus (AAV) manufacturing. Here, we report an optimized AAV production process developed to markedly increase upstream titers while preserving vector quality and potency. The process combines a redesigned plasmid system, an optimized plasmid ratio, and a novel synthetic transfection reagent and was benchmarked against a conventional triple-plasmid/PEI MAX workflow. Across multiple AAV capsids and independent production runs, the optimized process reproducibly increased crude harvest titers by approximately 10- to 33-fold relative to the standard process, while maintaining key vector quality attributes. Notably, within the detection limits of the assay, rcAAV was undetectable at 1 × 10¹⁰ vg input with the optimized process, whereas the conventional triple-plasmid (with native Rep-Cap sequence)/PEI MAX workflow remained rcAAV-positive under identical conditions. Importantly, the in vivo potency was comparable to that of vectors produced by the conventional process. These results position our optimized AAV production process as a promising strategy to materially reduce AAV manufacturing CoG per patient. Full article

(This article belongs to the Section Microbial Biotechnology)

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26 pages, 6076 KB

Open AccessArticle

Microbial Diversity and Hydrocarbon-Oxidizing Bacteria in Coastal Waters and Sands Contaminated by the Fuel Oil Spill in the Black Sea

by Ekaterina M. Semenova, Alexey P. Ershov, Tamara L. Babich, Diyana S. Sokolova, Nataliya G. Loiko, Elena A. Bakay, Ekaterina S. Kazak and Tamara N. Nazina

Microorganisms 2026, 14(8), 1856; https://doi.org/10.3390/microorganisms14081856 - 20 Aug 2026

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Abstract

In 2024, an accident involving two tankers in the Kerch Strait resulted in the release of approximately 2400 tons of fuel oil into the Black Sea, causing significant contamination of seawater and the coastal zone. This study presents the first microbiological and molecular–ecological [...] Read more.

In 2024, an accident involving two tankers in the Kerch Strait resulted in the release of approximately 2400 tons of fuel oil into the Black Sea, causing significant contamination of seawater and the coastal zone. This study presents the first microbiological and molecular–ecological assessment of prokaryotic community composition and hydrocarbon-oxidizing bacteria (HOB) in coastal seawater and sand near Anapa (Russian Federation) following the spill. The taxonomic composition of nine samples was analyzed using high-throughput sequencing of 16S rRNA genes (V3–V4 regions), identifying Bacteria as the dominant domain (85.3–99.8%). In seawater samples, bacteria of the phyla Pseudomonadota, Cyanobacteriota, and Bacteroidota and archaea of the phyla Thermoplasmatota and Crenarchaeota predominated. Eighteen aerobic bacterial strains, including members of the genera Shewanella, Pseudoalteromonas, Halopseudomonas, Marinomonas, Pseudomonas, Vibrio, Alcanivorax, Ectopseudomonas, Nitratireductor, and Echinicola, were isolated from the zone of fuel oil spill. Several isolates demonstrated heavy oil degradation and biosurfactant production. Screening of collection strains isolated from other habitats revealed that Rhodococcus erythropolis TG65 and Marinobacter lutaoensis Pd1 and Pd2 degraded 92–94% of fuel oil n-alkanes. Elevated dissolved iron concentrations in the seawater indicate the possibility of a metabolic coupling between hydrocarbon oxidation and microbial iron reduction, mediated by indigenous Shewanella and Pseudomonas species. These findings indicate that indigenous HOB may contribute to the natural attenuation of aliphatic hydrocarbons in fuel oil. Full article

(This article belongs to the Special Issue Microbiomes in the Oil Supply Chain: Applications and Drawbacks)

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16 pages, 1953 KB

Open AccessArticle

BTV Remodels the oISG15-Association Proteome

by Di Kang, Qinxue Gao, Mingxin Zhang, Rui Ha, Xinbing Hu, Meng Li, Zhongming Chen and Shijun Bao

Microorganisms 2026, 14(8), 1855; https://doi.org/10.3390/microorganisms14081855 - 20 Aug 2026

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Abstract

ISG15 is an interferon-induced ubiquitin-like protein that exerts diverse functions during viral infection. We previously reported that ovine ISG15 (oISG15) promoted bluetongue virus (BTV) replication by stabilizing viral NS1 and VP4 in an ISGylation-independent manner, although the mechanism remained unknown. Here, using the [...] Read more.

ISG15 is an interferon-induced ubiquitin-like protein that exerts diverse functions during viral infection. We previously reported that ovine ISG15 (oISG15) promoted bluetongue virus (BTV) replication by stabilizing viral NS1 and VP4 in an ISGylation-independent manner, although the mechanism remained unknown. Here, using the generated anti-oISG15 antibody, we performed immunoprecipitation (IP) coupled with label-free Liquid Chromatography-Tandem Mass Spectrometry (LC–MS/MS) to characterize the oISG15-associated proteome in BTV-infected and uninfected cells. The results showed that BTV infection markedly remodeled the oISG15 association landscape, with decreased enrichment of several autophagy- and trafficking-related proteins and increased enrichment of mitochondrial metabolic proteins in oISG15 immunoprecipitates. Functionally, oISG15 overexpression induced modest alterations in autophagy-related markers in uninfected cells yet attenuated these markers’ abundance during BTV infection. Together, this study revealed BTV-induced changes in the oISG15-associated proteome that coincided with alterations in autophagy-related markers. Full article

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

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25 pages, 3164 KB

Open AccessArticle

by Flor Alexia Esquivel-Barriga, Gerardo Vázquez-Marrufo, Adrián Gómez-Baltazar, Andrea Monserrat Negrete-Paz, Carlos Torres-Vega, Manuel López-Rodríguez, Elda Araceli Hernández-Díaz and Ma. Soledad Vázquez-Garcidueñas

Microorganisms 2026, 14(8), 1854; https://doi.org/10.3390/microorganisms14081854 - 20 Aug 2026

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Abstract

Foodborne illnesses caused by Salmonella Typhimurium remain a major public health concern worldwide. Although ST19 has historically been a dominant lineage within this serotype, ST213 has become increasingly prevalent in Mexico. The biological factors underlying this epidemiological shift remain incompletely understood. In this [...] Read more.

