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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41874170,
year = {2026},
author = {Chen, H and Liang, Y and Zhou, X and Cai, W and Qiu, H and Dandekar, AA and Dai, W},
title = {Novel dual regulatory roles of RpoA in quorum sensing regulation and social behavior switching in Pseudomonas aeruginosa.},
journal = {mBio},
volume = {},
number = {},
pages = {e0003226},
doi = {10.1128/mbio.00032-26},
pmid = {41874170},
issn = {2150-7511},
abstract = {Understanding the social structure and evolutionary dynamics of microbial communities requires the identification and characterization of relevant mutant subpopulations. While Pseudomonas aeruginosa employs quorum sensing (QS) to coordinate population-wide behaviors, the social traits of many QS mutants remain poorly defined. In this study, we developed an iterative "targeted gene duplication followed by mutant screening" (TGD-MS) approach to systematically identify noncanonical QS cheater mutants. We discovered that a single-nucleotide mutation in rpoA, which encodes the α subunit of RNA polymerase (RNAP), produces a QS-deficient phenotype resembling QS-null mutants. This RpoA variant mutant exhibits characteristic features of social cheating, including a competitive growth advantage in mixed populations, impaired QS-dependent virulence factor production, and attenuated pathogenicity. Structural and biochemical analyses revealed that the RpoA variant impairs RNAP binding to the promoters of core QS genes (lasI and lasR), leading to diminished QS activity. Further examination of natural RpoA variants uncovered a spectrum of QS-related phenotypes, suggesting that RpoA has a dual regulatory role in QS control. Within the C-terminal domain (α-CTD) of RpoA, we identified two distinct functional determinants that, through adaptive mutations, can acquire opposing regulatory effects on QS. This enables an environmentally dependent phenotypic switch between cooperation and cheating. Our discovery of noncanonical RpoA-mediated QS cheaters expands the framework of bacterial social evolution, demonstrating that mutations outside the canonical QS circuitry can disrupt cooperative behaviors. These findings underscore how core transcriptional machinery can be evolutionarily co-opted to modulate complex social interactions in dynamic environments.IMPORTANCETo understand how bacterial populations function and evolve, it is essential to identify socially significant subpopulations, including previously unrecognized types of cheaters. In this study, we uncover an unexpected role of RNA polymerase (RNAP) in regulating quorum sensing (QS) and QS-associated social behaviors in P. aeruginosa. Specifically, we demonstrate that the α subunit of RNAP (RpoA) is a key regulatory component in this process. A single-nucleotide mutation within the C-terminal domain of RpoA was found to alter QS activity, driving an environment-dependent transition between cooperative and cheating phenotypes. This discovery of this novel, noncanonical QS cheater mutant offers new insights into intra-population interactions, population stability, and evolutionary dynamics. These findings carry significant implications for microbial ecology and deepen our understanding of social evolution in bacterial communities.},
}

@article {pmid41874404,
year = {2026},
author = {Kück, AC and Leibrecht, L and Morel-Letelier, I and Gros, O and Wilkins, LGE and Yuen-Simović, B and Petersen, JM},
title = {Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag065},
pmid = {41874404},
issn = {1751-7370},
abstract = {Associations with microbial symbionts shape the ecology and evolution of almost all eukaryotes. One of their defining features is their specificity, but despite this, many symbioses show a degree of flexibility, with some symbiont species capable of colonizing multiple (often closely related) host species. Although widespread, the functional and evolutionary consequences of flexibility in host-symbiont pairings is poorly understood. Bivalves from the diverse, globally distributed, and ecologically important family Lucinidae are ideal for investigating this, as multiple host species can associate with the same symbiont species, often at the same location. We used metatranscriptomics to investigate the molecular responses of one symbiont species, Candidatus Thiodiazotropha endolucinida, in association with three different host species that co-occur in seagrass meadows in the Caribbean Sea. In replicated experiments, we identified host species-specific patterns of symbiont gene expression including those for key functions such as carbon fixation, cell division, and sulfide oxidation. Our work shows that the symbiont consistently responds in different ways to association with different host species. Because all samples were collected at the same site on the same day, and were thus exposed to the same environmental conditions, these differences are likely driven by host rather than environmental factors. In addition, host species had significantly different carbon isotope signatures, which were consistent with distinct modes of host-microbe interaction indicated by transcriptomics. Our results show that not only symbiont genotype, but also symbiont phenotype may enable coexistence of closely related host species, demonstrating the power of symbiosis in promoting and maintaining biodiversity.},
}

@article {pmid41874663,
year = {2026},
author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C},
title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02742-1},
pmid = {41874663},
issn = {1432-184X},
support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; },
}

@article {pmid41877017,
year = {2026},
author = {Ibanga, IA and Ekong, US and Akan, OD and Akpabio, U and Christopher, M},
title = {Antibiotic resistance in chicken gut bacteria: a study on bacterial diversity and drug sensitivity in some Nigerian poultry farms.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04972-2},
pmid = {41877017},
issn = {1471-2180},
}

@article {pmid41869816,
year = {2026},
author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K},
title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0250325},
doi = {10.1128/spectrum.02503-25},
pmid = {41869816},
issn = {2165-0497},
abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.},
}

@article {pmid41870091,
year = {2026},
author = {Garabello, E and Yoon, H and Reid, MC and Giometto, A},
title = {Tunable low-rate genomic recombination with Cre-lox in Escherichia coli: a versatile tool for anoxic environmental biosensing and synthetic biology.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0176825},
doi = {10.1128/aem.01768-25},
pmid = {41870091},
issn = {1098-5336},
abstract = {The ability to induce heritable genomic changes in response to environmental cues is valuable for environmental biosensing, for experimentally probing microbial ecology and evolution, and for synthetic biology applications. Site-specific recombinases provide a route to genetic memory via targeted DNA modifications, but their high specificity and efficiency are offset by leaky expression and limited tunability in prokaryotes. We developed a tightly regulated, titratable Cre recombinase system for Escherichia coli that achieves low recombination rates and minimal basal activity. Implemented on both plasmids and the chromosome, the latter showed superior retention of genetic memory across generations. These features make the system broadly useful for environmental biosensing and other applications. To demonstrate applicability to environmental biosensing, we developed a whole-cell recombination-based biosensor for arsenite, a toxic and ubiquitous pollutant that is primarily mobilized in anoxic environments, such as flooded soils, sediments, and aquifers. However, existing arsenite whole-cell biosensors face limitations in sensitivity and workflow in anaerobic settings. Our biosensor reliably recorded anoxic arsenite exposure as a stable genetic memory for delayed fluorescence readout in aerobic conditions, with detection sensitivity comparable to conventional wet chemical methods. By decoupling exposure from measurement, this approach offers a foundation for arsenite biosensing under field-relevant conditions, including redox variability and other physicochemical gradients, without the constraints of anoxic measurement. More broadly, the ability to induce low-rate, heritable genetic changes expands the genetic toolkit for environmentally responsive systems, with applications in environmental monitoring, bioproduction, and bioengineering, as well as experimental studies of microbial ecology, evolution, and host-microbe interactions.IMPORTANCEArsenic is a toxic and globally prevalent pollutant, mobilized primarily under anoxic conditions where detection is challenging. Whole-cell biosensors offer a promising route for monitoring bioavailable arsenic in situ, but their development has largely focused on aerobic conditions, with anoxic assays limited by sensitivity and workflow constraints. Genetic tools that enable heritable, low-frequency genomic changes in bacteria can expand biosensor capabilities by recording transient exposures and supporting applications in environmental monitoring, synthetic biology, and quantitative microbial population dynamics research. Here, we developed a tightly regulated, chemically inducible Cre-lox system in Escherichia coli that enables recombination at low, tunable rates. We demonstrate its utility by constructing an arsenite biosensor that reliably detects low concentrations and records exposures under both aerobic and anoxic conditions. This approach is broadly applicable for biosensors designed for field deployment and for experiments investigating microbial ecology and evolution, where controllable genetic diversification may be desirable.},
}

