@article {pmid41798180,
year = {2026},
author = {Cakin, I and Millington, R and Pawar, S and Buckling, A and Smirnoff, N and Padfield, D and Duffy, J and Yvon-Durocher, G},
title = {A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag024},
pmid = {41798180},
issn = {2730-6151},
abstract = {Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry ([Formula: see text] > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (∼30°C-35°C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninvasive and scalable tool for high-throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.},
}

@article {pmid41797016,
year = {2026},
author = {Ghannem, S and Labiadh, H and Ishak, S and Louiz, S and Derguini, A and Idres, T and Grassi, E and Semprucci, F and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Alsalamah, SA and Bendif, H and Rebai, A and Boufahja, F},
title = {Investigation of the impacts of second-generation antihistamines on free-living marine nematodes and their interaction with ZnS nanoparticles: Mechanistic insights from community and population approaches and molecular interactions modeling.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107969},
doi = {10.1016/j.marenvres.2026.107969},
pmid = {41797016},
issn = {1879-0291},
abstract = {The current research investigates the impact of loratadine and its active metabolite desloratadine, applied at environmentally relevant concentrations (40 and 80 ng/L), using community-level, population-based, and molecular modeling approaches, on meiofauna from the Dammam coast, Saudi Arabia. The results indicate a significant reduction in the abundance of meiobenthic organisms, accompanied by a marked decline in nematode diversity across treatments, especially under combined exposures at higher concentrations. Additionally, trophic groups 1B and 2B, characterized by clavate tail morphologies, were the main contributors to the observed dissimilarity patterns across treatments. The mixture of 40 ng/L of antihistamines with ZnS nanoparticles (4.1 nm) enhanced catalase and GST activities in Metoncholaimus pristiurus. An increase in growth rate was also observed, along with larger pharyngeal lumens, suggesting higher food pumping under stress. Locomotion issues and decreased fertility are also suggested, with signs of masculinization. This highlights the intensified toxic effects of antihistamines following the addition of ZnS NPs. Overall, the findings suggest synergistic or additive interaction between loratadine, desloratadine, and ZnS nanoparticles. Their toxicokinetic properties, along with strong binding affinities and stable molecular interactions with GLD-3 and SDP receptors, provide a mechanistic basis and support ecotoxicological impacts of these antihistamines and ZnS NPs on nematodes.},
}

@article {pmid41795790,
year = {2026},
author = {Özkan Vardar, D and Ekmen, B and Çalı, A},
title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/26896583.2026.2636868},
pmid = {41795790},
issn = {2689-6591},
abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.},
}

@article {pmid41794478,
year = {2026},
author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V},
title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118597},
doi = {10.1016/j.foodres.2026.118597},
pmid = {41794478},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.},
}

*Fermentation
*Microbiota
*Kombucha Tea/microbiology/analysis/economics
Food Microbiology
Bacteria/metabolism/classification
Yeasts/metabolism
Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry

@article {pmid41794468,
year = {2026},
author = {Wang, A and Qiu, C and Tang, J},
title = {Multidimensional synergy between yeast and lactic acid bacteria: mechanisms, quality formation, and precision fermentation strategies.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118586},
doi = {10.1016/j.foodres.2026.118586},
pmid = {41794468},
issn = {1873-7145},
mesh = {*Fermentation ; *Lactobacillales/metabolism/physiology ; Biofilms/growth & development ; *Microbial Interactions ; *Food Microbiology ; Quorum Sensing ; *Fermented Foods/microbiology ; *Yeasts/metabolism ; },
abstract = {The complex functional characteristics of fermented foods stem from dynamic microbial interactions rather than the activities of individual microorganisms. Traditional research has primarily focused on single-strain cultures and metabolic functions, whereas contemporary studies increasingly emphasize the pivotal role of interactions between different species in shaping fermentative ecosystems. This review explores the multifaceted interactions between yeast-lactic acid bacteria (LAB), focusing on three key aspects: (1) nutritional interactions and cross-feeding mechanisms; (2) molecular communication via metabolite exchange and quorum sensing; (3) collective adaptation strategies encompassing biofilm formation and environmental remodeling. Synergistic interactions promote metabolic complementarity, thereby enhancing substrate utilization efficiency and biosynthetic capacity beyond the limitations of single-strain cultures. Competitive interactions maintain ecological equilibrium within microbial communities while suppressing undesirable microorganisms. Quorum sensing mechanisms synchronize gene expression across entire populations, coordinating metabolic pathways and optimizing collective behavior. Biofilm formation creates structured microenvironments that enhance microbial resilience and metabolic specialization. Advanced methodologies, particularly multi-omics technologies and synthetic microbial ecology approaches, have become indispensable tools for unravelling these intricate interaction networks. Integrating genome-scale metabolic modelling with experimental validation offers unprecedented insights into the molecular mechanisms underpinning microbial interactions. This systems-level understanding enables the purposeful design of synthetic microbial communities and precise fermentation processes, highlighting the imperative shift from single-species optimization towards ecological management strategies. Future research should translate laboratory discoveries into industrial applications through standardized evaluation systems and dynamic regulatory strategies.},
}

*Fermentation
*Lactobacillales/metabolism/physiology
Biofilms/growth & development
*Microbial Interactions
*Food Microbiology
Quorum Sensing
*Fermented Foods/microbiology
*Yeasts/metabolism

@article {pmid41794110,
year = {2026},
author = {Wei, C and Hu, J and Wang, X and Chen, Y and Zhang, S and Peng, Y},
title = {Optimization of sulfate-reducing ammonium oxidation based on N/S: nitrogen and sulfur removal performance, microbial community, and response surface methodology.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124143},
doi = {10.1016/j.envres.2026.124143},
pmid = {41794110},
issn = {1096-0953},
abstract = {Sulfate-reducing ammonium oxidation (Sulfammox) offers a novel strategy for simultaneous nitrogen and sulfur removal. However, the microbial-driven metabolic pathways under different N/S and the optimal operational conditions remain unclear. This study operated three anaerobic sequencing batch reactors at N/S of 2.5, 2.0, and 1.5 to investigate the removal performance and microbial ecology. The reactor with an N/S of 1.5 (R3) achieved the highest removal efficiencies of 91.82% for NH4[+]-N and 47.95% for SO4[2-]-S, while the reactor with an N/S of 2.5 (R1) showed efficiencies below 15% for both, indicating that a lower N/S is critical for efficient removal. X-ray photoelectron spectroscopy confirmed the formation of elemental sulfur, indicating active sulfur transformation that alleviated sulfide inhibition and enhanced system stability. Batch tests identified optimal operating conditions: pH 8.0, hydraulic retention time 48 h, and COD 50 mg/L. When COD is greater than 300 mg/L, sulfate reduction dominated and inhibited the sulfammox process. Response surface methodology models (R[2]>0.98) predicted the optimal parameters in N/S 1.57, pH 7.66, HRT 46.53 h, and COD of 48.61 mg/L, achieving NH4[+]-N and SO4[2-]-S removal efficiencies of 93.13% and 47.35%. This represents 9.5% enhancement in NH4[+]-N removal over the pre-optimization phase. Microbial analysis revealed that N/S of 1.5 abundance of Desulfobacterota increased by 1.67%, driving sulfate reduction, while Chloroflexi constituted 26.07% in R3, the anammox bacterium Candidatus-Brocadia was inhibited, exhibiting a relative abundance of less than 0.1%. By elucidating sulfammox interactions, this study offers a practical, low-carbon and synergistic framework for the effective co-treatment of high NH4[+]-N and SO4[2-]-S wastewater.},
}

@article {pmid41792903,
year = {2026},
author = {Liang, MQ and Yuan, L and Liu, QH and Wu, J and Liu, DF and Sheng, GP},
title = {Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag046},
pmid = {41792903},
issn = {1751-7370},
abstract = {Although it is increasingly recognized that anthropogenic chemicals modulate horizontal gene transfer (HGT), the nature of these interactions is often more complex than a simple promotion or inhibition. The potential for a single chemical to exert opposing, concentration-dependent effects represent a critical and less-explored frontier in microbial ecology. Here, we investigate the last-resort antibiotic polymyxin B, a membrane-targeting peptide, and reveal a concentration-dependent, biphasic regulation of plasmid conjugation. Sub-inhibitory concentrations (0.125-0.5 mg/L) consistently inhibited the transfer of antibiotic resistance genes (ARGs) by up to 65.4%, whereas bactericidal concentrations (≥ 1 mg/L) strongly promoted it by up to 15.9-fold. This regulatory switch is driven by distinct physiological states: low-level exposure triggers defensive responses including reduced membrane permeability, whereas high-level exposure causes catastrophic membrane damage, inducing a synergistic stress response involving oxidative damage (>2-fold ROS increase) and a surge in cellular energy (up to 83.0% ATP increase) that facilitates HGT. High-concentration polymyxin B also promotes plasmid transfer in complex microbial communities derived from activated-sludge biofilms. Our findings reveal a new paradigm for the interaction between chemical stressors and microbial evolution, demonstrating that the ecological impact of contaminants on HGT cannot be predicted by monotonic models and highlighting the role of environmental hotspots in shaping the dissemination of antibiotic resistome.},
}

@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}

*Naphthalenes/metabolism
Biodegradation, Environmental
*Bacteria/metabolism/genetics
Systems Biology
Computer Simulation
*Environmental Pollutants/metabolism
Microbial Consortia

@article {pmid41790321,
year = {2026},
author = {Sahoo, A and Maity, A and Das, B and Paul, RC and Paul, P and Chakraborty, P and Chaudhuri, BN and Ghosh, MM and Das, S and Tribedi, P},
title = {Combined application of Vancomycin and Levofloxacin potentiates the antimicrobial activity against MRSA: a response surface methodology-based study.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41790321},
issn = {1874-9356},
support = {TNU/R&D/MG/24/02//The Neotia University, India/ ; TNU/R&D/MP/2021/010//The Neotia University, India/ ; },
}

@article {pmid41789424,
year = {2026},
author = {Katrak, C and Reed, S and Carter, M and Khatib, M and Peterson, A and Martin, K and Kajfasz, JK and Abranches, J},
title = {Oral hygiene agents at work: effects on Streptococcus mutans and caries risk.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1768512},
pmid = {41789424},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/prevention & control/microbiology ; *Streptococcus mutans/drug effects/physiology/growth & development ; Biofilms/drug effects/growth & development ; *Oral Hygiene/methods ; Probiotics/pharmacology ; Dental Plaque/microbiology/prevention & control ; Chlorhexidine/pharmacology/therapeutic use ; Hydrogen Peroxide/pharmacology ; Fluorides/pharmacology/therapeutic use ; Prebiotics ; Zinc/pharmacology ; },
abstract = {Dental caries remains one of the most prevalent chronic polymicrobial diseases worldwide, driven by acidogenic and aciduric bacteria, most notably Streptococcus mutans, that thrive within oral biofilms. Conventional strategies for caries prevention rely on mechanical plaque removal combined with agents that inhibit bacterial growth, disrupt biofilm formation, or enhance enamel remineralization. Here, we synthesize current evidence regarding a range of key agents that are incorporated into modern oral hygiene products. In addition to describing the mechanisms and efficacy of these agents, we describe their distinct biochemical and ecological effects on S. mutans metabolism, acid tolerance, and biofilm development. The agents that are relevant in the present day include fluoride, hydrogen peroxide, chlorhexidine, zinc, prebiotics (such as arginine and xylitol), and probiotics. Fluoride remains the cornerstone of caries prevention through its dual effects on enamel fluorapatite formation and inhibition of bacterial glycolysis, while chlorhexidine and hydrogen peroxide provide broad-spectrum antimicrobial activity. Zinc exhibits multifaceted roles in metabolic inhibition and plaque reduction, whereas pre- and probiotics aim to restore ecological balance by favoring health-associated commensal species. Finally, the review highlights evidence supporting combinatorial and synergistic use of these agents, particularly fluoride pairings, which may yield additive or enhanced protective effects. Understanding the molecular mechanisms that drive the efficacy of these compounds and gaining insight into cumulative influence on oral microbial ecology will drive the development of future treatment strategies.},
}

Humans
*Dental Caries/prevention & control/microbiology
*Streptococcus mutans/drug effects/physiology/growth & development
Biofilms/drug effects/growth & development
*Oral Hygiene/methods
Probiotics/pharmacology
Dental Plaque/microbiology/prevention & control
Chlorhexidine/pharmacology/therapeutic use
Hydrogen Peroxide/pharmacology
Fluorides/pharmacology/therapeutic use
Prebiotics
Zinc/pharmacology

