@article {pmid41945106,
year = {2026},
author = {Chiang, TH and J, SJP and Lin, YC and Chiang, KP},
title = {Dissolved Organic Carbon Regulates Bacterial Ingestion by Tetraselmis sp.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02752-z},
pmid = {41945106},
issn = {1432-184X},
support = {NSTC 114-2811-M-019-001//National Science and Technology Council, Taiwan/ ; NSTC 114-2611-M-019-003//National Science and Technology Council, Taiwan/ ; 113-2119-M-001-011//National Science and Technology Council/ ; },
}

@article {pmid41950827,
year = {2026},
author = {San Román, AX and Frey, SD and Knorr, MA and Tong, H and Melillo, JM and Simpson, MJ},
title = {Three decades of continuous warming in temperate forests destabilizes persistent forms of soil organic matter.},
journal = {The Science of the total environment},
volume = {1029},
number = {},
pages = {181777},
doi = {10.1016/j.scitotenv.2026.181777},
pmid = {41950827},
issn = {1879-1026},
abstract = {Rising temperatures have altered the balance of soil carbon stored versus respired in forest ecosystems worldwide. Yet, the molecular-level mechanisms driving changes to soil biogeochemical processes and the long-term changes to soil organic matter (SOM) dynamics remain unclear. Thus, we leveraged the world's longest soil warming experiment, spanning over three decades in a temperate forest, to investigate changes in SOM chemistry and microbial responses. Using advanced molecular-level techniques, we identified significant perturbations to SOM composition and novel shifts in microbial degradation pathways. Chronic warming enhanced the breakdown of plant-derived lipids typically thought resistant to microbial decomposition. Concomitant shifts in microbial communities indicate altered carbon use strategies, with microbes acclimating to warming and increasingly targeting persistent compounds. We provide new molecular-level evidence that chronic warming disrupts chemically resistant carbon compounds through altered microbial breakdown, revealing mechanisms by which persistent SOM pools may be lost. This further demonstrates that long-term stability is not solely governed by intrinsic chemical properties. Our findings underscore the need to fully elucidate long-term microbial functional shifts and their impacts on the stability of persistent SOM pools in a changing world.},
}

@article {pmid41950840,
year = {2026},
author = {Li, X and Cheng, X and Wu, M and Han, S and Wen, X and Tang, S and Cai, Z and Zhou, J},
title = {Auxin is a signal for algal-bacterial inter-kingdom interactions in marine diatom algal blooms.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141950},
doi = {10.1016/j.jhazmat.2026.141950},
pmid = {41950840},
issn = {1873-3336},
abstract = {Elucidating the signal molecules involved in algal-bacterial interactions is crucial for unraveling the mechanisms driving marine harmful algal blooms (HABs). As a cross-kingdom signaling molecule, indole-3-acetic acid (IAA), however, its chemical-ecological role in algal-bacterial interactions during HABs remains underexplored. Here, we induced a diatom bloom at mesocosm scale, and the role of IAA was explored using cellular, molecular and multi-omics approaches. The results demonstrated IAA-related functional gene abundance was strongly correlated with HAB stages, and two complete IAA synthesis pathways were detected. Non-targeted metabolite analysis showed that IAA's precursor-tryptophan was significantly enriched during the peak stage. PLS-PM analysis further showed that IAA-driven algal-bacterial interaction was significantly correlated with algal bloom trajectory. After co-culturing IAA-produced bacteria (Pseudoalteromonas phenolica) with model diatom Thalassiosira weissflogii, we found the wild type promotes algal photosynthetic efficiency and growth, while the mutant does not. Transcriptomic analysis and [13]C labeling revealed that IAA activates the auxin pathway to form amino acid conjugates (IAA-aa) through the GH3 gene, which are key molecular mechanisms for algal growth promotion. Our results indicated that IAA functions as a cross-talking signal driving algal-bacterial communication, providing new insights into algal bloom's formation mechanism and potential HABs control methods from a signal manipulation perspective.},
}

@article {pmid41950970,
year = {2026},
author = {Yang, R and Liu, Z and Liu, Y and Zhang, Y and Lei, J and Yang, Z and He, H and Wang, J and Chen, R},
title = {Multilayer microbial framework of aerobic granule microecosystems: Integrating community ecology, genetic networks, and enhancement strategies.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134569},
doi = {10.1016/j.biortech.2026.134569},
pmid = {41950970},
issn = {1873-2976},
abstract = {Aerobic granular sludge (AGS), a next-generation wastewater treatment technology, has advanced worldwide. Microbiological mechanisms underlying its formation and stability lack a unified explanation. Based on the concept that AGS construction involves progressive participation and stabilization of microbial organization under environmental selection, this review integrates evidence from community ecology and gene-regulatory networks and proposes a unified conceptual framework. The findings show that AGS formation follows a functional trait-driven self-organization process rather than simple cellular aggregation. Selection pressures shape community structure, promoting enrichment of microorganisms. On this basis, quorum-sensing (QS) system is activated with cell density. Rather than acting independently, QS is associated with the reinforcement of existing aggregates, the strengthening of metabolic synergy, and the stabilization of functional zonation. As a density-dependent coordination mechanism, it is involved in regulating the luxI/luxR pathway and key functional genes involved in extracellular polymeric substance synthesis, nitrogen removal, and phosphorus removal. This regulation primarily targets existing aggregates to enhance metabolic synergy and reinforce C/N/P-coupled functional zonation. Operational stability and system performance are improved, bridging community ecological processes with cross-scale gene-regulatory mechanisms. Within this framework, the rationale and limitations of enhancement strategies are evaluated, including QS regulation, microbial reinforcement, and synthetic biology. In the future, quantitative cross-scale coupling models and AI-driven process control may enable engineering universality and designability of AGS. Overall, the proposed paradigm of multilayer microbial programming provides a unified perspective on AGS formation and stability, supporting predictable and designable applications in next-generation biological wastewater treatment systems.},
}

@article {pmid41951653,
year = {2026},
author = {He, L and Yuan, D and Li, Q and Zhang, X and Niu, K and Li, X and Ou, Y and Du, H and Yuan, J and Duan, Y and Niu, H},
title = {Fecal virome transplantation attenuates arthritis in mice by remodeling gut ecology, systemic tryptophan metabolism, and innate immune responses.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00980-2},
pmid = {41951653},
issn = {2055-5008},
support = {2024VPPC-S02//the Open Project of the Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education/ ; 2025A1515012786//the Natural Science Foundation of Guangdong Province/ ; 2022YFF0710702 and 2022YFF0710701//the National Key &D Programs of China/ ; 202201020381//the Guangzhou Joint Fund for Key Laboratory/ ; YXJC2022004//the Medical Joint Fund of Jinan University/ ; },
abstract = {Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic joint inflammation and systemic immune dysregulation. Emerging evidence suggests that the gut microbiome plays an important role in immune modulation in RA, yet the role of the gut virome remains poorly understood. Here, using the K/BxN serum-transfer arthritis model, we systematically evaluated the potential role of fecal virome transplantation (FVT) in modulating gut ecology and innate inflammatory responses. Arthritic mice exhibited marked alterations in gut virome composition compared with healthy controls. Administration of purified virus-like particles (VLPs) from healthy donors correlated with reductions in paw swelling, histopathological inflammation, bone erosion, circulating proinflammatory cytokines, and myeloid cell infiltration in inflamed tissues. In parallel, 16S rRNA sequencing showed that FVT remodeled the gut bacterial community toward a composition more similar to that of healthy controls. Targeted serum metabolomics revealed increased levels of microbiota-derived tryptophan metabolites, including indole-3-lactic acid and related indole derivatives, suggesting a link between gut microbial remodeling and systemic immunometabolic regulation. Collectively, these findings indicate that FVT may attenuate inflammatory arthritis by remodeling gut microbial ecology, potentially involving virome-bacteriome interactions and immunometabolic pathways.},
}

@article {pmid41952630,
year = {2026},
author = {Wim, T and Mehraveh, S and Katalina, L and Cheah, CW and Pisha, P and Ana, C and Andy, T and Naiera, Z and Wannes, VH},
title = {Not a miracle, not a myth: The role of probiotics in periodontal health.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70039},
pmid = {41952630},
issn = {1600-0757},
support = {C3/24/081//KU Leuven/ ; },
abstract = {BACKGROUND: As the understanding of periodontal disease has evolved, therapeutic strategies have increasingly shifted from pathogen eradication toward ecological modulation of the oral microbiome. Within this paradigm, probiotics have emerged as potential adjuncts for maintaining periodontal health by promoting microbial balance and modulating host responses.

OBJECTIVE: To summarize the historical development, definitions, and mechanisms of probiotics and to critically evaluate the current clinical evidence supporting their use in periodontal therapy.

METHODS: This narrative review examines the conceptual framework of probiotics in oral health, distinguishing them from related approaches including prebiotics, postbiotics, and synbiotics. Literature from randomized controlled trials and meta-analyses was reviewed to assess the clinical effectiveness of probiotic interventions in periodontal therapy and to explore their proposed mechanisms of action.

RESULTS: Probiotic effects are highly strain-specific and involve multiple mechanisms, including production of antimicrobial compounds, competition for ecological niches, inhibition of biofilm formation and quorum sensing, strengthening of epithelial barrier integrity, and modulation of host immune and inflammatory responses. Evidence from randomized controlled trials and meta-analyses, particularly those evaluating Limosilactobacillus reuteri strains, suggests that probiotics used as adjuncts to nonsurgical periodontal therapy can significantly improve clinical parameters such as probing pocket depth, clinical attachment level, and bleeding on probing. However, substantial heterogeneity in study design, probiotic strains, delivery systems, and follow-up periods limits the comparability and generalizability of findings.

CONCLUSIONS: Probiotics represent a biologically plausible and ecologically oriented adjunct in periodontal therapy. While current evidence indicates beneficial clinical effects, further standardized and long-term clinical trials incorporating advanced microbiome analyses (e.g., next-generation sequencing) are needed to clarify mechanisms, optimize formulations, and support personalized probiotic strategies in periodontal care.},
}

@article {pmid41953022,
year = {2026},
author = {Han, W and Li, Q and Yuan, G},
title = {The gut microbiome as an actionable drug-sensitivity modulator for immune checkpoint blockade: clinical evidence for FMT, live biotherapeutics, and defined consortia.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1802676},
pmid = {41953022},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Fecal Microbiota Transplantation/methods ; Animals ; },
abstract = {Immune checkpoint inhibitors (ICIs) deliver durable benefit to only a subset of patients and can be limited by immune-related adverse events (irAEs). The gut microbiome has emerged as an actionable, host-level modulator of ICI drug sensitivity and toxicity. This mini-review links microbial ecology to antigen presentation, T-cell priming and fitness, metabolite signaling, and barrier inflammation, and summarizes interventional evidence across three modalities. Responder-derived fecal microbiota transplantation (FMT) provides the strongest proof-of-concept for re-sensitization in anti-PD-1-refractory melanoma. Microbiome repair can also improve refractory ICI-associated colitis. Early trials of live biotherapeutics and defined consortia support scalability but highlight context dependence and design pitfalls, including antibiotic preconditioning. We discuss practical determinants of reproducibility, including co-medications, diet, engraftment and functional readouts, and conclude with safety, regulatory, and reporting priorities for clinically deployable microbiome engineering.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Fecal Microbiota Transplantation/methods
Animals

@article {pmid41953448,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {Biohacking the human gut microbiome for precision health and therapeutic innovation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1776983},
pmid = {41953448},
issn = {1664-302X},
abstract = {Biohacking, the self-directed application of biotechnology, digital tools, and lifestyle interventions, has rapidly converged with gut microbiome science to create adaptive, individualized, and minimally invasive precision-health paradigms. This narrative review integrates current evidence on diet-based modulation, microbial therapeutics (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation), and synthetic-biology approaches (engineered strains and phage or synthetic consortia) within a multi-omics and continuous-phenotyping framework. Mechanistically, short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan catabolites operate as endocrine-like mediators linking gut microbial ecology with host immunity, metabolism, and neuroendocrine signaling. Pathways mediated by microbial metabolites underpin translational applications that span metabolic optimization, through improved insulin sensitivity, reduced adiposity, and attenuation of inflammation, and neurocognitive enhancement via the microbiome-gut-brain axis. Evidence from oncology further indicates that microbial metabolites and engineered taxa remodel stromal and immune niches, shaping therapeutic response and disease progression. Concurrently, emerging digital infrastructures, wearables, biosensors, metabolic avatars, and AI-driven "health twins," enable real-time, closed-loop modulation of host-microbe dynamics. Persistent challenges include methodological heterogeneity, safety concerns regarding live biotherapeutics and unsupervised fecal microbiota transplantation (FMT), fragmented regulation, and vulnerabilities in cyberbiosecurity and data equity. We propose a translational roadmap emphasizing standardized metadata (STORMS), validated reference frameworks, longitudinal multi-omics for causal inference, strain-level safety genomics, and governance integrating ethical and cybersecurity oversight. Under these conditions, microbiome-focused biohacking may evolve from anecdotal experimentation into a more reproducible and scientifically grounded component of preventive and personalized medicine. This manuscript is presented as a narrative and conceptual review, integrating validated microbiome research with emerging biohacking frameworks while explicitly distinguishing evidence-based findings from exploratory or speculative concepts.},
}

@article {pmid41954752,
year = {2026},
author = {Saha, S and Shah, AS and Wang, P and Burgess, TI and Bayliss, KL},
title = {Seed Potato Bacteria Transfer Across Generations Within the Tuber Flesh.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02758-7},
pmid = {41954752},
issn = {1432-184X},
abstract = {Potato crops are susceptible to pathogens and environmental extremes. Microbiomes support plant health and stress tolerance, and microbes can transfer across generations in vegetatively propagated potatoes. However, the extent and functional relevance of this transfer are poorly understood. This study investigated bacterial transfer across three tuber generations, from seed to granddaughter in two potato cultivars, Nadine and Royal Blue. Bacterial communities in the peel and flesh compartments were sequenced. The granddaughter generation was cultivated in two separate fields to determine the consistency of vertical transfer, and the tare soil bacterial community was a proxy for environmental acquisition. The overall community composition was influenced by generation, compartment, cultivar and field. Horizontal acquisition significantly increased across generations and was the primary source, accounting for more than 98% of the granddaughter tuber bacteria. Peel had a significantly higher number of horizontally acquired ASVs than flesh. Only a small set of seed tuber bacteria ASVs were vertically transferred to the granddaughter tubers. The overall vertical transfer probability was 1.8% across compartments, cultivars, and fields, and it was higher in flesh than in peel. Cultivar-specific probabilities were 1.8% for Nadine and 1.5% for Royal Blue. Field variance was minimal, indicating consistent vertical transfer regardless of where the tubers were grown. Taxa with stable vertical transfer included Streptomycetaceae, Xanthobacteraceae, Devosiaceae, Sphingomonadaceae, and Micrococcaceae. Vertically transferred ASVs were predicted to have functions associated with core metabolic and stress response pathways. This study confirmed consistent vertical transfer of bacteria across potato tuber generations, mainly in the flesh.},
}

@article {pmid41955218,
year = {2026},
author = {Yaakop, S and Senen, MA and Adila Rosli, NA and Mohammed, MA},
title = {Molecular identification and microbiome profiling of household casebearer, Phereoeca sp. (Lepidoptera: Tineidae) from Malaysia: Potential implications for human skin irritation.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346590},
doi = {10.1371/journal.pone.0346590},
pmid = {41955218},
issn = {1932-6203},
mesh = {Animals ; Malaysia ; *Microbiota/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Skin/microbiology ; *Lepidoptera/microbiology/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Moths/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Electron Transport Complex IV/genetics ; },
abstract = {In Malaysia, anecdotal accounts have linked the household casebearer (Lepidoptera: Tineidae) to skin lesions and localized inflammation; however, scientific evidence is lacking, and the species' taxonomic identity remains unclear. This study aimed to confirm the species identity and examine the bacteria associated with larvae that may be linked to skin irritation. Larvae were collected from three locations in Peninsular Malaysia and preserved. DNA was extracted from the larvae, and species identification was conducted by analyzing the cytochrome c oxidase subunit I (COI) gene through DNA barcoding. To study the bacteria present, the bacterial 16S rRNA gene was amplified and sequenced using Next-generation sequencing technology. The DNA sequences were analyzed to determine the species and profile the bacterial communities. The results identified the specimens as Phereoeca sp., suggesting they may represent an undescribed lineage. Microbiome analysis revealed that Proteobacteria (40.18%) and Actinobacteriota (32.13%) were the dominant bacterial phyla, with Cutibacterium acnes, Enterobacter, and Pseudomonas among the taxa previously associated with skin irritation or opportunistic infections. Several unclassified but potentially relevant taxa were also identified. These findings provide new insights into the microbial ecology and taxonomy of Phereoeca and underscore its potential role in medically significant interactions within human environments.},
}

Animals
Malaysia
*Microbiota/genetics
Humans
RNA, Ribosomal, 16S/genetics
Larva/microbiology
*Bacteria/genetics/classification/isolation & purification
Phylogeny
Skin/microbiology
*Lepidoptera/microbiology/genetics
DNA Barcoding, Taxonomic
DNA, Bacterial/genetics
*Moths/microbiology/genetics
High-Throughput Nucleotide Sequencing
Electron Transport Complex IV/genetics

@article {pmid41955350,
year = {2026},
author = {Moran, J and Graham, LC and Tikhonov, M},
title = {Emergent predictability in microbial ecosystems.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6794},
pages = {eadr1440},
doi = {10.1126/science.adr1440},
pmid = {41955350},
issn = {1095-9203},
mesh = {*Microbiota ; *Ecosystem ; Biodiversity ; *Bacteria/classification ; },
abstract = {A long-standing hypothesis of microbial ecology is that simple patterns might persist despite community complexity or even emerge because of it. However, the concept of "emergent simplicity" remains partly intuitive. Here, we defined emergent predictability of microbial ecosystems based on the predictive power of coarsened descriptions that group individual microbial strains into broader classes. We used two published datasets to show that coarse descriptions became more predictive for more species-rich communities. This behavior was not explained by simple averaging effects in large communities. To the contrary, our analysis indicates that emergent predictability arises when physiological or environmental feedback counteracts these averaging effects along certain axes of community variation, allowing these axes to become more informative as diversity increases.},
}

*Microbiota
*Ecosystem
Biodiversity
*Bacteria/classification

@article {pmid41955630,
year = {2026},
author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H},
title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/23744235.2026.2654559},
pmid = {41955630},
issn = {2374-4243},
abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.

METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.

RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n = 18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.

CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.},
}

@article {pmid41937469,
year = {2026},
author = {Wee, GN and Hwang, J and Kwon, B and Kim, J and Kim, S and Seo, SC and Jang, S},
title = {Human Contact Frequency as a Dominant Ecological Driver of Fungal Community Assembly and Homogenization in Public Built Environments.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2602016},
doi = {10.4014/jmb.2602.02016},
pmid = {41937469},
issn = {1738-8872},
mesh = {Humans ; *Fungi/classification/genetics/isolation & purification ; *Mycobiome/genetics ; *Air Microbiology ; Republic of Korea ; Cladosporium/isolation & purification/genetics ; Air Pollution, Indoor/analysis ; *Built Environment ; Public Facilities ; DNA, Fungal/genetics ; Malassezia/isolation & purification/genetics/classification ; Aspergillus/isolation & purification/genetics ; },
abstract = {As modern populations spend the majority of their time indoors, understanding indoor microbial ecology is crucial for public health. While research has addressed abiotic pollutants, the ecological dynamics of surface-associated mycobiomes remain insufficiently understood. This study assessed fungal communities across 25 types of public facilities in South Korea to evaluate the relative influence of environmental parameters and human-driven factors. A total of 327 surface samples from six surface types (handles, tables, chairs, walls, pillars, floors) were analyzed using internal transcribed spacer (ITS) sequencing, yielding 27 million reads and 31,721 amplicon sequence variants (ASVs). Although temperature and humidity significantly correlated with airborne fungal concentration, they exerted minimal influence on community diversity and structure. Instead, the intensity of human contact with indoor surfaces emerged as a primary driver of fungal community composition. We found that the relative abundance of the human-associated genus Malassezia is strongly associated with two distinct ecological states of indoor surface mycobiomes; high-Malassezia samples exhibited significantly distinct communities (ANOSIM R = 0.217, p < 0.001) and dense co-occurrence networks among genera of potential clinical relevance, with strong correlations between Malassezia and both Aspergillus and Cladosporium (|corr| = 0.81). These Malassezia-associated patterns persisting across diverse facilities demonstrate that human-driven microbes are the primary ecological drivers of surface mycobiomes in public spaces, providing foundational evidence for human contact-based microbial assessments in public health monitoring and hygiene-conscious environment design.},
}

Humans
*Fungi/classification/genetics/isolation & purification
*Mycobiome/genetics
*Air Microbiology
Republic of Korea
Cladosporium/isolation & purification/genetics
Air Pollution, Indoor/analysis
*Built Environment
Public Facilities
DNA, Fungal/genetics
Malassezia/isolation & purification/genetics/classification
Aspergillus/isolation & purification/genetics

@article {pmid41938569,
year = {2026},
author = {Yausheva, E and Kholodilina, T and Sizova, E and Shoshin, D and Ryazantseva, K and Nechitailo, K and Klimova, T and Mustafina, A},
title = {Dietary calcium citrate enhances nutrient digestibility and modulates cecal microbiota function in pre-laying hens.},
journal = {Veterinary world},
volume = {19},
number = {2},
pages = {821-839},
pmid = {41938569},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Calcium source and bioavailability are critical determinants of nutrient utilization, gut microbial ecology, and future productivity in laying hens, particularly during the pre-laying period. Organic calcium salts may exert additional functional effects through microbiota modulation beyond mineral supply alone. This study evaluated the effects of replacing calcium carbonate with calcium citrate on nutrient digestibility, cecal microbiota composition, short-chain fatty acid (SCFA) production, and predicted microbial metabolic pathways in pre-laying hens.

MATERIALS AND METHODS: Sixty Hisex Brown pre-laying hens (13-20 weeks of age) were allocated to two dietary treatments: a control diet containing calcium carbonate and an experimental diet in which calcium carbonate was fully replaced with calcium citrate. Diets were formulated to be isocaloric, isonitrogenous, and equal in total calcium content. Nutrient digestibility coefficients were determined using a physiological balance trial. Cecal SCFA concentrations were quantified by gas chromatography. Cecal microbiota composition was analyzed by 16S rRNA gene sequencing, and functional pathway prediction was performed using Kyoto Encyclopedia of Genes and Genomes-based bioinformatic analysis. Statistical significance was set at p < 0.05.

RESULTS: Replacement of calcium carbonate with calcium citrate significantly increased the digestibility of crude fat (+28.7%, p ≤ 0.001), crude protein (+7.29%, p ≤ 0.001), calcium (+7.56%, p ≤ 0.05), and phosphorus (+2.92%, p ≤ 0.05). Cecal concentrations of propionic, butyric, and valeric acids were significantly higher in the calcium citrate group (p ≤ 0.001). Microbiota analysis revealed a higher relative abundance of Bacillota, particularly Lactobacillaceae and Oscillospiraceae, and a reduced proportion of Bacteroidota, including Alistipes. Alpha diversity indices were higher in the experimental group. Functional prediction indicated enrichment of microbial genes associated with carbohydrate, amino acid (phenylalanine, tyrosine, tryptophan), and fatty acid metabolism, alongside reduced methane metabolism.

CONCLUSION: Dietary calcium citrate markedly improves nutrient digestibility and beneficially reshapes cecal microbiota composition and function in pre-laying hens. These findings highlight calcium citrate as a promising nutritional strategy to enhance gut health, mineral utilization, and feed efficiency, with potential implications for subsequent egg production and sustainable poultry systems.},
}

@article {pmid41941070,
year = {2026},
author = {de Leite, DPSBM and de Pinto, GOA and da Silva, MEUCM and da Silva, VV and Goncalves, LMT and de Albuquerque, MCF and Santos, RS and da Silva, LTR and Valença, YM and Beraldo, KRF and Juliano, MA and de Oliveira, PRF and da Silva, JG and Mota, RA},
title = {Antimicrobial Resistance and Biofilm in Bacteria from Rehabilitated Sapajus libidinosus.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {41941070},
issn = {1612-9210},
abstract = {Antimicrobial resistance (AMR) in natural environments and wildlife is an escalating threat to global health and biodiversity conservation. Neotropical primates of the genus Sapajus may act as reservoirs and ecological sentinels of resistant bacteria. The absence of systematic microbiological screening in wildlife rehabilitation centers, coupled with empirical antimicrobial use, can facilitate resistance spread in vulnerable ecosystems. This study characterized phenotypic and genotypic resistance profiles and biofilm-forming ability of Staphylococcus spp. and Mammaliicoccus sciuri isolated from Sapajus libidinosus undergoing rehabilitation in Northeastern Brazil. Rectal swabs were collected, and bacterial isolates identified by MALDI-TOF MS, followed by antimicrobial susceptibility testing, molecular detection of resistance genes, and biofilm assays. Nineteen isolates were recovered: 63.2% Staphylococcus spp. and 36.8% Mammaliicoccus spp. The predominant species were M. sciuri (36.8%) and S. simiae (31.6%). Rates of resistance to penicillin (63.2%) and tetracycline (57.9%) were the most frequent. The main resistance genes detected included tetM (36.8%), tet(38) (31.6%), blaZ (26.3%), msrA (26.3%), and mecA (5.3%). Perfect agreement existed between mecA presence and cefoxitin resistance (κ = 1.00; p < 0.01), with moderate agreement between msrA and non-susceptibility to erythromycin and clindamycin (j= 0.56; p = 0.0265). Biofilm production was mostly weak (94.7%), with moderate production in one isolate. Multidrug resistance occurred in 21.1% of isolates. This pioneering Brazilian study highlights wildlife rehabilitation centers as critical hotspots for AMR surveillance and contributes to understanding the ecological health and conservation of Neotropical primates.},
}

@article {pmid41943256,
year = {2026},
author = {Maciá-Vicente, JG and Gomes, SIF and Ampt, EA and Hennecke, J and Bakker, LM and van Ruijven, J and Mommer, L},
title = {The phylogenetic structure of plant communities drives the belowground transmission of fungal pathogens.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71156},
pmid = {41943256},
issn = {1469-8137},
support = {BG23/00164//Ministerio de Ciencia, Innovación y Universidades/ ; 864.14.006//Exacte en Natuurwetenschappen/ ; },
abstract = {Biodiversity is known to influence disease risk, yet the pathways of pathogen transmission within plant communities remain poorly understood, especially belowground. In particular, how soil-borne pathogens move from resident vegetation and soil to colonize new hosts is unresolved. We traced belowground pathogen transmission using phytometer seedlings of two plant species planted in a long-term grassland biodiversity experiment. After 3 months, we characterized the fungal communities of phytometer roots, resident plant roots, and soil using high-throughput sequencing and the FungalTraits database to identify associations between pathogen taxonomy and plant families. Next, we related pathogen abundance to phytometer growth. The phylogenetic similarity of phytometers with resident plant species strongly predicted the relative abundance of pathogens that were considered family-specific, but not of pathogens without a clear host preference. However, neither pathogen abundance in phytometers nor resident plant biomass affected phytometer growth, which was best explained by the resident communities' species richness. Combining sequencing of fungal communities with in situ field manipulations enabled us to track the associations between multiple soil-borne pathogens and plant hosts within the full complexity of plant-soil systems. While pathogen dynamics were readily detectable, their consequences for plant performance may only become apparent over longer ecological timescales.},
}

@article {pmid41936687,
year = {2026},
author = {Viswan, A and Augustine, N},
title = {Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02726-1},
pmid = {41936687},
issn = {1432-184X},
}

@article {pmid41936761,
year = {2026},
author = {Yang, T and Xu, A and Huang, Z and Wang, C and An, Y and Gong, X and Gao, D},
title = {Discharge strategy modulates microbial cooperation and nitrogen cycling in composite carbon-based tidal flow wetlands.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129591},
doi = {10.1016/j.jenvman.2026.129591},
pmid = {41936761},
issn = {1095-8630},
abstract = {Tidal flow constructed wetland (TFCW) cannot effectively remove excess nitrogen from municipal effluent under carbon-limited conditions. By adding a novel slow-release carbon source to TFCW, carbon utilization can be significantly accelerated, stimulating enhanced nitrogen transformation within the system. However, how HRT and discharge strategies shape the microenvironment-and in turn affect microbial processes, nitrogen cycling, and greenhouse gas emissions-remains poorly understood. Building upon previous research, this study investigated the impacts of different HRT and discharge modes on water quality characteristics and microbial community dynamics in TFCW equipped with a slow-release carbon source (BCP). Over 150 tidal cycles, TFCW performance and its influence on microbial ecology were evaluated. Results showed that the system operating at a 24-h HRT combined with full discharge achieved the highest TN removal efficiency (92.70%). This was primarily attributed to enhanced reoxygenation capacity, improved carbon utilization, and plant uptake, which synergistically promoted nitrification-denitrification processes. Microbial activity was more uniform, with key denitrifying enzymes (Nar, Nir) and electron transport system activity synergistically enhanced. High-throughput sequencing revealed Denitratisoma (1.55%) and Nitrospira (0.94%) involved in the cooperative removal of nitrate and ammonium. Correlation and redundancy analyses identified COD and DO as key drivers of microbial community assembly and function (rd ≥ 0.4). Overall, optimizing HRT and discharge strategies can effectively regulate microbial interactions and enhance nitrogen removal for TFCW with BCP. These findings provide new theoretical insights and practical guidance for the engineering design and operational management of advanced treatment systems for urban tailwater.},
}

@article {pmid41935026,
year = {2026},
author = {Pawaiya, A and Pradhan, RK and Johri, AK and Dua, M},
title = {Advanced breeding techniques in Brassica juncea L. for sustainable production under changing climate.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2648963},
doi = {10.1080/15592324.2026.2648963},
pmid = {41935026},
issn = {1559-2324},
mesh = {*Mustard Plant/genetics ; *Climate Change ; *Plant Breeding/methods ; Crops, Agricultural/genetics ; Stress, Physiological ; },
abstract = {Brassica juncea (L.) Czern. & Coss. is an agronomically important crop cultivated worldwide as a valuable source of oil. It is a major source of edible oil in South Asia because of its high oil content, nutraceutical value, and balanced fatty acid contents. In addition to being considered a relatively hardy crop with high economic value, its productivity potential is restricted by susceptibility to various biotic and abiotic stresses, including diseases, pests, drought, heat, frost, and salinity. These constraints adversely affect yield, often leading farmers to move towards alternative crops. In this context, the use of advanced genomics, transcriptomics, and proteomics approaches can provide molecular insight into the evolutionary history, genetic diversity and adaptive response of B. juncea under stress and at different developmental stages. A comprehensive understanding of its molecular architecture and advanced crop improvement strategies will culminate in the development of high-yielding, stress-resistant cultivars, facilitating sustainable mustard production under a changing climate.},
}

*Mustard Plant/genetics
*Climate Change
*Plant Breeding/methods
Crops, Agricultural/genetics
Stress, Physiological

@article {pmid41936227,
year = {2026},
author = {Alonso-Fernandes, E and Durante-Rodríguez, G and Cano, I and García-García, P and García-Salgado, S and Quijano, MÁ and Díaz, E and Carmona, M},
title = {Unraveling the arsenite response mechanisms in the,facultative anaerobe Aromatoleum sp. CIB.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128509},
doi = {10.1016/j.micres.2026.128509},
pmid = {41936227},
issn = {1618-0623},
abstract = {Arsenite is a highly toxic metalloid for living organisms; however, numerous microorganisms have evolved effective mechanisms to adapt to arsenic stress. The facultative anaerobic betaproteobacterium Aromatoleum sp. CIB exhibits a good level of arsenite tolerance, mediated by the coordinated action of multiple molecular systems involved in detoxification and cellular homeostasis. Here, we identified the arsSM genes, encoding enzymes responsible for the production of methylated arsenic species and putative precursors of arsenosugar biosynthesis. The organization of these genes within the arsSM operon suggests a role in arsenic homeostasis, potentially supported by their constitutive expression. This finding extends the known taxonomic distribution of arsSM-mediated arsenic transformation mechanisms beyond cyanobacteria and supports horizontal gene transfer as a likely route for arsSM operon acquisition. Moreover, we present the first comparative analysis of arsenite responses under aerobic and anaerobic conditions within a single bacterial species, revealing distinct physiological constraints and adaptive strategies. Transcriptomic profiling of Aromatoleum sp. CIB exposed to arsenite revealed a stronger global transcriptional response under aerobic conditions. Although canonical arsenic resistance genes (the ars cluster) were induced under both conditions, oxygen availability markedly intensified the global stress response, particularly oxidative stress-related pathways. In contrast, genes encoding protein-folding chaperones were preferentially upregulated under anaerobic conditions. These results indicate a context-dependent reorganization of cellular functions in response to arsenite stress, favoring survival over growth. Overall, this study highlights the complexity and flexibility of bacterial arsenic resistance and provides insights relevant to microbial ecology and arsenic biogeochemical cycling.},
}

@article {pmid41936639,
year = {2026},
author = {Aykut, TO and Crucitti-Thoo, RM and Rudak, A and Jasser, I},
title = {Caught Between Invasions: Community Structure and Environmental Drivers of Cyanobacteria in a Vulnerable Post-glacial Lake Region.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02749-8},
pmid = {41936639},
issn = {1432-184X},
support = {BOB-IDUB-622-666/2023//Ministerstwo Edukacji i Nauki/ ; },
}

@article {pmid41930262,
year = {2025},
author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C},
title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1757196},
pmid = {41930262},
issn = {1664-302X},
abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.},
}

@article {pmid41931990,
year = {2026},
author = {Gao, J and Yi, Y and Ran, W and Cheng, Y and Deng, W and Duan, S and Shi, F and Wei, Y and Zhang, Y and Gong, Q},
title = {Targeting astrocytic Nrf2 by Trilobatin alleviates lipopolysaccharide-induced depressive-like behaviors and cognitive impairment in mice: Mechanistic insights into gut microbiota and metabolites modulation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158118},
doi = {10.1016/j.phymed.2026.158118},
pmid = {41931990},
issn = {1618-095X},
abstract = {BACKGROUND: Clinical and preclinical evidence links major depressive disorder (MDD) and Alzheimer's disease (AD), suggesting MDD treatment could prevent some AD. Dysfunction within the microbiota-gut-brain axis contributes to MDD and AD pathogenesis via dysregulated microbial metabolites. Trilobatin (TLB) functions as a neuroprotective agent modulating gut microbiota. However, its capacity to alleviate depressive-like behavior and cognitive deficits through restoration of gut microbial ecology and metabolite profiles requires clarification.