@article {pmid41870584,
year = {2026},
author = {Muhammad, W and Zhou, X and Yu, X and Yang, K and Bai, R and Feng, L and Luo, Q and Zhou, Z and Wang, C and Li, J and Ji, K and Lu, HZ},
title = {Forest Succession Shapes Soil microbial Communities through Region-specific Edaphic Filters in Tropical and Subtropical Forests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02734-1},
pmid = {41870584},
issn = {1432-184X},
support = {32471599, 31872685//National Natural Science Foundation of China/ ; },
}

@article {pmid41871362,
year = {2026},
author = {Soto, C and Almendras, K and Orlando, J},
title = {Functional hierarchy and redundancy organize phosphorus cycling potential in Peltigera lichen microbiomes.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag029},
pmid = {41871362},
issn = {1574-6968},
abstract = {Lichen symbioses host complex microbial communities whose functional organization remains poorly understood. In Peltigera lichens, bacterial partners mediate key nutrient transformations, but it is unclear whether the spatial distribution of phosphorus-cycling functions follows the hierarchical control previously observed for community composition. We hypothesized that Peltigera microbiomes follow a thallus-to-soil gradient of control, in which host-driven specialization within thalli transitions toward environmentally driven reconfiguration in the substrate and soil. To test this, we quantified five bacterial genes involved in phosphorus turnover (gcd, phoD, phoN, phnX, and appA) across thalli, underlying substrates, and adjacent soils of several Peltigera species collected along contrasting Patagonian bioclimates. Absolute and relative gene abundances, together with diversity and variance partitioning analyses, were used to evaluate the influence of host identity, edaphic properties, and climate. Gene profiles revealed a shift from host-associated specialization to environmentally filtered assemblages, indicating that symbiotic and abiotic factors jointly structure phosphorus-cycling potential. The coexistence of functional specialization and redundancy provides a plausible mechanism for sustaining phosphorus turnover under changing environmental conditions.},
}

@article {pmid41871945,
year = {2026},
author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT},
title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337436},
pmid = {41871945},
issn = {1468-3288},
abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.},
}

@article {pmid41861947,
year = {2026},
author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S},
title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124311},
doi = {10.1016/j.envres.2026.124311},
pmid = {41861947},
issn = {1096-0953},
abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71 ± 102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34 ± 4.27 nmol/(kg·h)). On average, both N2ODen (115.34 ± 143.60 nmol/(kg·h)) and N2ONif (5.29 ± 4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56 ± 62.52 and 3.88 ± 4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.},
}

@article {pmid41862473,
year = {2026},
author = {Daniels, M and Wijayagunasekera, D and Berry, D},
title = {Widespread effects of catecholamines on growth of human gut bacteria.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00948-2},
pmid = {41862473},
issn = {2055-5008},
support = {Grant-DOI 10.55776/ESP558//Austrian Science Fund/ ; },
abstract = {The interactions between hosts and their microbiomes are driven in part by chemical communication, which influences immune responses, metabolism, and microbial community structure. Neuroendocrine signals are central to this bidirectional communication, forming the basis of microbial endocrinology. Although host-derived hormones, including catecholamines, are known to affect microbial physiology, much of the existing literature focuses on a limited number of model organisms or complex in vivo systems, where disentangling direct microbial responses from host-mediated effects is challenging. As a result, systematic comparative analyses of direct bacterial responses under controlled conditions remain scarce. Here, we performed a systematic in vitro screen under anaerobic conditions to assess catecholamine effects on the growth dynamics of phylogenetically diverse human gut bacteria. Catecholamines altered multiple growth parameters in a species-specific manner, with effects detectable at nanogram concentrations. Multivariate analyses, including principal component analysis and non-metric multidimensional scaling, revealed lineage-associated response patterns across taxa. Although derived from monoculture experiments, these intrinsic responses provide a comparative framework for understanding how direct hormone-microbe interactions may contribute to microbiome dynamics under host stress. Overall, this study provides a quantitative cross-species dataset to inform future systems-level investigations in microbial endocrinology.},
}

@article {pmid41865107,
year = {2026},
author = {Estruch, J and Almeida, T and Serrano, E and Pereira, L and Rouco, C and Lavín, S and Abrantes, J and Velarde, R and Lopes, AM},
title = {Temporal Dynamics and Turnover of Rabbit Hemorrhagic Disease Virus 2 (RHDV2/GI.2) in Wild Lagomorphs from Northeastern Spain.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02746-x},
pmid = {41865107},
issn = {1432-184X},
}

@article {pmid41865111,
year = {2026},
author = {Oliveira, AGG and Dias, MF and Haq, IU and Ferreira, JFG and Silva, CP and Moreira, M and da Silva Lanna, MC and Santos Rodrigues, LD and de Mâcedo Farias, L and Magalhães, PP},
title = {Seasonal and Source-Associated Microbiome Dynamics in Brazilian Drinking Water.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02735-0},
pmid = {41865111},
issn = {1432-184X},
}

@article {pmid41865966,
year = {2026},
author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J},
title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124325},
doi = {10.1016/j.envres.2026.124325},
pmid = {41865966},
issn = {1096-0953},
abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.},
}

@article {pmid41866381,
year = {2026},
author = {Wang, M and Xu, Z},
title = {PGPR-mediated enhancement of soil nutrients, rhizosphere microbial ecology, and plant growth: a review.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00966-0},
pmid = {41866381},
issn = {2055-5008},
support = {2025NC-YBXM-241//Key Research and Development Project of Shaanxi Provincial Department of Science and Technology (Agriculture and Rural Areas Field)/ ; 24JC028//2024 Shaanxi Provincial Education Department Service Local Special Scientific Research Project (Industrialization Cultivation project)/ ; 2025-CXY-071//Yulin City Science and Technology Program/ ; },
abstract = {Plant Growth-Promoting Rhizobacteria (PGPR) are key bio-agents for sustainable agriculture. This review conceptualizes PGPR as rhizosphere engineers that enhance soil nutrients, restructure microbial networks, and boost plant stress tolerance. While their mechanisms are well-understood in the lab, a significant translational gap limits field efficacy due to inconsistent colonization and environmental context-dependency. We critically analyze this gap and propose integrated strategies-from advanced formulations to synthetic consortia-to unlock the reliable application of PGPR for global food security.},
}

@article {pmid41866413,
year = {2026},
author = {Berkelmann, D and Zuñiga-Umaña, JM and Chaverri, P and Solano, W and Gatica-Arias, A},
title = {Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866413},
issn = {1573-0972},
support = {111-C1-472//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; },
mesh = {*Plant Diseases/microbiology ; *Coffea/microbiology ; Plant Leaves/microbiology ; *Basidiomycota/genetics/classification/isolation & purification ; DNA, Fungal/genetics ; Costa Rica ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; *Fungi/genetics/classification/isolation & purification ; Coffee/microbiology ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.},
}

*Plant Diseases/microbiology
*Coffea/microbiology
Plant Leaves/microbiology
*Basidiomycota/genetics/classification/isolation & purification
DNA, Fungal/genetics
Costa Rica
Phylogeny
Sequence Analysis, DNA
Biodiversity
*Fungi/genetics/classification/isolation & purification
Coffee/microbiology
DNA, Ribosomal Spacer/genetics

@article {pmid41866874,
year = {2026},
author = {Iriarte-Mesa, C and Juère, E and Bileck, A and Kremsmayr, T and Goodson, ML and Ehrlich, A and Hodžić, A and Kunert, M and Gerner, C and Kählig, H and Marko, D and Muttenthaler, M and Berry, D and Del Favero, G and Kleitz, F},
title = {Mesoporous Silica Nanoparticles-Based Formulations for Enhanced Oral Delivery of Peptide Drugs: A Case Study on Insulin.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e13347},
doi = {10.1002/smll.202513347},
pmid = {41866874},
issn = {1613-6829},
support = {714366/ERC_/European Research Council/International ; FT210100266//Australian Research Council/ ; 2037680//National Health and Medical Research Council/ ; 10.55776/P36130//Austrian Science Fund/ ; //University of Vienna/ ; },
abstract = {Peptide drugs have revolutionized modern medicine owing to their high potency, selectivity, and excellent tolerability. However, oral delivery remains limited, and most peptide drugs are administered parenterally due to their inherent instability to proteolytic digestion and poor ability to cross gastrointestinal barriers, which hinders efficient absorption into the bloodstream. This study presents a multifunctional oral delivery system based on mesoporous silica nanoparticles (MSN) customized for insulin administration. Insulin-loaded MSN were co-formulated with succinylated β-lactoglobulin to produce pH-responsive tablets that limited premature gastric release (≤13% after 2 h at pH 1.2) and protected insulin from enzymatic degradation, while enabling controlled intestinal release (up to 88%-98% at pH 7.4). Surface functionalization with polyethylene glycol and phosphonate moieties improved colloidal stability and increased insulin solubility by ∼2.5-fold. The interaction of phosphonated MSN with intestinal epithelial cells further induced transient reorganization of tight junction proteins, enhancing paracellular insulin transport (26% after 24 h, compared with 13% for non-confined insulin). Delivered insulin retained bioactivity, as demonstrated by activation of insulin-responsive signaling pathways in vitro and reduced blood glucose levels in hyperglycemic mice. These results highlight MSN as a promising platform for oral peptide delivery with improved efficacy and patient compliance.},
}