Foodborne illnesses caused by Salmonella Typhimurium remain a major public health concern worldwide. Although ST19 has historically been a dominant lineage within this serotype, ST213 has become increasingly prevalent in Mexico. The biological factors underlying this epidemiological shift remain incompletely understood. In this study, we compared virulence-associated gene repertoires and stress-related phenotypes in representative S. Typhimurium ST19 and ST213 strains with distinct virulotypes (VTs). Comparative genomic analysis identified 119 virulence-associated genes distributed across 26 VTs, with most genes broadly conserved between genotypes. Representative strains were evaluated under simulated gastrointestinal tract (GIT) stress conditions, in post-stress recovery assays, and in a Caenorhabditis elegans infection model. Under the experimental conditions evaluated, the representative ST213 strains SAL109 (VT1), SAL115 (VT1), and SAL016 (VT12) tended to show higher persistence under host-associated stress conditions and greater intestinal colonization capacity in C. elegans than the ST19 strain SAL004 (VT23). However, strains sharing the same VT did not necessarily exhibit similar phenotypes, indicating that virulence-associated gene repertoires alone do not fully explain stress tolerance or host colonization behavior. Overall, these findings highlight phenotypic variability among strains with similar virulence gene content and support the importance of integrating genomic and phenotypic approaches to better understand the biology of emerging S. Typhimurium lineages. Full article

(This article belongs to the Special Issue Salmonella and Food Safety)

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18 pages, 4620 KB

Open AccessArticle

Contrasting the Microbial Communities in Rhizosphere and Bulk Soils Across Different Eucommia ulmoides Planting Sites and Their Soil Chemical Driving Mechanisms

by Panfeng Liu, Huaxiang Wang, Furong Lin, Hongyan Du, Liwei Xing, Kunhao Xie and Qingxin Du

Microorganisms 2026, 14(8), 1853; https://doi.org/10.3390/microorganisms14081853 - 20 Aug 2026

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Abstract

Soil multifunctionality (SMF) is a core indicator of plantation soil ecological function, and microbial diversity plays a vital role in sustaining it. However, cross-site rhizosphere and bulk SMF disparities and their microbial driving mechanisms remain unclear in Eucommia ulmoides plantations. Here, we collected [...] Read more.

Soil multifunctionality (SMF) is a core indicator of plantation soil ecological function, and microbial diversity plays a vital role in sustaining it. However, cross-site rhizosphere and bulk SMF disparities and their microbial driving mechanisms remain unclear in Eucommia ulmoides plantations. Here, we collected rhizosphere and bulk soils from three typical sites (Mengzhou, MZ; Liangyuan, LY; and Yuanyang, YY). Soil chemical properties, extracellular enzymes, microbial alpha diversity, community composition and cross-kingdom network topology were measured. Correlation heatmaps, random forest, Redundancy analysis (RDA) and Partial least path modeling (PLS-PM) were adopted to quantify SMF predictors and regulatory pathways. Rhizosphere soils possessed significantly higher alkaline hydrolyzable nitrogen (AN), available phosphorus (AP) and available potassium (AK) than bulk soils at all sites. LY rhizosphere showed the greatest soil organic carbon (SOC), total potassium (TK), available nutrients and enzyme activities, while YY had higher total nitrogen (TN) and AP, yet the lowest enzyme levels. Rhizosphere bacterial and fungal alpha diversity was consistently higher across locations. SMF varied distinctly by site and compartment: LY had substantially higher SMF than MZ and YY in both rhizosphere and bulk soils, with rhizosphere SMF being consistently greater than bulk values across all sites. The PLS-PM (GOF = 0.70) indicated that soil chemical properties regulated SMF via dual pathways: they directly promoted microbial co-occurrence networks and indirectly modified network structure by altering fungal diversity, while suppressing bacterial diversity. Total effect analysis identified soil chemical properties and microbial co-occurrence networks as the core drivers of SMF variation. This work clarifies that rhizosphere effects and soil chemical properties jointly drive SMF by regulating microbial diversity and co-occurrence networks, offering theoretical guidance for sustainable soil management in E. ulmoides plantations. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 4660 KB

Open AccessArticle

Itaconic Acid Directly Binds to the Cysteine Residue of PurF: A Novel Mechanism for Inhibiting Purine Metabolism in Porcine Pathogenic Escherichia coli

by Haozhen Liu, Xin Li, Xinyu Zhang, Yao Ge, Yinfeng Chen, Xinjian Li and Zhenlong Wu

Microorganisms 2026, 14(8), 1852; https://doi.org/10.3390/microorganisms14081852 - 20 Aug 2026

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Abstract

Itaconic acid has been reported to possess anti-inflammatory and antibacterial properties. However, its specific mechanisms of action against pathogenic bacteria, especially in the context of purine metabolism, remain poorly understood. Here, we investigate the impact of itaconic acid on the purine metabolism of [...] Read more.

Itaconic acid has been reported to possess anti-inflammatory and antibacterial properties. However, its specific mechanisms of action against pathogenic bacteria, especially in the context of purine metabolism, remain poorly understood. Here, we investigate the impact of itaconic acid on the purine metabolism of PCN033, a highly pathogenic porcine extraintestinal pathogenic Escherichia coli (ExPEC) strain. Our in vitro and in vivo experiments demonstrated that itaconic acid significantly inhibited the proliferation of PCN033. Multi-omics analyses, including transcriptome and metabolome sequencing, revealed that itaconic acid severely disrupted the purine metabolism pathway of PCN033. Further mechanistic studies identified PRPP amidotransferase (PurF), a key enzyme in de novo purine synthesis, as a direct target of itaconic acid. Molecular docking and click chemistry experiments provided compelling evidence that itaconic acid specifically binds to the second cysteine residue (2C) of PurF, leading to the inhibition of its enzymatic activity. These data reveal a novel and critical mechanism by which itaconic acid exerts its antibacterial effects in response to bacterial infection. Importantly, our in vivo data show that supplementation with itaconic acid alleviated weight loss, organ damage, and inflammatory responses induced by PCN033 infection in mice and nursery pigs. These novel findings enhance our understanding of the antibacterial mechanisms of itaconic acid. Supplementation with itaconic acid could serve as a therapeutic strategy for treating pathogenic bacterial infections in humans and other animals. Full article

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

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29 pages, 4824 KB

Open AccessArticle

Isolation, Biocontrol Efficacy and Genomic Analysis of Trichoderma harzianum Snef3255 Against Peanut Root-Knot Nematode Disease

by Xuesong Bai, Zhigang Li, Chenjun Duan, Di Zhao, Hai Dong, Xiaofeng Zhu, Haiyan Fan, Xiaoyu Liu, Yuxi Duan and Lijie Chen

Microorganisms 2026, 14(8), 1851; https://doi.org/10.3390/microorganisms14081851 - 20 Aug 2026

Viewed by 327

Abstract

Peanut root-knot nematode (RKN) disease caused by Meloidogyne hapla is among the most destructive soil-borne diseases threatening peanut production worldwide. We isolated Trichoderma harzianum strain Snef3255 from peanut rhizosphere soil, which exhibited high virulence against second-stage juveniles, with a mortality rate of 86.08%. [...] Read more.