@article {pmid41788582,
year = {2026},
author = {Wang, E and Chen, C and Li, Q},
title = {Current obstacles for continuous cropping of Panax species and mitigation strategies.},
journal = {Journal of ginseng research},
volume = {50},
number = {2},
pages = {100925},
pmid = {41788582},
issn = {1226-8453},
abstract = {Panax species-represented here by Panax ginseng Meyer, Panax quinquefolius L., and Panax notoginseng (Burk.) F. H. Chen-are valued for their saponins and polysaccharides and thus have significant clinical and commercial value. Rising global demand has driven intensive, large-scale cultivation, but repeated monoculture has produced persistent continuous cropping obstacles that now threaten the sustainability of the industry. These obstacles are not attributable to a single factor. Rather, they arise from interacting processes including degradation of soil physical and chemical properties, accumulation of plant-derived toxins that inhibit growth (allelopathic autotoxicity), and shifts in the soil microbial community that impair soil health and plant resilience. Together, these changes lead to stunted growth, reduced yields, and increased disease incidence. This review synthesizes recent advances in understanding continuous cropping obstacles in Panax species. It evaluates evidence for the primary causal factors, assesses current mitigation strategies, and highlights areas where findings are robust or still uncertain. By integrating soil science, plant physiology, and microbial ecology, the review identifies practical approaches already in use and emerging technologies with potential to improve outcomes. Finally, we identify critical knowledge gaps and outline priority directions for future research aimed at clarifying mechanisms and translating that knowledge into an effective management framework. The ultimate goal is to provide a theoretical basis to guide the development of scalable, evidence-based practices that alleviate continuous cropping obstacles in the cultivation of Panax species.},
}

@article {pmid41788258,
year = {2026},
author = {Keles, E and Celik, O},
title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.},
journal = {Microbial cell (Graz, Austria)},
volume = {13},
number = {},
pages = {117-130},
pmid = {41788258},
issn = {2311-2638},
abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.},
}

@article {pmid41787281,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Rasschaert, G and Demaître, N and Sadiq, FA and Boon, N and Cools, A and De Reu, K},
title = {Hidden threats: exploring biofilm communities in broiler houses and pig nursery units drinking water lines.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04790-6},
pmid = {41787281},
issn = {1471-2180},
support = {HBC.2021.1060//VLAIO-LA/ ; },
}

@article {pmid41787131,
year = {2026},
author = {Stanovcic, S and Milisavljevic, M and Azanjac, N and Kojic, S and Kojic, M},
title = {Biomolecules Generated During Programmed Cell Death (PCD) Enhance the Capacity of Proliferating Ustilago maydis Cells to Overcome the Negative Impacts of Non-PCD Necromass.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02736-z},
pmid = {41787131},
issn = {1432-184X},
support = {7730230//Science Fund of the Republic of Serbia/ ; },
}

@article {pmid41786226,
year = {2026},
author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF},
title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134333},
doi = {10.1016/j.biortech.2026.134333},
pmid = {41786226},
issn = {1873-2976},
abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.},
}

@article {pmid41778806,
year = {2026},
author = {Wasson, PA and McRose, DL},
title = {Nitrous oxide produced by denitrifying pseudomonads inhibits the growth of rhizosphere bacteria by inactivating the cobalamin-dependent methionine synthase.},
journal = {mBio},
volume = {},
number = {},
pages = {e0269925},
doi = {10.1128/mbio.02699-25},
pmid = {41778806},
issn = {2150-7511},
abstract = {Microbial communities are shaped by complex metabolic interactions, whereby the byproducts of one organism influence the physiology of others. This is exemplified in the microbial nitrogen cycle, where diffusion of free intermediates can drastically reshape the chemical landscape of the environment. One such intermediate, nitrous oxide (N2O), is often overlooked as biologically inert. However, emerging evidence suggests this gas may inhibit the activity of some cobalamin-dependent enzymes through a reaction with the cofactor. This raises the possibility that, through such an interaction, N2O-producing organisms may shape the microbial communities in which they reside, selecting against organisms that rely on these sensitive cobalamin enzymes. At the plant root, a hotspot of microbial activity, the impact of such interactions may be especially important. To investigate this, we focused on microbial N2O production and its effect on methionine biosynthesis, a ubiquitous bacterial process carried out by cobalamin-dependent (MetH) or independent (MetE) methyltransferases. In this study, we show that deleting metE and forcing reliance on MetH sensitizes the denitrifier Pseudomonas aeruginosa to exogenous and self-produced N2O. We extend these findings to plant-associated bacteria, where we find that a significant portion of an Arabidopsis thaliana rhizosphere culture collection relies exclusively on cobalamin-dependent methionine synthases and experimentally demonstrate their sensitivity to N2O. Finally, we show that the growth of one MetH-reliant rhizosphere isolate is suppressed in co-culture with N2O-producing P. aeruginosa. Together, these findings suggest that N2O producers can shape microbial ecology at the plant root.IMPORTANCEMicrobes that live on plant roots can make important contributions to plant health and often exist in tight-knit communities held together by chemical exchanges. This study investigates an interaction between two such metabolites: the climate-active gas nitrous oxide (N2O) and cobalamin. N2O can become toxic through a reaction with methionine synthase enzymes that use cobalamin as a cofactor. We asked whether the production of N2O by some bacteria curtails the growth of others that rely on these enzymes. Using genetic mutants of a model bacterium and natural isolates from the roots of the plant Arabidopsis thaliana, we showed that N2O-producing microbes suppress growth of their sensitive neighbors and that N2O sensitivity is common in rhizosphere bacteria. As natural and agricultural soils periodically experience bursts of N2O, our results suggest that exposure to this gas may shape the assembly of plant-beneficial microbial communities.},
}

@article {pmid41786065,
year = {2026},
author = {Wang, X and Liu, R and Liu, J and Lin, Y and Zhou, M},
title = {Gut microbiota-derived indole metabolites in depression: mechanisms and therapeutic potential.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178720},
doi = {10.1016/j.ejphar.2026.178720},
pmid = {41786065},
issn = {1879-0712},
abstract = {Depression, a prevalent neuropsychiatric disorder with complex pathophysiology and often insufficient treatment efficacy, is increasingly associated with disruptions in the gut-brain axis. This review focuses on the underappreciated role of the microbial indole pathway, a key route in tryptophan metabolism orchestrated by the gut microbiota. We synthesize recent evidence demonstrating that gut microbiota-derived indole metabolites, such as indole-3-propionic acid (IPA) and indole-3-aldehyde (IAld), are significantly reduced in depression. These metabolites exert multifaceted antidepressant effects by enhancing intestinal and blood-brain barrier integrity, suppressing neuroinflammation, and promoting neuroplasticity. Furthermore, we explore the therapeutic potential of targeting this axis through interventions like specific probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation to restore microbial ecology and indole metabolite levels. By highlighting the microbiota-indole-brain pathway as a critical mechanistic and therapeutic frontier, this review provides a novel perspective on the pathogenesis and treatment of depression, moving beyond conventional monoaminergic theories.},
}

@article {pmid41785727,
year = {2026},
author = {Wang, C and Luo, M and Chen, Q and Zheng, L and Jiang, T and Dai, M},
title = {Hedyotis diffusa Willd. extract alleviates CCl4-induced liver fibrosis via modulation of the gut microbiota and FXR/SHP/CYP7A1-mediated bile acid metabolism.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121450},
doi = {10.1016/j.jep.2026.121450},
pmid = {41785727},
issn = {1872-7573},
abstract = {Liver fibrosis is a critical stage in the progression of chronic liver diseases, yet effective therapeutic agents are limited. Hedyotis diffusa Willd., a traditional Chinese medicine herb with heat-clearing and detoxifying properties, has long been used to treat inflammatory disorders, hepatic dysfunction and malignancies. Although accumulating studies suggest that Hedyotis diffusa Willd. Extract (HDW) possesses hepatoprotective and antifibrotic potential, the underlying mechanisms, particularly those involving gut microbiota and bile acid (BA) metabolism along the gut-liver axis, remain largely undefined.

AIM OF THE STUDY: To investigate the protective effects of HDW against carbon tetrachloride (CCl4)-induced liver fibrosis in mice, and to determine whether its antifibrotic efficacy is mediated by modulation of the gut microbiota-bile acid-FXR/SHP/CYP7A1 axis.

MATERIALS AND METHODS: Liver fibrosis was induced by intraperitoneal injection of 10% CCl4 in olive oil for five weeks. Histopathological changes were evaluated using H&E, Sirius red and Masson staining. Liver function was assessed using serum levels of ALT, AST, ALP and γ-GT. Collagen deposition was evaluated by measuring hepatic hydroxyproline (HYP) and fibrosis-related markers (HAase, IV-C, LN and PC-III). Activation of hepatic stellate cells was determined by α-SMA and Col1a1 expression. The composition of the gut microbial was profiled using 16 S rRNA sequencing, and the necessity of gut microbiota for HDW efficacy was evaluated through an antibiotic (ABX) cocktail intervention. Targeted BA metabolomics quantified BA profiles, while RT-qPCR and Western blotting evaluated FXR/SHP/CYP7A1 pathway activity. Intestinal barrier integrity was assessed by villus morphology, tight junction protein levels (Claudin-1, ZO-1, Occludin), and serum lipopolysaccharide (LPS).

RESULTS: HDW treatment markedly alleviated CCl4-induced liver fibrosis, demonstrated by improved hepatic architecture, reduced serum transaminases and ALP/γ-GT, decreased hydroxyproline levels, and downregulation of α-SMA and Col1a1. HDW reshaped the gut microbial composition by enriching beneficial taxa, whereas ABX treatment markedly attenuated its antifibrotic effects, indicating that the therapeutic action of HDW is largely microbiota-dependent. HDW restored BA homeostasis and significantly increased fecal odeoxycholic acid. Consequently, hepatic FXR/SHP/CYP7A1 signaling was upregulated at both the mRNA and protein levels. Furthermore, HDW strengthened the intestinal epithelial barrier by enhancing tight junction integrity and reducing serum LPS.

CONCLUSION: HDW exerts significant antifibrotic effects in CCl4-induced liver fibrosis via a gut microbiota-dependent mechanism involving the restoration of BA metabolism and the activation of the hepatic FXR/SHP/CYP7A1 axis. Given its ability to modulate gut microbial ecology, BA homeostasis and intestinal barrier integrity simultaneously, HDW is a promising therapeutic candidate for targeting the gut microbiota in the treatment of liver fibrosis.},
}

@article {pmid41785576,
year = {2026},
author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I},
title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.},
journal = {The Science of the total environment},
volume = {1023},
number = {},
pages = {181623},
doi = {10.1016/j.scitotenv.2026.181623},
pmid = {41785576},
issn = {1879-1026},
abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.},
}

@article {pmid41782409,
year = {2026},
author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q},
title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2639216},
doi = {10.1080/19490976.2026.2639216},
pmid = {41782409},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Mice ; Homeostasis ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; *Guanidines/metabolism/pharmacology ; Colitis, Ulcerative/microbiology/metabolism ; Mice, Inbred C57BL ; Bacteroides/metabolism ; *Butyrates/metabolism ; Disease Models, Animal ; Stem Cells/metabolism ; Feedback, Physiological ; *Amino Acid Transport System y+/metabolism/genetics ; Akkermansia ; },
abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Humans
Mice
Homeostasis
*Intestinal Mucosa/metabolism/microbiology/drug effects
*Guanidines/metabolism/pharmacology
Colitis, Ulcerative/microbiology/metabolism
Mice, Inbred C57BL
Bacteroides/metabolism
*Butyrates/metabolism
Disease Models, Animal
Stem Cells/metabolism
Feedback, Physiological
*Amino Acid Transport System y+/metabolism/genetics
Akkermansia

@article {pmid41781688,
year = {2026},
author = {Cinek, O and Hubáčková, K and Litošová, K and Hlináková, L},
title = {Heterogeneity Primer Spacers Improve the Performance of Massively Parallel Amplicon Sequencing of the V3-V4 Region of the 16 S rDNA as well as the 18 S Region for Blastocystis Subtyping.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02708-3},
pmid = {41781688},
issn = {1432-184X},
}

@article {pmid41779172,
year = {2026},
author = {Roldán, DM and Carrizo, D and Sánchez-García, L and Menes, RJ},
title = {Temperature Response of Aerobic Methane-Oxidizing Bacteria in Lake Sediments from King George Island, Maritime Antarctica.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02717-2},
pmid = {41779172},
issn = {1432-184X},
}

@article {pmid41779071,
year = {2026},
author = {Lygis, V and Marčiulynas, A and Plepytė, T and Šulčius, S and Menkis, A},
title = {Metabarcoding Reveals Rich and Diverse Aeromycobiota in Protected Oak Forests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02714-5},
pmid = {41779071},
issn = {1432-184X},
abstract = {Old-growth oak (Quercus robur) forests in Europe are biodiversity hotspots, yet their airborne fungal diversity remains poorly studied. We investigated aeromycobiota in three Lithuanian oak stands (Punia, Dūkštos and Šilinė) using passive spore traps combined with DNA metabarcoding. Weekly sampling between August and September 2022 yielded 75 spore samples, producing 262,755 high-quality fungal sequences clustered into 1,881 operational taxonomic units (OTUs) representing six phyla and 36 classes. Ascomycota (53.1% of OTUs) and Basidiomycota (44.3%) dominated in richness, while Basidiomycota prevailed in relative sequence abundance (62.8%). Major taxa included Exobasidiaceae sp., Cladosporium sp., Melampsora sp., and Thelephora terrestris. Airborne fungal communities exhibited a substantial core assemblage shared among stands, accompanied by stand-associated differences in species richness and relative sequence abundance. The Punia stand showed the highest richness and the greatest proportion of stand-specific OTUs. Temporal variation was detectable but moderate relative to spatial differences among stands. Functional guild analysis revealed dominance of saprotrophs (46.5% of assigned OTUs), followed by pathotrophs (14.5%) and symbiotrophs (13.2%). Overall, our results demonstrate that passive spore traps-based airborne metabarcoding captures high fungal diversity and resolves both widespread and stand-associated community patterns in old-growth oak forests. This study provides the first characterization of aeromycobiota in old-growth Q. robur forests of Northern Europe and highlights the value of airborne metabarcoding for fungal biodiversity assessment and long-term forest monitoring.},
}