OBJECTIVE: The present research was designed to examine the impact of TLB on depressive-like behavior and cognitive impairments, and the role of the gut microbiota and metabolites.

METHODS: Neuroprotective effects of TLB on MDD and AD were evaluated using an LPS mouse model exhibiting depressive-like behavior and memory impairment. The principal molecular target of TLB was identified through a combination of single-cell sequencing, surface plasmon resonance, and gene knockout approaches. Mechanistic insights into gut microbiota and metabolites were gained through 16S rRNA sequencing and fecal microbiota transplantation (FMT).

RESULTS: TLB attenuated LPS-induced depressive-like behaviors manifested as lowered sucrose preference, extended immobility, and improved cognitive deficits as reflected by Y-maze and novel object recognition. Mechanistically, TLB directly bound Nrf2, enhanced Nrf2-ARE activity, and suppressed neuroinflammation and oxidative stress. TLB restored gut microbiota homeostasis, elevated Akkermansia muciniphila (AKK) abundance and short-chain fatty acids, and strengthened intestinal tight junction proteins. FMT from TLB-treated mice replicated these benefits in wild-type but not Nrf2-knockout mice. AKK supplementation similarly ameliorated behavioral and cognitive deficits via Nrf2 activation.

CONCLUSION: Our findings reveal that TLB mitigates neuropsychiatric deficits by activating Nrf2, remodeling restructuring gut microbiota and fortifying intestinal barrier function. The Nrf2-mediated microbiota-gut-brain axis is suggested as a potential therapeutic target for MDD and AD, positioning TLB as a promising natural Nrf2 activator.},
}

@article {pmid41933473,
year = {2026},
author = {Spieck, E and Koch, H and Kop, LFM and Keuter, S and Malinowski, M and Sass, K and Sand, W and Donati, E and Garcia, PP and Lücker, S and Giaveno, A},
title = {Cultivation-Based Detection of a Novel High-GC Nitrospira Derived From the Argentinian Copahue Volcano Area.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70290},
pmid = {41933473},
issn = {1462-2920},
support = {SP 667/7-1//Deutsche Forschungsgemeinschaft/ ; SP 667/7-2//Deutsche Forschungsgemeinschaft/ ; SP 667/11-1//Deutsche Forschungsgemeinschaft/ ; SP 667/11-2//Deutsche Forschungsgemeinschaft/ ; doi.org/10.55776/COE7//Austrian Science Fund/ ; VI.Veni.192.086//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 024.002.002//SIAM/ ; },
mesh = {Argentina ; *Hot Springs/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Nitrification ; Nitrites/metabolism ; },
abstract = {Nitrification is an essential process within the global nitrogen cycle and also occurs under extreme conditions, such as in geothermal environments. The nitrite-oxidizing group Nitrospira represents key nitrifiers in these systems, as several species inhabit hot springs worldwide. Using different initial incubation temperatures, two novel moderately thermophilic Nitrospira enrichments, Nitrospira sp. Vd2 and Ca. N. neuquenensis E2OT, were obtained from sulfur-rich mud pools in the geothermal field Las Máquinas (Neuquén Province, Argentina). Nitrospira sp. Vd2 belongs to the N. bockiana lineage V, whereas the second enrichment (E2OT) represents the novel taxonomic lineage VIII, together with cultures from Kamchatka (Kam-Ns4a) and Garga hot springs (Ga3a). The vibrioid morphology of Ca. N. neuquenensis E2OT is strikingly different from all described, twisted rod-shaped Nitrospira. Our study expands the knowledge of the taxonomic and genomic diversity of moderately thermophilic Nitrospira, by comparing the high-quality draft genomes with those of previously described species. The recent discovery of quorum-sensing genes outside the Nitrospira lineage II was confirmed for both Argentinian cultures. Notably, the genome GC contents of the enrichments Vd2 and E2OT are 60.6% and 69.4%, respectively. The latter is the highest observed for Nitrospira to date and might support thermotolerance up to 50°C.},
}

Argentina
*Hot Springs/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Genome, Bacterial
Nitrification
Nitrites/metabolism

@article {pmid41934143,
year = {2026},
author = {Cruz-Paredes, C and Brangarí, AC and Tájmel, D and Hicks, L and Leizeaga, A and Wondie, M and Sandén, H and Rousk, J},
title = {Soil Microbial Communities Adjust Thermal Traits and Carbon Allocation in Response to Climate Manipulations in Subtropical Forest and Cropland.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70836},
pmid = {41934143},
issn = {1365-2486},
support = {2016-06327//Vetenskapsrådet/ ; 9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Climate Change ; *Microbiota ; *Carbon/metabolism ; Temperature ; Tropical Climate ; Carbon Cycle ; Soil/chemistry ; Bacteria/metabolism ; Fungi ; Droughts ; },
abstract = {Soil microorganisms regulate carbon (C) cycling, and their growth and respiration are strongly dependent on temperature. Yet it remains unclear how warming alters microbial thermal traits, community structure, and the balance between microbial respiration and growth, particularly in subtropical ecosystems where high temperatures coincide with low soil moisture, potentially constraining microbial activity. In this study, we investigated soil microbial thermal traits for growth and respiration, and the microbial community composition in two subtropical land-uses with contrasting microclimates: a cooler, moist pristine forest and a warmer, drier cropland. Using open top chambers (OTCs) or rain exclusion shelters over 1.5 years, we quantified how experimental warming and drought altered microbial functioning and upscaled these effects using field soil temperature and moisture records. Field warming increased the abundance of warm-adapted bacterial and fungal taxa and led to shifts in microbial thermal trait distributions toward higher minimum temperature values for microbial growth, indicating community-level thermal adaptation. These thermal trait adaptations resulted in a modeled 36% reduction in annual soil CO2 efflux in warmed plots. Overall, our results show that thermal trait adaptation, driven partly by community restructuring, buffers soil C losses under warming and may enhance soil C sequestration in subtropical ecosystems. These findings showcase the importance of integrating microbial thermal traits into soil C models to improve predictions of climate-carbon feedbacks.},
}

*Soil Microbiology
*Forests
*Climate Change
*Microbiota
*Carbon/metabolism
Temperature
Tropical Climate
Carbon Cycle
Soil/chemistry
Bacteria/metabolism
Fungi
Droughts

@article {pmid41926446,
year = {2026},
author = {Lelis, ALJ and da Silva, LAF and Casali, DM and Leiva, T and Rodrigues, MC and Barroso, JPR and Lasmar, PVF and Tomaz, CL and Barbosa, AJ and Sartini, CCF and de Souza, JM and Millen, DD},
title = {The effects of increasing dosages of narasin on ruminal fermentation patterns, bacterial community composition, and nutrient digestibility in beef cattle receiving feedlot diets.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346130},
pmid = {41926446},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Rumen/microbiology/drug effects/metabolism ; *Fermentation/drug effects ; *Digestion/drug effects ; Animal Feed ; Male ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Bacteria/drug effects ; Dietary Supplements ; Hydrogen-Ion Concentration ; Nutrients/metabolism ; },
abstract = {This study evaluated the effects of increasing narasin doses on ruminal fermentation, nutrient digestibility, ruminal pH stability, papillae histology, and microbial composition in Angus cattle fed feedlot diets. Three rumen-cannulated Angus steers (average body weight: 680 kg) were assigned to a 3 × 3 Latin square design and received diets containing 13, 20, or 27-ppm of narasin. Each experimental period consisted of 14 days of adaptation followed by seven days of sampling. Ruminal degradability was assessed on days 15-17, apparent digestibility on days 15-19, continuous ruminal pH on days 19-20, and samples for short-chain fatty acids (SCFA), microbiota, and ruminal histology were collected on days 20 and 21. Ruminal degradability was not affected by narasin dose. Digestibility of acid detergent fiber (ADF) was significantly influenced, with the greatest values observed at 27-ppm (P = 0.01). Increasing narasin doses improved ruminal pH stability, as indicated by a linear increase in minimum pH (P = 0.01) and a reduction in the duration of pH below 5.6 (P = 0.10). At 13 ppm, SCFA production, particularly acetate and propionate, increased (P < 0.05), indicating enhanced fermentation efficiency. In contrast, supplementation with 27-ppm reduced ammonia (P < 0.01), acetate (P = 0.02), and butyrate (P < 0.01) concentrations and increased the acetate-to-propionate ratio (P < 0.01). Lactate concentration decreased linearly with increasing narasin doses (P = 0.03). Narasin supplementation altered ruminal microbial composition, increasing the relative abundance of Lachnospiraceae and Isotricha while reducing lactic acid-producing bacteria. In terms of ruminal morphology, supplementation with 20-ppm of narasin increased the keratin layer thickness of ruminal papillae (P = 0.02), suggesting enhanced epithelial development. Overall, narasin supplementation modulated ruminal function and microbial ecology, with doses between 13 and 20-ppm providing the most favorable balance between fermentative efficiency and ruminal health in feedlot cattle.},
}

Animals
Cattle
*Rumen/microbiology/drug effects/metabolism
*Fermentation/drug effects
*Digestion/drug effects
Animal Feed
Male
Fatty Acids, Volatile/metabolism
Gastrointestinal Microbiome/drug effects
Diet/veterinary
Bacteria/drug effects
Dietary Supplements
Hydrogen-Ion Concentration
Nutrients/metabolism

@article {pmid41926667,
year = {2026},
author = {Chen, Y and Duan, R and Zhang, C and Li, G and Ji, X and Zhang, Q and Pei, F and Wang, K and Duan, L},
title = {Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e16931},
doi = {10.1002/advs.202516931},
pmid = {41926667},
issn = {2198-3844},
support = {2021YFA1301300//National Key R&D Program of China/ ; 82470578//National Natural Science Foundation of China/ ; 7254451//Beijing Natural Science Foundation/ ; },
abstract = {The early-life microbiome plays a pivotal role in host development and lifelong health. Maternal factors are increasingly recognized as crucial in shaping offspring microbiome. However, how maternal preconception perturbations affects offspring health remain unclear. Thus, we combined animal and clinical data to elucidate whether preconception microbial perturbations disrupt microbial succession and increase offspring susceptibility to colitis. In animals, preconception antibiotic exposure induced long-lasting disruptions in offspring microbial ecology, through enhanced maternal-offspring microbial transmission, altered microbial developmental trajectories, and increased selective pressures during microbial community assembly. Ultimately, these alterations resulted in persistent gut mucosal immaturity and heightened susceptibility to colitis in adulthood. Complementary clinical studies revealed concordant alterations in gut microbiome and metabolome of children with inflammatory bowel disease (IBD) and their seemingly healthy mothers, characterized by pro-inflammatory taxa and metabolites. Notably, mothers of IBD children reported significantly higher antibiotic exposure than controls, which was also associated with enhanced maternal-offspring microbial transmission and increased selective pressures during microbial community assembly. Our findings reveal a potential intergenerational mechanism in which preconception perturbations are associated with disrupted microbial succession, transgenerational propagation of gut mucosal immaturity, and susceptibility to colitis. These results underscore the importance of judicious antibiotic use during the often-overlooked preconception period.},
}

@article {pmid41929694,
year = {2026},
author = {Srivastava, A and Kim, M and Lee, SA and Yun, JH},
title = {Editorial: Microalgae-microbe interactions: advances and applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1815619},
doi = {10.3389/fmicb.2026.1815619},
pmid = {41929694},
issn = {1664-302X},
}

@article {pmid41923642,
year = {2026},
author = {Gallego-Del-Sol, F and Sin, D and Chmielowska, C and Mancheño-Bonillo, J and Li, Y and Zamora-Caballero, S and Quiles-Puchalt, N and Penadés, JR and Marina, A},
title = {Phages communicate across species to shape microbial ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.004},
pmid = {41923642},
issn = {1097-4172},
abstract = {Arbitrium is a communication system that helps bacteriophages to decide between lysis and lysogeny through secreted peptides. In this system, the arbitrium communication peptide (AimP) binds its cognate arbitrium receptor (AimR) to repress aimX (a negative regulator of lysogeny) expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we challenge this view by demonstrating cross-communication between arbitrium systems. Using prototypical arbitrium phages, we show that AimP peptides can bind and repress non-cognate AimR receptors, promoting lysogeny and reducing prophage induction. Structural and biochemical analyses reveal conserved receptor features that permit cross-recognition of non-cognate peptides while preserving recognition of cognate partners. In mixed lysogenic cultures, these interactions alter induction outcomes, underscoring their ecological significance. Extending to infection contexts, we demonstrate that crosstalk favors lysogeny of incoming phages in cells harboring compatible systems. These findings establish that phages engage in cross-species communication via peptide signaling, reshaping microbial communities in unexpected ways.},
}

@article {pmid41924123,
year = {2026},
author = {Grinshpan, I and Lavy, O and Zorea, A and Amit, I and Levin, L and Furman, O and Somekh, D and Guevara, N and Moraïs, S and Cordero, OX and Mizrahi, I},
title = {Endemic within endemics: the microbiota of the Galapagos marine iguanas.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag040},
pmid = {41924123},
issn = {2730-6151},
abstract = {The ecological processes shaping host-associated microbial communities in geographically isolated ecosystems remain poorly understood-particularly the interplay between dispersal, selection, and microbial speciation. Here, we characterize the fecal microbiota of the Galápagos marine iguana (Amblyrhynchus cristatus), an iconic endemic vertebrate that depends on its microbiota to digest an algae-based diet. We analyzed fecal samples from 111 individuals across three remote colonies and found that fecal microbial composition is dominated by Clostridia, closely following a neutral dispersal model. Yet, ecological and phylogenetic analyses revealed novel, host-restricted Clostridia clades-spanning species to family level-that appear to have diversified within marine iguanas. These lineages are consistently retained across host populations through strong purifying selection, resulting in striking microbiota homogenization. Our findings demonstrate that endemic hosts can support microbially distinct lineages shaped by stochastic dispersal and parallel selection, advancing our understanding of microbial community assembly in obligate host-microbiota systems.},
}

@article {pmid41925447,
year = {2026},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {The rhizosphere microbiome as a decentralized immune system.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.006},
pmid = {41925447},
issn = {1878-4380},
abstract = {Plant immunity should be reconsidered beyond the boundaries of the plant genome. We propose that the rhizosphere microbiome may function analogously to a decentralized immune system, contributing adaptive defenselike properties and memory effects. In this forum article, we discuss how this perspective reframes immunity as an emergent property of plant-microbiome interactions, shifting the focus from a solitary host toward an integrated holobiont.},
}