Peanut root-knot nematode (RKN) disease caused by Meloidogyne hapla is among the most destructive soil-borne diseases threatening peanut production worldwide. We isolated Trichoderma harzianum strain Snef3255 from peanut rhizosphere soil, which exhibited high virulence against second-stage juveniles, with a mortality rate of 86.08%. Field trials demonstrated that TC and TS provided control efficacies of 70.85% and 61.88%, respectively, while boosting peanut yields by 18.15% and 13.61%. We report a high-quality chromosome-level genome assembly of T. harzianum Snef3255 using Oxford Nanopore, Illumina and high-throughput chromatin conformation capture (Hi-C) sequencing data. This assembly comprised seven chromosomes (40,811,729 bp) with a BUSCO completeness of 99.31%. A total of 13,611 protein-coding genes were predicted. Systematic comparative genomic analysis of T. harzianum Snef3255 with other Trichoderma species was performed, and putative functional gene clusters were investigated. Furthermore, we identified two candidate secreted proteins, ThCP1 and ThLysM1, and screened their interacting proteins in peanut, respectively. This study demonstrated the potential of Snef3255 as a biocontrol agent for peanut RKN disease and provided a genomic basis for understanding Trichoderma–peanut interactions. Full article

(This article belongs to the Special Issue Biological Control of Microbial Pathogens in Plants)

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21 pages, 10618 KB

Open AccessArticle

Isolate-Specific Modulation of Growth, Carbon Allocation, and Transcriptomic Responses in Spirodela polyrhiza by Duckweed-Associated Bacteria

by Karnjana Ruenpham, Kazuhiro Mori, Yasuhiro Tanaka, Arinthip Thamchaipenet, Masaaki Morikawa and Tadashi Toyama

Microorganisms 2026, 14(8), 1850; https://doi.org/10.3390/microorganisms14081850 - 20 Aug 2026

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Abstract

Duckweed-associated plant growth-promoting bacteria have attracted attention for their potential to enhance duckweed biomass production. However, the mechanisms underlying isolate-specific growth promotion are unclear. This study compared the effects of two duckweed-associated bacterial isolates, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the [...] Read more.

Duckweed-associated plant growth-promoting bacteria have attracted attention for their potential to enhance duckweed biomass production. However, the mechanisms underlying isolate-specific growth promotion are unclear. This study compared the effects of two duckweed-associated bacterial isolates, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the growth, biomass composition, colonization behavior, and transcriptomic responses of Spirodela polyrhiza. Biomass composition and transcriptome analyses were performed to characterize the host responses. Both isolates enhanced duckweed biomass; PS02 increased it 1.2-fold, whereas PS05 induced a significant 1.4-fold increase compared to the uninoculated control. PS05 established bacterial populations approximately one order of magnitude higher than those of PS02 and formed dense extracellular polymeric substance-mediated microcolonies on the surface. Transcriptome analysis revealed that PS05 induced 1108 differentially expressed genes, compared with 454 in PS02, indicating greater host transcriptomic reprogramming. Functional enrichment of transcriptome responses showed that PS05 preferentially regulates carbohydrate biosynthesis, central carbon metabolism, and starch biosynthesis, significantly enhancing starch accumulation and turion formation without reducing protein or photosynthetic pigment content. This study provides evidence linking bacterial colonization, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, offering a basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production. Full article

(This article belongs to the Section Plant Microbe Interactions)

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19 pages, 2669 KB

Open AccessArticle

Convergent Bacterial but Divergent Fungal Communities in the Tobacco Rhizosphere Under Intensive Management on Contrasting Soils

by Shuang Peng, Dan Song, Beibei Zhou and Yiming Wang

Microorganisms 2026, 14(8), 1849; https://doi.org/10.3390/microorganisms14081849 - 20 Aug 2026

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Abstract

The rhizosphere microbiome is critical for plant health, yet how soil type and intensive management jointly govern its assembly remain unclear. Here, we hypothesized that soil type acts as a primary environmental filter, while intensive cultivation (plant growth plus fertilization) imposes additional selective [...] Read more.

The rhizosphere microbiome is critical for plant health, yet how soil type and intensive management jointly govern its assembly remain unclear. Here, we hypothesized that soil type acts as a primary environmental filter, while intensive cultivation (plant growth plus fertilization) imposes additional selective pressures that differentially shape bacterial versus fungal communities. Using flue-cured tobacco (K326) grown in clay loam and sandy loam soils under field conditions, we examined the rhizosphere microbiome at the topping stage. Intensive cultivation significantly altered rhizosphere physicochemical properties. Key nutrients, including organic matter (OM), dissolved total nitrogen (DTN), available phosphorus (AP), and available potassium (AK), were markedly enriched. Rhizosphere soil pH exhibited a bidirectional shift relative to the corresponding bulk soil, converging to a narrow range (7.4–7.8) in both soil types. Root activity and fertilization imposed contrasting selective pressures on the two microbial kingdoms: bacterial diversity declined slightly, indicating strong deterministic selection, whereas fungal diversity increased, reflecting adaptation to root-generated niches. Differential abundance analysis identified 38 bacterial OTUs as a core rhizosphere-adapted microbiome shared across both soil types, demonstrating robust fitness in the nutrient-enriched rhizosphere environment under intensive management. No shared core fungal OTUs were detected, underscoring strong soil legacy effects and higher habitat specificity in fungi. Notably, the core bacterial microbiome was dominated by K-strategists (slow-growing, resource-efficient taxa) that exhibited opportunistic traits capable of rapidly exploiting nutrient pulses in the rhizosphere. Together, these findings reveal that soil type acts as a critical filter modulating plant–microbe interactions under intensive agriculture, while bacteria and fungi employ divergent ecological strategies in response to selection pressures. This work provides both theoretical and practical insights for optimizing tobacco cultivation and sustaining soil microecological health. Full article

(This article belongs to the Special Issue Agricultural Microbial Ecology: Plant–Soil–Microbe Interactions)

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29 pages, 4274 KB

Open AccessArticle

ESM2-Guided Context-Aware Annotation Completion Supplements Carbohydrate Metabolism Coverage in Silage Microbial Metagenomes

by Jiewei Zhang, Xinyu Du, Jinbiao Tang, Xiaoning Dong, Xusheng Guo, Mingxue Li and Dongmei Xu

Microorganisms 2026, 14(8), 1848; https://doi.org/10.3390/microorganisms14081848 - 20 Aug 2026

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Abstract

Functional annotation gaps limit the interpretation of carbohydrate metabolism in silage microbiomes. We developed Context-Aware Annotation Completion (CAAC), a framework integrating ESM2 embeddings, genomic-neighborhood features, three-class classification, confidence-tiered neighbor voting, and Enzyme Commission (EC)-to-KEGG Orthology (KO) mapping. CAAC was applied to 21 metagenomes [...] Read more.