@article {pmid41777393,
year = {2026},
author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D},
title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1685007},
pmid = {41777393},
issn = {1664-462X},
abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.},
}

@article {pmid41776739,
year = {2026},
author = {Tang, X and Liu, H and Qin, P and Wang, T and Du, W and Zhang, M and Zhu, M and Feng, J},
title = {Identification and Fungicide Efficacy of Leaf Spot on Euonymus fortunei Caused by Alternaria alternata in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-26-0167-RE},
pmid = {41776739},
issn = {0191-2917},
abstract = {Leaf spot disease has recently emerged on Euonymus fortunei in Shanxi Province, China, causing noticeable foliar lesions and reducing ornamental value. The causal agent was identified as Alternaria alternata based on morphological characteristics and multilocus phylogenetic analysis using five loci (Alt a1, gapdh, RPB2, ITS, and OPA10-2). Biological characterization showed that mycelial growth was optimal at 27 ℃ on oatmeal agar, whereas conidial germination was favored under alkaline conditions (pH 9.0). The pathogen was sensitive to NaCl stress but showed no significant response to different light regimes. In vitro fungicide sensitivity assays revealed marked differences in inhibitory efficacy between mycelial growth and conidial germination, indicating strong developmental stage-dependent responses. Certain fungicide mixtures exhibited enhanced inhibitory effects compared with single compounds, suggesting potential synergistic interactions. Microscopic observations further revealed fungicide-induced morphological abnormalities, including hyphae swelling, roughened surfaces, reduced sporulation, and deformation of conidial germ tubes. This study represents the first report of A. alternata causing leaf spot disease on E. fortunei in China and provides a basis for understanding pathogen biology and developing effective chemical management strategies for this emerging ornamental disease.},
}

@article {pmid41774190,
year = {2026},
author = {Noirungsee, N and Pitaktham, T and Nakkaew, A and Chantanaorrapint, S and Klinnawee, L},
title = {Microbial Communities of the Mycoheterotrophic Plant Thismia Gardneriana in a Lowland Tropical Rainforest of Southern Thailand.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02727-0},
pmid = {41774190},
issn = {1432-184X},
support = {N25A650472//National Research Council of Thailand/ ; },
}

@article {pmid41773092,
year = {2026},
author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS},
title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.},
journal = {Research and reports in urology},
volume = {18},
number = {},
pages = {580953},
pmid = {41773092},
issn = {2253-2447},
abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).

METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.

RESULTS: Baseline β diversity did not differ between groups. Post-instillation, β diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.

CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.},
}

@article {pmid41772134,
year = {2026},
author = {Sadiq, FA and Yang, N and Goeteyn, J and De Reu, K and Heyndrickx, M and Burmølle, M},
title = {Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02701-w},
pmid = {41772134},
issn = {1432-184X},
abstract = {Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence in situ hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising Stenotrophomonas rhizophila, Microbacterium lacticum, and Bacillus licheniformis. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24 h, with S. rhizophila as the dominant species and M. lacticum exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions - commensalism, exploitation, and neutral interaction. Transcriptomic profiling of S. rhizophila revealed extensive gene expression changes in dual-species biofilms with M. lacticum, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with B. licheniformis induced minimal transcriptional changes in S. rhizophila, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.},
}

@article {pmid41771260,
year = {2026},
author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR},
title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70309},
pmid = {41771260},
issn = {1758-2229},
support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; },
abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.},
}

@article {pmid41770930,
year = {2026},
author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G},
title = {High bacterial diversity drives the suppression of a soilborne plant disease.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {10},
pages = {e2509303123},
doi = {10.1073/pnas.2509303123},
pmid = {41770930},
issn = {1091-6490},
abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.},
}

@article {pmid41770403,
year = {2026},
author = {D'Souza, R and Pujare, K and Balu, SK and Kanojiya, D and Garg, Y and Ghag, SB},
title = {Differential Response of Banana Root Exudates and its Components on the Growth and Development of Banana Wilt Pathogen.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02693-z},
pmid = {41770403},
issn = {1432-184X},
}

@article {pmid41770335,
year = {2026},
author = {Suarez-Silva, R and Saucedo-Bazalar, M and Ramirez Saenz, M and La Torre Ramirez, RD and Caycho Ortiz, E and Orjeda, G},
title = {Exploring the Algarrobo Decline in the Pómac Forest: Unraveling the Relationship between the Endomicrobiome of Neltuma Pallida and Enallodiplosis Discordis.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02711-8},
pmid = {41770335},
issn = {1432-184X},
support = {No. 042-2022-RFNP//Servicio Nacional de Áreas Naturales Protegidas Servicio Nacional de Áreas Naturales Protegidas/ ; R. R. No 009412-2021-UNMSM and Project number B2110006i - PINTERDIS - 2021//Universidad Nacional Mayor de San Marcos/ ; },
}

@article {pmid41770002,
year = {2026},
author = {Feliu-Paradeda, L and Amorós-Espuña, Q and Perona-Vico, E and Casals, E and Esteve-Codina, A and Puig, S and Bañeras, L},
title = {Synergies revealed: RNA-seq study of C. acetobutylicum and C. carboxidivorans co-cultured in the presence of conductive materials.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326225},
doi = {10.1128/spectrum.03262-25},
pmid = {41770002},
issn = {2165-0497},
abstract = {Co-cultures can improve substrate utilization and product yields, yet the dynamics between species remain highly variable and poorly understood. In this study, we investigated the metabolic and transcriptional interplay between Clostridium acetobutylicum and Clostridium carboxidivorans when co-cultured in the presence of activated carbon or magnetite, with the aim of evaluating these materials as metabolism enhancers. Fermentation profiling showed that magnetite accelerated glucose consumption and favored acid over alcohol production, with butyrate and acetate reaching yields of 0.65 and 0.62 mol/mol glucose, respectively. Alcohols (ethanol and butanol) accumulated in late fermentation and occurred concomitantly to a metabolic shift from acidogenesis to solventogenesis, potentially driven by interspecies dynamics as RNA-seq data suggested. RNA-seq analysis detected 7,369 genes and revealed C. carboxidivorans dominated in early fermentation, and C. acetobutylicum was activated later (in view of the number of reads detected for each species). Magnetite-treated samples displayed the most transcriptional variation, and species-specific patterns emerged. Changes in electron-active genes (e.g., hydA and rnf genes) suggest enhanced redox communication, highlighting the capacity of conductive materials to influence metabolic flow and regulatory pathways in microbial consortia, opening possibilities for improved bioproduction and carbon utilization.IMPORTANCEMicrobial co-cultures offer a promising strategy to expand metabolic capabilities beyond those of individual strains, yet their internal coordination remains poorly understood. This study demonstrates that conductive materials not only accelerate substrate utilization but also modulate cooperation in a co-culture of Clostridium carboxidivorans and Clostridium acetobutylicum. According to gene expression levels, we demonstrate a clear temporal division of labor between the two partners, with C. carboxidivorans initiating acidogenesis and C. acetobutylicum later driving solventogenesis. Magnetite and activated carbon addition had little effect, but changes in the expression pattern of electron-active genes (hydA and rnf) could be detected for the two species. Understanding and controlling these dynamics are key to optimizing co-cultures for industrial fermentation and biofuel production.},
}

@article {pmid41769348,
year = {2026},
author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J},
title = {Epistemic compression in large language model explanations of the gut-liver axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1773593},
pmid = {41769348},
issn = {2235-2988},
abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.

METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.

RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.

CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.},
}

@article {pmid41769190,
year = {2026},
author = {Al-Jamal, FF and Abuassaf, RA and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD},
title = {Ethanolic extracts from deep marine sponges: A new frontier in antibacterial discovery from the Jordanian Gulf of Aqaba.},
journal = {Biomedical reports},
volume = {24},
number = {4},
pages = {44},
pmid = {41769190},
issn = {2049-9442},
abstract = {The urgent need for new antibiotics to counter bacterial resistance has led to renewed interest in marine natural products. The present study evaluated the antibacterial potential of ethanolic extracts from three deep-sea sponges: Stelletta sp., Dactylospongia cf. elegans (D. cf. elegans) and Axinella sp., which were collected from the Gulf of Aqaba off the coast of Jordan. Antibacterial activity was assessed against Gram-negative and Gram-positive bacteria using the well diffusion method, followed by determination of the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Only D. cf. elegans exhibited potent activity, which was limited to Gram-positive bacteria and showed inhibition zones of 7 to 21 mm and MIC and MBC values of 1 and 2 mg/ml, respectively. Stelletta sp. showed no detectable activity, and Axinella sp. displayed minimal effects. DNA barcoding (28S rRNA) confirmed that all three species belong to the class Demospongiae. LC-MS/MS analysis of the extract from D. cf. elegans identified bioactive constituents, including bolinaquinone, dactyloquinone, gallic acid and caffeic acid, which are compounds known for antibacterial properties and likely contributed to the observed activity. Thus, D. cf. elegans could be a promising source of antibacterial agents against Gram-positive pathogens and warrants further evaluation of the mechanisms involved, its toxicity, and its effects in vivo.},
}

@article {pmid41767570,
year = {2026},
author = {Souza, JM and Silva, LAF and Casali, DM and Souza, JCSM and Wolfe, LA and Skarlupka, JH and Zuniga-Chaves, I and Steinberger, AJ and Deblois, CL and Scheftgen, AJ and Lelis, ALJ and Leiva, T and Rodrigues, MC and Barroso, JPR and Lasmar, PVF and Suen, G and Millen, DD},
title = {Rumen and cecum microbial dynamics following narasin inclusion in Nellore cattle diets.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1645979},
pmid = {41767570},
issn = {1664-302X},
abstract = {This study investigated the effects of narasin supplementation on the ruminal and cecal bacterial communities of feedlot Nellore cattle. We hypothesized that narasin would selectively modulate microbial populations in distinct gastrointestinal compartments without causing broad-scale disruption of overall community diversity. Sixty-four Nellore bulls (393 ± 24 kg) were assigned to a completely randomized block design and fed finishing diets containing either 0 or 20 ppm of narasin for 112 days. Rumen and cecal contents were collected at slaughter and analyzed using 16S rRNA gene sequencing to characterize bacterial community structure and composition. Overall, the rumen exhibited greater bacterial diversity and richness than the cecum, regardless of dietary treatment. Narasin supplementation did not affect Shannon diversity in either the rumen (p = 0.182) or the cecum (p = 0.298); however, Chao richness was reduced in the rumen of narasin-fed cattle (p = 0.028). Beta-diversity analyses based on Bray-Curtis and Jaccard dissimilarities revealed no significant differences in overall community structure between treatments in either compartment (p > 0.198). At the phylum level, narasin supplementation was associated with a reduction in Firmicutes and a concomitant increase in Bacteroidetes in the rumen. In contrast, Firmicutes predominated in the cecum, and narasin significantly increased the relative abundance of this phylum, particularly members of the order Clostridiales (p = 0.05). In conclusion, narasin exerts selective effects on specific bacterial populations rather than inducing widespread shifts in microbial diversity. These results provide novel insights into how narasin modulates microbial ecology in both the rumen and the understudied cecum, highlighting compartment-specific responses that may contribute to improved feed efficiency in beef cattle.},
}

@article {pmid41764142,
year = {2026},
author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL},
title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02706-5},
pmid = {41764142},
issn = {1432-184X},
support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; },
}

@article {pmid41763651,
year = {2026},
author = {Angebault, C and Bardoul, M and Fillâtre, P and Bouju, P and Rieul, G and Fedun, Y and Launey, Y and Reizine, F},
title = {Clinical landscape and mortality risk in Intensive Care Unit peritonitis in a low-MultiDrug Resistant setting: A multicentre cohort study.},
journal = {Anaesthesia, critical care & pain medicine},
volume = {},
number = {},
pages = {101783},
doi = {10.1016/j.accpm.2026.101783},
pmid = {41763651},
issn = {2352-5568},
abstract = {INTRODUCTION: Peritonitis is a frequent cause of sepsis in the intensive care unit (ICU) and is characterized by substantial microbiological variability, including multidrug-resistant organisms (MDROs).

METHOD: We conducted a retrospective, multicenter cohort study including ICU patients diagnosed with intra-abdominal infection across 4 hospitals 2020-2022). The primary objective was to describe clinico-biological features, and microbiological characteristics according to the setting of the peritonitis (Community peritonitis (CP), early nosocomial peritonitis (ENP), or late nosocomial peritonitis (LNP)). Additionally, we analyzed 90-day survival using Kaplan-Meier curves and multivariable Cox regression.