@article {pmid41868377,
year = {2026},
author = {Cui, Y and Sun, W and Wei, L and Fan, S and Li, Q and Duan, L},
title = {Complex interactions of gut-derived short-chain fatty acids in hyperuricemia and gout pathophysiology.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1772631},
pmid = {41868377},
issn = {1664-302X},
abstract = {Hyperuricemia is a common metabolic disorder associated with gout, kidney injury, cardiovascular disease, and chronic low-grade inflammation. Increasing evidence indicates that abnormalities in intestinal uric acid handling and gut microbial metabolism contribute substantially to systemic urate imbalance, particularly when renal excretion is impaired. Among microbiota-derived metabolites, short-chain fatty acids (SCFAs) have emerged as key regulators linking gut microbial ecology with uric acid metabolism through coordinated effects on epithelial barrier integrity, inflammatory signaling, and urate transport. Growing interest in prebiotics and probiotics has further highlighted the therapeutic potential of targeting SCFAs production as a complementary strategy to traditional urate-lowering drugs. Given that hyperuricemia is the primary pathogenic precursor to gout, this review also examines the role of SCFAs in modulating gout-associated inflammation. This review integrates current findings on the microbiota-SCFA-urate axis and outlines how SCFA-centered gut modulation may provide a viable framework for managing hyperuricemia and gout.},
}

@article {pmid41869502,
year = {2026},
author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T},
title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.},
journal = {Environmental science and ecotechnology},
volume = {30},
number = {},
pages = {100683},
pmid = {41869502},
issn = {2666-4984},
abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.},
}

@article {pmid41860729,
year = {2026},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Ledesma-Hernandez, G and Cuezva, S and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V},
title = {Habitat Specialization and Airborne Dispersal Shape the Microbiome of a Gypsum Karst Cave.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02745-y},
pmid = {41860729},
issn = {1432-184X},
}

@article {pmid41860788,
year = {2026},
author = {Duarte, GCK and Crispim, D and Wittée, SC and Lemos, JRN and Lemos, NE and de Oliveira, MS and Alves, MD and Massignam, ET and Assmann, TS and Pellenz, FM},
title = {An ultra-processed food-based cafeteria diet induces obesity, metabolic dysfunction, and tissue-specific gene dysregulation in C57BL/6 mice.},
journal = {Animal models and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/ame2.70160},
pmid = {41860788},
issn = {2576-2095},
support = {//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; //Financiamento e Incentivo à Pesquisa e Eventos (FIPE) - Hospital de Clínicas de Porto Alegre/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //Postgraduation Program in Medical Sciences: Endocrinology at Universidade Federal do Rio Grande do Sul, Brazil/ ; },
abstract = {BACKGROUND: The cafeteria diet (CAFD) model has been used to mimic the Western-style "junk food" eating pattern, inducing obesity in rodents. As the dietary composition varies across studies, we developed a CAFD model based on commonly consumed Brazilian ultra-processed foods to evaluate its effect on weight gain, metabolic parameters, and gene expression in C57BL/6 mice.

METHODS: Forty male C57BL/6 mice were assigned to either a standard diet (SD) group or a CAFD group for 16 weeks. Biometric data, glycemic control, insulin resistance (IR), hepatic steatosis, and serum leptin and adiponectin levels were assessed. Expressions of 27 genes involved in adipocytokine signaling, inflammation, apoptosis, lipid, and glucose metabolism were analyzed using quantitative real-time polymerase chain reaction in visceral (VAT) and subcutaneous (SAT) adipose tissues, liver, and skeletal muscle.

RESULTS: CAFD-fed mice exhibited significantly greater weight gain, hyperglycemia, elevated IR, and hepatic steatosis compared to SD controls. Circulating leptin and adiponectin levels increased in the CAFD group. Gene expression analysis revealed significant dysregulation in VAT (19 genes), SAT (6 genes), liver (11 genes), and muscle (4 genes) of the CAFD group, affecting pathways related to adipocytokine signaling, oxidative stress, inflammation, apoptosis, and lipid and glucose metabolism. Additionally, an increased Itgax-to-Llgl1 ratio in VAT of the CAFD mice indicated a phenotypic shift in macrophages from M2 to pro-inflammatory M1.

CONCLUSION: This CAFD model efficiently induces obesity, metabolic dysfunction, and tissue-specific alterations in gene expression in C57BL/6 mice, supporting its use as a relevant model for studying the molecular and inflammatory mechanisms underlying diet-induced obesity.},
}

@article {pmid41861859,
year = {2026},
author = {Ye, Q and Fang, H and Tang, R and Li, M and Li, X},
title = {Synergistic parameter optimization Unlocks High-Efficiency H2/CO2 Bio-methanation: Decoupling mass transfer enhancement from microbial Trade-offs.},
journal = {Bioresource technology},
volume = {450},
number = {},
pages = {134459},
doi = {10.1016/j.biortech.2026.134459},
pmid = {41861859},
issn = {1873-2976},
abstract = {The advancement of CO2 biomethanation represents a crucial pathway for renewable energy storage and carbon neutrality. However, its widespread application is often constrained by inefficient gas-liquid mass transfer of H2 and suboptimal operational parameters. This study investigates the synergistic effects and underlying mechanisms of three key engineering parameters-agitation intensity, gas recirculation rate, and H2/CO2 feed ratio-on the performance of an in-situ H2/CO2 biomethanation process at mesophilic temperature (37 ± 1℃). Enhanced agitation (up to 160 rpm) and increased gas recirculation (up to 1200 mL·min[-1]) significantly improved (p＜0.05) the volumetric mass transfer coefficient (kla) for H2, thereby boosting the maximum volumetric methane production (VMP) to 0.97 L·L[-1]·d[-1]. Optimizing the H2/CO2 feed ratio to 5:1 strengthened the thermodynamic driving force for hydrogenotrophic methanogenesis, increasing methane content by ∼15% compared to the stoichiometric 4:1 ratio. High-throughput sequencing revealed that intensified mass transfer selectively enriched dominant hydrogenotrophic methanogenic archaea phylum (e.g., Methanobacteriota reached 75.2% at an H2/CO2 feed ratio of 5:1), while suppressing hydrolytic and acidogenic bacterial phylum (e.g., Bacteroidetes decreased from 23.7% to 6.8%, under intensified agitation), indicating a functional trade-off between enhanced methanogenic efficiency and complex organic degradation. This work emphasized the long-term, integrated evaluation of hydrodynamics and microbial ecology of the biomethanation systems, leading to superior methane yield and system stability. The findings provide critical insights and practical guidance for scaling up efficient and stable biomethanation systems, addressing a key bottleneck in industrial Power-to-Gas applications.},
}

@article {pmid41860227,
year = {2026},
author = {Chaput, G and Hanley, TC and Eisen, JA and Sogin, EM and Hughes, AR and Hays, C},
title = {Microbiota characterization of Zostera marina seeds at early stage development.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0116325},
doi = {10.1128/mra.01163-25},
pmid = {41860227},
issn = {2576-098X},
abstract = {Understanding seagrass seed microbiomes is crucial for developing microbial-mediated methods to improve germination in restoration efforts. Here, we used 16S rRNA gene and ITS2 amplicon sequencing to characterize the bacterial and fungal communities of seeds from the model seagrass, Zostera marina.},
}

@article {pmid41610050,
year = {2026},
author = {Moreno-Mirón, JM and Ruiz-Argüelles, GJ and Gallardo-Pérez, MM and Moreno-Mirón, A and Rivera-Aguilar, AP and Gale, RP},
title = {The Gastro-Intestinal Microbiota in Haematology.},
journal = {Acta haematologica},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000550689},
pmid = {41610050},
issn = {1421-9662},
abstract = {BACKGROUND: The gastro-intestinal microbiota is a key regulator of systemic immunity and inflammatory tone and it contributes to normal haematopoiesis through microbial metabolites, barrier integrity, and host-microbe immune signalling. Disruption of this has been increasingly linked to the development, clinical course, and treatment-related complications of haematological disorders, including clonal haematopoiesis of indeterminate potential (CHIP), leukaemias, and plasma cell neoplasms (PCNs).