Functional annotation gaps limit the interpretation of carbohydrate metabolism in silage microbiomes. We developed Context-Aware Annotation Completion (CAAC), a framework integrating ESM2 embeddings, genomic-neighborhood features, three-class classification, confidence-tiered neighbor voting, and Enzyme Commission (EC)-to-KEGG Orthology (KO) mapping. CAAC was applied to 21 metagenomes from uninoculated and Lacticaseibacillus paracasei-inoculated silages sampled before ensiling and at 7 and 90 days. Five-fold cross-validation yielded an F1-macro of 84.64% for negative, positive, and hard-sequence classification. Among 800,000 selected annotation-poor sequences, 545,671 Tier 1 or Tier 2 predictions passed the annotation-validity and EC-to-KO mapping criteria, of which 524,814 were eligible for sample-level annotation supplementation. After silage-focused filtering and KO–EC summarization, these predictions yielded 102 KO–EC features repeatedly detected across the silage metagenomes and increased coverage in 25 of 47 carbohydrate-metabolism pathways, mainly by recovering enzyme-level components related to starch and sucrose, cellulose and cellobiose, xylan and hemicellulose, and pectin and glucuronate metabolism. Taxon-linked analyses further revealed treatment- and stage-associated patterns in the taxonomic sources of the supplemented annotations. A database-derived temporal benchmark using the July 2025 CAZy release showed 94.94% Tier 1 family-level annotation-transfer consistency. CAAC extends the enzyme-level interpretation of under-annotated silage metagenomes, while the inferred assignments remain computational predictions requiring experimental validation. Full article

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

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29 pages, 16546 KB

Open AccessArticle

Biochar Application Improves Soil Aggregate Stability and Aggregate-Associated Carbon Fractions Through Microbial Community Regulation in Eucalyptus Plantations—A Seven-Year Field Experiment

by Jialin Liao, Yuyi Shen, Denan Zhang, Yingjie Sun, Qiumei Teng, Guangping Xu, Yunhuang Luo, Kechao Huang, Hao Shi, Zhiwen Tan, Junzhi Chu and Yu Cao

Microorganisms 2026, 14(8), 1847; https://doi.org/10.3390/microorganisms14081847 - 20 Aug 2026

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Abstract

Biochar has been used to improve soils and promote sustainable agricultural development. The effects of applying different doses of biochar on soil aggregate structure and stability, aggregate-associated microbial communities, aggregate carbon fractions, and underlying mechanisms in planted forest soil ecosystems remain unclear. This [...] Read more.

Biochar has been used to improve soils and promote sustainable agricultural development. The effects of applying different doses of biochar on soil aggregate structure and stability, aggregate-associated microbial communities, aggregate carbon fractions, and underlying mechanisms in planted forest soil ecosystems remain unclear. This study aimed to explore the effects of biochar amendment (7 years) on carbon stabilization in plantation soils. The effects of biochar application (0%, 0.5%, 1.0%, 2%, 4%, and 6%) on water-stable aggregate distribution, stability indices such as mean weight diameter (MWD), geometric mean diameter (GMD), and fractal dimension (D), aggregate-associated microbial communities (fungal and bacterial phospholipid fatty acids (PLFAs)), and carbon fractions such as soil organic carbon (SOC), easily oxidized organic carbon (EOC), dissolved organic carbon (DOC), particulate organic carbon (POC), microbial biomass carbon (MBC), recalcitrant organic carbon (ROC) and black carbon (BC) were investigated based on a seven-year in situ field experiment in a Eucalyptus plantation in northern Guangxi. The results showed that after 7 years, biochar application significantly increased the proportion of macroaggregates (≥0.25 mm). The MWD and GMD increased significantly with increasing biochar application rates, whereas D decreased significantly, indicating enhanced soil structural stability. Biochar significantly increased the abundance of fungi and bacteria across all aggregate size classes and changed the microbial community structure towards conditions that promoted increased carbon stabilization. Additionally, biochar application significantly increased both recalcitrant (ROC and BC) and labile carbon (EOC, POC, DOC, and MBC) in all aggregate fractions, with the largest increments in macroaggregates. Based on correlation analysis and structural equation modeling (SEM), we speculated that biochar might enhance the physical protection and chemical sequestration of organic carbon by optimizing the physical structure of the aggregates and synergizing with the microbial carbon pump. The 7-year application of biochar significantly enhanced the SOC content in plantation soils, primarily by increasing recalcitrant organic carbon, demonstrating that biochar application constitutes a viable approach to augmenting persistent soil carbon stabilization in plantation ecosystems. The 4% and 6% treatments produced the largest responses for most of the measured indicators, underscoring the importance of biochar application. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 3715 KB

Open AccessArticle

Seasonal Occurrence, Population Diversity, and Mobilome Features of Environmental Vibrio parahaemolyticus in Coastal and Estuarine Waters of Haiyan, Zhejiang, China

by Jingyu Xu, Yangang He and Peiyan He

Microorganisms 2026, 14(8), 1846; https://doi.org/10.3390/microorganisms14081846 - 20 Aug 2026

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Abstract

Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, yet the ecological and genomic significance of environmental populations as potential reservoirs remains incompletely characterized. From May to October 2024, 108 water samples were collected monthly at one coastal and two estuarine sites in [...] Read more.

Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, yet the ecological and genomic significance of environmental populations as potential reservoirs remains incompletely characterized. From May to October 2024, 108 water samples were collected monthly at one coastal and two estuarine sites in Haiyan, Zhejiang. Confirmed isolates (n = 39) underwent whole-genome sequencing, MLST/cgMLST, virulence and AMR gene screening, integron characterization with BLASTp (+2.17.0) integrase family typing, and viral-region prediction. Culture-based detection was absent in May and rose to 66.7% in October (Cochran–Armitage trend, p = 0.003), with descriptively higher detection at the coastal site. MLST identified 28 STs including four novel types (Simpson’s diversity = 0.953). All isolates lacked tdh, trh, and T3SS2 but retained T3SS1 and MAM7. One estuarine isolate carried CALIN-associated dfrA31 and qnrVC5. All integrases matched VpaIntIA (95.9–100% identity), not mobile class 1–3 integrases. Viral regions were detected in 38/39 isolates; filamentous phage annotations in 52.6%. Haiyan coastal V. parahaemolyticus shows seasonal and spatial patterns, high diversity, and a mobilome dominated by chromosomal super-integrons, underscoring the need for integrase family typing in environmental surveillance. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 21674 KB

Open AccessArticle

Isolation and Genomic Characteristics of the First Bovine Viral Diarrhea Virus Subgenotype 2b Isolate from Buffalo in Guangxi Province, China

by Shuhong Zhong, Shaomin Qin, Shiwen Feng, Cuilan Wu, Lan Jia, Xiongbiao Xuan, Huili He, Hao Peng, Shuai Hu, Jinfeng Liu, Jun Lin and Jun Li

Microorganisms 2026, 14(8), 1845; https://doi.org/10.3390/microorganisms14081845 - 19 Aug 2026

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Abstract

(1) Background: Bovine viral diarrhea virus (BVDV) is an economically important pathogen affecting cattle worldwide. The genetic diversity of BVDV-2 in buffalo remains poorly understood. This study aimed to elucidate the genomic and antigenic features of GX24, the first BVDV-2b isolate identified from [...] Read more.

(1) Background: Bovine viral diarrhea virus (BVDV) is an economically important pathogen affecting cattle worldwide. The genetic diversity of BVDV-2 in buffalo remains poorly understood. This study aimed to elucidate the genomic and antigenic features of GX24, the first BVDV-2b isolate identified from dairy buffalo in China. (2) Methods: The virus was isolated from a rectal swab through three blind passages in MDBK cells and identified through immunofluorescence and RT-PCR. The near-complete genome was sequenced using the Illumina platform and subjected to phylogenetic and recombination analysis. B-cell epitopes and glycosylation sites were predicted using BepiPred-3.0, Epitope1D, DiscoTope-3.0, NetNGlyc-1.0, and NetO-Glyc-4.0. (3) Results: The 12,267-nt GX24 genome (GenBank: PX682047) was classified as BVDV-2b. Recombination analysis detected a putative recombination signal within the NS5A gene involving Chinese BVDV-2b and Italian BVDV-2a strains. Integrative analyses predicted conserved linear and conformational epitope clusters in the N- and C-terminal regions of the E2 protein. Spatial analysis indicated that several epitope residues may be masked by glycan shielding. (4) Conclusions: This study provides the first genomic evidence of a BVDV-2b isolate from dairy buffalo in China, suggesting that BVDV-2b may be present in this population. The putative recombination signal and antigenic characteristics offer valuable insights for the development of diagnostics and vaccine design in the future. Full article

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

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16 pages, 4456 KB

Open AccessArticle

Microbial Quotients and Stoichiometric Imbalance Reflect Divergent Responses to Wetland Land-Use Conversion

by Zehao Wang, Ye Li and Jiuwang Jin

Microorganisms 2026, 14(8), 1844; https://doi.org/10.3390/microorganisms14081844 - 19 Aug 2026

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Abstract

Wetland degradation alters soil nutrient cycling and microbial functioning, yet how microorganisms adjust resource-use strategies after wetland conversion remains poorly understood. This study examined the effects of wetland degradation-induced land-use conversion on soil-microbial quotients (qMBC, qMBN, qMBP) and soil-microbial stoichiometric imbalance (C:Nimb, C:Pimb, [...] Read more.

Wetland degradation alters soil nutrient cycling and microbial functioning, yet how microorganisms adjust resource-use strategies after wetland conversion remains poorly understood. This study examined the effects of wetland degradation-induced land-use conversion on soil-microbial quotients (qMBC, qMBN, qMBP) and soil-microbial stoichiometric imbalance (C:Nimb, C:Pimb, N:Pimb) in the A’er Xiang lake marsh wetland, northeastern China. Five sites were compared: native wetland, 5- and 10-year forestland converted from wetland, and 5- and 10-year cropland converted from wetland. The qMBP increased from 11.15% in native wetland to 30.40% in 10-year cropland, while qMBC rose from 5.97% to 9.81%, indicating that microbial P and C quotients were highly sensitive to wetland conversion. C:Nimb increased to 2.93 in 10-year cropland, whereas N:Pimb rose from 4.93 in native wetland to 13.79 and 10.59 in 5-year and 10-year forestland, respectively. Correlation analysis demonstrated that soil, microbial, and enzyme stoichiometry jointly regulated microbial quotients. Specifically, C:Nimb was strongly and negatively correlated with N:Pimb (r = −0.839, p < 0.01), and microbial biomass showed contrasting responses, being positively correlated with C:Nimb but negatively correlated with C:Pimb and N:Pimb. These indicators can guide future land-use decisions by integrating water availability with microbial adaptation in degraded sandy wetland regions. Full article

(This article belongs to the Section Environmental Microbiology)

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13 pages, 2144 KB

Open AccessSystematic Review

Gut Microbiota Recovery After Direct-Acting Antiviral Therapy for Chronic Hepatitis C: A Systematic Review and Meta-Analysis

by Jing-Hong Hu, Ming-Ling Chang, Tung-Jung Huang, Yung-Yu Hsieh, Nai-Jen Liu, Kai-Feng Sung and Jui-Hsiang Tang

Microorganisms 2026, 14(8), 1843; https://doi.org/10.3390/microorganisms14081843 - 19 Aug 2026

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Abstract

Direct-acting antivirals (DAAs) cure most chronic hepatitis C virus (HCV) infections, yet whether the gut microbiota returns toward a healthy state after viral clearance remains uncertain. We systematically reviewed DAA-era adult HCV studies using sequencing-based fecal microbiota assessment (PROSPERO CRD420261374682). Longitudinal alpha-diversity change [...] Read more.