RESULTS: Among the 392 patients included in the study period, 195 experienced a CP, 88 an ENP, and 109 an LNP. Extended-spectrum beta-lactamase-producing bacteria were identified in 24 patients (6.1%), and carbapenem-resistant bacteria in 5 patients (1.3%). MDRO rates differed significantly: carbapenem-resistant bacteria were more frequent in LNP patients (3.7% vs. 0.0% in CP and 0.5% in ENP; p = 0.03), and cephalosporinase-producing bacteria were more common in nosocomial settings (40.4% in LNP vs. 19.0% in CP; p < 0.001). Ninety-day mortality was 34.7% overall and did not differ across settings (p = 0.345). Age and SAPS II were independently associated with mortality. Finally, appropriate empirical antimicrobial therapy was not associated with improved 90-day survival (p = 0.128).

CONCLUSION: Through this large cohort study of ICU patients with peritonitis, we observed a low prevalence of MDRO. Our findings challenge the relevance of broad-spectrum empirical therapy in low-MDRO regions and underscore the need for tailored antimicrobial stewardship strategies.},
}

@article {pmid41762238,
year = {2026},
author = {Phauk, S and Sin, S and Terenius, O},
title = {Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02724-3},
pmid = {41762238},
issn = {1432-184X},
}

@article {pmid41757148,
year = {2025},
author = {Bektaş, A and Ulusoy, M},
title = {Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity.},
journal = {Euroasian journal of hepato-gastroenterology},
volume = {15},
number = {2},
pages = {185-189},
pmid = {41757148},
issn = {2231-5047},
abstract = {AIM AND BACKGROUND: Celiac disease (CD) and nonceliac gluten sensitivity (NCGS) are increasing in public and scientific focus. Interestingly, regions with traditionally high gluten consumption such as Turkey, Iran, and the Mediterranean show lower CD prevalence than the Western countries. This paradox indicates that genetic predisposition alone, such as HLA DQ2 or DQ8 carriage, does not fully explain gluten intolerance. Understanding environmental, microbial, and cultural contributors may clarify the development of gluten tolerance.

METHODS: This narrative review synthesizes current evidence from epidemiology, microbiology, immunology, and nutritional science to propose an integrative hypothesis. Relevant literature was examined to explore interactions among diet, gut microbiota, and immune tolerance mechanisms that influence responses to gluten exposure.

RESULTS: Findings suggest that early life gluten exposure, microbial diversity, and long-term dietary adaptation enhance mucosal tolerance to gluten. Specific microorganisms such as Lactobacillus, Bifidobacterium, and Prevotella can enzymatically degrade immunogenic gluten peptides including the 33-mer α2-gliadin fragments. Reduced microbial diversity and the consumption of ultra-processed foods may contribute to heightened gluten sensitivity and immune dysregulation.

CONCLUSION: Gluten is not inherently toxic; its immunogenicity depends on host microbiota composition, environmental exposures, and dietary context. A systems biology approach that integrates microbial ecology, evolutionary adaptation, and immunonutrition may better explain gluten tolerance variability across populations.

CLINICAL SIGNIFICANCE: Recognizing gluten tolerance as a modifiable, microbiota influenced process may guide more individualized dietary recommendations, reduce unnecessary gluten avoidance, and promote evidence-based clinical management of gluten-related disorders.

HOW TO CITE THIS ARTICLE: Bektaş A, Ulusoy M. Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity. Euroasian J Hepato-Gastroenterol 2025;15(2):185-189.},
}

@article {pmid41757127,
year = {2026},
author = {Saha, A and Jones, JM and Plummer, A and Larkin, JW},
title = {Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.707077},
pmid = {41757127},
issn = {2692-8205},
abstract = {Microbes across species and environments form biofilms, living materials composed of cells and extracellular polymers. Biofilm-dwelling cells benefit from emergent soft matter physics that sculpts three-dimensional morphologies and osmotically absorbs nutrients. Although biofilms are modeled as viscoelastic gels, the physical origins of the phase transition underlying their conversion from groups of cells to living gels have not been systematically investigated. Here, we show that Bacillus subtilis biofilms use polymer composition to tune their physical properties and drive gel formation. Using imaging and water immersion experiments with matrix knockout strains, we demonstrate the complementary roles of two polymers in this developmental transition: hydrophilic poly- γ -glutamate swells colonies by absorbing water and exopolysaccharides serve as effective cross-linkers, causing a sol-gel-like phase transition that imparts structural integrity. With matrix knockout co-culture biofilms, we independently modulate the production of each polymer and reveal a phase space of biofilm morphologies. Colonies that produce both polymers develop macroscopic wrinkles. A thin-film model predicts biofilm wrinkling from swelling-generated internal strain coupled to elasticity. The model reproduces the shape of our observed morphological phase diagram. Our results demonstrate that bacteria leverage gelation to vary their material properties and morphologies, with implications for microbial ecology and engineering living matter.},
}

@article {pmid41754095,
year = {2026},
author = {Mafe, AN and Büsselberg, D},
title = {The Diet-Microbiota-Polyamine Axis in Intestinal Aging: Microbial Pathways, Functional Foods, and Physiological Implications.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754095},
issn = {2072-6643},
support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; },
abstract = {Intestinal aging is characterized by a gradual decline in epithelial renewal capacity, barrier function, immune balance, and metabolic regulation, often accompanied by shifts in gut microbial composition. Polyamines, including putrescine, spermidine, and spermine, are vital microbial-host metabolites that support intestinal cell growth, autophagy, immune modulation, and mucosal repair. With advancing age, both host-derived and microbiota-mediated polyamine production declines, contributing to intestinal dysfunction and heightened vulnerability to inflammation and age-related disorders. This review explores the diet-microbiota-polyamine axis as a key biological framework influencing intestinal aging. It aims to integrate evidence on how dietary components and functional foods shape gut microbial ecology and, in turn, regulate microbial polyamine biosynthetic pathways that impact intestinal health. The review highlights major microbial contributors to polyamine metabolism, particularly lactic acid bacteria, and outlines mechanistic pathways linking polyamines to epithelial regeneration, inflammatory control, and gut barrier maintenance. It further discusses how age-associated dysbiosis disrupts these interactions and evaluates nutritional and microbial-based strategies such as fermented foods, prebiotics, and probiotics that may enhance polyamine availability and restore gut homeostasis. From the standpoint of food microbiology and human physiology, this synthesis underscores the translational potential of targeting microbial polyamine production through diet-based interventions. This article presents a narrative review synthesizing experimental, animal, and emerging human evidence on microbial and dietary polyamines in intestinal aging. In conclusion, modulating the diet-microbiota-polyamine axis represents a promising strategy to promote healthy intestinal aging, meriting deeper mechanistic exploration and validation through clinical studies.},
}

@article {pmid41753780,
year = {2026},
author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC},
title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753780},
issn = {2076-2607},
support = {2020-67017-30776//USDA-NIFA/ ; },
abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.},
}

@article {pmid41753774,
year = {2026},
author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B},
title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753774},
issn = {2076-2607},
abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.},
}

@article {pmid41753768,
year = {2026},
author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K},
title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020482},
pmid = {41753768},
issn = {2076-2607},
support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; },
abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.},
}

@article {pmid41753753,
year = {2026},
author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J},
title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020467},
pmid = {41753753},
issn = {2076-2607},
abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.},
}

@article {pmid41753641,
year = {2026},
author = {Pérez-García, LA and Sáenz-Mata, J and Fortis-Hernandez, M and Preciado-Rangel, P},
title = {Plant Growth-Promoting Rhizobacteria as a Strategy to Enhance Enzymatic and Metabolic Tolerance of Cucumis sativus L. Under Salinity Stress.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020351},
pmid = {41753641},
issn = {2076-2607},
abstract = {Cucumis sativus L., a salt-sensitive horticultural crop, is severely affected by soil salinity, which disrupts photosynthetic efficiency and metabolic homeostasis. This study quantified the effects of Plant Growth-Promoting Rhizobacteria (PGPR)-Pseudomonas paralactis, Bacillus cereus, Sinorhizobium meliloti, and Acinetobacter radioresistens-on key enzymatic indicators of cucumber seedlings exposed to 0, 50, 100, and 150 mM NaCl. PGPR inoculation significantly enhanced bacterial stress-mitigation and hormonal pathways, with ACC-deaminase activity increasing by up to 78.8% (A. radioresistens, 150 mM NaCl) and nitrilase activity by 50.5% (S. meliloti, 50 mM NaCl). Auxin-related pathways were strongly induced, as reflected by increases of up to 51.1% in the IAM pathway (P. paralactis) and 42.9% in the IPA pathway (A. radioresistens). In plant tissues, key metabolic enzymes exhibited high stability under salinity, with ProDH and NDPK activities increasing by up to 4.5% and 2.35%, respectively, while RuBisCO activity remained unaffected across treatments. These results demonstrate that PGPR function as effective bioestimulants by coordinating hormonal regulation and metabolic resilience, providing a sustainable biotechnological strategy to enhance cucumber tolerance to salinity stress.},
}

@article {pmid41751059,
year = {2026},
author = {Tapingkae, W and Srinual, O and Srinual, P and Khamtavee, P and Pintalerd, N and Chaiyaso, T and Yachai, M and Tapingkae, T and Kanmanee, C},
title = {Dietary Coffee Silverskin Supplementation: Effect on Growth Performance, Carcass Traits, and Gastrointestinal Health of Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/ani16040598},
pmid = {41751059},
issn = {2076-2615},
support = {FF66/045//Fundamental Fund 2023, Chiang Mai University/ ; },
abstract = {Coffee silverskin (CSS) remains a neglected poultry additive; investigating its bioactive potential is essential for optimizing agricultural productivity and enhancing food security via advanced nutrition. This study analyzed how dietary CSS supplementation influences broiler growth, slaughter characteristics, meat quality, cecal microbial ecology, and intestinal histomorphology. A total of 400 one-day-old male Ross 308 broilers were randomly assigned to four dietary treatments with 10 replicates of 10 birds each. Experimental treatments consisted of a negative control (NC, basal diet) and CSS-supplemented groups (0.5, 1.0, and 2.0 g/kg, designated CSS0.5, CSS1.0, and CSS2.0, respectively). All data were subjected to one-way ANOVA using the procedure of SPSS 23.0. Coffee silverskin supplementation, specifically at 1.0-2.0 g/kg, optimized broiler growth performance, significantly elevating body weight and average daily gain (p < 0.05). While carcass yield improved in a dose-dependent manner, fundamental meat quality-pH and shear force-remained stable. Crucially, CSS inclusion reconfigured cecal ecology, selectively suppressing Escherichia coli and Salmonella sp. while enhancing Lactobacillus populations (p < 0.001). This microbial shift mirrored histological gains, notably enhanced villus height and villus height-to-crypt ratios (p < 0.05). These findings demonstrate that CSS, particularly at 1.0-2.0 g/kg, enhances broiler performance, carcass quality and gut health.},
}

@article {pmid41750824,
year = {2026},
author = {Oh, SC and Lee, SJ and Ding, K and Shen, J and Huang, C and Kang, SN and Reaney, MJT and Kim, YJ and Shim, YY},
title = {Kimchi Fermentation-Driven Detoxification of Flaxseed: Impact on Physicochemical Quality and Antioxidant Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/foods15040632},
pmid = {41750824},
issn = {2304-8158},
support = {RS-2023-00263064//Ministry of Science and ICT/ ; },
abstract = {Flaxseed (Linum usitatissimum L.) is a rich source of α-linolenic acid (ALA) and lignans but contains toxic cyanogenic glycosides (CGs) that limit its application in foods. This study investigated the efficacy of a specialized Lactobacillaceae consortium in detoxifying flaxseed and the subsequent effects of adding this cyanogenic glycoside-depleted flaxseed (CGDF) to a kimchi matrix. Ground flaxseed and CGDF were added to the kimchi seasoning mixture at concentrations of 0.5%, 1.0%, and 2.0% (w/w) and fermented at 4 °C for 8 weeks. Analytical results confirmed that the fermentation process reduced linustatin and neolinustatin to undetectable levels (<500 mg/kg) and reduced total hydrogen cyanide (HCN) to below the Japanese regulatory limit of 10 mg/kg established under the Food Sanitation Act. During fermentation, CGDF-supplemented groups exhibited a delayed decrease in pH and higher retention of free sugars and vitamin C compared to the control and raw flaxseed groups. Notably, the 2.0% CGDF group maintained high oxidative stability of ALA, which we attribute to a putative antioxidant protection mechanism driven by the bioconversion of lignan glycosides into bioactive aglycones. These findings suggest that incorporating biologically detoxified flaxseed into kimchi creates a functional food system that ensures safety while enhancing nutritional stability. Overall, this work provides foundational evidence for developing safe, nutritionally enhanced functional foods within the One Health framework, integrating food safety, microbial ecology, and improved bioactive compound availability.},
}

@article {pmid41750446,
year = {2026},
author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A},
title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/antibiotics15020148},
pmid = {41750446},
issn = {2079-6382},
support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.},
}