@article {pmid41742154,
year = {2026},
author = {Ullah, H and Selvarajan, R and Lau Vetter, MCY},
title = {Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {41742154},
issn = {1475-2859},
support = {Scholarship//Alliance of International Science Organizations/ ; IDSSE-SJBS-202501//Institute of Deep-sea Science and Engineering/ ; Y970011001//Knowledge Innovation Program of Chinese Academy of Sciences/ ; E2500001//Hainan Provincial Talent Development Bureau/ ; },
abstract = {UNLABELLED: Biosurfactants produced by microorganisms play essential roles in ecosystem function and hold significance promise for biotechnological applications. However, their diversity and distribution remain poorly depicted due to the limitations of culture-based approaches. In this study, we conducted a large-scale genomic data mining of 142,135 microbial genomes of putative biosurfactant-producing taxa, spanning 21 distinct ecosystems, to systematically profile gene association with 10 major biosurfactant classes. Using a list of 18 key functional genes, we mapped their taxonomic and ecological distribution and analyzed patterns of gene co-occurrence. We found that rhamnolipid biosynthesis genes are nearly ubiquitous across microbial lineages, reflecting their fundamental role in microbial adaptation. In contrast, emulsan and serrawettin pathways are more restricted to plant-associated and fungal ecosystems. The highest diversity of biosurfactant-related genes was found in genomes recovered from nutrient-rich habitats, including plant-associated, algal, and wastewater ecosystems. Co-occurrence network analysis revealed two distinct organizational strategies: a rare, conserved core cluster of genes associated with fengycin, surfactin, iturin lichenysin and plipastatin production, and a widespread, modular periphery linked to rhamnolipid, emulsan, and serrawettin W1 pathways, that are likely driven by the need to adapt to environmental complexity. Notably, we identified previously unreported genomes with biosurfactant production potential, significantly expanding the known biodiversity and ecological range of potential producers. Our findings establish biosurfactant production as a key microbial trait shaped by habitat, with broad implications for microbial ecology, ecosystem monitoring and sustainable biotechnology. This work provides comprehensive genomic resource for biosurfactant research, laying the foundation for targeted bioprospecting and integrative functional studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-026-02932-z.},
}

@article {pmid41916728,
year = {2026},
author = {Henry, GBL and Tremblay, J and Stenuit, BA and Gerin, PA},
title = {Microbial Ecology of Mixotrophic Chain Elongation: Megasphaera spp. as Drivers of Medium-Chain Carboxylate Production From H2, CO2, and Carboxylates.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70287},
doi = {10.1111/1462-2920.70287},
pmid = {41916728},
issn = {1462-2920},
support = {SPW-DGO3-D65-1454//Service Public de Wallonie/ ; SPW-DGO3-D31-1397//Service Public de Wallonie/ ; 2019-BRIDGE-4D//Région de Bruxelles-Capitale/ ; //European Regional Development Fund/ ; },
mesh = {*Carbon Dioxide/metabolism ; *Hydrogen/metabolism ; *Carboxylic Acids/metabolism ; Fermentation ; Bioreactors/microbiology ; Clostridium/metabolism ; },
abstract = {The production of medium-chain carboxylates (MCC) by mixed culture fermentation of complex organic feedstocks is often constrained by the availability of reducing equivalents. Therefore, mixotrophic fermentation processes, which integrate diverse carbon and reducing equivalents sources, are gaining more attention. However, the microbial communities evolving in such complex environments, where organic and inorganic substrates interact, remain insufficiently understood. To identify the key microorganisms involved in mixotrophic MCC production, two bioreactors were initially fed with brewer's spent grain as organic feedstock and supplemented daily with H2 and CO2 as inorganic substrates. Time-course analyses of net metabolite production rates and microbial community composition identified Megasphaera spp. (likely M. elsdenii and M. hexanoica) as the main chain elongators in the system. The results suggest that these Megasphaera species metabolize short-chain carboxylates, H2 and CO2, with potential cross-feeding interactions with acetogens (likely Clostridium ljungdahlii and Clostridium luticellarii). The homoacetogenic acetate produced is subsequently elongated, likely by Megasphaera species, using H2 and CO2 as electron and carbon sources for production of elongated carboxylates. This study paves the way for the development of MCC production strategies that integrate organic waste valorization with direct CO2 utilization, using H2 as an electron donor, a process that aligns with low-carbon-footprint technologies.},
}

*Carbon Dioxide/metabolism
*Hydrogen/metabolism
*Carboxylic Acids/metabolism
Fermentation
Bioreactors/microbiology
Clostridium/metabolism

@article {pmid41919917,
year = {2026},
author = {Mall, A and Rode, KJ and Marx, CJ},
title = {Evolution uncovers a general tradeoff between recovery after heat shock and growth at elevated temperatures.},
journal = {mBio},
volume = {},
number = {},
pages = {e0330525},
doi = {10.1128/mbio.03305-25},
pmid = {41919917},
issn = {2150-7511},
abstract = {Fitness tradeoffs between different environments enable the maintenance of microbial diversity. While the importance of tradeoffs is clear, it has been surprisingly difficult to predict which traits they will occur between and at how granular a level. For example, it is unclear whether performance between a constant versus pulsed exposure of the same stress tends to be positively correlated, independent of each other, or negatively correlated. Empirically, it has been shown that a critical feature structuring microbial communities is temperature. However, the compatibility between strategies to deal with different forms of heat stress is unclear. For instance, are strains that grow well at higher temperatures also stronger at withstanding heat shock? To understand how environmental microbes can adapt to better deal with heat stress, we performed an evolution experiment using a dominant phyllosphere microbe Methylobacterium extorquens in a regime of intermittent heat shock. We identified the genetic basis of adaptation, discovering a large number of loci capable of mediating adaptation to heat shock, many of which had not been previously linked to heat stress. Despite the genetic divergence among evolved isolates, we discovered a general tradeoff between heat shock resistance and growth at consistently elevated temperatures. We found this tradeoff was not limited to evolved isolates, but also represented across a sample of environmentally isolated Methylobacterium strains. These findings indicate a generic conflict between strategies to deal with heat shock recovery and growth at elevated temperatures, suggesting even variation in intensities of a stressor can drive diversity in microbial strategies.IMPORTANCEOne of the key forces shaping the microbial diversity in nature is temperature. However, temperature in ecological settings is variable, and it is unknown if strategies to deal with different intensities of high temperature are compatible or not. Using evolution experiments, we identify the genetic basis of adaptation to heat shock in Methylobacterium extorquens, a dominant member of the phyllosphere microbiome. We discover a number of genetic targets where beneficial mutations improve heat shock resistance, most of which have not been implicated with heat stress before. For both the evolved isolates and a set of environmentally isolated Methylobacterium strains, we discover a general tradeoff between recovery after heat shock and growth at elevated temperatures. While the strategies to deal with increasing temperatures have garnered significant interest, our results suggest that even different intensities of heat stress can select for distinct and incompatible strategies and can drive microbial diversification in ecological settings.},
}

@article {pmid41920852,
year = {2026},
author = {Kim, H and Kim, S and Kimbrel, JA and Morris, MM and Mayali, X and Buie, CR},
title = {Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014102},
doi = {10.1371/journal.pcbi.1014102},
pmid = {41920852},
issn = {1553-7358},
abstract = {Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination method, "F-informed MDS," which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community's response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.},
}

@article {pmid41922370,
year = {2026},
author = {López-Gálvez, J and Schönfelder, E and Mayer, H and Schiessl, K and Silva, MOD and Harms, H and Müller, S},
title = {A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors.},
journal = {NPJ systems biology and applications},
volume = {12},
number = {1},
pages = {},
pmid = {41922370},
issn = {2056-7189},
support = {No 101000733//Horizon 2020/ ; },
mesh = {*Flow Cytometry/methods ; *Bioreactors/microbiology ; *Staining and Labeling/methods ; Escherichia coli/growth & development ; *Bacteria/growth & development ; },
abstract = {In biotechnological processes, cell density and physiology are critical parameters for controlling the feed rate, harvest time, and process performance. We developed an automated flow cytometry approach that enables continuous, real-time (fully automated, hourly) monitoring of bacterial populations in continuous bioreactors. The method employed a double-staining protocol that combined DAPI to assess total DNA content and Alexa Fluor 488-EdU via Click-iT technology to identify the proportions of cells undergoing active DNA replication through EdU incorporation. The integrated workflow included fixation, permeabilization, staining, and measurement steps and was applied to three Gram-negative strains: Bradyrhizobium sp., Escherichia coli, and Stenotrophomonas rhizophila. Automated analysis captured growth dynamics and cell cycle progression, providing insights into population behavior under different dilution rates. In this study, automated on-line sampling enabled hourly flow cytometry measurements of cell concentration and physiological indicators during continuous cultivation, supporting real-time monitoring and control in industrial biotechnology.},
}

*Flow Cytometry/methods
*Bioreactors/microbiology
*Staining and Labeling/methods
Escherichia coli/growth & development
*Bacteria/growth & development

@article {pmid41922553,
year = {2026},
author = {Cloud, RE and Irwin, P and Muturi, EJ and Cáceres, CE},
title = {Characterizing the Microbiome and Prevalence of Wolbachia in Culex pipiens Complex and Culex restuans Mosquitoes in the Midwest United States.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02750-1},
pmid = {41922553},
issn = {1432-184X},
support = {DEB - 1754115//National Science Foundation/ ; DEB - 1754115//National Science Foundation/ ; DBI - 2022049//Genomics and Eco-evolution of Multi-scale Symbioses Institute/ ; },
}

@article {pmid41914961,
year = {2026},
author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W},
title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258725},
doi = {10.1128/spectrum.02587-25},
pmid = {41914961},
issn = {2165-0497},
abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.},
}

@article {pmid41915129,
year = {2026},
author = {Kang, L and Dumack, K},
title = {Protistan Predators Outshine Fungi in Forest Soil Activity.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {3},
pages = {e70072},
pmid = {41915129},
issn = {1550-7408},
support = {2023-57678375//China Scholarship Council - Deutscher Akademischer Austauschdienst (CSC - DAAD)/ ; 24JK0749//Shaanxi Provincial Department of Education/ ; 2023GK84//Yulin University/ ; 2024XZGY05//Yulin University/ ; 20250710//Yulin University/ ; },
mesh = {Forests ; *Soil Microbiology ; *Fungi/genetics/classification/physiology/isolation & purification ; *Soil/chemistry/parasitology ; Biodiversity ; *Eukaryota/classification/genetics ; Spain ; Ecosystem ; Canada ; France ; Sweden ; },
abstract = {Despite extensive research on fungal communities in forest soils, our understanding of the whole eukaryotic diversity and distribution remains limited. Moreover, traditional amplicon sequencing methods often introduce severe PCR and primer biases, further hindering accurate assessment of the microbial community composition in forest soils. To address these challenges, this study used a public metatranscriptomic data set to analyze 51 forest soil samples comprising four countries (Canada, France, Spain, and Sweden). Our results reveal that Arcellinida, a eukaryotic order of shell-bearing amoebae, represent the most abundant eukaryotic taxon in forest soils, with an average relative abundance of 12.6%. This finding challenges the conventional view that fungi dominate eukaryotic diversity in these ecosystems. Furthermore, our study demonstrates that Arcellinida (R[2] = 0.066, p = 0.006) and soil pH (R[2] = 0.126, p < 0.001) are key biological and environmental drivers, respectively, shaping the composition of eukaryotic communities in forest soils, suggesting distinct impact on the microbial community through predation. These findings offer novel insights into the ecological significance of microbial eukaryotes in forest ecosystems and provide a new framework for investigating the predatory dynamics centered on Arcellinida in forest soil microbial networks.},
}

Forests
*Soil Microbiology
*Fungi/genetics/classification/physiology/isolation & purification
*Soil/chemistry/parasitology
Biodiversity
*Eukaryota/classification/genetics
Spain
Ecosystem
Canada
France
Sweden

@article {pmid41915160,
year = {2026},
author = {Kou, C and Li, D and Liu, Z and Gao, W and Zhang, W and Xiong, L and He, L and Li, M and Shu, A and Ma, J and Gao, Z},
title = {Correction to: Rare Microbial Taxa Dominate the Microecological Landscape of Cadmium Exposure in Rice Rhizosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
doi = {10.1007/s00248-026-02737-y},
pmid = {41915160},
issn = {1432-184X},
}

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02730-5},
pmid = {41915167},
issn = {1432-184X},
}

@article {pmid41910204,
year = {2026},
author = {Green, L and Marchesani, A and Joyner, JL},
title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag084},
pmid = {41910204},
issn = {1365-2672},
abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.

METHODS & RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.

CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.},
}

@article {pmid41910273,
year = {2026},
author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P},
title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0179025},
doi = {10.1128/msystems.01790-25},
pmid = {41910273},
issn = {2379-5077},
abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.

IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.},
}

@article {pmid41910276,
year = {2026},
author = {Woodruff, GC and Moser, KA and Wang, J},
title = {The bacteria of a fig community.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301324},
doi = {10.1128/spectrum.03013-24},
pmid = {41910276},
issn = {2165-0497},
abstract = {Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach toward tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata, such as foundress wasp number and nematode occupancy, were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 2,000 ASVs were detected, and microbial communities were dominated by members of Proteobacteria, Bacteroidota, and Actinobacteriota. Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. A joint analysis of fig and previously published C. elegans substrate microbiomes revealed similarities and differences among the biotic environments of these nematode sister species. Fig microbial community composition was driven in large part by variation among individual plants. Conversely, nematodes had no detectable impact on microbial community composition or alpha diversity. A handful of ASVs (associated with the genera Ochrobactrum and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.IMPORTANCEUnraveling why different species live in different places is a longstanding open question in ecology. It is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata, a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Additionally, microbial diversity is driven in large part by individual plant of origin. Likewise, we found that nematode occupancy does not appear to impact microbial composition. Moreover, we show that as the number of foundress wasps increases, the microbial α-diversity decreases. Finally, we identified ASVs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a community wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.},
}

@article {pmid41910755,
year = {2026},
author = {Liu, L and Zhao, X and Wang, X and Zhao, Y and Luo, P and Sun, C and Li, W and Zhu, J and Fan, G and Ying, Y and Zhang, J and Xu, Q and Mu, X},
title = {Dynamics of Micro-Diatoms in the Austral Autumn/Winter Reveal Ecological Strategies in the Northern End of the Antarctic Peninsula.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02748-9},
pmid = {41910755},
issn = {1432-184X},
support = {42306259//the National Natural Science Foundation of China/ ; 2022YFC2807504//National Key Research and Development Program of China/ ; 2025TD02//the Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences, China/ ; },
}

@article {pmid41912631,
year = {2026},
author = {Liu, L and Liu, Y and Tang, S and Zhang, B and Zhong, Y and Liu, D and Zhou, J and Cai, Z},
title = {The coexistence of r and K strategy in a unicellular microalga Haematococcus lacustris.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09922-2},
pmid = {41912631},
issn = {2399-3642},
abstract = {Understanding how organisms balance growth and defence is a general goal in biology. r (high reproductivity but stress-sensitive offspring) and K (low reproductivity but high stress-resistant offspring) selection are two classical life history strategy theories. Contrary to the common belief that an organism can only be classified as either r or K strategist, by integrating physiological, microscopic and transcriptomic data, we present experimental evidence for the coexistence of both strategies in the unicellular microalga Haematococcus lacustris. Under standard conditions, swimming vegetative cells (SVCs) normally grow and reproduce via binary fission (r strategy) and gradually transform into non-swimming cells (NSCs) over time. Intriguingly, unlike the prevailing notion that NSCs cannot propagate, they are found to reproduce via multiple fission at a barely detectable growth rate, resulting in stress-resistant, non_mobile daughter cells, demonstrating a complete life history (thus are defined as K strategy). Collectively, our findings suggest that H. lacustris adopts both r and K strategies, enhancing the understanding of the adaptation and survival of microbial populations in challenging environments.},
}

@article {pmid41914631,
year = {2026},
author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS},
title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219825},
doi = {10.1128/spectrum.02198-25},
pmid = {41914631},
issn = {2165-0497},
abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.},
}

@article {pmid41914732,
year = {2026},
author = {Pasman, R and Krom, BP and Zhang, J and Brul, S and Zaat, SAJ},
title = {Secreted factors of Staphylococcus aureus promote co-invasion with Candida albicans by inducing hypha formation and invasion.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0196125},
doi = {10.1128/aem.01961-25},
pmid = {41914732},
issn = {1098-5336},
abstract = {Interkingdom interactions between Candida albicans and Staphylococcus aureus promote lethal dissemination of the bacterium. During this process, C. albicans hypha invasion aids S. aureus dissemination through Als1p/Als3p-facilitated co-invasion. The effects of S. aureus on C. albicans hypha formation and invasion are, however, unknown. In this study, we used both liquid mDMEM-DMP as well as a previously constructed semi-solid adaptation of the medium (mDMEM-DMPA) to study the effects of C. albicans/S. aureus co-culturing on hypha formation and invasion. Semi-solid-based co-culturing significantly increased colony size and generally increased hypha invasion. Liquid growth-based time-lapse microscopy showed that S. aureus significantly promoted both C. albicans hypha length and elongation rate. Further semi-solid-based growth results revealed that >3 kDa-secreted S. aureus factors were accountable for the increase in C. albicans hypha growth. A newly constructed in vitro assay confirmed the co-invasion of S. aureus during co-culturing and showed that deletion of C. albicans Als1p/Als3p abolished the co-invasion of S. aureus during co-culturing. In conclusion, our study shows that S. aureus affects C. albicans virulence by actively stimulating C. albicans hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to co-invade. Therefore, S. aureus can stimulate C. albicans epithelial invasion even prior to attaching to its hyphae, providing the foundation for subsequent co-invasion.IMPORTANCEEpithelial barriers normally protect against invasion and systemic infection by S. aureus, but frequently, such infections occur without a port of entry. One route of S. aureus epithelial traversal is through co-invasion with the highly invasive Candida albicans. Understanding this interaction in detail is of high importance in view of the prevention of these infections. Our study shows how the S. aureus and C. albicans interaction results in mutual benefit. S. aureus appeared to affect C. albicans virulence by actively stimulating C. albicans hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to bind to the hyphae and co-invade. These insights are important from a microbial ecological perspective and offer important potential targets for interfering with the interaction and reducing the virulence of these opportunistic pathogens.},
}