Direct-acting antivirals (DAAs) cure most chronic hepatitis C virus (HCV) infections, yet whether the gut microbiota returns toward a healthy state after viral clearance remains uncertain. We systematically reviewed DAA-era adult HCV studies using sequencing-based fecal microbiota assessment (PROSPERO CRD420261374682). Longitudinal alpha-diversity change was pooled by REML random-effects meta-analysis with Hartung–Knapp adjustment, and compositional/functional findings were synthesized narratively. Seven studies met qualitative criteria and five longitudinal reports were extractable. Because participant overlap between two Thai reports could not be excluded, the primary conservative non-overlap analysis of four reports (180 paired observations) gave Hedges’ g = 0.13 (95% CI −0.53 to 0.80; I² ≈ 89%); the five-report sensitivity estimate was directionally positive but imprecise (g = 0.35, 95% CI −0.38 to 1.07). Recovery concentrated in richness (Chao1), whereas evenness-weighted diversity (Shannon, Hill) barely moved; beneficial taxa such as Faecalibacterium and Blautia increased after SVR. These findings are consistent with uneven, richness-led microbial recovery, but the overall certainty of the pooled evidence is very low (GRADE); functional and clinical recovery remain insufficiently characterized and undemonstrated. Full article

(This article belongs to the Section Gut Microbiota)

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19 pages, 14335 KB

Open AccessArticle

Isolation, Identification, Drug Sensitivity, Pathogenicity and Genomic Analysis of Vibrio mimicus from Pelteobagrus fulvidraco

by Shao Peng, Kai Zhang, Zichun Zhou, Zhi Meng, Chunyu Zhang, Wenjing Li, Tongpu Guo, Lei Tang, Wei Xu, Wenli Zhou, Xuying Jia and Jinwei Gao

Microorganisms 2026, 14(8), 1842; https://doi.org/10.3390/microorganisms14081842 - 19 Aug 2026

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Abstract

In this study, pathogenic bacteria were isolated from diseased Pelteobagrus fulvidraco collected from a yellow catfish farm in northern China. The recovered isolate was subjected to Gram staining, transmission electron microscopy observation, 16S rRNA gene sequencing and whole-genome sequencing, followed by systematic analyses [...] Read more.

In this study, pathogenic bacteria were isolated from diseased Pelteobagrus fulvidraco collected from a yellow catfish farm in northern China. The recovered isolate was subjected to Gram staining, transmission electron microscopy observation, 16S rRNA gene sequencing and whole-genome sequencing, followed by systematic analyses of its antimicrobial resistance, pathogenicity and genomic characteristics. Combined with artificial infection assays and multiple comparative verifications, the pathogen was identified as Vibrio mimicus. Clinical observation of naturally infected fish revealed that superficial skin ulcers of varying severity constituted the hallmark clinical sign of this disease. Genomic analysis uncovered major virulence-related genes, including tlh, vmh and tdh, as well as key antimicrobial resistance genes such as crp and ugd. Artificial infection trials confirmed the strong virulence of this isolate against P. fulvidraco, with distinct clinical manifestations triggered by injections of bacterial suspensions at different concentrations. Mortality was first observed in the high-dose group at 2–3 days post-injection, yet no cutaneous ulceration was detected at this stage. The peak incidence and mortality occurred between 3 and 7 days post-challenge, with diseased fish exhibiting lesions identical to those seen in naturally infected individuals. The median lethal dose (LD₅₀) of the isolate was determined to be 1.72 × 10⁵ CFU/mL. Growth gradient assays across varying temperatures and pH values identified the optimal culture conditions for this strain: 33 °C and pH 8.5. Antimicrobial susceptibility testing demonstrated that the isolate was highly susceptible to piperacillin, norfloxacin, roxithromycin, azithromycin, furazolidone, ceftriaxone and tetracycline, whereas it displayed high-level resistance to compound sulfamethoxazole and clindamycin. Collectively, this work lays a scientific foundation for the isolation, identification and comprehensive research of Vibrio mimicus-induced ulcerative disease in yellow catfish. Full article

(This article belongs to the Special Issue Research on Bacterial Pathogens in Fish)

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16 pages, 4318 KB

Open AccessArticle

by Siyu Li, Xuefei Zhao, Minjia Chen, Yi Cheng, Qiwei Wu, Yangyang Feng, Ailin Yi, Lu Chen, Yuting Tian and Yanling Wei

Microorganisms 2026, 14(8), 1841; https://doi.org/10.3390/microorganisms14081841 - 19 Aug 2026

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Abstract

As global aging accelerates, identifying age- and lifestyle-associated gut microbiota alterations has become critical for understanding healthy aging and microbiota-targeted interventions. To explore the associations of age and lifestyle factors with gut microbiota profiles in community-dwelling adults, 159 Chongqing residents were divided into [...] Read more.

As global aging accelerates, identifying age- and lifestyle-associated gut microbiota alterations has become critical for understanding healthy aging and microbiota-targeted interventions. To explore the associations of age and lifestyle factors with gut microbiota profiles in community-dwelling adults, 159 Chongqing residents were divided into young (18–39, n = 44), middle-aged (40–59, n = 71) and elderly (60–89, n = 44) groups. Fecal samples were analyzed by 16S rRNA gene sequencing, and lifestyle factors were assessed using a study-specific structured questionnaire. The Shannon index differed significantly between the young and middle-aged groups (p < 0.05), whereas other α-diversity and β-diversity analyses showed no significant differences. Age-related shift trends included decreased Bacillota and increased abundance of Bacteroidota. Young adults were enriched in Parasutterella, the [Eubacterium] ventriosum group and Anaerostipes; middle-aged adults were enriched in Clostridium sensu stricto 4, Clostridium sensu stricto 1 and Holdemanella; and elderly adults were enriched in Prevotellaceae UCG-004, Helicobacter, Lactobacillus, Streptococcus and Fusobacterium. Lifestyle factors were independently associated with specific microbial signatures, including tea-related enrichment of Catenibacterium and Escherichia–Shigella, exercise-related enrichment of Dialister and Bavariicoccus, and milk-related enrichment of Bacillus and Klebsiella (formerly Raoultella). Overall, these findings provide population-based evidence linking age and lifestyle factors with gut microbial profiles and may inform microbiota-targeted strategies for healthy aging. Full article

(This article belongs to the Special Issue Fecal Microbiota Transplantation in Humans and Animals)

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12 pages, 2012 KB

Open AccessArticle

Molecular Survey of Selected Tick-Borne Pathogens and Genetic Diversity of Theileria equi in Donkeys from Croatia

by Nika Konstantinović, Daria Jurković Žilić, Antun Kostelić, Adnan Hodžić, Ana Marija Kovač, Gordan Šubara and Relja Beck

Microorganisms 2026, 14(8), 1840; https://doi.org/10.3390/microorganisms14081840 - 19 Aug 2026

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Abstract

Tick-borne pathogens remain insufficiently investigated in donkeys, particularly in southeastern Europe. This study investigated the occurrence of piroplasms, Anaplasmataceae, and hemotropic Mycoplasma spp. in donkeys from Croatia and assessed the genetic diversity of detected Theileria equi. Blood samples from 135 apparently healthy [...] Read more.