SUMMARY: This review synthesises current evidence on how gut microbiota composition and function intersect with haematopoietic regulation and haematological disease biology. We summarise proposed mechanisms - including microbe-derived metabolites (e.g., short-chain fatty acids), pattern-recognition receptor signalling, intestinal permeability, and cytokine-mediated inflammation - that may influence haematopoietic stem and progenitor cell behaviour and immune cell differentiation. We then discuss disease-specific associations of dysbiosis with CHIP, leukaemias, and PCN, as well as the impact of common haematology interventions (antibiotics, chemotherapy, immunomodulatory therapies, and transplantation) on microbial ecology and downstream clinical outcomes. Finally, we highlight methodological challenges and outline priorities for longitudinal, mechanistic, and multi-omics studies to enable microbiota-informed risk stratification and therapeutic modulation.

KEY MESSAGES: (1) The gut microbiota influences haematopoiesis via immune signalling, microbial metabolites, and maintenance of mucosal barrier function. (2) Dysbiosis is associated with CHIP, leukaemias, and PCN, and may contribute through chronic inflammation and altered immune homeostasis. (3) Haematological therapies frequently reshape the microbiota; these changes may affect infection risk, treatment tolerance, and outcomes. (4) Current evidence is largely associative; rigorously designed longitudinal and interventional studies are needed to establish causality and guide clinical translation.},
}

@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}

*Ecosystem
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Metagenome
*Lakes/microbiology
*Fresh Water/microbiology
Metagenomics
Transcriptome

@article {pmid41854259,
year = {2026},
author = {Almela, P and Hamilton, TL},
title = {Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0003126},
doi = {10.1128/aem.00031-26},
pmid = {41854259},
issn = {1098-5336},
abstract = {High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic, like snow. Nucleic acid extraction significantly impacts these analyses, often introducing more variation between samples than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields, where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, DNA extraction remains challenging, as the thick, resilient walls of snow algal cysts can limit cell lysis, and differences among extraction methods may therefore affect the estimates of community composition and richness. Here, we compared three common extraction methods (Qiagen DNeasy PowerSoil Pro, Qiagen DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced the resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of DNA from resilient cells, including mature-phase snow algae, likely due to improved cell lysis. Our findings provide insights to improve standardization and facilitate comparison among studies in snow and ice environments.IMPORTANCEHigh-throughput sequencing has transformed environmental microbiology, allowing for detailed, culture-independent analyses of microbial communities. However, multiple methodological factors, including DNA extraction, can introduce variability in results, making cross-study comparisons challenging. This research contributes to improving our understanding of snow algae, which play a role in alpine and polar ecosystems by influencing biogeochemical cycles and snow reflectivity. By evaluating common DNA extraction techniques for snow algae, this study helps improve the reliability and reproducibility of sequencing data, supporting broader efforts toward methodological standardization in microbial ecology.},
}

@article {pmid41855561,
year = {2026},
author = {Berne, C and Debidour, M and Paniconi, M and Danis, N and Sprowls, ED and Kavanagh, K and Gilbert, L and Brun, Y},
title = {Exploring the diversity of bacterial holdfast polar adhesins from Québec aquatic environments.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0310},
pmid = {41855561},
issn = {1480-3275},
abstract = {Biofilms are complex microbial communities that adhere to surfaces, often in response to their environment. Irreversible attachment in these biofilms is mediated by bacterial adhesins, and, in many Alphaproteobacteria, those adhesins are located at the cell pole. To examine the prevalence and natural variation of polar adhesins, 76 water samples were collected across Québec through a citizen science initiative. Environmental isolates were screened for their ability to form biofilms, and strains exhibiting polar attachment were selected. A subset of 21 representative strains was used for phenotypic assays and whole-genome sequencing. Phylogenetic analysis showed that most belonged to the order Caulobacterales, and microscopic characterization indicated variability in the polysaccharide composition of polar adhesins in these environmental strains. By integrating comparative genomics with phenotypic assays, this work establishes a unique framework for linking microbial ecology to molecular mechanisms of adhesion. Our results highlight intra-order natural variations in polar adhesin structure and composition. Such variations may be signatures of adaptive adhesive performances across diverse environments. These findings not only advance the understanding of biofilm biology but also open avenues for bio-inspired applications, including the development of next-generation adhesives and anti-biofouling materials.},
}

@article {pmid41855876,
year = {2026},
author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J},
title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129409},
doi = {10.1016/j.jenvman.2026.129409},
pmid = {41855876},
issn = {1095-8630},
abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.},
}

@article {pmid41856914,
year = {2026},
author = {Sorouri, B and Bernardin, J and Favier, AI and Garces, KR and McMullen, JG and McGuire, RM},
title = {Microbial ecology for all: A vision of accessibility, unity, and responsibility.},
journal = {Ecology},
volume = {107},
number = {3},
pages = {e70342},
doi = {10.1002/ecy.70342},
pmid = {41856914},
issn = {1939-9170},
support = {2305844//National Science Foundation/ ; 2305876//National Science Foundation/ ; 2305992//National Science Foundation/ ; },
mesh = {*Ecology ; Ecosystem ; Biodiversity ; Microbiota ; },
abstract = {Microorganisms are ubiquitous in nature, representing a significant portion of global biodiversity and playing vital roles in ecosystem functions, biogeochemical cycles, and organismal health. The growing recognition of microbial importance and their potential to address ecological and global challenges has inspired a renewed interest and innovation in microbial ecology. This field has benefited immensely from sequencing technologies that allow scientists to explore diversity at scales previously unimaginable. While the rapid growth of the field has offered significant positive advancements and foreshadows promising potential, there are aspects that need careful consideration. New technology has led to exponential growth in available microbial data, yet not everyone has easy access to sequencing technology, data mining and analysis tools, or the time to acquire new skills. Thus, we are at a crossroads in ensuring that these resources are accessible for all, and that traditional methods of microbiology are still appreciated as tools to progress the field in meaningful ways. As early-career researchers, we want to raise these points as principles for shaping the future of microbial ecology. Here, we outline a vision for a more accessible, united, and responsible microbial ecology field, one with applications equipped to address the needs of both society and the environment. To democratize the field, we advocate to destigmatize microbes and increase awareness of their beneficial roles by integrating microbes into early education. We believe unity and collaboration among microbial ecologists, as well as with professionals and community members in other STEM fields, are essential for advancing the field. Data should be accessible and standardized for collaboration, and greater integration across disciplines is essential to address future ecological challenges effectively and innovatively. It is our responsibility to ensure that we are asking relevant research questions with the potential to engage with socio-environmental issues and prioritize sustainable practices. As a collective field, our research should strive to not only expand scientific knowledge but also support community resilience and policy-making for a sustainable future. Together, this vision will promote a more equitable, diverse, and collaborative future for microbial ecology; and has applications for the broader ecology field.},
}

*Ecology
Ecosystem
Biodiversity
Microbiota

@article {pmid41857392,
year = {2026},
author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J},
title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02722-5},
pmid = {41857392},
issn = {1432-184X},
support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science & Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; },
}

@article {pmid41859237,
year = {2026},
author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H},
title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag011},
pmid = {41859237},
issn = {2730-6151},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.},
}