@article {pmid41749772,
year = {2026},
author = {Shang, J and Dong, C and Zhou, Q and Chai, J and Wei, Y},
title = {The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/bioengineering13020233},
pmid = {41749772},
issn = {2306-5354},
abstract = {Temperature fluctuations strongly affect microbial viability, often inducing adaptive responses. In this study, we employed the psychrophilic bacterium Bacillus mycoides 41-22 and its associated phage VMY22, originally isolated from the Mingyong Glacier, to investigate phage adaptability under varied temperature conditions. Through selective enrichment at 4 °C, 15 °C, 28 °C, and 32 °C, we observed clear differences in phage infectivity, as assessed by plaque assays, along with genomic mutations and protein structural changes. Notably, mutations predominantly occurred in functional genes (ATPase, endolysin), while the examined structural loci remained conserved. Homology modeling revealed distinct adaptations in protein tertiary structures corresponding to environmental temperatures, suggesting that phage evolution mainly affects post-adsorption processes. Our findings elucidate a novel mechanism of temperature-driven functional protein evolution among cold-adapted bacteriophages (phage) and providing insights into their potential applications in microbial ecology and biotechnology.},
}

@article {pmid41748761,
year = {2026},
author = {de Lima, LVA and da Silva, MF and de Oliveira, LM and de Assis, MCT and Carvalho, ICO and Fuzinatto, IM and Semprebon, SC and de Oliveira Nocetti, RV and Lazarin-Bidoia, D and Nakamura, CV and Felicidade, I and Lepri, SR and Favaron, PO and Dealis, ML and Cabeça, LF and Filho, GA and Mantovani, MS},
title = {PEGylated liposomal fluopsin C triggers cuproptosis and ferroptosis pathways and suppresses 3D tumor spheroid growth in NCI-H460 cells.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {41748761},
issn = {1432-0738},
}

@article {pmid41747730,
year = {2026},
author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C},
title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.021},
pmid = {41747730},
issn = {1097-4172},
abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.},
}

@article {pmid41746386,
year = {2026},
author = {Wang, Z and Wang, Q and Liu, Y and Du, W and Hong, L and Zhou, D and Asiegbu, FO and Wu, P and Ma, X and Wang, K},
title = {Soil Nutrient Availability By Beneficial Bacteria of Forest Trees: From Mechanisms To Applications.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02728-z},
pmid = {41746386},
issn = {1432-184X},
abstract = {As global environmental challenges intensify, enhancing forest health and soil quality has emerged as a crucial area of research. Understanding and application of beneficial bacteria in forestry industry is urgently needed as an environmentally friendly and sustainable approach. Although thousands of patents have been registered for microbial application in agriculture and forestry, the mechanisms and application of beneficial bacteria on the soil nutrient availability have not been well summarized. This review investigated the role of beneficial bacteria in tree growth, particularly their contributions to soil nutrient availability in forest trees. We summarized that beneficial bacteria significantly enhance the availability of essential elements such as nitrogen, phosphorus, potassium, and iron by promoting nutrient cycling and transformation within the soil. This process supports tree growth and improves soil quality. Additionally, beneficial bacteria facilitate plant growth by synthesizing plant hormones and inducing resistance to biotic and abiotic stresses. This review concludes by discussing practical implications of beneficial bacterial colonization and application for enhancing soil nutrient levels, along with potential future research directions. We have enriched the theoretical framework of forest-associated bacteria and provided a scientific basis that can inform forest management and ecological restoration.},
}

@article {pmid41745260,
year = {2026},
author = {Christinaki, AC and Floudas, D and Myridakis, AI and Gonou-Zagou, Z and Kouvelis, VN},
title = {Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {41745260},
issn = {2309-608X},
support = {19620//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph-anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov.},
}

@article {pmid41744634,
year = {2026},
author = {Pérez, E and Sanjuán, E and Jůzl, M and Raposo, A and Saraiva, A and Jaber, JR and Carrascosa, C},
title = {Active Antimicrobial Packaging Systems: Mechanisms of Microbial Control and Applications in Food Preservation.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744634},
issn = {2079-7737},
abstract = {Microbial spoilage and foodborne pathogens remain central challenges in food safety, driven by the metabolic resilience and ecological adaptability of bacteria, yeasts, and molds across diverse food matrices. Active antimicrobial packaging has emerged as a biologically informed strategy that directly targets microbial physiology through controlled release or contact-mediated mechanisms. These systems employ natural antimicrobials, bacteriocins, essential oils, and metal nanoparticles to disrupt cell membranes, inhibit enzymatic pathways, generate reactive oxygen species, or interfere with quorum sensing, resulting in substantial reductions in microorganisms such as Listeria monocytogenes, Salmonella spp., E. coli O157:H7, Pseudomonas spp., Brochothrix thermosphacta, and spoilage fungi. In real food environments, these interventions achieve multi-log reductions and attenuate microbial metabolism, though efficacy varies with pH, water activity, fat content, and storage temperature. Oxygen scavengers further reshape microbial ecology by suppressing aerobic spoilage organisms while inadvertently favoring anaerobic competitors. Despite promising outcomes, concerns regarding nanoparticle migration, microbial resistance potential, and matrix-dependent performance highlight the need for deeper microbiological validation. Future progress will require integrative research linking microbial ecology, packaging material science, and mechanistic toxicology. By aligning with microbial behavior at the cellular and ecosystem levels, active antimicrobial packaging represents a powerful, biologically grounded approach to mitigating foodborne risks.},
}

@article {pmid41744504,
year = {2026},
author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T},
title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0137325},
doi = {10.1128/msystems.01373-25},
pmid = {41744504},
issn = {2379-5077},
abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.},
}

@article {pmid41743866,
year = {2025},
author = {Tarigan, MB and Saragih, RM and Tarigan, KA and Ginting, F},
title = {Antimicrobial resistance and empirical antibiotic use in diabetic foot infections: A retrospective study from Indonesia.},
journal = {Narra J},
volume = {5},
number = {3},
pages = {e2895},
pmid = {41743866},
issn = {2807-2618},
abstract = {Diabetic foot infection (DFI) represents a major complication of diabetes mellitus with significant morbidity, frequently leading to amputation if not optimally managed. The aim of this study was to analyze clinical, microbiological, and antibiotic susceptibility data from patients with type 2 diabetes who presented with foot infections in Indonesia. The retrospective study, conducted at St. Elisabeth Hospital in North Sumatra, Indonesia, predominantly comprised male farmers with a mean diabetes duration of 8.6 years, most of whom exhibited advanced ulcer severity (64.5% at Wagner grade III). Surgical debridement was performed in 79.0% cases, and amputation in 21.0% of cases. Laboratory investigations revealed poor glycemic control (mean HbA1c 10.12%) and biochemical markers indicative of systemic inflammation and renal impairment. Microbial cultures identified a predominance of Gram-negative bacteria (58.1%), primarily Klebsiella pneumoniae, Proteus mirabilis, and Escherichia coli, whereas Gram-positive isolates (41.9%) were dominated by Staphylococcus aureus, including methicillin-resistant strains. Empirical outpatient and inpatient antibiotic regimens commonly included amoxicillin, ciprofloxacin, metronidazole, and ceftriaxone; however, in vitro susceptibility testing demonstrated limited efficacy of β-lactams such as ampicillin and amoxicillin (<10% sensitivity). In contrast, linezolid, amikacin, vancomycin, carbapenems, and fosfomycin exhibited superior activity against the isolated pathogens. These findings emphasize the critical need for empirical antibiotic guidelines tailored to local microbial ecology and resistance profiles, integrated with early surgical management, stringent glycemic control, and multidisciplinary care. This comprehensive approach is essential to reduce the risk of amputation and improve clinical outcomes in tropical, resource-limited settings.},
}

@article {pmid41743643,
year = {2026},
author = {Markfeld, M and Talpaz, I and Biton, B and Maheriniaina Randriamoria, T and Soarimalala, V and Goodman, SM and Nunn, CL and Titcomb, G and Pilosof, S},
title = {Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag026},
pmid = {41743643},
issn = {2730-6151},
abstract = {The occurrence of microbes in animal hosts is highly heterogeneous, shaped by interactions among host traits, environmental context, and microbial diversity. Understanding this heterogeneity is particularly critical for endoparasite infections, where some hosts harbor diverse, high-burden assemblages that elevate disease spread and spillover risk. Yet the mechanisms underlying such heterogeneity remain poorly understood in wild systems, especially at the individual-host level. We addressed this challenge by studying protozoan infections in introduced black rats (Rattus rattus) across environmental gradients in Madagascar. Using network-based stochastic block modeling, we identified three infection profiles capturing meaningful variation in protozoan richness and composition, providing a structured framework for understanding heterogeneity. To uncover the predictors of these profiles, we trained machine-learning models incorporating host traits with environmental variables. Our models consistently outperformed no-skill baselines, with host traits contributing [Formula: see text]40% more to predictions than environmental factors. Body mass and gut microbiome composition emerged as the strongest host predictors, while rat and other non-native species densities were the most influential environmental predictors. These results show that infection heterogeneity arises from the interplay of intrinsic host traits and extrinsic environmental conditions. Our approach illustrates how combining network analysis with predictive modeling can (i) uncover latent heterogeneity in host-microbe associations, (ii) identify the relative contribution of the factors driving this heterogeneity, and (iii) predict host infection profiles. Our framework advances microbial ecology by linking host traits, microbial communities, and environmental context, while also informing disease ecology at human-animal interfaces where zoonotic pathogens circulate.},
}

@article {pmid41743513,
year = {2025},
author = {Hylling, O and Forero-Junco, LM and Ellegaard-Jensen, L and Dedon, PC and Cui, L and Nielsen, TK and Hansen, M and Neve, H and Johansen, A and Kot, W},
title = {Novel Modification Sites of dPreQ0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {6},
number = {4},
pages = {250-258},
pmid = {41743513},
issn = {2641-6549},
abstract = {BACKGROUND: Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting Aminobacter niigataensis, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.

MATERIALS AND METHODS: The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography-mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.

RESULTS: Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the Kleczkowskaviridae family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ0 modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.

CONCLUSIONS: This is the first report of a phage infecting the genus Aminobacter, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.},
}

@article {pmid41743133,
year = {2026},
author = {Zhang, W and Jiang, H and Zhu, Q and Shi, Z and Chen, W and Xu, X and Peng, F and Chi, Y},
title = {Microbial diversity and water quality changes in mangrove sediments in Quanzhou Bay.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743704},
pmid = {41743133},
issn = {1664-302X},
abstract = {This study investigated the diversity, composition, and environmental drivers of bacterial communities in the mangrove sediments of Quanzhou Bay, a subtropical estuary under anthropogenic pressure. Using high-throughput sequencing of the 16S rRNA gene, we analyzed samples from four sites (Fengze-FZ, Jinjiang-JJ, Luojiang-LJ, and Shishi-SS) representing a gradient of terrestrial influence and environmental conditions. The bacterial communities were predominantly composed of Pseudomonadota and Chloroflexi, a pattern consistent with global mangrove ecosystems but with distinct local structuring. Beta-diversity analyses (NMDS/PCA) revealed a significant spatial divergence, with the FZ site forming a distinct cluster separate from JJ, LJ, and SS, correlating with its unique environmental profile. Redundancy analysis (RDA) identified dissolved oxygen (LDO) and salinity as the key environmental factors shaping community structure. Functional prediction indicated a conserved potential for core metabolic processes (e.g., amino acid biosynthesis, bacterial chemotaxis) across sites, suggesting functional redundancy, while differences in the relative abundance of these pathways pointed to adaptive metabolic adjustments along the environmental gradient. Our findings demonstrate that the sedimentary microbial community structure in Quanzhou Bay is primarily shaped by localized environmental heterogeneity, providing critical insights into the microbial ecology of mangroves in urbanized coasts and a baseline for assessing ecosystem health and biogeochemical functioning under anthropogenic influence.},
}

@article {pmid41740962,
year = {2026},
author = {Scheuerl, T and Rivett, DW},
title = {A Concept Using α-Niche Evolution Within Bacterial Communities to Direct β-Niche Evolution of Focal Species.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70255},
doi = {10.1111/1462-2920.70255},
pmid = {41740962},
issn = {1462-2920},
support = {316807//UIBK/ ; 325779//Tyrolian Science Foundation/ ; 101067338//MSCA Postdoctoral Fellowship/ ; EP/X024830/1//EPSRC Postdoc Fellowship/ ; ISS-2021-109666//Vertex Pharmaceuticals Research/ ; },
abstract = {The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits-α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.},
}

@article {pmid41739277,
year = {2026},
author = {Silva, MLOM and Martins, AKS and Sandes, SHC and Alvim, LB and Nunes, ÁC and Camargo, ILBC and Tinoco, HP and Nicoli, JR and Martins, FS},
title = {Isolation and evaluation of antagonistic activity against pathogenic bacteria by Lactobacillus and Enterococcus spp. from the saliva of Speothos venaticus and Chrysocyon brachyurus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41739277},
issn = {1678-4405},
abstract = {UNLABELLED: Saliva plays a crucial role in oral defense across mammals by combining host-derived antimicrobial factors with antagonistic indigenous microbiota. Understanding the composition of the oral lactic microbiota in wild canids may provide valuable insights into microbial ecology and animal health. In this study, Lactobacillus and Enterococcus spp. isolated from the saliva of South American bush dogs (Speothos venaticus) and maned wolves (Chrysocyon brachyurus) were enumerated, identified, and evaluated for their antagonistic activity against pathogenic bacteria. For bacterial isolation, MRS agar and BHI agar supplemented with sodium azide (BHI-SA) were used for Lactobacillus and Enterococcus, respectively. Identification of the bacterial isolates was performed using PCR-ARDRA and multiplex PCR. Antagonistic activity was assessed using a double-layer agar diffusion assay, which detects diffusible inhibitory effects without identifying the compounds involved. A total of 23 bacterial isolates were obtained from BHI-SA and 24 from MRS for bush dogs, while 15 were recovered from BHI-SA and 23 from MRS for maned wolves. Salivary bacterial counts ranged from 4.0 to 5.0 log10 CFU/mL. In bush dogs, Enterococcus faecalis and Enterococcus faecium were identified, while E. faecalis and Enterococcus hirae were found in maned wolves. Limosilactobacillus reuteri, Lactiplantibacillus paraplantarum, Lactiplantibacillus plantarum and Lactobacillus johnsonii were isolated from bush dogs, while Ligilactobacillus salivarius and Latilactobacillus curvatus were identified in maned wolves. Antagonistic activity against indicator pathogens was more frequent among Lactobacillus isolates. These results suggest that the antibacterial properties observed in the saliva of these wild canids may be partly attributed to indigenous Lactobacillus and Enterococcus species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01877-0.},
}