Tick-borne pathogens remain insufficiently investigated in donkeys, particularly in southeastern Europe. This study investigated the occurrence of piroplasms, Anaplasmataceae, and hemotropic Mycoplasma spp. in donkeys from Croatia and assessed the genetic diversity of detected Theileria equi. Blood samples from 135 apparently healthy donkeys originating from 15 herds in six Croatian counties were examined using PCR. Positive T. equi samples were further characterized by sequencing, haplotype determination, and phylogenetic analysis. Theileria equi DNA was detected in 31/135 animals (22.96%; 95% CI: 15.99–29.94%), whereas no Anaplasmataceae or hemotropic Mycoplasma spp. DNA was detected. Infection showed marked geographical and herd-level variation. The highest prevalence was recorded in Šibensko-Kninska County (17/34; 50.0%), while all positive animals originated from three herds in the Croatian littoral region. Prevalence differed significantly among herd-size categories (p = 0.012), with no positive animals detected in small herds. Sequence analysis identified three T. equi haplotypes: D was predominant (22/31; 70.97%), followed by A (8/31; 25.81%) and E (1/31; 3.23%). Phylogenetic analysis confirmed all Croatian sequences as T. equi and indicated the presence of multiple genetic lineages within the sampled donkey population. These findings provide new molecular epidemiological data on T. equi in Croatian donkeys and demonstrate a heterogeneous distribution of infection among the investigated regions and herds. Among the selected tick-borne pathogens investigated, T. equi was the only pathogen detected. Further studies integrating larger and longitudinal datasets with detailed management, environmental, and tick-vector data are needed to better understand the factors underlying the observed epidemiological patterns. Full article

(This article belongs to the Special Issue Ticks and Threats: Insights on Tick-Borne Diseases)

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23 pages, 5499 KB

Open AccessArticle

Fermentation Improves the Antioxidant Activity, Flavor Components and Metabolic Characteristics of Coffee Pulp Beverage

by Runhua Gong, Weixin Sun, Tao Pan, Li Zhuang, Shichao Peng, Jianyong Wang, Mingduo Yang, Jingjing Bai and Lili Zhao

Microorganisms 2026, 14(8), 1839; https://doi.org/10.3390/microorganisms14081839 - 19 Aug 2026

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Abstract

This study aimed to evaluate the impact of four strains, Bifidobacterium longum BL11, Streptococcus thermophilus LB42, Lacticaseibacillus casei LC15, and Lactiplantibacillus plantarum XJ25, on the antioxidant activity, flavor components and metabolic characteristics of fermented coffee pulp beverage (CPB). Results indicated that the antioxidant [...] Read more.

This study aimed to evaluate the impact of four strains, Bifidobacterium longum BL11, Streptococcus thermophilus LB42, Lacticaseibacillus casei LC15, and Lactiplantibacillus plantarum XJ25, on the antioxidant activity, flavor components and metabolic characteristics of fermented coffee pulp beverage (CPB). Results indicated that the antioxidant activities were remarkably enhanced in the fermented CPB samples (p < 0.05). A total of 103 volatile compounds (VOCs) were detected by HS-SPME-GC-MS and GC-IMS, with 37 types of VOCs newly generated after fermentation, including esters, alcohols and ketones, thereby enhancing the flavor quality of CPB. In addition, a total of 334 differential non-volatile metabolites covering 20 subclasses were obtained in all CPB samples, such as D-tagatose, glyceraldehyde, isorhynchophylline and pyruvic acid, which showed remarkably increased levels after fermentation (p < 0.05). Organic acids, amino acids and derivatives were the two major classes of differential metabolites. The CPB samples had a different flavor profile after fermentation, while the group of Lactiplantibacillus plantarum showed the highest overall acceptability. These findings provide a systematic comparison of single-strain fermentation effects on VOCs and non-volatile metabolites in CPB samples, promoting its high-value utilization in innovative food applications. Full article

(This article belongs to the Special Issue Microbial Fermentation in Food Processing)

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17 pages, 2730 KB

Open AccessArticle

Variation in Soil Bacterial and Fungal Diversity, Community Composition, and Co-Occurrence Patterns Across Nearshore Islands in the Northern South China Sea

by Jian Gong, Yechen Qiao, Rui Pan, Hu Du, Xionghui Liao and Wanxia Peng

Microorganisms 2026, 14(8), 1838; https://doi.org/10.3390/microorganisms14081838 - 19 Aug 2026

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Abstract

Soil microbial biogeography on nearshore islands remains less well understood than that on remote archipelagos, particularly when bacterial and fungal diversity, community composition, and co-occurrence associations are evaluated together. We characterized bacterial 16S rRNA gene and fungal ITS communities in 36 topsoil samples [...] Read more.

Soil microbial biogeography on nearshore islands remains less well understood than that on remote archipelagos, particularly when bacterial and fungal diversity, community composition, and co-occurrence associations are evaluated together. We characterized bacterial 16S rRNA gene and fungal ITS communities in 36 topsoil samples collected from five nearshore islands in the northern South China Sea and examined their associations with plant diversity, soil physicochemical properties, and climatic and geographic conditions. Bacterial Shannon diversity, ACE richness, and Simpson diversity differed significantly among islands, as did fungal ACE richness, whereas fungal Shannon and Simpson diversity showed no significant differences. Bray–Curtis-based analyses revealed island-associated differentiation in bacterial community composition and fungal community composition, although multivariate dispersion also differed among islands. Sample-level subnetworks derived from an integrated co-occurrence network showed that the number of bacteria–bacteria edges differed significantly among islands, whereas the numbers of bacteria–fungi and fungi–fungi edges did not. Exploratory Spearman correlation analyses and variation partitioning indicated that microbial properties were more broadly associated with soil physicochemical properties and climatic–geographic conditions than with plant diversity. By evaluating both microbial kingdoms within the same field campaign, this study identifies partly distinct bacterial and fungal biogeographic and co-occurrence patterns and provides a baseline for future microbial biodiversity monitoring on nearshore islands. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)

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13 pages, 1678 KB

Open AccessArticle

Climatic Associations of Akabane Virus Occurrence in East Asia: Temperature-Driven Patterns Based on the Köppen–Geiger Classification

by Jung Won Kim and Jung-Yong Yeh

Microorganisms 2026, 14(8), 1837; https://doi.org/10.3390/microorganisms14081837 - 19 Aug 2026

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Abstract

Akabane virus (AKAV) is a Culicoides-borne arbovirus that causes congenital malformations and reproductive losses in ruminants, resulting in substantial economic losses in livestock production. Because vector activity and virus transmission are strongly influenced by environmental conditions, defining climatic factors associated with AKAV [...] Read more.