@article {pmid41859451,
year = {2026},
author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L},
title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755652},
pmid = {41859451},
issn = {1664-302X},
abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.},
}

@article {pmid41860215,
year = {2026},
author = {Chaudhary, A and Lin, H and Guo, L and Poretsky, R},
title = {Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026326},
doi = {10.1128/aem.00263-26},
pmid = {41860215},
issn = {1098-5336},
abstract = {Bacterial communities in freshwater ecosystems play a critical role in biogeochemical and food web dynamics. However, our understanding of environmental controls on bacterial community function, particularly in large lakes, is limited. We characterized Lake Michigan water chemistry, bacterial community function, and substrate preferences to better understand bacteria-water chemistry relationships. Using metatranscriptomics, we investigated bacterioplankton gene expression in surface waters across a nearshore-to-offshore transect during 2017-2018. Additionally, we measured nutrients, dissolved organic carbon (DOC), chromophoric dissolved organic matter (DOM), as well as changes in major fluorescent DOM components across this transect. The results highlighted similarities in inorganic N and P measurements and a minor reduction in DOC levels from nearshore to offshore. However, significant changes in the composition of DOM were observed across the transect, including a higher presence of terrestrially derived and high-molecular-weight DOM in the nearshore. These differences in DOM quality were associated with the differential expression of several gene families between nearshore and offshore bacterioplankton. Notably, genes involved in the acquisition of various DOM, N, and P substrates, including peptidases, proteases, and transporter genes for amino acids, nucleobases, sugars, urea, and inorganic phosphate, were over-represented in the offshore bacterioplankton. A focused analysis of all the transporter gene expression for C, N, and P substrates revealed similar trends-higher expression of DOM transporter genes in the offshore versus nearshore. When viewed in the context of changing DOM quality across the transect, these results imply that offshore bacterial communities are more substrate-limited (particularly C) than in nearshore and are investing more energy in acquiring DOM substrates.IMPORTANCEVarious environmental, geological, and climatic factors influence bacterial community dynamics in freshwater ecosystems in complex and interactive ways. It thus becomes challenging in microbial ecology studies to disentangle the specific effects of these factors on microbial community function. Spatial environmental gradients in large lake ecosystems can provide a unique opportunity to test important questions about bacterial function and water chemistry relationships in a relatively consistent geological and climatic framework. Lake Michigan, one of the five largest lakes in the world, is one such example. The lake has witnessed significant ecological changes in the last few decades, and the impact of these changes on the physico-chemical environment and bacterioplankton function is not fully understood. In a relatively novel approach for freshwater systems, this study assesses Lake Michigan bacterial metabolism using robust transcriptomics techniques in the context of rich environmental data, including characterization of the lake chromophoric DOM and fluorescent DOM pool.},
}

@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}

@article {pmid41846605,
year = {2026},
author = {Allner, R and Decewicz, P and Allner, T and Bluszcz, A and Dziewit, L},
title = {Development of molecular biomarkers for monitoring of arable crops colonization with Methylobacterium symbioticum SB0023/3, a methylotrophic bacterium commonly used as a biostimulant in agriculture.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1718185},
pmid = {41846605},
issn = {1664-462X},
abstract = {INTRODUCTION: The intensive use of synthetic fertilizers has led to increased nitrous oxide emissions, declining soil fertility, and reduced biodiversity. Biological alternatives, such as the use of endophytic bacteria to improve plant growth, are promising alternatives but require reliable monitoring tools to assess colonization success and biological effectiveness under field conditions. One of the most commonly used microbial biostimulants is Methylobacterium symbioticum SB0023/3; thus, monitoring the efficacy of inoculation and maintenance of this strain is required for adequate evaluation of fertilization practices.

METHODOLOGY: The resequencing of the genome of M. symbioticum SB0023/3, followed by comparative genomics and functional annotation were performed. Specific real-time PCR primers were developed and validated for strain-specific detection. The colonization of various crops (wheat, corn, rapeseed, peas, and tomatoes) was tested under controlled conditions using developed molecular markers.

RESULTS: The resequencing of the SB0023/3 genome revealed novel genetic content and updated previous records. The resequenced genome showed 121 novel regions with 165 protein-coding genes and five tRNA. Based on the newly obtained genome, two highly specific biomarker genes (copG and ubik) were identified and, together with the (Methylobacterium spp./methylotrophs-specific) xoxF gene, validated for their strain/genus-specificity. The developed real-time PCR assays using copG and ubik biomarkers demonstrated high specificity for M. symbioticum SB0023/3, distinguishing it from related species. In contrast, the xoxF gene showed relaxed specificity and cannot be used for SB0023/3 detection. Successful endophytic colonization was confirmed in all tested crops, with high detection rates exceeding 80% in tomatoes. Classical culturing on a novel nitrogen-free medium additionally confirmed colonization, with the same validating the real-time PCR assays.

DISCUSSION: This study provides a robust, genome-informed molecular detection system for monitoring M. symbioticum SB0023/3 in crops. The presented approach enables direct detection from plant tissues, facilitating studies on colonization dynamics and biosafety. This methodology can be extended to other microbial biostimulants, supporting sustainable agricultural practices.},
}

@article {pmid41848198,
year = {2026},
author = {Skoupý, S and Stanojković, A and Johansen, JR and Casamatta, DA and McGovern, C and Jungblut, AD and Fastner, J and Dvořák, P},
title = {Population and herbarium genomics provide a comprehensive framework for a revision of Microcoleus (Cyanobacteria).},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70145},
pmid = {41848198},
issn = {1529-8817},
support = {//European Community Research Infrastructure Action under the FP7 "Capacities" Program/ ; 23-06507S//Grantová Agentura České Republiky/ ; },
abstract = {Microcoleus is a cosmopolitan, filamentous cyanobacterium and a key component of biological soil crusts-complex microbial communities essential for primary production in diverse terrestrial environments. Here, we performed a taxonomic revision of several species of Microcoleus based on a large population genomic dataset. The dataset was based on a Microcoleus speciation continuum characterized by variable levels of gene flow between the species. The putative species ranged from cryptic to distinctly morphologically defined lineages. We identify the type herbarium specimen and obtained a genome for the type species M. vaginatus and herein describe 10 novel species of Microcoleus. We provide epitypifications for the previously described species M. vaginatus and M. attenuatus. This research contributes to a more comprehensive understanding of terrestrial cyanobacterial biodiversity and cryptic species in cyanobacteria. It highlights the need for an extensive genomic and phenotypic dataset in the taxonomy of Cyanobacteria.},
}

@article {pmid41850628,
year = {2026},
author = {Tumeo, A and Kovářová, A and McDonagh, F and Ryan, K and Clarke, C and Miliotis, G},
title = {Patient colonization with Phytobacter spp. co-harboring blaIMP-4, blaSHV-12, and mcr-9.1 highlights its role as an under-recognized reservoir of antimicrobial resistance.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108562},
doi = {10.1016/j.ijid.2026.108562},
pmid = {41850628},
issn = {1878-3511},
abstract = {We report two uncommon identifications of patient colonization with multidrug-resistant, carbapenemase-encoding Phytobacter in Ireland. Phytobacter is a recently delineated genus within the Enterobacterales that is frequently misidentified in clinical laboratories. Two isolates were recovered from rectal swabs in 2024 and were initially identified as Phytobacter ursingii by MALDI-TOF. Whole-genome sequencing with in silico species typing (average nucleotide identity and digital DNA-DNA hybridization) resolved them as Phytobacter diazotrophicus E787336 and P. ursingii E980862. We reconstructed a genus-wide maximum-likelihood core-genome phylogeny and profiled all publicly available Phytobacter genomes to contextualize antimicrobial resistance (AMR) and plasmid content. Across the dataset, we detected 22 plasmid replicon types and a resistome comprising 71 genes, over half predicted to be plasmid-borne. These included carbapenemases in 26.5% (9/34) of the genomes, and disinfectant-associated resistance determinants in 29.5%. E787336 and E980862 represent the first Phytobacter isolates identified to co-harbor plasmid-borne blaIMP-4, blaSHV-12, and mcr-9.1 in association with IncHI2A plasmid reconstructions. Phenotypic testing confirmed resistance to aztreonam, aminoglycosides, cephalosporins, fluoroquinolones, and piperacillin-tazobactam, yet susceptibility to carbapenems and colistin. These findings expand the clinical and genomic evidence that Phytobacter can act as an under-recognized colonizer and reservoir for plasmid-borne AMR, including carbapenemases, and underscore the need for improved clinical identification, genomic surveillance, and preparedness for limited therapeutic options.},
}