@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}

@article {pmid41847008,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR},
title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41847008},
issn = {2692-8205},
abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA), which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.},
}

@article {pmid41902972,
year = {2026},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S},
title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02712-7},
pmid = {41902972},
issn = {1432-184X},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; },
}

@article {pmid41903008,
year = {2026},
author = {Heyse, J and Props, R and Defoirdt, T and Boon, N},
title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41903008},
issn = {1573-0972},
support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; },
}

@article {pmid41903868,
year = {2026},
author = {Manfredonia, I and Chioso, L and Mateescu, I and Konu, M and Brons, JK and Deelman-Driessen, C and Viljakainen, L and Wertheim, B and Lequime, S},
title = {Prevalence and distribution of two polycipiviruses in wild black garden ants (Lasius niger L.) in the Netherlands.},
journal = {Journal of invertebrate pathology},
volume = {217},
number = {},
pages = {108611},
doi = {10.1016/j.jip.2026.108611},
pmid = {41903868},
issn = {1096-0805},
abstract = {Metagenomic studies have revealed diverse viruses in insects. Yet, our understanding of the ecology of insect viruses, especially in ants, remains limited, despite the insects' ecological importance. Viruses of the family Polycipiviridae are increasingly recognized as widespread yet poorly characterized components of ant viromes. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria. In the Netherlands, LniV-1 was detected in 17.5% of colonies, whereas MsaV-1 was detected in 27.5%, including evidence of co-infection at the colony level. Neither the geographical distribution of infected colonies nor the inferred phylogenies for both viruses showed strong geographic structuring. The prevalence in workers within colonies was variable, ranging from 10 to 60%. These findings suggest that polycipiviruses are common in natural L. niger populations and may transmit via both horizontal and vertical routes. This study provides baseline data on ant-virus interactions in natural environments, advancing understanding of viral ecology in social insects and informing future research on virus transmission dynamics in natural ecosystems.},
}

@article {pmid41904277,
year = {2026},
author = {M Davidson, I and Nikbakht, E and M O'Neill, H and Haupt, LM and Dunn, PJ},
title = {Shaping the Female Microbiome: A Review of Lifestyle Factors Influencing the Vaginal, Gut, Oral, and Skin Microenvironments.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02747-w},
pmid = {41904277},
issn = {1432-184X},
abstract = {The female microbiome, spanning the vaginal, gut, oral, and skin sites, harbours distinct microbial communities. Although the diversity and function of microbial communities across these sites are becoming increasingly understood, the extent to which modifiable lifestyle and environmental factors such as smoking, diet, alcohol intake, obesity, physical activity, stress, hygiene, and sexual behaviours shape these microbiomes remains underexplored. This review is restricted to modifiable lifestyle and environmental factors and does not comprehensively assess pharmaceutical exposures (e.g., antibiotics or hormonal therapies) or hormonal influence. To date, no review has comprehensively assessed and compiled evidence across the four microbial sites in females, despite their unique hormonal, physiological, and reproductive characteristics that distinctly influence microbial composition and function. This review provides a comprehensive examination of how such factors influence the dynamics of microbial composition and function along with site-specificity while also assessing cross-site microbial interactions. We focus exclusively on females to address a critical knowledge gap to provide a foundation from which future research and interventions can be tailored to women's health. This review discusses the underlying mechanisms driving microbial shifts and their impact on host health, highlighting critical gaps in our current knowledge. The integration of findings from multi-site microbiome research, highlights the potential to inform targeted, preventative, and therapeutic strategies that utilise the inherent dynamic nature of the microbiome to improve health outcomes across the female lifespan.},
}

@article {pmid41904356,
year = {2026},
author = {Vojtkuf, I and Čačković, A and Soares, AR and Probst, AJ and Orlić, S},
title = {Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02743-0},
pmid = {41904356},
issn = {1432-184X},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; },
}

@article {pmid41908552,
year = {2026},
author = {Yu, N and Pang, S and Li, Y and Diao, H},
title = {Integrated microbiome-metabolome analysis reveals multiorgan toxicity of 1-nitropyrene and the limited efficacy of ferroptosis inhibitor Fer-1 in rats.},
journal = {Frontiers in toxicology},
volume = {8},
number = {},
pages = {1771766},
pmid = {41908552},
issn = {2673-3080},
abstract = {INTRODUCTION: 1-Nitropyrene (1-NP), a prevalent nitro-polycyclic aromatic hydrocarbon, is increasingly recognized as a potential metabolic disruptor, yet its systemic biological effects remain insufficiently characterized.

METHODS: This study investigated the metabolic, immunological, hepatic, and microbiome alterations induced by chronic 1-NP exposure in rats and assessed whether ferroptosis inhibition via Fer-1 could mitigate these effects.

RESULTS: Although body weight was not significantly altered overall, high-dose exposure impaired growth from week 4. Exposed groups exhibited progressively elevated fasting blood glucose and impaired glucose tolerance, indicating significant disruption of glucose homeostasis. Serum biochemistry revealed dose-dependent reductions in HDL and total cholesterol, while histopathology confirmed hepatocyte ballooning, inflammation, and steatosis consistent with NAFLD-like progression. Hematological changes, including shifts in neutrophil and lymphocyte populations, suggested chronic inflammatory activation. Untargeted metabolomics identified extensive alterations in pathways related to glycolysis, tryptophan metabolism, glycerophospholipid metabolism, and ABC transporters. Gut microbiota analysis demonstrated reduced richness and significant compositional shifts, with functional predictions linking dysbiosis to xenobiotic degradation, lipid metabolism, and phosphotransferase systems. Integrated microbiome-metabolome analysis revealed coordinated disruptions in host-microbial metabolic networks. Fer-1 intervention modified specific metabolic and microbial signatures but did not substantially alleviate major toxic outcomes.

CONCLUSION: Overall, chronic 1-NP exposure causes widespread metabolic injury driven by combined effects on host metabolism, immune regulation, hepatic function, and gut microbial ecology. These findings highlight 1-NP as a potent environmental metabolic disruptor and underscore the need for further mechanistic studies to inform mitigation strategies.},
}

@article {pmid41909255,
year = {2026},
author = {Sai, LO and Zhu, X and Lipson, DA and Xu, X},
title = {Spatial biogeography of microbes in soils vs. aquatic ecosystems in U.S.'s major natural biomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752205},
pmid = {41909255},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial macroecology has gained recognition as a critical component of microbial ecology. Using data from the National Ecological Observatory Network (NEON), this study examined the spatial patterns of microbial abundance and their environmental controls in soil and aquatic ecosystems across major natural biomes in the United States.

METHODS: Microbial cell density in aquatic ecosystems and soil microbial biomass carbon in terrestrial ecosystems were analyzed, and their relationships with environmental variables were evaluated using correlation analyses.

RESULTS: In aquatic ecosystems, microbial cell density ranged from 1.8 × 10 5 to 4.1 × 10 6 cells mL[-1] and was positively associated with specific conductance (r = 0.32, p < 0.01) and water temperature (r = 0.19, p = 0.03), but negatively associated with dissolved oxygen (r = -0.21, p = 0.01). Across all locations, the cell density averaged approximately 1.4 × 10 6 cells mL[-1]. In terrestrial ecosystems, soil microbial biomass carbon ranged from 27 to 2.5 × 10 4 μg C g[-1] dry soil and was positively correlated with soil moisture (r = 0.57, p < 0.01), soil carbon content (r = 0.67, p < 0.01), and soil nitrogen content (r = 0.66, p < 0.01). It was negatively associated with soil temperature (r = -0.42, p < 0.01) and soil pH (r = -0.42, p < 0.01). Across all locations, the microbial biomass carbon averaged approximately 2.9 × 10 3 μg C g[-1]. Bacteria were dominant across both aquatic and terrestrial environments, ranging from 28% to 88%, while Eukarya ranged from 0% to 48%. Archaea made a minor contribution to the microbial community across all sites. Unclassified microbes varied across the United States, ranging from less than 1% at the Lower Tombigbee River in southwest Alabama to 57% at Sycamore Creek in Arizona.

DISCUSSION: In aquatic systems, cell density increased with specific conductance and water temperature but decreased where dissolved oxygen was high. In terrestrial ecosystems, biomass was higher in soils with greater soil nitrogen content, soil carbon content, and moisture, indicating that nutrient-rich and humid environments favored microbial growth. In contrast, abundances declined in warmer and more alkaline soils. These biogeographic patterns show divergent environmental factors driving microbial abundance in various ecosystems, reflecting high microbial adaptation to surrounding physical and chemical conditions.},
}

@article {pmid41909260,
year = {2026},
author = {Wang, XL and Zhang, C and Lu, DS and Dong, ZY and Jin, BM and Wan, SY and Zhang, ZW and Zhang, CJ and Li, L},
title = {Paeoniflorin protects against NAFLD through antioxidant, anti-inflammatory effects and restoration of gut microbiota homeostasis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1766068},
pmid = {41909260},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a widespread chronic metabolic disorder characterized by hepatic lipid accumulation, oxidative stress, inflammation and gut dysbiosis. Paeoniflorin (PAF) exhibits potential against NAFLD, yet its antioxidant mechanism via the gut-liver axis remains unclear. In a high-fat/sucrose (HFS) diet-induced NAFLD mouse model, C57BL/6 mice received PAF (50 or 100 mg/kg/day) for 10 weeks. Oxidative stress markers, histopathology, gut microbiota, and serum metabolomics were conducted, with fecal microbiota transplantation (FMT) applied for causal validation. PAF ameliorated metabolic disorders by suppressing hepatic lipogenesis and promoting cholesterol excretion. PAF significantly ameliorated oxidative stress by enhancing hepatic and colonic anti-oxidant capacity, evidenced by increased SOD activity and decreased MDA levels. It concurrently reduced systemic inflammation and enhanced intestinal barrier integrity via upregulation of tight junction proteins. Furthermore, PAF reshaped the gut microbiota, elevating beneficial Akkermansia and microbial-derived SCFAs, while suppressing pro-oxidant and pro-inflammatory pathogens like Desulfovibrio and Helicobacter. FMT confirmed that these antioxidant and metabolic benefits were mediated by the gut microbiota. In conclusion, PAF alleviates NAFLD primarily through potent antioxidant actions and anti-inflammatory, achieved via remodeling gut microbial ecology and reinforcing intestinal barrier.},
}

@article {pmid41900402,
year = {2026},
author = {Mokrani, S and Benouguef, Z and Houali, K and Bensidhoum, L and Derguini, A and Ibrahim, NA and Basher, NS and Nabti, EH},
title = {Resistance Mechanisms of Rhizospheric Bacillus and Pseudomonas Strains Against Heavy Metal Contamination (Cu, Cr and Cd) and Their Antifungal Properties.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
pmid = {41900402},
issn = {2076-2607},
support = {IMSIU-DDRSP2601//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Environmental pollution caused by persistent chemical compounds, particularly heavy metals, poses a significant global challenge. Current strategies focus on eco-friendly and sustainable approaches, such as the application of microorganisms, to mitigate this issue. In this study, four strains of Bacillus and Pseudomonas were phylogenetically identified and assessed for their resistance to three heavy metals: copper (Cu), chromium (Cr), and cadmium (Cd) up to 500 µg/mL. Various tolerance mechanisms related to heavy metal resistance were elucidated, including salinity tolerance, antibiotic resistance, production of exopolysaccharides (EPS), and biosurfactant synthesis. The antifungal activities of these strains were evaluated against the fungal isolates Fusarium oxysporum fs. phaseoli (Fop) and Stemphylium botryosum (St-bt) using dual culture assays. Phylogenetic analysis revealed that three strains belong to the genus Bacillus, while one strain is classified under Pseudomonas. Additionally, these strains exhibited diverse mechanisms for heavy metal tolerance, including salinity tolerance (up to 600 mM), multi-antibiotic resistance (to imipenem, ampicillin, and sodium fusidate), and the production of viscous, slimy colonies indicative of EPS synthesis. Biosurfactant production led to a significant reduction in surface tension, ranging from 10.51 ± 3.87% to 82.89 ± 5.01%. The antifungal assays demonstrated that the strains effectively inhibited the mycelial growth of the fungal isolates, with inhibition percentages varying from 0% to 83.34 ± 2.22%. The strains characterized in this study exhibit considerable potential for application in the bioremediation of metal-contaminated soils and as biocontrol agents.},
}

@article {pmid41900653,
year = {2026},
author = {Constantin, CE and Holban, AM and Iordache, F and Curutiu, C},
title = {Antimicrobial Nanomaterials in the Food Industry: Applications in Meat Packaging.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {6},
pages = {},
pmid = {41900653},
issn = {1996-1944},
abstract = {A thorough understanding of the microbial ecology of meat products, dominated by critical pathogens such as Salmonella spp., Campylobacter jejuni, Escherichia coli, and Listeria monocytogenes, and marked by risks of resistant biofilm formation and vulnerabilities specific to informal commercial sectors, underscores the need to transition from conventional inert barriers to active nanostructured packaging systems. This review critically analyses the current state of antimicrobial nanomaterials, dissecting their molecular mechanisms of action and dynamic interactions designed to preserve sensory and nutritional food quality. Beyond technical effectiveness, the paper highlights the inherent tension between technological innovation and toxicological uncertainties, addressing major challenges related to migration kinetics in complex lipid matrices and the uneven global regulatory landscape. Main limitations of frequently investigated materials, along with regulatory discrepancies among international authorities and safety variables, are discussed to contextualise the current barriers to industrial implementation. We conclude that although nanotechnology represents a transformative force for extending shelf life, safety validation through rigorous assessment of migration remains imperative to harmonise scientific progress with public health protection. This integrative perspective highlights the imperative of calibrating nanostructural architecture to the bioactive profile, providing strategic design directions essential for the sustainable translation of experimental innovation to industrial scale.},
}

@article {pmid41900772,
year = {2026},
author = {Karimian Azari, E and Govaert, M and Duysburgh, C and Glab, S and Marzorati, M and Saiyed, Z},
title = {Evaluation of Targeted-Release Capsule Formulations for Protection of the Acid-Sensitive Enzyme Pancreatin Under Fasted and Fed Intestinal Conditions In Vitro.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900772},
issn = {1999-4923},
support = {N/A//Lonza Capsules & Health Ingredients/ ; },
abstract = {Objective: This study assessed the ability of capsule formulations to improve the oral delivery and retain activity of an acid-sensitive enzyme during gastrointestinal transit. Methods: The dissolution characteristics of five capsule formulations-single DRcaps[®] [DR], single Vcaps[®] Plus [VCP], and three DUOCAP[®] capsule-in-capsule combinations, DRcaps[®] inside DRcaps[®] (DR-in-DR), DRcaps[®] inside Vcaps[®] Plus (DR-in-VCP), and Vcaps[®] Plus inside DRcaps[®] (VCP-in-DR)-were evaluated in an in vitro simulation of a healthy human upper gastrointestinal tract under fasting and fed conditions using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME)[®] platform. Capsules contained caffeine as a marker of capsule dissolution, and pancreatin as an active ingredient for which activity was determined by the conversion of tributyrin. Readouts included visual capsule scoring, the analysis of caffeine release, and the quantification of tributyrin-to-butyrate conversion at the end of each gastrointestinal tract segment. Results: The single VCP capsules had a high level of caffeine release at the end of the stomach incubation with low butyrate recovery (16-21%), suggesting the rapid release and gastric degradation of the unprotected enzyme. The single DR, DR-in-VCP, and VCP-in-DR formulations showed caffeine release at the end of the duodenum and/or jejunum and had high butyrate recovery, ranging from 53% to 87%. The DR-in-DR formulation had the most delayed release, with incomplete caffeine release and low-to-moderate butyrate recovery (10-36%). Conclusions: Fast capsule dissolution led to the reduced enzymatic activity of the active ingredient, while delayed dissolution resulted in inadequate time for the enzymatic conversion of tributyrin to butyrate. These results highlight that capsule selection should align with the intended use and targeted nutrient delivery, with DUOCAP[®] formulations being best suited for small intestinal (VCP-in-DR and DR-in-VCP) and colonic (DR-in-DR) delivery.},
}