Akabane virus (AKAV) is a Culicoides-borne arbovirus that causes congenital malformations and reproductive losses in ruminants, resulting in substantial economic losses in livestock production. Because vector activity and virus transmission are strongly influenced by environmental conditions, defining climatic factors associated with AKAV distribution is critical for understanding its epidemiology. However, such relationships have not been systematically evaluated in East Asia. In this study, we applied the Köppen–Geiger climate classification to characterize regional climatic zones in South Korea and Japan and examined their associations with AKAV case counts. AKAV cases were predominantly observed in temperate climate zones (Cfa and Cwa). Temperature-related variables showed consistent positive associations with AKAV case counts, with a 1 °C increase in annual mean temperature associated with approximately 1.38–1.56-fold increases in reported cases. In contrast, precipitation variables exhibited weak or negative associations. These findings indicate that temperature is an important climatic factor associated with AKAV case counts, suggesting that climate-dependent modulation of vector dynamics may contribute to observed patterns of AKAV occurrence. This study provides a climate-based framework for understanding the spatial distribution of AKAV and supports the development of targeted surveillance and control strategies under changing environmental conditions. Full article

(This article belongs to the Special Issue Emerging Vector-Borne Viruses: Transmission and Epidemiology)

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32 pages, 2516 KB

Open AccessReview

Adaptive Laboratory Evolution in Synechocystis sp. PCC 6803: Current Status and Perspectives

by Dielle P. Procópio, Anna Santin and Cassius V. Stevani

Microorganisms 2026, 14(8), 1836; https://doi.org/10.3390/microorganisms14081836 - 19 Aug 2026

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Abstract

With the increasing environmental concerns about carbon dioxide emissions and the pressing demand for sustainable resources, photosynthetic microorganisms have gained considerable attention as alternative platforms for the environmentally friendly production of fuels and chemicals. These organisms function as green cell factories capable of [...] Read more.

With the increasing environmental concerns about carbon dioxide emissions and the pressing demand for sustainable resources, photosynthetic microorganisms have gained considerable attention as alternative platforms for the environmentally friendly production of fuels and chemicals. These organisms function as green cell factories capable of directly converting carbon dioxide into organic carbon metabolites using solar energy, offering a promising platform for more sustainable biomanufacturing. Among these organisms, cyanobacteria, and particularly Synechocystis sp. PCC 6803, have emerged as particularly attractive hosts due to their relatively simple cellular organization, efficient photosynthetic metabolism, and amenability to genetic manipulation. In addition to rational metabolic engineering approaches, Adaptive Laboratory Evolution (ALE) has recently been proposed as a powerful strategy to improve Synechocystis strain robustness, enhance tolerance to environmental and metabolic stresses, and optimize cellular performance under specific growth conditions. By selecting beneficial spontaneous mutations over successive generations, ALE could complement genetic engineering strategies and further expand the potential of cyanobacterial platforms for efficient and sustainable bioproduction. Full article

(This article belongs to the Special Issue Microbial Taxonomy and Environmental Metagenomics: Diversity, Dynamics, and Functional Genes)

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Open AccessArticle

Stage-Specific Dynamic of Gut Microbiota Across the Musk-Secretion Cycle in Forest Musk Deer (Moschus berezovskii)

by Gangning Wei, Jianhao Ji, Mengheng Feng, Zhixiang Xiao, Biao Chen, Huirong Mao, Yunlin Zheng and Xiaolong Hu

Microorganisms 2026, 14(8), 1835; https://doi.org/10.3390/microorganisms14081835 - 19 Aug 2026

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Abstract

Musk secretion in forest musk deer (Moschus berezovskii) involves unique physiological processes, yet the paradox of heightened energy expenditure concurrent with voluntary fasting during this period remains poorly understood. Given the role of gut microbiota in host energy metabolism and health, [...] Read more.

Musk secretion in forest musk deer (Moschus berezovskii) involves unique physiological processes, yet the paradox of heightened energy expenditure concurrent with voluntary fasting during this period remains poorly understood. Given the role of gut microbiota in host energy metabolism and health, we characterized its compositional and functional dynamics across the musk-secretion cycle. Fecal samples were collected from male forest musk deer at three stages—before (BMS), during (DMS), and after musk secretion (AMS)—and analyzed via full-length 16S rRNA gene sequencing. Results showed that alpha diversity differed significantly among groups (Simpson index: p = 0.027). Beta diversity analysis revealed significant community restructuring across stages (Adonis, R² = 0.173, p < 0.01), while LEfSe analysis (LDA > 4.0) identified a series of stage-specific taxa, further corroborating the existence of inter-group differences. In terms of species composition, Firmicutes and Bacteroidetes dominated across all stages. Significant inter-stage differences were observed in Verrucomicrobiota (highest in DMS), Patescibacteria (lowest in DMS), Proteobacteria (progressively declining), and Actinobacteria (progressively declining). At the genus level, Akkermansia, Candidatus Saccharimonas, Roseburia, and Butyricicoccus showed significant variation across the musk-secretion cycle. Notably, Akkermansia muciniphila varied significantly across stages despite high inter-individual variability. Functional prediction revealed the enrichment of hydrocarbon degradation and nitrogen fixation in BMS, and anaerobic respiration and reductive acetogenesis in DMS. This study provides foundational insights into the gut microecological mechanisms underlying musk secretion in forest musk deer. Full article

(This article belongs to the Section Gut Microbiota)

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Microorganisms, Volume 14, Issue 8 (August 2026) – 261 articles

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