@article {pmid41850929,
year = {2026},
author = {Garcés-Ruiz, M and Díaz-Otero, BG and Antonielli, L and Saraiva, JP and Karpouzas, D and Declerck, S},
title = {Machine learning for designing low-risk microbial consortia pesticides.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.12.027},
pmid = {41850929},
issn = {1879-3096},
abstract = {Microbial consortia, considered low-risk pesticides (LRPs), appear to be valuable tools for reducing our dependence on chemical pesticides. However, their use is limited by inconsistent product efficacy and registration difficulties. Artificial intelligence (AI) and machine learning (ML) offer solutions for designing and evaluating synthetic microbial communities (SynComs), predicting their compatibility, ecological stability, and biocontrol efficacy. The transition from laboratory discovery of SynCom-based LRPs to field application and commercialization could be significantly accelerated. Here, we review the methods and steps necessary to establish reliable SynComs and describe how AI and ML approaches could improve the construction and validation of SynCom-based LRPs to obtain more specific results that can contribute to their risk assessment.},
}

@article {pmid41851145,
year = {2026},
author = {Shen, J and Han, M and Sun, J and Yu, H and Yang, Y and Shen, K and Su, Y and Chen, X and He, H and Shao, H and Sun, J and McMinn, A and Wang, M and Liang, Y},
title = {Diversity and ecological potential of sediment viruses from Chinese continental shelf seas.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00940-w},
pmid = {41851145},
issn = {2055-5008},
abstract = {Continental shelves are important areas for global biogeochemical cycling, yet the roles of sediment viruses in these areas remain poorly understood. Here, 48 surface sediment samples from the Chinese continental shelf were analyzed, and 12,540 viral operational taxonomic units (vOTUs) were identified. Taxonomic classification found that 93.6% of the vOTUs could not be assigned at the family level, and protein-sharing networks showed that 60.4% were singletons. Viral community structure was shaped primarily by temperature and water depth. A total of 557 auxiliary metabolic genes (AMGs) were identified, including those involved in sulfur reduction and phosphorus acquisition (Pho-family proteins). Additionally, diverse antibiotic resistance genes (ARGs) were detected, suggesting anthropogenic influence. This study reveals the diversity, ecological function, and environmental drivers of viral communities in continental shelf sediments, providing new insights into viral contributions to microbial ecology and biogeochemical processes.},
}

@article {pmid41852400,
year = {2025},
author = {Fischer, A and Singh, JP and Van Hamme, J and Bottos, E and Fraser, LH},
title = {Investigating impacts from topsoil stockpile height on soil microbial communities.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1607677},
pmid = {41852400},
issn = {2813-4338},
abstract = {Mining activities are often severely disruptive to the landscape, and a significant barrier to reclamation following mining operations is the lack of quality topsoil. This project addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted a microbial profiling of two topsoil stockpiles in the interior of British Columbia, Canada. Both stockpiles show depleted soil quality and significant changes compared to reference soils. Notably, there were declines in microbial diversity and significant shifts in community structure with increasing stockpile depths in one of the stockpiles. These results highlight the influence of topsoil-stockpile height on microbial communities in the soil, which ultimately influences the success of restoration. This research can help the industry to optimize restoration and expedite recovery in their mine-closure practices and provides insights into the general structure of the microbiome existing across a gradient in severely disturbed mining soils.},
}

@article {pmid41852403,
year = {2025},
author = {Helal, M and Bari, VK},
title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1549166},
pmid = {41852403},
issn = {2813-4338},
abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.},
}

@article {pmid41852418,
year = {2025},
author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S},
title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1619859},
pmid = {41852418},
issn = {2813-4338},
abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.},
}

@article {pmid41853343,
year = {2023},
author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y},
title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1329925},
pmid = {41853343},
issn = {2813-4338},
abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.},
}

@article {pmid41853537,
year = {2024},
author = {Klimasmith, IM and Wang, B and Yu, S and Yoshikuni, Y and Kent, AD},
title = {Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1452476},
pmid = {41853537},
issn = {2813-4338},
abstract = {The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.},
}

@article {pmid41841797,
year = {2026},
author = {Coskun, ÖK and Orsi, WD and Marshall, IPG and Muschler, KA and Mitschke, N and Ferdelman, TG and Gomez-Saez, GV},
title = {Hypoxia increases microbial carbon assimilation of taurine in a seasonally anoxic fjord.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag057},
pmid = {41841797},
issn = {1751-7370},
abstract = {Hypoxic zones are expanding globally altering marine biogeochemical cycles. Within these low-oxygen regions, microbial communities play a key role in the production, degradation, and transformation of dissolved organic sulfur (DOS) compounds. Taurine is a bioavailable DOS compound widely utilized by marine microbes with a central role in nutrients exchange, energy production and biomass generation. However, in stratified water columns with varying oxygen conditions, the specific microbial taxa assimilating taurine as a carbon source remain poorly characterized. Here, we applied quantitative stable isotope probing (qSIP) experiments using 13C-labeled organosulfur compounds (taurine and methionine) and 13C-glucose to identify active microbial utilizers in oxic and hypoxic waters in the seasonally anoxic Mariager Fjord (Denmark, Kattegat Sea). Our qSIP results were supported by physicochemical measurements and geochemical data. Taurine-derived 13C-carbon was assimilated into microbial biomass exclusively under hypoxic conditions, primarily by Flavobacteriaceae (Bacteroidota), indicating that taurine serves as a carbon source only when oxygen is limited. 13C-taurine and 13C-methionine assimilation were strongly associated, suggesting a flexible metabolic strategy for utilizing organosulfur compounds in hypoxic waters. In oxic waters, 13C-methionine and 13C-glucose were assimilated by distinct taxonomic groups, dominated by Bacteroidota and Verrucomicrobiota, respectively. Overall, our study identifies active microbial communities assimilating organosulfur compounds under varying oxygen levels in the seasonally anoxic Mariager Fjord, providing new insights into key microbial processes in low-oxygen coastal systems.},
}

@article {pmid41842987,
year = {2026},
author = {Reardon, CL and Manter, DK},
title = {Amplification Efficiency of Quantitative PCR Reactions is Improved by Addition of Non-Target DNA.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02719-0},
pmid = {41842987},
issn = {1432-184X},
}

@article {pmid41843121,
year = {2026},
author = {Dou, WH and Li, TC},
title = {Rapid Genomic Adaptation of Drosophila Melanogaster to Wolbachia Elimination.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02732-3},
pmid = {41843121},
issn = {1432-184X},
support = {ZR2024QC383//Natural Science Foundation of Shandong Province/ ; ZR2024QC222//Natural Science Foundation of Shandong Province/ ; },
}