@article {pmid41901002,
year = {2026},
author = {Chang, J and Yang, W and Jin, Y and Zhou, Z and Song, Z and Zhao, W and Liang, S and Ma, Y},
title = {Microbial Biosurfactants: A Bridge from Aquatic Environments to Subsurface Oil Recovery: Mechanisms, Challenges, Prospects.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
pmid = {41901002},
issn = {2075-1729},
support = {Study on the Structure of Hydration layers on Clay Mineral Surfaces and the Regulatory Mechanisms of Aggregation-Dispersion Behavior of Fine Mineral Particles//2024 Annual Xi'an University of Science and Technology Excellent Youth Science Foundation Project/ ; },
abstract = {Microbial biosurfactants, derived from diverse aquatic and extreme ecosystems, offer a sustainable and environmentally compatible strategy for enhanced oil recovery by fundamentally altering subsurface rock wettability. These biologically produced amphiphiles can efficiently transform oil-wet rock surfaces into water-wet states, thereby mobilizing otherwise trapped crude oil. The primary aim of this review is to provide an integrative understanding of how these biomolecules function at the interface between aquatic microbial ecology and subsurface petroleum engineering, with a particular focus on wettability alteration as a key mechanism for enhancing oil recovery. This review surveys major biosurfactant classes-glycolipids, lipopeptides, and polymeric bioemulsifiers-and their core mechanisms, emphasizing their relevance to challenging reservoir conditions such as high temperature and salinity. A detailed assessment is devoted to persistent hurdles such as stability, adsorption onto rock formations, and economic scalability. Future prospects center on three key approaches: advancing synergistic "bio-hybrid" systems that integrate biosurfactants with complementary agents such as biopolymers and nanomaterials; achieving cost-effective production through the valorization of waste feedstocks; and expanding targeted bioprospecting of microbial diversity from extreme aquatic environments. Together, these strategies are reviewed to drive the advancement of robust, green microbial-enhanced oil recovery (MEOR) technologies, charting a course from fundamental insights to field-scale implementation.},
}

@article {pmid41901079,
year = {2026},
author = {Cirio, S and Mantegazza, G and Salerno, C and Guglielmetti, S and Allam, A and Campus, G and Cagetti, MG},
title = {Assessing the Impact of Heyndrickxia coagulans Administered Through Sugar-Free Chewing Gum on Dental Biofilm: A Double-Blind Randomized Controlled Trial.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901079},
issn = {2072-6643},
mesh = {Humans ; *Chewing Gum ; Double-Blind Method ; *Biofilms/drug effects ; Male ; Female ; Adult ; *Dental Plaque/microbiology ; *Probiotics/administration & dosage ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background:Heyndrickxia coagulans has emerged as a candidate for oral health applications, and chewing gum offers a promising delivery method. This study evaluates whether H. coagulans delivered via sugar-free chewing gum can induce detectable changes in plaque microbial ecology. Methods: A randomized, double-blind, placebo-controlled clinical trial was conducted on 52 healthy adults. Participants consumed probiotic or control gum for 4 weeks. Dental plaque was collected at baseline (T0), mid-intervention (T1), end of intervention (T2), and one week post-intervention (T3). qPCR quantified H. coagulans, while 16S rRNA gene profiling assessed microbial diversity and taxonomic composition. Statistical analyses included rank-based difference-in-differences models, Wilcoxon and Mann-Whitney tests, and differential abundance inference based on negative binomial modeling. Results: Forty-four subjects completed the study. In the Intervention group, the strain was detected in 71.4% of participants at T1 and 61.9% at T2, and it persisted in 9.5% at T3. Differential abundance analysis revealed a broad depletion of taxa linked to oral dysbiosis at T2 with partial persistence at T3, along with selective enrichment of beneficial strains. Conclusions:H. coagulans delivered via chewing gum can reach the dental biofilm and induce modest, transient shifts in microbial composition. However, these biofilm ecology findings should be interpreted in the context of clinical outcomes.},
}

Humans
*Chewing Gum
Double-Blind Method
*Biofilms/drug effects
Male
Female
Adult
*Dental Plaque/microbiology
*Probiotics/administration & dosage
Middle Aged
Young Adult
RNA, Ribosomal, 16S/genetics

@article {pmid41889812,
year = {2026},
author = {Leisch, N and Baars, S and Beavis, T and Bertucci, P and Bhickta, C and Bonadonna, M and Brannon, CM and Burgués-Palau, L and Cherek, P and Chevalier, F and Decelle, J and Demulder, M and Dey, G and Dudin, O and Duke, E and Engel, BD and Flaum, E and Flori, S and Gallet, B and Guichard, P and Halavatyi, A and Hamel, V and Jacobovitz, M and Juery, C and Laporte, M and Mattei, S and Mikus, F and Mocaer, K and Moog, K and Olivetta, M and Pavie, M and Pepperkok, R and Perez-Boerema, A and Planat, L and Prakash, M and Pyle, EW and Rhodes, CR and Romero-Brey, I and Ronchi, P and Rosa, H and Ramos, AR and Saint-Donat, C and Schwab, Y and Shah, H and Steyer, AM and Svetlove, A and Toullec, G and Vincent, F and Wiegand, T and Wietrzynski, W and Yee, D and Zwahlen, S},
title = {An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.23.707475},
pmid = {41889812},
issn = {2692-8205},
abstract = {Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand life's diversity in the environment.},
}

@article {pmid41891698,
year = {2026},
author = {Li, Y and Ji, M and Tu, Q},
title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143425},
doi = {10.1128/msystems.01434-25},
pmid = {41891698},
issn = {2379-5077},
abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.},
}

@article {pmid41892593,
year = {2026},
author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A},
title = {Sulfoquinovose degradation by cow rumen microbiota.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag069},
pmid = {41892593},
issn = {1751-7370},
abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.},
}

@article {pmid41895437,
year = {2026},
author = {Rinanda, T and Riani, C and Artarini, A and Sasongko, L},
title = {Exploring the role of gut methanogenic archaea in childhood stunting in Aceh Province, Indonesia.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103040},
doi = {10.1016/j.anaerobe.2026.103040},
pmid = {41895437},
issn = {1095-8274},
abstract = {BACKGROUND: Emerging evidence highlights the critical role of gut microbiota in childhood growth; however, the contribution of methanogenic archaea remains underexplored. In this study, we investigated the involvement of gut methanogens in linear growth impairment by analyzing their abundance, diversity, methanogenesis, and interactions with bacterial short-chain fatty acids (SCFAs) and glucagon-like peptide-1 (GLP-1) levels in stunted versus normal children.

METHODS: This case-control study included 42 children aged 24-59 months from Pidie, Aceh, Indonesia. Gut archaea were profiled through 16S rDNA amplicon sequencing, and mcrA gene expression was measured using quantitative Polymerase Chain Reaction. SCFAs were analyzed using gas chromatography-mass spectrometry, and GLP-1 levels were quantified using immunoassay. The microbial co-occurrence networks were also assessed.

RESULTS: Archaeal 16S rDNA amplicon sequencing revealed a lower abundance of Methanobacteriaceae, particularly Methanobrevibacter, in stunted children, although their presence contributed to greater microbial diversity. Reduced mcrA gene expression in stunted children indicates a decrease in methanogenesis. Although not statistically significant, mcrA gene expression positively correlated with height, SCFA concentrations, and GLP-1 levels. Microbial network analysis revealed a lower density of microbial networks, indicating reduced stability and resilience in stunted children, with Methanobrevibacter playing a substantial role. Notably, Methanobrevibacter exhibited a positive association with Elusimicrobium, a rare human-associated microbe, and a negative correlation with Lachnospiraceae in normal children, indicating unique microbial interactions that may influence metabolic health.

CONCLUSION: Methanogens, particularly Methanobrevibacter, may play a crucial role in shaping gut microbial ecology and supporting metabolic pathways relevant to linear growth during early childhood.},
}

@article {pmid41895935,
year = {2026},
author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T},
title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118849},
doi = {10.1016/j.foodres.2026.118849},
pmid = {41895935},
issn = {1873-7145},
mesh = {Animals ; *Cultured Milk Products/microbiology ; China ; *Metagenomics/methods ; *Lactobacillales/genetics/classification/isolation & purification ; Cattle ; *Milk/microbiology ; *Food Microbiology ; Fermentation ; Geography ; Horses ; },
abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.},
}

Animals
*Cultured Milk Products/microbiology
China
*Metagenomics/methods
*Lactobacillales/genetics/classification/isolation & purification
Cattle
*Milk/microbiology
*Food Microbiology
Fermentation
Geography
Horses

@article {pmid41896360,
year = {2026},
author = {Yang, X and Tang, J and Lai, Z and Dong, Z and Liao, J and Guo, Y and Wang, Z},
title = {Comparative Analysis of Nasal and Cloacal Bacterial Communities in Three Sea Turtle Species under Rescue Center Conditions.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02751-0},
pmid = {41896360},
issn = {1432-184X},
support = {No. 2021B1212110005//Science and Technology Infrastructure Project of Department of Science and Technology of Guangdong Province/ ; },
}

@article {pmid41896556,
year = {2026},
author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O},
title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00941-9},
pmid = {41896556},
issn = {2055-5008},
support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; },
abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.},
}

@article {pmid41896600,
year = {2026},
author = {Lajoinie, DM and Rocco Welsh, R and Rey, C and Nilsson, JF and Toscani, AM and Djurhuus, AM and Sauka, D and Hansen, LH and Jofré, E and Pistorio, M},
title = {Comparative genomics and biocontrol potential of five Bacillus strains isolated from grapevine rhizosphere.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44555-9},
pmid = {41896600},
issn = {2045-2322},
support = {PICT2021-0277//Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina)/ ; PIP2022-0367//Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina)/ ; },
}

@article {pmid41897466,
year = {2026},
author = {Lyu, X and Zhang, L and Si, J and Dai, S and Su, H and Lyu, S and Chen, L and Sun, J and Jin, X and Li, H},
title = {Activation of the Nrf2 Signaling Pathway by a Ginseng-Salvia Root-Notoginseng Composite Alleviates Ulcerative DSS-Induced Colitis via Restoring Gut Microbiota and the Intestinal Barrier.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antiox15030320},
pmid = {41897466},
issn = {2076-3921},
support = {JJKH20250214CY//the Jilin Provincial Department of Education Scientific Research Project/ ; },
abstract = {Current treatments for ulcerative colitis (UC) often fail to adequately address its multifactorial pathogenesis, which involves oxidative stress, barrier dysfunction, and gut microbiota dysbiosis. This study evaluated the therapeutic potential and multi-targeting mechanism of a ginseng, salvia root, and notoginseng oral solution (GSNS) in a mouse model of colitis induced by dextran sulfate sodium (DSS). Based on high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) technology, 25 major bioactive components were identified. Following the induction of colitis with 3.5% DSS in C57BL/6J mice, the animals were treated with the GSNS (40, 80, or 160 mg/kg/day) or 5-Amino Salicylic Acid (5-ASA). The therapeutic efficacy was assessed via disease activity, histopathological staining, cytokines and oxidative stress analysis, and a barrier integrity test. Combined data from Western blot, qPCR, immunohistochemistry, electron microscopy, and 16S rRNA sequencing indicate that the therapeutic effect of the GSNS against colitis is attributable to its dual role in dampening pro-inflammatory cytokines and potentiating antioxidant defenses via the Nrf2/HO-1 signaling pathway. It also upregulated Occludin expression, repaired tight junctions, and was associated with beneficial alterations in the gut microbiota, as evidenced by increased Prevotellaceae and suppressing Escherichia-Shigella. These findings demonstrated that the GSNS exerts a multi-target effect against colitis by synergistically enhancing antioxidant defense, repairing the intestinal barrier, and modulating microbial ecology, supporting its potential as a promising natural compound-based candidate for DSS-induced colitis treatment.},
}

@article {pmid41897732,
year = {2026},
author = {Lee, H and Na, W and Sohn, C},
title = {Comparative Microbiome Profiles of Korean Fermented Foods Based on Production Type and Additive Use.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/foods15061010},
pmid = {41897732},
issn = {2304-8158},
support = {NRF-RS-2024-00463020//National Research Foundation of Korea/ ; },
abstract = {Fermented foods are produced through controlled microbial activity and are valued for their extended shelf life, sensory attributes, and potential health benefits. This study examined the effects of production methods on microbial ecology by comparing microbial community structure, Shannon diversity, and pH changes in traditional and commercially produced Korean fermented foods. Cabbage and radish kimchi were fermented for four weeks to assess microbial succession and physicochemical changes, and additional fermented foods, including soy sauce, soybean paste, pepper paste, fruit vinegar, yogurt, and aged kimchi, were compared according to production method. Microbial communities were analyzed using amplicon sequencing targeting the V3-V4 regions of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region. Traditionally produced cabbage kimchi exhibited high microbial diversity at the early fermentation stage, initially dominated by Weissella and Leuconostoc, followed by a gradual shift toward lactic acid bacteria dominance at later stages. In contrast, commercially produced cabbage kimchi maintained a simplified microbial community dominated by a limited number of lactic acid bacteria throughout fermentation. Radish kimchi showed production-method-dependent patterns, with the rapid dominance of lactic acid bacteria during traditional fermentation and partial recovery of microbial diversity during commercial fermentation. Shannon diversity was consistently higher in traditionally produced kimchi during fermentation. In contrast, commercially produced kimchi exhibited more rapid acidification. Across other fermented foods, traditionally produced soy-based products exhibited complex microbial communities dominated by Bacillus spp., whereas commercially produced products were characterized by yeast-dominant profiles. Fruit vinegar and yogurt showed low microbial diversity regardless of the production method. These findings demonstrate the importance of production strategies in shaping microbial ecology, fermentation dynamics, and resulting product characteristics across various Korean fermented foods.},
}

@article {pmid41897857,
year = {2026},
author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L},
title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/ani16060880},
pmid = {41897857},
issn = {2076-2615},
support = {42367014//The National Natural Science Foundation of China/ ; },
abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.},
}

@article {pmid41898277,
year = {2026},
author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J},
title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.},
journal = {Biomedicines},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/biomedicines14030630},
pmid = {41898277},
issn = {2227-9059},
support = {3502Z20227102//Qinyu Xu/ ; },
abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.},
}

@article {pmid41898837,
year = {2026},
author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P},
title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.},
journal = {Genes},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/genes17030303},
pmid = {41898837},
issn = {2073-4425},
mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; },
abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.},
}

*Soil Microbiology
Rhizosphere
Metagenomics/methods
*Microbiota/genetics
*Plants/microbiology/genetics
Genomics/methods
Metabolomics/methods
Plant Roots/microbiology/genetics
Crops, Agricultural/microbiology/genetics
Multiomics

@article {pmid41898972,
year = {2026},
author = {Derguini, A and Basher, NS},
title = {Cockroaches as Vectors of Pathogens and Antimicrobial Resistance: Evidence from Healthcare, Community, and Agricultural Settings.},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/insects17030310},
pmid = {41898972},
issn = {2075-4450},
support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; },
abstract = {Synanthropic cockroaches, especially Blattella germanica and Periplaneta americana, are persistent pests of human dwellings, healthcare facilities, food establishments, farms, and transport infrastructure. Accumulating field and laboratory studies indicate that synanthropic cockroaches carry clinically important bacteria, fungi, and parasites, including multidrug-resistant strains harbouring extended-spectrum β-lactamase, carbapenemase, and other antimicrobial-resistant determinants. Cockroaches acquire these organisms from sewage, waste, food residues, animal excreta, and contaminated clinical environments, and retain them on the cuticle and within a complex gut microbiota. Dissemination is predominantly mechanical, via contact transfer and deposition of regurgitate and faeces on food, equipment, and surfaces, but may be amplified by gut colonisation, microbial interactions, and horizontal gene transfer within the cockroach microbiome. In hospitals, cockroaches can connect high-burden reservoirs (drains, waste areas, kitchens) with vulnerable units, including intensive care units (ICUs), neonatal intensive care units (NICUs), burn units, and haemato-oncology wards. In food and livestock systems, they may contaminate housing, ingredients, and finished products, enabling spillover along supply chains and at ports. This review synthesises current evidence and highlights the following priorities: integrate cockroaches into infection prevention, food safety, and biosecurity; incorporate cockroach sampling into antimicrobial resistance (AMR) and genomic surveillance; and advance mechanistic research on cockroach-microbiota-pathogen interactions to improve pest management and safely explore cockroach-derived antimicrobial compounds. In this review, we distinguish external mechanical carriage (cuticular contamination) from internal gut carriage; we use "gut colonisation" only when persistence/replication or prolonged shedding is demonstrated.},
}