@article {pmid41739174,
year = {2026},
author = {Sánchez-Astráin, B and Borrego-Ramos, M and Viso, R and de la Hoz, CF and Blanco, S and Juanes, JA},
title = {Unravelling Diatom-Microbiome Dynamics in the Red Alga Gelidium Corneum (Florideophyceae, Rhodophyta).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02723-4},
pmid = {41739174},
issn = {1432-184X},
}

@article {pmid41738851,
year = {2025},
author = {Kim, M and Hakeem, WGA and Rothrock, MJ},
title = {Key Farm-to-Fork Factors Influencing E. coli Levels in Pastured Poultry Production.},
journal = {Avian diseases},
volume = {69},
number = {4},
pages = {395-406},
doi = {10.1637/aviandiseases-D-25-00033},
pmid = {41738851},
issn = {1938-4351},
mesh = {Animals ; *Escherichia coli/isolation & purification/physiology ; *Animal Husbandry/methods ; *Chickens ; Feces/microbiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; Soil Microbiology ; *Poultry Diseases/microbiology/epidemiology ; Farms ; Southeastern United States ; },
abstract = {Pastured poultry farms offer a unique model for investigating microbial ecology in less controlled environments, presenting challenges and opportunities for food safety management. This study aims to identify the key factors that influence Escherichia coli levels with two complementary modeling approaches: a linear mixed-effect model (LMM) and a random forest (RF) model. Data were collected from 11 pastured poultry farms in the southeastern United States from 2014 to 2017. Five sample types were analyzed: soil (n = 812), feces (n = 817), ceca (n = 206), postprocessing whole carcass rinse (WCR-P; n = 235), and final product whole carcass rinse (WCR-F; n = 230). Two different sets of predictor variables were used separately: 1) 32 farming practices and 26 physicochemical properties and 2) 80 meteorological factors. The model performance was compared with the randomized mean squared error (RMSE) with a test dataset. LMM was not used for meteorological factors because of the multicollinearity. Significant differences (α = 0.05) in E. coli levels were observed between all sample types, with feces samples showing the highest level. Compared to LMMs, RF models generally showed higher predictive accuracy (lower RMSE) on the test dataset. For soil samples, higher pH and sodium levels were linked to higher E. coli levels. The same trend with pH was observed in fecal samples. WCR-P samples showed that the organic acid treatment in the rinse water led to lower E. coli levels than other treatments. In WCR-F samples, longer storage time led to lower E. coli levels. Meteorological factors showed a weaker relationship with E. coli levels compared to farming practices and physicochemical properties, but in soil samples, mild and stable temperature played an important role in E. coli survival. This study can help stakeholders develop data-driven management strategies targeting key factors to aid in the reduction of food safety and animal health risk.},
}

Animals
*Escherichia coli/isolation & purification/physiology
*Animal Husbandry/methods
*Chickens
Feces/microbiology
*Escherichia coli Infections/veterinary/microbiology/epidemiology
Soil Microbiology
*Poultry Diseases/microbiology/epidemiology
Farms
Southeastern United States

@article {pmid41736367,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS},
title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.71150/jm.2511012},
pmid = {41736367},
issn = {1976-3794},
abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.},
}

@article {pmid41735517,
year = {2026},
author = {Piaszczyk, W and Lasota, J and Foremnik, K and Błońska, E},
title = {Tree species determine soil microbial diversity: variation in fungal and bacterial communities in temperate forests.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41297-6},
pmid = {41735517},
issn = {2045-2322},
support = {2022/06/X/NZ9/00006//Narodowe Centrum Nauki/ ; },
abstract = {This study investigates the influence of three deciduous tree species: small-leaved linden (Tilia cordata), common beech (Fagus sylvatica), and sessile oak (Quercus petraea) on soil microbial diversity in temperate forest ecosystems. Conducted on loess soils in southern Poland, the research clarifies species-specific effects on soil microbiota and chemical properties, providing insights into tree-microbe-soil interactions in forest environments. Soil samples were collected from monospecific stands and analysed using next-generation sequencing (NGS). Fungal and bacterial DNA was extracted, and libraries targeting the ITS1 (fungi) and 16 S rRNA V3-V4 (bacteria) regions were sequenced using the Illumina MiSeq platform. Microbial communities were evaluated in relation to soil pH, nutrient content, and exchangeable cations. Linden soils had the highest pH (5.1-7.0) and calcium content (18.9 cmol(+)·kg[-1]), while beech soils were the most acidic (pH 3.8-5.7) with the lowest calcium (8.0 cmol(+)·kg[-1]). Fungal communities were dominated by Basidiomycota, Ascomycota, and Mortierellomycota, with varying proportions across species. Bacterial diversity was highest in linden and oak stands. Dominant bacterial phyla included Actinobacteriota, Proteobacteria, and Acidobacteriota. Each tree species hosted a distinct microbial community, reflecting its impact on soil properties and microbial structure. Tree species significantly shape soil microbial diversity and chemistry. Incorporating microbial data into forest management may enhance soil function, biodiversity conservation, and ecosystem resilience. Broader spatial sampling is recommended to generalize findings.},
}

@article {pmid41734518,
year = {2026},
author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD},
title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110940},
doi = {10.1016/j.vetmic.2026.110940},
pmid = {41734518},
issn = {1873-2542},
abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.},
}

@article {pmid41733768,
year = {2026},
author = {Zhou, S and Yao, Y and Yuan, R and Chu, W},
title = {Comparative Microbiome Analysis of Rhodiola fastigiata Rhizosphere Versus Bulk Soil in Xizang with Targeted Isolation of Rhizosphere-Derived Functional Strains.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41733768},
issn = {1559-0305},
support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Rhodiola fastigiata, a critically endangered medicinal plant of the Qinghai-Xizang Plateau, faces severe threats from habitat degradation. This study aimed to support its microbial-assisted conservation by characterizing the rhizosphere microbiome and isolating functional plant growth-promoting (PGP) bacteria. Using high-throughput sequencing of the 16S rRNA gene and ITS region, we found the rhizosphere community to be distinct and enriched in key taxa (e.g., Sphingomonas, Mortierella). Metabolic predictions suggested upregulated stress-adaptive pathways. Crucially, from 126 isolates, we obtained four Bacillus strains that concurrently produce protease, amylase, and cellulase and solubilize phosphate-quantifying a multifunctional PGP profile critical for nutrient-poor soils. These culturable, spore-forming strains provide direct resources for developing synthetic inoculants. Our work bridges microbial ecology with applied biotechnology, delivering both a foundational microbial map and candidate strains to enable the cultivation and conservation of this endangered species in extreme environments.},
}

@article {pmid41733363,
year = {2026},
author = {Ziegert, ZA and Troester, A and Frebault, J and Goffredo, P and Gaertner, WB and Jahansouz, C and Staley, C},
title = {SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0397325},
doi = {10.1128/spectrum.03973-25},
pmid = {41733363},
issn = {2165-0497},
abstract = {The intestinal microbiota plays a critical role in post-surgical wound healing following bowel resection; however, perioperative, prophylactic antibiotic administration may deleteriously affect it. We previously used 16S rRNA amplicon sequencing of stool samples to assess perioperative and longitudinal changes in the microbiome through 6 months in patients undergoing (i) colonoscopy after mechanical bowel prep (MBP) alone, (ii) non-resectional colorectal surgery after MBP with oral antibiotics and prophylactic intravenous antibiotics no longer than 24 h post-operative (surgical bowel prep [SBP]), and (iii) resectional colorectal surgery with SBP. Our objective in this study was to investigate the translational utility of SparCC co-occurrence networking to uncover biologically relevant patterns. Network topological parameters and hub species were calculated using NetCoMi, and permutational statistical tests were used to compare parameters. Network similarity among cohorts and time points generally matched changes in beta diversity, except in the resectional cohort, where all networks could not be differentiated statistically. Similarity in centrality measures among hub species was frequently significantly less similar than expected by chance and corresponded to an increased edge density and modularity, suggesting the latter parameters may reflect re-stabilization of the microbiome following surgery. We further noted the infrequently reported genera Enterocloster and Ruthenibacter were hub species during time points associated with surgical recovery, suggesting potentially novel roles for these genera in wound healing. Streptococcus, frequently implicated in surgical site infections at our center, was also frequently positively associated with Blautia throughout all networks, suggesting an increasing abundance of commensal bacteria serves as a prophylactic strategy.IMPORTANCEThis study employs the emerging approach of co-occurrence networking to assess ecological dynamics in the microbiome following colonoscopy and colorectal surgery. We expand upon applications of this approach to determine hub species and investigate clinically translational interpretations of network topological parameters in the context of recovery across three different trajectories of perturbation. Our results provide a context in which to interpret these network parameters biologically and represent a foundational step in beginning to quantitatively leverage network-based approaches to study microbial ecology. Furthermore, we identify network hub taxa that may play previously unexplored roles in wound healing.},
}

@article {pmid41733159,
year = {2026},
author = {Diab, E and Du, C and Tigani, W and Elsayed, SS and van Wezel, GP},
title = {Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01626},
pmid = {41733159},
issn = {1520-6025},
abstract = {The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.},
}

@article {pmid41732360,
year = {2026},
author = {Yash, and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P},
title = {Dataset on ecological health and microbial communities of coastal aquaculture ponds from surrounding region of Sundarban mangroves.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112542},
pmid = {41732360},
issn = {2352-3409},
abstract = {Integrated Mangrove Aquaculture (IMA) and Sustainable Aquaculture in Mangrove Ecosystem Fisheries (SAIME) are key activities undertaken across coastal regions globally to meet growing demand for brackish-water aquaculture products through sustainable practices. An in-depth biomonitoring study was conducted to map the ecological health of IMA and non-IMA aquaculture ponds in the surrounding region of the Indian Sundarbans mangroves located along the northeast coast of Bay of Bengal. Surface water samples were collected from six aquaculture ponds, four IMA (IMA_C1, IMA_C3, IMA_DB1, and IMA_DB4) and two non-IMA (C6_NM and DB5_NM) in the month of October 2022, for characterizing niche-specific biological communities using the environmental DNA (eDNA) approach. During sampling, in-situ environmental parameters were recorded. Mangrove litter-derived phenolics (tannic and gallic acids) and dissolved nutrients were estimated using a UV-Vis spectrophotometer, while dissolved organic carbon (DOC) was measured with the elemental analyzer. Metal and metalloid concentrations were determined by inductively coupled plasma mass spectrometry approach (ICP-MS). IMA ponds showed ideal conditions for shrimp aquaculture, with pH ranging from 7.913 to 8.633 and dissolved oxygen (DO) between 5.32 and 6.03 mg/L, indicating no hypoxic conditions despite higher concentrations of phenolics. High-throughput sequencing (HTS) based on Oxford Nanopore Technologies (ONT) sequencing chemistry was undertaken on the MinION platform, revealing the predominance of Proteobacteria among prokaryotes and Bacillariophyta as well as Chlorophyta among eukaryotes from extracted eDNA in each studied pond. Additionally, members of the family Cyprinidae were also detected, reflecting the biodiversity of fish population in these ponds. Functional gene profiling indicated signatures associated with nitrogen, phosphorus, sulphur, potassium and iron acquisition and metabolism, along with pathways related to aromatic compound degradation. Overall, dissolved nutrients, dissolved organic carbon (DOC), metal and metalloid ion concentrations as well as structure and functional profiles of biological communities provide a comprehensive basis for evaluating the ecological health of aquaculture ponds. This study generates important baseline information for long-term monitoring and represents the first eDNA-based high-throughput sequencing assessment of IMA and non-IMA aquaculture ponds from surface water in close proximity to the Sundarbans mangrove.},
}

@article {pmid41729252,
year = {2026},
author = {Li, Y and Chen, D and Liu, X and Li, Y and Chen, F},
title = {Zooplankton-associated Bacterial Communities are Dominated by Host-Specific Rather than Environmentally Random Taxa.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02702-9},
pmid = {41729252},
issn = {1432-184X},
}

@article {pmid41725809,
year = {2026},
author = {Zenati, K and Braun, SD and Belhadi, D and Moawad, AA and Müller, E and Diezel, C and Brandt, C and Mostefaoui, R and Monecke, S and Zaidi, FZ and Belmahdi, M and Touati, A and Ehricht, R},
title = {The oral cavity as a reservoir for resistance- and hypervirulence-associated genes of Klebsiella pneumoniae in hospitalized patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1751947},
pmid = {41725809},
issn = {1664-302X},
abstract = {INTRODUCTION: This study investigated the epidemiology and distribution of carbapenem resistance and virulence genes in Klebsiella pneumoniae strains isolated from the oral cavity of hospitalized patients, highlighting their role as reservoirs in non-epidemic contexts.