@article {pmid41900294,
year = {2026},
author = {Ramírez-Saad, HC and Hernández-Rodríguez, CH},
title = {Editorial for Special Issue "Genomics Approaches in Microbial Ecology".},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030534},
pmid = {41900294},
issn = {2076-2607},
abstract = {Microbial ecology has entered a phase of methodological consolidation where genomic and molecular tools are being used to address ecological questions rather than being subordinate to culture-based approaches [...].},
}

@article {pmid41900372,
year = {2026},
author = {Faragó, V and Borsodi, AK and Nagy, B},
title = {The Taxonomic Diversity of Prokaryotic Communities from Permafrost Active Layers of the Chilean Andes.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030613},
pmid = {41900372},
issn = {2076-2607},
support = {NKFIH OTKA K147424//National Research, Development and Innovation Office, Hungary/ ; EKÖP-25-3-I-ELTE-244//Ministry for Culture and Innovation, Hungary/ ; },
abstract = {The study of microorganisms inhabiting extreme environments offers a valuable opportunity to explore their potential ecological roles. This study aimed to reveal and compare the microbial taxonomic diversity of largely unexplored permafrost regions located in different climatic zones (dry and wet) in the Chilean Andes, separated by thousands of kilometers. Permafrost active layer samples were collected from the Ojos del Salado (Atacama Desert) and the Torres del Paine (Patagonia) from different sampling depths. Illumina 16S rRNA gene-based amplicon sequencing revealed that the Andean permafrost active layer provides diverse habitats for distinct microbial communities, with higher taxonomic diversity of Bacteria than Archaea. The wet Patagonian Andes samples showed higher diversity, with a greater abundance of Chloroflexota and Bacteroidota, while the dry Ojos del Salado samples were dominated by Actinomycetota, indicating desiccation stress. Archaea were classified as ammonia-oxidizing members of the Thermoproteota phylum. Beta-diversity analyses suggested that differences in environmental conditions (mainly available moisture) contributed more to community structure differentiation than geographical distances. Nevertheless, the effect of sampling depth on microbial diversity was insignificant.},
}

@article {pmid41883800,
year = {2026},
author = {Diao, N and Cai, A and Zhou, Y and Long, B and Mo, Z and Shang, S and Liu, Y and Xu, J and Hu, W and Feng, K and Sarengaowa, },
title = {Recent advances on fermentation of mustard plant (Brassica juncea L.): microbial community, fermentation processing and sensorial quality: a review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1784857},
pmid = {41883800},
issn = {1664-302X},
abstract = {Mustard (Brassica juncea L.), rich in vitamins, minerals, and glucosinolates, yields fermented products valued for their distinct flavor and health benefits, particularly across East and Southeast Asia. The fermentation process is primarily driven by a complex microbial community dominated by lactic acid bacteria (LAB) such as Lactobacillus fermentum, Lactobacillus pentosus, and Lactobacillus plantarum. These microbes metabolize substrates to generate organic acids, volatile compounds, and free amino acids, which collectively shape the product's flavor and sensory quality. This review systematically summarizes recent progress in mustard fermentation, focusing on: the composition, succession, and function of microbial communities across different regions and fermentation stages and their influence on fermentation characteristics; the regulatory effects of key processing parameters-including fermentation vessel, temperature, and salt concentration-on microbial ecology, metabolic pathways, and final product quality; the chemical basis of taste attributes such as sourness, umami, bitterness, and pungency alongside the formation and evolution of aroma compounds during fermentation, and their links to microbial metabolism and biochemical pathways like glycolysis and the tricarboxylic acid cycle; and the formation patterns of potential risk factors such as biogenic amines and nitrite during fermentation, along with strategies to control their levels through process optimization and starter culture selection. Finally, future research directions are outlined, emphasizing the integration of omics and synthetic biology technologies to elucidate flavor formation mechanisms, develop stable starter cultures, and establish standardized processes. These advances aim to achieve consistent flavor, improved quality, and safe production of fermented mustard products, supporting the sustainable development of the industry.},
}

@article {pmid41884457,
year = {2026},
author = {Saeed, NK and Elbeltagi, YM and Al-Beltagi, M},
title = {Unveiling the viral dimension: The paediatric gut virome as a key modulator of gastrointestinal metabolic, and neurodevelopmental health.},
journal = {World journal of virology},
volume = {15},
number = {1},
pages = {118362},
pmid = {41884457},
issn = {2220-3249},
abstract = {Paediatric gut microbiome research has long been bacteriocentric, overlooking the extensive viral component known as the gut virome. Composed of bacteriophages, eukaryotic viruses, and endogenous viral elements, the paediatric gut virome is the most abundant and genetically diverse biological entity in the intestine. Emerging evidence indicates that the virome is a key regulator of microbial ecology, immune maturation, and systemic physiological programming during early life. This narrative review synthesizes current knowledge on the establishment, development, and functional roles of the paediatric gut virome, with emphasis on its interactions with the bacterial microbiome and host immune system. We highlight how early-life viral exposures influence mucosal immune imprinting, epithelial barrier integrity, and immune tolerance, particularly during the first 1000 days of life. Virome dysbiosis is increasingly associated with paediatric gastrointestinal disorders, including inflammatory bowel disease, necrotizing enterocolitis, celiac disease, and functional gastrointestinal disorders. Beyond the gut, the virome also contributes to metabolic regulation, type 1 diabetes risk, and gut-brain axis signaling, influencing neurodevelopment. Mechanistic pathways involving phage-mediated bacterial modulation, innate immune sensing, cytokine signaling, and metabolic intermediates are discussed, positioning the paediatric gut virome as a central regulator of gastrointestinal and systemic homeostasis.},
}

@article {pmid41884809,
year = {2026},
author = {Ren, L and Li, M and Wu, L and Lin, Z and Chen, A},
title = {Microbial transformation of secondary bile acids: roles in gut ecology and autoimmune diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1769792},
pmid = {41884809},
issn = {1664-3224},
mesh = {*Bile Acids and Salts/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; Humans ; *Autoimmune Diseases/immunology/microbiology/metabolism/etiology ; Animals ; },
abstract = {Secondary bile acids (SBAs) attracted interest due to their regulatory functions in gut microbial ecology and immune responses. These intricate microbial transformations decisively shape the biochemical properties of SBAs. Recent advancements in artificial intelligence and mass spectrometry technologies have substantially expanded our understanding of the diversity within the SBAs pool. To date, hundreds of SBAs, a minor portion of the natural SBA repertoire, have been identified, alongside the prediction of tens of thousands of associated enzymes. Integrative multi-omics studies have further substantiated the role of SBAs in the pathogenesis of autoimmune diseases. This review synthesizes current knowledge on the microbial modification of bile acids, their effects on gut microbial ecology and immune function, with a particular emphasis on autoimmune disorders. Collectively, these findings highlight SBAs as critical regulators of gut microbiota and immune system homeostasis, with their functions intricately linked to their molecular structures.},
}

*Bile Acids and Salts/metabolism/immunology
*Gastrointestinal Microbiome/immunology
Humans
*Autoimmune Diseases/immunology/microbiology/metabolism/etiology
Animals

@article {pmid41886209,
year = {2026},
author = {Singh, AP and Dongre, S and Sharma, S and Joshi, K and Bagdare, H and Bobade, R and Prakash, O and Sharma, R},
title = {Decolourizing distillery spent wash using fungal biotechnologies: from pollution to potential.},
journal = {Bioresources and bioprocessing},
volume = {13},
number = {1},
pages = {},
pmid = {41886209},
issn = {2197-4365},
}

@article {pmid41887850,
year = {2026},
author = {Fang, K and He, Y and Rao, S and Wang, J and Xu, J and Shi, J},
title = {Neglected but significant: High mercury alkylation but low carbon sequestration in paddy field as revealed by soil profiles survey.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {301-310},
doi = {10.1016/j.jes.2025.08.016},
pmid = {41887850},
issn = {1001-0742},
mesh = {*Mercury/analysis/chemistry ; *Soil Pollutants/analysis ; *Soil/chemistry ; *Environmental Monitoring ; Alkylation ; *Carbon Sequestration ; Oryza ; Carbon ; Soil Microbiology ; Methylation ; },
abstract = {The global environmental crisis caused by simultaneous increasing mercury (Hg) alkylation and organic carbon deficit has restricted the implementation of the "One Health" framework. Here, we report a neglected but significant phenomenon of high Hg alkylation but low carbon sequestration in paddy field through soil profiles survey deep to the parent material horizon (defined as deepsoil). We found that ratios of Hg methylation and ethylation were increased by 69.0 % and 64.2 % in deepsoil compared to that in topsoil (P < 0.05). This inhibition of Hg alkylation in topsoil is likely regulated by Nitrosomonadaceae (enriched by 64.9 % vs. deepsoil), which harbors the merA gene (Hg demethylation marker). Furthermore, through deciphering molecular level of dissolved organic matter, we found the content of labile carbon increased by 12.7 %, compared to those in topsoil. Conversely, in deepsoil, labile carbon (e.g., carbohydrates) enriches Spirochaetaceae (abundance +69.2 %, carrying the hgcA gene for Hg methylation), thereby facilitating Hg alkylation. This microbial shift enhanced Hg alkylation in deepsoil relative to topsoil. In summary, this study bridges human health, microbial ecology, and climate resilience (carbon storage) within the "One Health" paradigm, revealing depth-dependent mechanisms that reconcile soil Hg remediation with carbon management for sustainable agroecosystems.},
}

*Mercury/analysis/chemistry
*Soil Pollutants/analysis
*Soil/chemistry
*Environmental Monitoring
Alkylation
*Carbon Sequestration
Oryza
Carbon
Soil Microbiology
Methylation

@article {pmid41888223,
year = {2026},
author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K},
title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44250-9},
pmid = {41888223},
issn = {2045-2322},
support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; },
abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.},
}

@article {pmid41888251,
year = {2026},
author = {Perliński, P and Mudryk, ZJ and Zdanowicz, M and Kubera, Ł},
title = {Culturable Airborne Microorganisms in Urban and Coastal Recreation Areas (Southern Baltic Sea).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02729-y},
pmid = {41888251},
issn = {1432-184X},
}

@article {pmid41878569,
year = {2026},
author = {Uma Mageswary, M and Hanglian, L and Li, P and Richmond, RV and Azianey, Y and Tan, JS and Liong, MT and Ali, A and Vejayantheran, M and Hua, J and Jian, H and Abd Hamid, IJ and Taib, F and Zhang, Y},
title = {Probiotic improves respiratory and gastrointestinal health, immune homeostasis, and gut microbiota composition in infants: a randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1746679},
pmid = {41878569},
issn = {2296-861X},
abstract = {INTRODUCTION: The early postnatal period is a critical window for shaping the gut microbiota, which plays a pivotal role in immune maturation, infection resistance, and metabolic programming. Disruptions to this process may predispose infants to infections and allergic or metabolic disorders. Probiotics such as Bifidobacterium infantis have shown promise in modulating gut microbial ecology and immune function, but strain-specific and mechanistic evidence in infants remains limited. This study aimed to evaluate the effects of B. infantis YLGB-1496 supplementation on clinical outcomes, immune markers, and gut microbiota composition in healthy infants below one year of age.

METHODS: In a 12-week, randomized, double-blind, placebo-controlled trial, 119 healthy infants were enrolled (B. infantis YLGB-1496 n=59, placebo n=60). Participants received one daily sachet of B. infantis YLGB-1496 (1 × 10¹⁰ CFU) or placebo. Clinical outcomes for respiratory health and gastrointestinal (GI) health were assessed via validated questionnaires. Oral and fecal samples were collected for analysis of sIgA, cortisol, and cytokines (TNF-α, IFN-γ, IL-1β, IL-10, calprotectin). Gut microbiota was profiled by 16S rRNA sequencing, and diversity indices and taxonomic shifts were analyzed.

RESULTS: Compared with placebo, B. infantis YLGB-1496 supplementation was associated with consistent numerical reductions in respiratory symptom days, although these did not remain statistically significant after false discovery rate (FDR) adjustment. In contrast, gastrointestinal outcomes showed robust improvements after FDR correction, including reduced stomach ache (q = 0.010), lower diarrhea incidence (q < 0.001), and fewer diarrhea-related clinical visits (q < 0.001). Fecal sIgA remained elevated in the B. infantis YLGB-1496 group (P = 0.138 vs P = 0.000 in placebo), accompanied by increased IL-10 (P < 0.001) and reduced IL-1β (P = 0.002). Oral sIgA was enhanced (P = 0.001), while cortisol declined similarly in both groups. Microbiota analysis revealed enrichment of beneficial taxa in the B. infantis YLGB-1496 group with concurrent reductions in pathobionts. In contrast, the placebo group exhibited increases in Campylobacter, Staphylococcus, and Desulfovibrio desulfuricans, and decreases in Faecalibacterium prausnitzii and Anaerostipes caccae, indicative of dysbiosis. These compositional changes support improved gut barrier function and immune development.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05794815?term=NCT05794815&rank=1, Identifier: NCT05794815.},
}

@article {pmid41879866,
year = {2026},
author = {Finch, JTD and Riegler, M and Cook, JM and Brettell, LE},
title = {Filth Flies, Flowers and Food: Pollination by Flies (Calliphoridae) Does Not Affect the Strawberry Microbiome.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02741-2},
pmid = {41879866},
issn = {1432-184X},
support = {PH16002//Horticultural Innovation Australia Limited/ ; },
}

@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41879886},
issn = {1869-1889},
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}

@article {pmid41879986,
year = {2026},
author = {Couradeau, E and Vanegas, J and Betancurt-Anzola, D and Glass, S and Eckert, K and Bechtold, EK and Ellenbogen, JB and Zaragoza, LR and Wrighton, K and Vanegas, JS},
title = {Soil Microbial Diversity in Páramos Wetland of the Colombian Andes Reveals Novel and Unique Features Within a Global Wetland Database.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02738-x},
pmid = {41879986},
issn = {1432-184X},
support = {2325922//NSF/ ; 7006508//USDA Hatch/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; },
abstract = {Tropical wetlands are the largest natural source of methane on Earth, yet they remain the least studied, particularly high-altitude wetlands like those in the Páramo of Chingaza, Colombia. These ecosystems are crucial for water provisioning, carbon sequestration, and biodiversity conservation but are threatened by rapid climate change. While the páramo biome supports thousands of endemic plant species and plays a vital role in balancing carbon inputs and greenhouse gas outputs (CO2 and CH4), its soil microbial diversity and functional roles in soil processes are largely unexplored. To fill this knowledge gap, we conducted amplicon sequencing of the ITS, 16S rRNA, and 18S rRNA genes to examine microbial diversity across three distinct ecosites at Laguna Seca, Chingaza, characterized by different macrotopographies, water-table levels, and vegetation assemblages. Our findings revealed significant variations in microbial community structure, with the peatland ecosite showing the highest diversity across all amplicons. Comparative analysis with global wetland datasets indicated that microbial communities at Laguna Seca share similarities with subarctic Stordalen Mire fen and other peat-forming wetlands. Notably, our targeted assessment identified a diversity of potential methanogens and methanotrophs exclusively within the peatland ecosite, at low but comparable abundance to other wetlands. This suggests that methane cycling in the other ecosites of this wetland may either be less prominent than expected or involve organisms not previously associated with known methane processes. These findings establish a baseline for understanding microbial diversity in tropical high-montane wetlands and underscore the unique ecological significance of páramo peatlands amid climate change.},
}