METHODS: Carbapenem-resistant Klebsiella spp. were isolated from the oral cavity of 180 hospitalized patients in medical wards at two hospitals in Bejaia, Algeria. Screening for carbapenem resistance was performed on oral mucosa and saliva using Carba-MTL broth. Antibiotic susceptibility was assessed with the Vitek2 system and interpreted according to EUCAST guidelines. Whole genome sequencing (WGS) was carried out using Oxford Nanopore Technologies, with ABRicate used for resistance/virulence gene detection and Kleborate for hypervirulence assessment. Whole-genome sequences were further examined to identify single-nucleotide polymorphisms (SNPs) and to reconstruct a SNP-based phylogenetic tree in order to assess the genetic relatedness among the isolates.

RESULTS: Twenty Klebsiella strains were identified as K. pneumoniae. Among these, 85% were carbapenem-resistant, carrying OXA-48 (80%) or NDM-5 (5%), and all harbored blaCTX-M-15. WGS of the 20 K. pneumoniae strains revealed a broad resistome, including β-lactamases (CTX-M-15, CMY-4, OXA-1, TEM-1), sulfonamide (sul1, sul2), aminoglycoside (aac(3)-IIa, aadA2, aph(3')-VI, armA, strA, strB), trimethoprim (dfrA12, dfrA5, dfrA14), and tetracycline (tetA). Quinolone resistance was linked to QRDR mutations (gyrA S83I, parC S80I) and plasmid-mediated genes (qnrS1, qnrB10, qnrS10, aac(6')-Ib-cr). Five distinct sequence types (STs) were identified, including high-risk clones ST13 and ST48. Virulence profiling revealed yersiniabactin (85%), frequently linked to ICEKp elements (ICEKp4, ICEKp10), and colibactin (40%) among OXA-48 isolates. Notably, a single K. pneumoniae isolate harboring NDM-5 (K21) carried both hypervirulence markers (ybt9/ICEKp3, iuc1, rmp1/kpvp-1) and carbapenem resistance, documenting, for the first time in Algeria, the convergence of these traits in oral isolates. ICEKp was identified as the key vehicle for dissemination of yersiniabactin and colibactin, and a novel association between ICEKp and kpvp-1 was observed. Capsular typing showed predominance of K57-O1/O2v2 among OXA-48 producers and K27/O4 among NDM-5 strains.

CONCLUSION: This study provides the first evidence in Algeria of OXA-48- and NDM-5-producing K. pneumoniae in the oral cavity of hospitalized patients. The coexistence of carbapenem resistance and hypervirulence underscores the oral cavity as a critical reservoir, potentially fueling nosocomial infections and the dissemination of high-risk clones within hospitals and the wider community.},
}

@article {pmid41720792,
year = {2026},
author = {Mohammadzadeh, R and Mahnert, A and Zurabishvili, T and Wink, L and Kumpitsch, C and Habisch, H and Sprengel, J and Filek, K and Mertelj, P and Pernitsch, D and Hingerl, K and Durdevic, M and Gorkiewicz, G and Diener, C and Loy, A and Kolb, D and Trautwein, C and Madl, T and Moissl-Eichinger, C},
title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69711-7},
pmid = {41720792},
issn = {2041-1723},
support = {10.55776/P32697//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
abstract = {The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of Methanobrevibacter smithii in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of M. smithii with CRC-causing bacteria such as Fusobacterium nucleatum, including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.},
}

@article {pmid41720095,
year = {2026},
author = {Wang, T and George, AB and Maslov, S},
title = {Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101491},
doi = {10.1016/j.cels.2025.101491},
pmid = {41720095},
issn = {2405-4720},
abstract = {Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counterintuitive effect considering their dependence on essential resources from other species. To address the ecological roles of auxotrophs, our study introduced a consumer-resource model (CRM) to capture the complex higher-order interactions within these communities. We also developed an intuitive graphical and algebraic framework, which assesses the feasibility of auxotroph communities and their stability under resource fluctuations and biological invasions. Validated against experimental data from synthetic E. coli auxotroph communities, the model accurately predicted outcomes of community assembly. Our findings highlight the critical role of higher-order interactions and resource dependencies in maintaining the diversity and stability of microbial ecosystems dominated by auxotrophs. A record of this paper's transparent peer review process is included in the supplemental information.},
}

@article {pmid41716220,
year = {2026},
author = {Gomes-Neto, JC and Crook, A and Hestrin, R and Li, G and Liew, CS and Rosa, G and Singh, KD and Tuggle, CK and Summers, KL and Valdes, C and Fahlgren, N and Clarke, J},
title = {Challenges and opportunities: computational biology and the future of agriculture.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag003},
pmid = {41716220},
issn = {2635-0041},
abstract = {MOTIVATION: The world of agriculture is rapidly changing with advances in artificial intelligence and demands for greater feed and food security considering environmental and sustainability challenges. The 30th Conference on Intelligent Systems in Molecular Biology (ISMB) held in July 2022 featured an invited session on the role of computational biology in Digital and Precision Agriculture. This session featured presentations by experts from various subdisciplines on novel research discoveries and a panel discussion on Digital Agriculture at Scale. Topics discussed during the session included genetics, epigenetics, and genomics of agriculturally relevant species; foodborne pathogen genomics and epidemiology; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and findable, accessible, interoperable, and reproducible (FAIR) data standards; biotechnology; and soil microbial ecology and biogeochemistry.

RESULTS: We present several of the current and future challenges and opportunities for computational biology in agriculture including why these challenges are important to address, what barriers exist, and what skills and competencies are required to be successful as a computational biologist in agriculture. We intend this summary to engage the computational biology community and attract them to the opportunities available for interesting and impactful work toward ensuring sustainable food security.},
}

@article {pmid41715924,
year = {2026},
author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K},
title = {Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2026.02.022},
pmid = {41715924},
issn = {1542-0086},
abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared to archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.},
}

@article {pmid41715245,
year = {2026},
author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD},
title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {22},
pmid = {41715245},
issn = {2524-4671},
abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.

RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.

CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.},
}

@article {pmid41714654,
year = {2026},
author = {Rabaey, JS and Lewis, ASL and Attermeyer, K and Aurich, P and Bansal, S and Bartosiewicz, M and Bertolet, BL and Bussmann, I and Cadieux, SB and Calamita, E and Capelli, C and Carey, CC and Cillero, C and Clayer, F and D'Ambrosio, SL and Davidson, TA and Deemer, BR and Denfeld, BA and Eckert, W and Esposito, C and Ford, P and Gorsky, A and Griffiths, NA and Grossart, HF and Hamilton, DP and Holgerson, MA and Huser, BJ and Iwata, T and Jansen, J and Jones, SE and Juutinen, S and Kortelainen, P and Koschorreck, M and Kragh, T and Laas, A and Larmola, T and Läubli, S and Laurion, I and Lehmann, MF and Liu, L and Martikainen, PJ and Matoušů, A and McCord, SA and Montes-Pérez, JJ and Nizzoli, D and Ordóñez, C and Peacock, M and Pilla, RM and Prėskienis, V and Pu, J and Riis, T and Saarela, T and Santoso, AB and Schubert, CJ and Sepulveda-Jauregui, A and Sherman, BS and Sø, JS and Stenehjem, KJ and Strock, KED and Tsuchiya, K and Wendt-Potthoff, K and Weyhenmeyer, GA and Znachor, P and Zopfi, J},
title = {Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06751-0},
pmid = {41714654},
issn = {2052-4463},
abstract = {Lakes, ponds, and reservoirs (hereafter: "lakes") are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Emissions of CO2 and CH4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO2 and CH4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.},
}

@article {pmid41714186,
year = {2026},
author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W},
title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag037},
pmid = {41714186},
issn = {1751-7370},
abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.},
}

@article {pmid41713418,
year = {2026},
author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD},
title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.007},
pmid = {41713418},
issn = {1097-4172},
abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
}

@article {pmid41713400,
year = {2026},
author = {Wang, XW and Wang, T and Liu, YY},
title = {Artificial intelligence for microbiology and microbiome research.},
journal = {Cell systems},
volume = {17},
number = {2},
pages = {101531},
doi = {10.1016/j.cels.2026.101531},
pmid = {41713400},
issn = {2405-4720},
mesh = {*Artificial Intelligence/trends ; *Microbiota/physiology ; Humans ; Machine Learning ; *Microbiology/trends ; },
abstract = {Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine-learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We first introduce foundational AI techniques and offer guidance on choosing between traditional machine-learning and sophisticated deep-learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas from taxonomic profiling, functional annotation and prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, and clinical microbiology to prevention and therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.},
}

*Artificial Intelligence/trends
*Microbiota/physiology
Humans
Machine Learning
*Microbiology/trends

@article {pmid41708342,
year = {2026},
author = {Alfahl, Z and Lynch, R and O'Dwyer, C and Kelly, JP},
title = {Medical versus science students: Knowledge, perceptions and learning of core pharmacology concepts.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70498},
pmid = {41708342},
issn = {1365-2125},
abstract = {AIMS: Pharmacology is a core discipline underpinning both medical and biomedical science education, essential for understanding drug action, safety and therapeutic efficacy. This study compared pharmacology knowledge, perceptions and learning experiences between second-year medical and science students to evaluate how effectively each curriculum supports acquisition of internationally defined core pharmacology concepts.

METHODS: A mixed-methods design was employed, involving pre- and post-module surveys and curriculum mapping against the global pharmacology core concept framework. Quantitative data were analysed using chi-squared tests, while qualitative responses were evaluated thematically. Participants included students enrolled in MD214 Introduction to Pharmacology (medical) and PM208 Fundamental Concepts in Pharmacology (science) at the University of Galway.

RESULTS: Medical students demonstrated stronger baseline and post-module understanding of pharmacokinetic and pharmacodynamic principles, particularly in applied pharmacokinetics such as drug-drug interactions and variability in drug response. Science students showed significant improvement over time, reflecting effective conceptual learning. Both cohorts reported positive perceptions of module relevance and teaching effectiveness (mean scores 7.7-8.9/10) and moderate to high confidence in mastering core concepts. YouTube and textbooks were the most common supplementary resources. Curriculum mapping showed alignment with 23 of 24 core concepts in the medical module and 20 in the science module.

CONCLUSIONS: Medical students exhibited greater initial competence and perceived relevance, whereas science students benefited substantially from targeted instruction. Findings highlight the value of concept-based, contextually integrated pharmacology teaching and support continued curriculum development guided by international core concept frameworks.},
}

@article {pmid41705859,
year = {2026},
author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM},
title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0134625},
doi = {10.1128/mra.01346-25},
pmid = {41705859},
issn = {2576-098X},
abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.},
}

@article {pmid41705204,
year = {2026},
author = {Verbunt, J and Mennens, L and Jocken, J and Blaak, EE and Savelkoul, P and Stassen, FRM},
title = {From food to vesicle: nutritional influences on gut microbial inflammatory signaling.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1756462},
pmid = {41705204},
issn = {2296-861X},
abstract = {Diet is a pivotal determinant of gut microbial ecology, giving not only rise to specific bacterial compositionality but also its functional output. Studying functional readouts-such as microbial metabolite production-could provide a more accurate and mechanistically informative measure of intervention outcome than traditional compositional profiling alone. Bacterial membrane vesicles (bMVs) are gaining attention as mediators of microbial metabolism and output. These nanoparticles are selectively released as carriers of bioactive proteins, lipids, nucleic acids, and metabolites reflective of the activity of the parent bacteria. Importantly, bMVs are rigid, can efficiently be isolated from feces, and are able to stably transport their cargo to interact with the host. In interacting with immune cells or pathogen recognition receptors, they can potentiate inflammatory responses. Given their extensive, multifaceted involvement in inter-Kingdom communication, bMVs represent an important biomarker for evaluating dietary modulation of gut microbial function. We propose that characterization of gut-derived bMVs offers a highly sensitive, mechanistically grounded approach to titrating impact of dietary interventions. By capturing shifts in microbial metabolic activity and inflammatory potential, bMV-based assessments could complement or surpass traditional measures of microbiome compositional change. Integrating bMV profiling into dietary intervention studies may therefore provide new insight into the functional consequences of diet-microbiome interactions and help refine strategies aimed at reducing inflammation and promoting host health.},
}

@article {pmid41704769,
year = {2026},
author = {Yinhang, W and Xueli, J and Zheng, W and Xiaojian, Y and Shu, X and Qingjie, Z and Ying, L and Shuwen, H},
title = {Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114664},
pmid = {41704769},
issn = {2589-0042},
abstract = {The gut microbiota is a key hallmark of colorectal cancer (CRC), yet gut fungi remain understudied. We characterized the gut fungal landscape and its associations with bacteria, metabolites, and trace elements in CRC using fecal samples from healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). Fungal annotation was performed using genomic data from NCBI (PRJNA833221) as reference. Fungal diversity increased in CRC patients, with seven genera showing differential abundance. Rhizopus was specifically enriched in CRC, while Sporisorium, etc. enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacteria and three fungi) that effectively distinguished intestinal disease groups (AUC = 0.89). Structural equation modeling revealed three fungal markers-Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera-that influence bacterial-metabolite-trace element networks. This study delineates the gut fungal atlas in CRC and reveals complex cross-kingdom interactions, offering new insights into CRC pathogenesis.},
}