@article {pmid41880444,
year = {2026},
author = {Moore, PJ and Kent, LA and Hunter, RC},
title = {Anaerobic microbiota promote pathogen association with the airway epithelium.},
journal = {Journal of medical microbiology},
volume = {75},
number = {3},
pages = {},
doi = {10.1099/jmm.0.002149},
pmid = {41880444},
issn = {1473-5644},
mesh = {Humans ; *Pseudomonas aeruginosa/physiology ; *Bacteria, Anaerobic/physiology ; *Microbiota ; Epithelial Cells/microbiology ; *Sinusitis/microbiology ; Mucins/metabolism ; *Rhinitis/microbiology ; *Respiratory Mucosa/microbiology ; Cell Line ; *Pseudomonas Infections/microbiology ; Chronic Disease ; },
abstract = {Introduction. Chronic rhinosinusitis (CRS) is a prevalent condition characterized by mucus stasis, persistent inflammation and infection of the paranasal sinuses. CRS often involves infection by the bacterium Pseudomonas aeruginosa, especially in individuals with cystic fibrosis or a history of antibiotic use. While P. aeruginosa is a well-established opportunistic pathogen that deploys a diverse array of virulence factors to drive airway infections, its persistence in the airway mucosa is also likely influenced by its local microbial ecology. For instance, anaerobic bacterial genera, such as Streptococcus, Veillonella and Prevotella, are also commonly found in CRS and may contribute to pathogen establishment.Hypothesis. Although anaerobes are common members of the CRS microbiota, their role in promoting P. aeruginosa association with the airway epithelium remains poorly defined. We hypothesized that anaerobes facilitate P. aeruginosa attachment by degrading mucin glycoproteins that decorate the epithelial surface.Aim. To determine whether CRS-associated anaerobic microbiota enhance P. aeruginosa colonization of the airways through mucin modification.Methodology. Using a novel dual oxic-anoxic culture platform, Calu-3 epithelial cells were co-cultured with a CRS-derived anaerobic microbial community. Inflammatory gene expression, mucin integrity and subsequent P. aeruginosa epithelial association were assessed. Additionally, mucins isolated from anaerobe-treated cells were evaluated for their ability to promote P. aeruginosa attachment in vitro.Results. Anaerobe exposure increased epithelial inflammatory marker gene expression and led to degradation of mucin glycoproteins. Anaerobe pre-treatment significantly enhanced P. aeruginosa association with the epithelial surface. Moreover, mucins isolated from anaerobe-treated cells promoted greater pathogen attachment in vitro compared to intact mucins.Conclusion. CRS-associated anaerobic microbiota can remodel the sinonasal microenvironment in ways that enhance P. aeruginosa epithelial association. These findings highlight the importance of polymicrobial interactions in CRS pathogenesis and suggest that targeting anaerobe-mediated mucin degradation may represent a novel therapeutic strategy for chronic airway disease.},
}

Humans
*Pseudomonas aeruginosa/physiology
*Bacteria, Anaerobic/physiology
*Microbiota
Epithelial Cells/microbiology
*Sinusitis/microbiology
Mucins/metabolism
*Rhinitis/microbiology
*Respiratory Mucosa/microbiology
Cell Line
*Pseudomonas Infections/microbiology
Chronic Disease

@article {pmid41882188,
year = {2026},
author = {Anokyewaa, MA and Wang, Z and Amenyogbe, E and Lu, Y and Zhen, G},
title = {Impacts of Probiotics on Microbial Populations in Aquaculture Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02710-9},
pmid = {41882188},
issn = {1432-184X},
support = {(2022A1515110243)//Guangdong Basic and Applied Basic Research Foundation/ ; },
}

@article {pmid41882189,
year = {2026},
author = {Chewe, M and Shembo, TK and Dumfeh, EP and Zhou, S and Odinga, ES and Yang, G and Ohore, OE},
title = {Assessing the Ecological Roles of Resistomes within Microbial Communities in Antibiotic-contaminated Ecosystems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02740-3},
pmid = {41882189},
issn = {1432-184X},
support = {Hnky2025ZC-3//Hainan Province Higher Education Scientific Research Project/ ; RZ2300006042//Hainan Medical University Talent Research Launch Fund/ ; },
}

@article {pmid41883376,
year = {2026},
author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W},
title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {3},
pages = {420-433},
pmid = {41883376},
issn = {2833-8278},
abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.},
}

@article {pmid41883787,
year = {2026},
author = {Lin, H and Shao, C and Yu, J and Chen, H and Ren, Y and Ren, J and Zeng, Y and Wu, Y and Zhang, Q and Xiao, X},
title = {Maternal probiotic and prebiotic supplementation on glucose metabolism in pregnant women and their offspring: effects and related mechanisms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1782361},
pmid = {41883787},
issn = {1664-302X},
abstract = {INTRODUCTION: The global diabetes epidemic has brought gestational diabetes mellitus (GDM) and its long-term impacts on maternal-child health into sharp focus. Emerging evidence indicates that early-life metabolic programing, mediated significantly by gut microbiota, profoundly influences offspring glucose homeostasis. Notably, microbial-targeted nutritional interventions, including probiotic and prebiotic supplementation, have considerable potential as innovative therapeutic approaches. These strategies may effectively prevent intergenerational transmission of metabolic diseases by improving glucose metabolism in both mother and offspring.

METHODS: This narrative review synthesizes evidence from clinical trials and animal studies investigating the effects of maternal probiotic and prebiotic supplementation on glucose metabolism. We searched and analyzed literature focusing on glycemic outcomes in pregnant women with or without GDM and their offspring, as well as studies exploring underlying mechanisms including gut microbiota modulation, metabolite production, inflammatory pathways, and epigenetic regulation.

RESULTS: Clinical and animal studies have shown that probiotics and prebiotics can significantly alleviate metabolic parameters such as elevated fasting glucose and insulin resistance in patients with GDM, but their preventive effect on the incidence of GDM is unclear. In addition, maternal supplementation with probiotics or prebiotics may positively affect glucose metabolism in offspring through multiple interconnected mechanisms, which include the modulation of intestinal microbial ecology, the increased generation of microbial- derived metabolites such as short-chain fatty acids (SCFAs), the mitigation of inflammatory responses, and epigenetic regulation (e.g., DNA methylation, lncRNA and miRNA modification).

DISCUSSION: Despite some heterogeneity in the results of existing studies, there is overall support for the therapeutic potential of probiotic and prebiotic interventions in optimizing metabolic outcomes for both maternal and pediatric populations. Future studies need to further define the optimal type, dose and timing of intervention for probiotics and prebiotics and explore precise intervention strategies on the basis of individual gut microbiota characteristics. In conclusion, probiotic and prebiotic supplementation during pregnancy and lactation may become an adjunctive tool to improve glucose metabolism in mothers and infants, resulting in innovative approaches for the primary prevention of metabolic diseases.},
}

@article {pmid41883797,
year = {2026},
author = {Sui, C and Qiao, H},
title = {The Type VI secretion system in enteric pathogen colonization: molecular mechanisms, ecological dynamics, and therapeutic potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809019},
pmid = {41883797},
issn = {1664-302X},
abstract = {The Type VI Secretion System (T6SS) is a sophisticated, phage-tail-like contractile nanomachine that mediates contact-dependent protein translocation in a wide range of Gram-negative enteric pathogens. As a primary weapon for interference competition, T6SS enables pathogens like Salmonella and Vibrio cholerae to directly eliminate commensal rivals. This targeted elimination allows pathogens to dismantle microbiota-mediated colonization resistance and seize essential nutritional niches. Beyond interbacterial warfare, the system facilitates "exploitative competition" by secreting effectors for the acquisition of limited micronutrients such as iron and zinc. Furthermore, T6SS acts as a crucial virulence determinant by manipulating host cell signaling, disrupting cytoskeletal integrity, and even enhancing intestinal contractions to physically expel competitors. The expression and activity of T6SS are dynamically regulated by gastrointestinal cues, including bile salts, pH fluctuations, and quorum sensing signals, ensuring its activation is precisely timed during infection. Elucidating these multifaceted roles not only deepens our understanding of microbial ecology in the gut but also highlights T6SS as a promising target for microbiome engineering and the development of customizable, precision antimicrobial therapies.},
}

@article {pmid41689060,
year = {2026},
author = {Li, M and Lin, J and Ma, C and Wei, G and Hu, Q and Li, X},
title = {Effects of L-selenomethionine supplementation on nutrient digestibility and metabolism, antioxidant capacity, hormone levels, and fecal microbiota diversity in pregnant Yili mares during mid- to late gestation.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41689060},
issn = {1746-6148},
abstract = {BACKGROUND: L-selenomethionine (L-SeMet), a highly bioavailable organic form of selenium, plays a critical role in maintaining antioxidant homeostasis, regulating reproductive hormone secretion, and improving intestinal microbial ecology. Previous studies have demonstrated that appropriate supplementation with L-SeMet can significantly enhance the production performance and health status of ruminants. However, the nutritional regulatory mechanisms and physiological effects of L-SeMet in monogastric herbivores, particularly horses during mid- to late gestation, remain inadequately understood. Therefore, this study investigated the effects of different levels of L-SeMet supplementation on nutrient digestibility and metabolism, antioxidant capacity, reproductive hormone profiles, and fecal microbiota diversity in pregnant Yili mares.

RESULTS: The results showed that selenium (L-SeMet) supplementation at 0.4, 0.6, or 0.8 mg Se mare⁻¹ day⁻¹ significantly increased apparent crude protein digestibility and serum glutathione peroxidase (GSH-Px) activity in pregnant mares compared with controls. Compared with the control group, the 0.6 and 0.8 mg Se mare⁻¹ day⁻¹ groups exhibited significantly higher neutral detergent fiber (NDF) digestibility, nitrogen metabolism rate, total antioxidant capacity (T-AOC), catalase (CAT) activity, progesterone, and estradiol levels, while malondialdehyde (MDA) and urinary estrone levels were reduced. Fecal microbiota analysis further revealed an increased relative abundance of methanogens and Actinobacteriota, particularly in the 0.6 mg Se mare⁻¹ day⁻¹ group. Functional predictions indicated enrichment of microbial metabolic pathways related to carbohydrates and energy metabolism.

CONCLUSIONS: Collectively, these findings indicate that selenium supplementation (provided as L-SeMet) enhances nutrient utilization, antioxidant defenses, and the endocrine milieu during pregnancy, with 0.6–0.8 mg Se mare⁻¹ day⁻¹ appearing to confer the broadest benefits; dose optimization and long term outcomes warrant further investigation.},
}

@article {pmid41699524,
year = {2026},
author = {Tshimbila Kabangu, JMV and Tsiwedi-Tsilabia, E and Faida-Kitoga, and Cizungu-Namugusha, J and Muhindo-Kabuyaya, P and Arung Kalau, W and Lundimu Tugirimana, P and Mushagalusa Kasali, F and Kadima Ntokamunda, J and Mukadi-Bamuleka, D},
title = {Prevalence of wound infections and related antimicrobial resistance in Goma, Democratic Republic of the Congo: a multicenter cross-sectional study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41699524},
issn = {1471-2334},
abstract = {BACKGROUND: The morbidity and mortality related to wound infections and microbial resistance are real public health concern in low-income settings where data are lacking, empirical antibiotic use is common and microbiological diagnostics are limited. This study aimed to describe the prevalence and antimicrobial resistance (AMR) patterns resulting from wound infections.

METHODS: We conducted a one-year multicenter cross-sectional study across hospitals in Goma, Democratic Republic of the Congo. Consecutive patients with clinically infected wounds were enrolled. Wound swabs were processed using standard culture and susceptibility testing. Firth’s bias-reduced logistic regression was used to assess factors associated with surgical site infection (SSI) and AMR, with analyses stratified by Gram staining.

RESULTS: Most patients were below 40 years old, with a median age of 27 years (IQR: 22–39), predominantly males (64.5%). Gunshot injuries (33.2%), road traffic accidents (24.5%) and cesarean section  (14.8%) were the leading cause of wounds. SSIs accounted for 21.25% of all clinically diagnosed infected wounds; they were significantly associated with female sex (OR = 3.65, 95% CI: 1.18–11.92, p = 0.03) and abdominal surgery (OR = 272.92, 95% CI: 85.66–1208.58, p < 0.001). In female patients, a high rate of SSIs was observed following cesarean section  (86.8%). Overall microbial swab cultures were negative in 21.0%. Among 18 isolated species, Gram-negative bacteria were predominant with Proteus mirabilis (24.1%), Pseudomonas aeruginosa (13.6%), and Escherichia coli (12.7%), as the leading pathogens. In Gram-stratified Firth models, empirical antibiotic therapy was not independently associated with increased in vitro AMR. Amikacin showed a protective association among Gram-negative isolates, while estimates for Gram-positive cocci were imprecise due to small sample size. Pseudomonas aeruginosa exhibited reduced susceptibility to multiple drug classes.

CONCLUSION: Wound infections in Goma are largely linked to trauma and cesarean deliveries, with Gram-negative microorganisms dominating. The microbial ecology comprises ESKAPE pathogens and species known for their emerging resistance patterns such as Proteus mirabilis, Pseudomonas aeruginosa and Escherichia coli. Empirical antibiotic therapy was not independently associated with AMR after adjustment. These findings underscore the urgent need for enhanced diagnostic strategies, strengthened infection prevention measures, and effective antimicrobial stewardship in this resource-limited and conflict-affected setting.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12867-w.},
}

@article {pmid41873801,
year = {2026},
author = {Martins, GL and Zandt, DI' and Merloti, LF and Bieluczyk, W and Rocha, GS and Timmers, R and Rodrigues, RR and Tsai, SM and van der Putten, WH},
title = {Connectivity and Age of Restored Atlantic Forest Fragments Drives Composition and Functionality of the Fungal Community in the Leaf Litter Layer.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70325},
pmid = {41873801},
issn = {1365-294X},
support = {2018/19000-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/19000-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/05561-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; Process 2021/00976-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/18333-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 101110604//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Forests ; *Plant Leaves/microbiology ; Brazil ; Biodiversity ; *Fungi/classification/genetics ; Trees/microbiology ; Soil Microbiology ; Conservation of Natural Resources ; Ecosystem ; },
abstract = {The restoration of biodiversity and functional tropical forests is critical to mitigating global biodiversity losses. Aboveground, increasing the connectivity of regenerating forest fragments facilitates the recolonization of tropical forest biodiversity. However, restoring functional ecosystems also requires the recovery of decomposition processes as these are essential in shaping aboveground biodiversity. Therefore, we investigate the role of forest connectivity in restoring the composition and functioning of fungal communities in the leaf litter layer during a chronosequence of forest restoration. In the Brazilian Atlantic Forest, we studied secondary forests regrown between 18 and 55 years after deforestation and different levels of forest connectivity and compared their litter to recently abandoned pastures and undisturbed primary forests. We quantified how forest age and connectivity between fragments influenced the litter fungi composition in relation to tree diversity, litter chemistry and litter isotopes. We show that fungal composition was highly heterogeneous in forest litter, whereas pasture litter exhibited a more homogeneous community. Moreover, forest connectivity had stronger effects on litter fungal composition compared to forest age. Connectivity promoted wood saprotrophs and endophytes, while suppressing soil saprotrophs, with its effects being more evident during later stages of restoration. Fungal guilds such as endophytes and saprophytes were primarily influenced by tree diversity and leaf litter chemistry. We conclude that forest connectivity promotes the re-establishment of saprophytic fungi capable of decomposing recalcitrant litter substrates, driven mainly by enhancing tree diversity and litter quality. Practical implications of increasing connectivity may relate to forest resilience in front of future climate change scenarios.},
}

*Forests
*Plant Leaves/microbiology
Brazil
Biodiversity
*Fungi/classification/genetics
Trees/microbiology
Soil Microbiology
Conservation of Natural Resources
Ecosystem

@article {pmid41873837,
year = {2026},
author = {Kazmi, SSUH and Batool, SM and Pastorino, P and Barcelò, D and Grossart, HP and Yaseen, ZM and Khan, ZH and Azeem, M and Li, G},
title = {The plastisphere as a nexus for antimicrobial resistance: micro(nano)plastics in pathogen colonization, gene transfer, and global health risks.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/brv.70163},
pmid = {41873837},
issn = {1469-185X},
support = {42595620//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2023J05078//Natural Science Foundation of Fujian Province, China/ ; //Fujian Province Excellent Postdoctoral Project/ ; 2021-DST-004//Ningbo S&T Project/ ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) have emerged as pervasive vectors of antimicrobial resistance (AMR), with the plastisphere being a microbial niche on plastic surfaces acting as a nexus for pathogen colonization, gene transfer, and global health risks. These particles adsorb antibiotics, transport pathogens, and serve as reservoirs for antibiotic resistance genes (ARGs), fostering pathogen-ARG coevolution and horizontal gene transfer (HGT) through biofilm-mediated mechanisms. Despite their recognized role in AMR dissemination, critical gaps persist in understanding how environmental stressors (e.g. salinity, pH) modulate plastisphere dynamics and socioeconomic disparities in exposure. This review synthesizes evidence positioning MPs/NPs as triple threats: microbial habitats, ARG reservoirs, and HGT conduits. We also discuss synergistic interactions of plastisphere biofilms with antibiotics to amplify selective pressures, enabling resistance dissemination across ecosystems and food chains, thereby escalating global health risks. Current research lacks mechanistic insights into real-world plastisphere interactions and longitudinal data linking MPs/NPs to clinical AMR outcomes. We propose actionable One Health strategies including artificial intelligence (AI)-enhanced surveillance, circular economy frameworks, and pathogen-resistant biodegradable polymers to disrupt the plastisphere-driven AMR nexus. Our synthesis underscores the urgency of integrating environmental science, epidemiology, and policy to mitigate risks to ecological and human resilience.},
}