@article {pmid41703880,
year = {2026},
author = {Mipun, P and Sarma, P and Dey, G and Terangpi, L and Hajong, B and Chakraborty, D and Kshetriya, D and Mandal, SM and Dinata, R and Baindara, P},
title = {Ethnic fermentation secrets of Northeast India and emerging functional food insights.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118431},
doi = {10.1016/j.foodres.2026.118431},
pmid = {41703880},
issn = {1873-7145},
mesh = {India ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; *Functional Food/microbiology ; *Food Microbiology ; *Ethnicity ; Probiotics ; },
abstract = {Northeast India is home to an incredible variety of ethnic fermented foods, shaped over centuries by cultural wisdom and adaptation to the local environment. From bamboo shoots, soybeans, and rice to fish, dairy, vegetables, and traditional beverages, these foods are deeply woven into daily life and are rich in beneficial microorganisms with probiotic potential. Understanding the microbial ecology, biochemical transformations, and functional metabolites of Northeast India's traditional fermented foods provides a scientific basis for improving safety, identifying bioactive ingredients, and guiding the development of next-generation fermented products. This review brings together insights from ethnomicrobiological surveys and culture-based studies to explore the microbes, fermentation pathways, and biochemical changes that give these foods their distinctive qualities, as well as their nutritional benefits and safety considerations. We highlight lesser-known products, examine toxin-producing pathogens, and profile antimicrobial peptides (AMPs), uncovering varying levels of pathogen risk across products. Additionally, fermentation space analysis reveals exciting opportunities to create new foods by creatively combining local ingredients. Finally, we look at how modern tools, including artificial intelligence (AI) and machine learning (ML), can help scale up production, standardize quality, and ensure safety. Overall, by blending traditional knowledge with modern biotechnology and AI, these unique fermentation foods could find their place globally while preserving their cultural roots.},
}

India
*Fermentation
*Fermented Foods/microbiology
Humans
*Functional Food/microbiology
*Food Microbiology
*Ethnicity
Probiotics

@article {pmid41568973,
year = {2026},
author = {Downing, BE and Gupta, D and Shalvarjian, KE and Nayak, DD},
title = {Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.},
journal = {Journal of bacteriology},
volume = {208},
number = {2},
pages = {e0044825},
doi = {10.1128/jb.00448-25},
pmid = {41568973},
issn = {1098-5530},
support = {F32GM150233/NH/NIH HHS/United States ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation/ ; S589706//U.S. Department of Energy/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation/ ; Beckman Young investigator Award//Arnold and Mabel Beckman Foundation/ ; Searle Scholars Award//Kinship Foundation/ ; 202299857//National Science Foundation Graduate Research Fellowship Program/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Methanosarcina/metabolism/genetics ; *Energy Metabolism ; Acetates/metabolism ; *Carbon/metabolism ; Archaeal Proteins/metabolism/genetics ; Gene Expression Regulation, Archaeal ; Acetyl Coenzyme A/metabolism ; },
abstract = {UNLABELLED: Methanogenic archaea (methanogens) are microorganisms that obligately produce methane as a byproduct of their energy metabolism. While most methanogens grow on CO2+H2, isolates of the genera Methanosarcina and Methanothrix can use acetate as the sole substrate for methanogenesis. Methanogenic growth on acetate, i.e., acetoclastic methanogenesis, is hypothesized to require two distinct genetic modules: one for the activation of acetate to acetyl-CoA and another for producing a chemiosmotic gradient using electrons derived from ferredoxin. In Methanosarcina spp., the activation of acetate to acetyl-CoA is mediated by acetate kinase (Ack) and phosphotransacetylase (Pta), whereas Methanothrix spp. encode AMP-forming acetyl-CoA synthetases (Acs). The Rhodobacter nitrogen fixation complex (Rnf) or energy-converting hydrogenase (Ech) is critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:methanophenazine oxidoreductase-like complex (Fpo') likely plays an analogous role in Methanothrix spp. Here, we tested the proposed modularity of these pathways to facilitate acetoclastic methanogenesis. First, we surveyed over 100 genomes within the class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations that might support acetoclastic methanogenesis. Our results indicate that Acs, while functional, cannot replace Ack+Pta to rescue acetate growth in M. acetivorans. Similarly, the Fpo' bioenergetic complex cannot replace Rnf. As such, our work suggests that, in addition to horizontal gene transfer of core catabolic modules, acetoclastic metabolism in methanogens requires changes to core energy metabolism too.

IMPORTANCE: A large fraction of biogenic methane is derived from acetate, yet acetoclastic methanogens, i.e., methanogens that grow on acetate, remain poorly characterized due to their slow growth. Two groups of methanogens, Methanosarcina spp. and Methanothrix spp., perform acetoclastic methanogenesis using distinct sets of genes for acetate activation and energy conservation. It is widely hypothesized that these genetic modules from Methanosarcina spp. and Methanothrix spp. are functionally analogous and would thus be interchangeable. To test this hypothesis, we engineered different combinations of modules for acetoclastic growth in Methanosarcina acetivorans. Our results challenge this hypothesized paradigm of modularity, and we posit that other changes to the carbon and electron transfer pathways are crucial for the emergence of acetoclastic methanogenesis.},
}

*Methane/metabolism/biosynthesis
*Methanosarcina/metabolism/genetics
*Energy Metabolism
Acetates/metabolism
*Carbon/metabolism
Archaeal Proteins/metabolism/genetics
Gene Expression Regulation, Archaeal
Acetyl Coenzyme A/metabolism

@article {pmid41703847,
year = {2026},
author = {Gil, MI and Tudela, JA and Illán, G and Hernández, N and Andújar, S and Sabater, D and Allende, A and Truchado, P},
title = {Industrial-scale application of bacteriophages on baby spinach: One-year study of Listeria control, quality and microbial community shifts.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118384},
doi = {10.1016/j.foodres.2026.118384},
pmid = {41703847},
issn = {1873-7145},
mesh = {*Spinacia oleracea/microbiology ; *Bacteriophages ; *Food Microbiology/methods ; *Listeria/virology ; Listeria monocytogenes/virology ; Microbiota ; *Food Preservation/methods ; Food Handling/methods ; Food Contamination/prevention & control ; },
abstract = {Bacteriophages have emerged as promising biocontrol agents against pathogenic bacteria due to their strong antimicrobial activity and host specificity. In this study, we evaluated a previously validated industrial bacteriophage cocktail (PhageGuard Listex™) for its performance on baby spinach, focusing on product quality and microbial community dynamics. Twenty industrial trials conducted over one year compared non-treated and phage-treated baby spinach samples after processing (day 0) and after 10 days of storage under commercial (3 d at 4 °C followed by 7 d at 7 °C) and abusive (continuous 10 °C) temperature conditions. Phage stability was confirmed in the application solution and persistence on the product surface after storage. Although Listeria monocytogenes was not detected in any sample (0/600), the proportion of samples positive for Listeria spp. was significantly lower in the phage-treated group (6%) than in the non-treated group (12%). The preventive phage application did not affect headspace gas composition, sensory attributes, or objective color parameters. Quality deterioration was observed only at 10 °C, regardless of phage treatment. Despite the reduction in Listeria spp. prevalence, microbial diversity and community structure were unaffected by phage application, consistent with the low relative abundance of Listeria spp. in the microbiota and the narrow host range of the phage cocktail; storage conditions, particularly temperature, were the most influential factor affecting bacterial taxonomic composition. The relative abundance of Pseudomonas and Flavobacterium increased during storage, while Bacillus and Exiguobacterium decreased. These findings support the feasibility of using this bacteriophage-based treatment as a preventive intervention that does not affect product quality and preserves the natural microbial ecology of baby spinach during storage.},
}

*Spinacia oleracea/microbiology
*Bacteriophages
*Food Microbiology/methods
*Listeria/virology
Listeria monocytogenes/virology
Microbiota
*Food Preservation/methods
Food Handling/methods
Food Contamination/prevention & control

@article {pmid41703844,
year = {2026},
author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y},
title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118381},
doi = {10.1016/j.foodres.2026.118381},
pmid = {41703844},
issn = {1873-7145},
mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; },
abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.},
}

*Fermentation
*Phenols/metabolism/analysis
*Plant Leaves/microbiology/metabolism/chemistry
*Microbiota
*Tea/microbiology/chemistry/metabolism
*Metabolome
Anaerobiosis
Metabolomics/methods
Bacteria/metabolism
*Camellia sinensis/microbiology
Flavonoids/metabolism

@article {pmid41700860,
year = {2026},
author = {Machushynets, NV and Elsayed, SS and Du, C and Lysenko, V and de la Cruz, M and Sanchez, P and Genilloud, O and Martin, NI and Liles, MR and van Wezel, GP},
title = {Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149625},
doi = {10.1128/msystems.01496-25},
pmid = {41700860},
issn = {2379-5077},
abstract = {The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin, and tridecaptins. Here, we use a targeted mass spectrometry query language (MassQL)-based approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics-guided and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery.IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs). A collection of plant-associated Paenibacillus spp. were analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with mass spectrometry query language queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus, we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new sub-family of bacitracins active against multidrug-resistant gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.},
}

@article {pmid41700805,
year = {2026},
author = {Zhou, S and Bai, X and Xue, B and Chu, W},
title = {A Vaginal Microbiota-Ovary Axis in Chemotherapy-Accelerated Ovarian Aging: Single-Cell Insights into Cellular Dysregulation.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag042},
pmid = {41700805},
issn = {1529-7268},
abstract = {BACKGROUND: Chemotherapy-induced premature ovarian failure (POF) represents a major challenge to female reproductive health, yet the potential regulatory role of vaginal microbiota in this process remains largely unexplored.

RESULTS: Using a well-established model of chemotherapy-induced ovarian aging, we observed significant disruptions in vaginal microbial ecology characterized by depletion of Lactobacillus species and concomitant enrichment of pathogenic bacteria. Microbiota transplantation effectively reversed these dysbiosis patterns and restored ovarian function. Single-cell transcriptomic analysis revealed that microbial intervention promoted the recovery of granulosa and luteal cell populations while simultaneously suppressing inflammatory activation in ovarian stromal cells, demonstrating the vaginal microbiota's capacity to maintain follicular integrity. Further mechanistic insights showed that microbiota transplantation upregulated key antioxidant defense systems and ribosomal protein networks within ovarian cells, suggesting coordinated actions to mitigate oxidative stress and enhance cellular repair capacity, although the specific microbial metabolites mediating these effects require further elucidation.

CONCLUSIONS: Our findings establish for the first time the existence of a functional vaginal microbiota-ovary axis and delineate its critical role in protecting against chemotherapy-induced ovarian damage. This work not only advances our fundamental understanding of microbial-endocrine crosstalk but also identifies concrete microbial targets for developing innovative strategies to preserve fertility in cancer patients.},
}

@article {pmid41697449,
year = {2026},
author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J},
title = {Correction to: Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.},
journal = {Photosynthesis research},
volume = {164},
number = {2},
pages = {14},
doi = {10.1007/s11120-026-01203-7},
pmid = {41697449},
issn = {1573-5079},
}

@article {pmid41697388,
year = {2026},
author = {Ding, Z and Guo, Y and Guo, L and Ren, B and Yang, J and Li, J and Bai, L},
title = {Reintroduction of Grassland Plant Species Shapes Soil Bacterial Ecological Groups and Contributes Differently To Bacterial Diversity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02718-1},
pmid = {41697388},
issn = {1432-184X},
support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; },
}

@article {pmid41696024,
year = {2026},
author = {Pendleton, A and Schmidt, ML},
title = {Interpreting UniFrac with absolute abundance: a conceptual and practical guide.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf250},
pmid = {41696024},
issn = {2730-6151},
abstract = {[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU[A] and show that although computationally slower than conventional alternatives, GU[A] is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.},
}

@article {pmid41695957,
year = {2026},
author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H},
title = {Chloroflexota in agricultural soils: current knowledge and future research directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705889},
pmid = {41695957},
issn = {1664-302X},
abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.},
}

@article {pmid41695945,
year = {2026},
author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD},
title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759987},
pmid = {41695945},
issn = {1664-302X},
abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.},
}

@article {pmid41695141,
year = {2025},
author = {Uh, YR and Park, SN and Song, MJ},
title = {Characterization of the gut micro biota in Koreans and investigation of its association with probiotic consumption: implications for microbial ecology and host health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745533},
pmid = {41695141},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.

METHODS: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.

RESULTS: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.

CONCLUSION: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.},
}

@article {pmid41695122,
year = {2026},
author = {Yash, and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P},
title = {Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond.},
journal = {Access microbiology},
volume = {8},
number = {2},
pages = {},
pmid = {41695122},
issn = {2516-8290},
abstract = {Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.},
}