@article {pmid41844028,
year = {2026},
author = {Sun, L and Huang, L and Jia, S and Wei, Y and Cao, Z and Zhang, P and Zhang, G},
title = {Enhancing wastewater denitrification in constructed wetlands: microbial mechanisms driven by lotus leaf-based carbon.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129368},
doi = {10.1016/j.jenvman.2026.129368},
pmid = {41844028},
issn = {1095-8630},
abstract = {The performance of constructed wetlands (CWs) in treating low C/N domestic wastewater is often constrained by limited carbon availability for denitrification. This study proposes an innovative approach using alkali-pretreated lotus leaves as a biodegradable, slow-release carbon source to enhance denitrification efficiency and uncover the underlying metabolic and microbial mechanisms. Results demonstrated that wet lotus leaves-especially those wet-4% NaOH-released carbon more efficiently than dried leaves, with a peak rate of 25.93 mg g[-1]·h[-1] (calculated as ΔCOD/Δt normalized to wet mass and measured within the first 20 h of the static experiment). This pretreatment also mitigated nitrogen and phosphorus leaching risks. Supplementation with 400 g of 4% NaOH-treated wet lotus leaves (CW2) significantly improved the TN removal efficiency, reaching a peak of 91.89 ± 3.56% during days 1-16, with an overall average of 85.63% ± 7.72%. Mechanistically, tryptophan-like DOM signals (EEM) suggest that small-molecule soluble organics released from plant-derived carbon sources can be rapidly taken up and utilized by denitrification-associated microorganisms, thereby supporting the denitrification process. Microbial characteristics analysis revealed that CW2 enriched microbial richness (Shannon = 6.96; Chao 1 = 2015.9) and shifted community composition toward denitrification-favorable taxa. Notably, Proteobacteria abundance increased from 21.5% to 38.5%, accompanied by the proliferation of key genera including Pseudomonas and Janthinobacterium. The taxa associated with nitrifiers, denitrifiers, and anammox bacteria collectively contributed to a more robust nitrogen removal pathway. These findings suggest that the supplementary carbon source-by regulating dissolved oxygen distribution, supplying bioavailable carbon, and establishing spatially structured redox gradients-strategically modulates microbial ecology and functional metabolism, offering a low-cost and sustainable solution for enhancing nitrogen removal in constructed wetlands.},
}

@article {pmid41844516,
year = {2026},
author = {Muratore, TJ and Chari, NR and Phillips, RP and Taylor, BN and Knorr, MA and Frey, SD},
title = {Increased root-derived carbon buffers soil carbon loss under simultaneous warming and nitrogen addition.},
journal = {Ecology},
volume = {107},
number = {3},
pages = {e70351},
doi = {10.1002/ecy.70351},
pmid = {41844516},
issn = {1939-9170},
support = {DEB-1832110//U.S. National Science Foundation (NSF) Long Term Ecological Research Program/ ; DEB-1456610//U.S. National Science Foundation (NSF) Long-Term Research in Environmental Biology/ ; 2106096//Macrosystems Biology and NEON-Enabled Science" (MSB-NES)/ ; 1950364//U.S. National Science Foundation (NSF) Directorate for Biological Sciences Division of Biological Infrastructure/ ; 3018//New Hampshire Agricultural Experiment Station/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; },
mesh = {*Soil/chemistry ; *Nitrogen/chemistry ; *Carbon/chemistry/metabolism ; *Plant Roots/metabolism/physiology ; *Global Warming ; Soil Microbiology ; *Carbon Cycle ; },
abstract = {Plant roots are primary drivers of soil organic matter dynamics, mediating belowground carbon (C) inputs, stabilization, and losses. Yet, how global changes such as rising temperatures and altered nitrogen (N) availability interact to affect these dynamics has rarely been tested empirically in the field. Here, we quantify how inputs to soil organic matter from fine-root production, root exudates, and root-associated fungi respond to long-term (16 years) soil warming (+5°C), nitrogen (N) enrichment (+5 g N m[-2] year[-1]), and their combination in a temperate hardwood forest. Warming alone reduced root-derived C inputs by 21% and increased microbial respiration by 46%, resulting in a net soil C loss of 135 g C m[-2] year[-1]. In contrast, N enrichment increased root-derived soil organic carbon (SOC) accumulation by 47% and reduced root respiration by 40%, contributing to a near-neutral soil C balance. When combined, warming × N addition increased root-derived SOC fourfold (from 70 to 281 g C m[-2] year[-1]), fully offsetting warming-induced C losses and maintaining soil C stocks at control levels. Root-derived SOC accumulation was positively related to fine-root production (r[2] = 0.42) and to maple:oak exudate ratios (r[2] = 0.31), highlighting species-specific control over C stabilization. These findings demonstrate that interacting global change factors can have balancing effects on root C allocation and microbial losses, highlighting soil N availability as a critical control determining whether warming accelerates SOC depletion or stabilizes new root-derived C.},
}

*Soil/chemistry
*Nitrogen/chemistry
*Carbon/chemistry/metabolism
*Plant Roots/metabolism/physiology
*Global Warming
Soil Microbiology
*Carbon Cycle

@article {pmid41844664,
year = {2026},
author = {Ruiz-Muñoz, B and Bretscher, KM and Carrión, VJ and Cazorla, FM and Gutiérrez-Barranquero, JA},
title = {Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00957-1},
pmid = {41844664},
issn = {2055-5008},
support = {PID2021-123713OB-I00//Ministerio de Ciencia, Innovacion y Universidades (Spain)/ ; },
abstract = {Long-term farming practices leave an imprint on soil microbiomes, but how these changes influence crop drought resilience remains poorly understood. Here, we examined avocado orchards managed organically or conventionally for two decades and recurrently exposed to drought, to assess how management history shapes the rhizosphere microbiota and its contribution to plant stress tolerance. Organic and conventional systems resulted in distinct soil physicochemical profiles that were associated with shifts in rhizosphere microbial community composition. Organic management was characterized by higher soil pH, phosphorus availability, water content, and C:N ratio, together with a consistent enrichment of spore-forming bacteria, especially members of the Bacillaceae family. We established a culture collection from the organic rhizosphere, dominated by Bacillaceae, and identified three top-performing strains: Bacillus halotolerans B19 and B21, and Bacillus subtilis B26. In greenhouse assays, B. halotolerans strains mitigated drought stress by preserving biomass and reducing leaf proline accumulation, while B. subtilis provided partial protection. Gene expression analysis revealed strain-specific responses that nonetheless converged on bdh (2,3-butanediol dehydrogenase) induction, highlighting a common mechanism for drought mitigation. Together, these findings establish a mechanistic link between long-term organic farming and microbial functions underpinning drought resilience in perennial agroecosystems, paving the way for climate-smart farming strategies.},
}

@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Metagenomics
Animals
*Diet
Metabolomics
Bacteria/classification/genetics/metabolism/isolation & purification
Proteomics
Multiomics

@article {pmid41834869,
year = {2026},
author = {Ruff, SE and Murali, R and Rubin-Blum, M and Teske, AP},
title = {Editorial: Rising stars in geomicrobiology: microbial life in subsurface, seep and hydrothermal ecosystems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808625},
doi = {10.3389/fmicb.2026.1808625},
pmid = {41834869},
issn = {1664-302X},
}

@article {pmid41835129,
year = {2026},
author = {Milke, F and Garcia, SL and Simon, M and Pacheco-Valenciana, A and Lennartz, ST},
title = {Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag037},
pmid = {41835129},
issn = {2730-6151},
abstract = {Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to infer community structure, revealing (not exclusively) potential biotic interactions. Such networks have been inferred for diverse biomes and repeatedly found to be modular, yet the ecological significance of this modularity remains underexplored. We tested whether clusters within co-occurrence networks ("cohorts"), are universal and ecologically meaningful units by assessing their ubiquity, stability, and environmental specificity across diverse ecosystems. Our meta-analysis spans 25 previously published 16S rRNA gene amplicon sequencing datasets (14 160 samples) and covers high environmental variability ranging from aquatic, terrestrial to anthropogenic environments. Microbial co-occurrence networks consistently exhibited high modularity across biomes. Inferred cohorts were ubiquitous and represented up to 90% of the community composition. Our findings demonstrate that modularity is a fundamental and generalizable feature of microbial community organization, indicating the existence of stable subcommunities. Highly similar cohorts were inferred even across different, unconnected environments and datasets, and showed consistent responses to environmental gradients, indicating that their composition is to a large degree deterministic and predictable. The overall cohort structure and environmental preferences were independent of the sample size and the inference algorithm, underlining the robustness and applicability of the results. Recognizing these microbial cohorts as a meaningful level of microbial organization will refine microbial community ecology, cultivation strategies, and predictive modelling of microbial dynamics.},
}

@article {pmid41836789,
year = {2026},
author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P},
title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2641915},
pmid = {41836789},
issn = {2000-2297},
abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.

OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).

METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.

RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.

CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.},
}

@article {pmid41837593,
year = {2026},
author = {Mailem, RC and Tsai, PW and Tayo, L and Hsueh, CC and Hsieh, CY and Chen, BY},
title = {Uncovering the Redox and Immunoregulatory Basis of the Chinese Herbal Formula Ping An Fang Yu Yin using Network Pharmacology and In Silico Target Profiling.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128418247251211153057},
pmid = {41837593},
issn = {1873-4286},
abstract = {INTRODUCTION: Ping An Fang Yu Yin (PAFYY) is a traditional Chinese herbal tea formula commonly used to treat respiratory infections, including COVID-19. Previous research indicates potential antiinflammatory activities; however, the underlying mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the therapeutic effects of PAFYY, specifically its electron-transport and bioenergetic properties, through network pharmacology, electrochemical analysis, and Microbial Fuel Cell (MFC) assessments.

METHODS: Active compounds and their respective targets were identified via database searches. Proteinprotein interaction networks were constructed using the STRING database and further analyzed using Cytoscape and MCODE software. Molecular docking was employed to assess the binding affinity between identified key compounds and their targets. Cyclic voltammetry (CV) and MFC assays evaluated the electrontransport characteristics of PAFYY water and ethanol extracts.

RESULTS: The analysis identified 298 active compounds associated with 1,940 biological targets, highlighting key targets including EP300, CREBBP, ESR1, AKT1, MAPK3, MAPK1, and STAT3. GO and KEGG pathway enrichment analyses revealed that PAFYY significantly influences immune system processes and neuronal signaling pathways. Molecular docking confirmed the anti-inflammatory and antiviral potential of the identified active compounds. Additionally, electrochemical studies demonstrated that PAFYY contains electroactive substances mediating electron-driven redox reactions.

DISCUSSION: Recent studies have demonstrated that traditional Chinese herbal teas contain electron shuttles capable of mediating electron transfer in electrogenic bacteria. Emerging evidence further indicates that electroactive plant polyphenols can modulate microbial ecology through redox-mediated mechanisms. Our findings suggest that PAFYY may act on the microbiota-immune axis, with its electron-shuttling constituents contributing not only to direct cellular effects and antioxidant activity but also to modulation of the gut microbiome in ways that support antiviral immunity and attenuate inflammation. These results may inform future research into the mechanistic basis of medicinal herbs, while highlighting the potential of MFCs as a functional screening platform for identifying bioactive redox compounds.

CONCLUSION: The anti-COVID-19 properties of PAFYY may be largely attributed to its electron-transport capabilities, mediated through electroactive compounds. These findings provide novel insights into the mechanistic basis of traditional Chinese medicine prescriptions, potentially enhancing their therapeutic application.},
}

@article {pmid41839398,
year = {2026},
author = {Kawuribi, V and Awere-Duodu, A and Adjei, FA and Osman, AH and Bomansaan, H and Madadi, MM and Tampuri, JU and Adu-Amankwaah, J},
title = {The Gut-Tumor Metabolic Axis: A Comprehensive Exploration of Bidirectional Crosstalk in Cancer Immunotherapy.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105280},
doi = {10.1016/j.critrevonc.2026.105280},
pmid = {41839398},
issn = {1879-0461},
abstract = {The gut-tumor metabolic axis represents a bidirectional immunometabolic network in which tumor-derived metabolites reshape microbial ecology, while gut microbiome-derived metabolites recalibrate systemic and intratumoral immunity, ultimately influencing cancer progression and immunotherapy outcomes. Tumor aerobic glycolysis generates excess lactate and acidity that suppress cytotoxic immune function, remodel the tumor immune microenvironment, and indirectly perturb intestinal microbial composition. In turn, microbial metabolites including short-chain fatty acids, bile acid derivatives, tryptophan catabolites, inosine, and trimethylamine N-oxide signal through defined host pathways such as GPR109A, AHR, and adenosine A2A receptors to regulate antigen presentation, T-cell differentiation, macrophage polarization, and immune checkpoint sensitivity. Preclinical and emerging clinical evidence demonstrates that dietary modulation, rational probiotics, and fecal microbiota transplantation can enhance immune checkpoint inhibitor efficacy in selected contexts. However, metabolite effects are highly context dependent, with dose, timing, tumor type, and immune state critically shaping therapeutic benefit or resistance. This review integrates mechanistic insights and clinical evidence, highlights translational challenges including safety, donor heterogeneity, and biomarker validation, and proposes a framework for biomarker-guided microbiome-based strategies to advance precision cancer immunotherapy.},
}

@article {pmid41840154,
year = {2026},
author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A},
title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41840154},
issn = {1678-4405},
support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
}

@article {pmid41841597,
year = {2026},
author = {Ye, Z and Kuang, J and Bates, CT and Escalas, A and Ning, D and Wu, L and Liu, S and Deng, S and Lei, J and Chen, X and Pett-Ridge, J and Saha, M and Hale, L and Wang, G and Tian, R and Fu, Y and Tang, Y and Firestone, M and Zhou, J and Yang, Y},
title = {Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18964},
doi = {10.1002/advs.202518964},
pmid = {41841597},
issn = {2198-3844},
support = {KY-23ZK01//Hainan Institute of National Park/ ; 32161123002//National Natural Science Foundation of China/ ; //Office of Science/ ; DE-SC0014079//Office of Biological and Environmental Research Genomic Science program/ ; //UC Berkeley/ ; //Nobel Research Institute/ ; //University of Oklahoma/ ; //Lawrence Livermore National Laboratory (LLNL)/ ; AC52-07NA27344//Lawrence Berkeley National Laboratory/ ; SCW1555//Lawrence Berkeley National Laboratory/ ; EF-2025558//Lawrence Berkeley National Laboratory/ ; },
abstract = {Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.},
}

@article {pmid41841793,
year = {2026},
author = {Dey, R and Coenen, AR and Solonenko, NE and Burris, MN and Mackey, AI and Galasso, J and Sun, CL and Demory, D and Muratore, D and Beckett, SJ and Sullivan, MB and Weitz, JS},
title = {Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag041},
pmid = {41841793},
issn = {1751-7370},
abstract = {Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coexistence is often attributed to coevolutionary processes mediated by complex, pairwise infection networks. Here, using in vitro experiments and mathematical models, we explore how higher-order interactions function as a complementary, ecological feedback mechanism to stabilize phage-bacteria communities. To do so, we examine an environmentally-derived, synthetic phage-bacteria community comprised of five marine heterotrophic bacteria (Cellulophaga baltica and Pseudoalteromonas strains) and five associated phage. We used Bayesian inference to reconstruct free phage production in one-step growth experiments and then forecasted pairwise phage-bacteria community dynamics over multiple infection cycles. In contrast to model predictions of rapid bacterial population collapse, each bacterial strain persisted in the community. We hypothesized and then experimentally validated the relevance of infection attenuation at relatively high viral densities. We extended models into a community context, corroborating complex coexistence of all phage and bacteria. Life history traits inferred in community fits often differed from those inferred in a pairwise context, implicating higher-order interactions as an additional, ecological stabilization mechanism. Follow-up experiments confirm that phage traits (including burst size) can shift when infecting single vs. multiple strains. More broadly, these findings suggest that complex community coexistence of phage and bacteria may be more common than anticipated when including feedback mechanisms outside of the growth-dominated regimes of fitted pairwise models that do not reflect the full scope of ecologically relevant contexts.},
}

@article {pmid41826531,
year = {2026},
author = {Eckertová, T and Palyzová, A and Műllerová, M and Řezanka, T},
title = {Radioactive Springs and Archaeal Life in Deep Groundwater Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02720-7},
pmid = {41826531},
issn = {1432-184X},
support = {(VEGA project No. 1/0019/22//Scientific Grant Agency/ ; CZ.02.01.01/00/22_008/0004597//Grant Talking Microbes/ ; APVV-21-0356//Slovak Research and Development Agency/ ; RVO 61388971//Institutional Research Concept/ ; },
}

@article {pmid41826538,
year = {2026},
author = {Teban-Man, A and Erdem, ED and Berendonk, TU and Klümper, U and Coman, C and Szekeres, E},
title = {Hydrodynamics Shape Antibiotic Resistance in Wastewater-Impacted River Biofilms.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02725-2},
pmid = {41826538},
issn = {1432-184X},
}

@article {pmid41828603,
year = {2026},
author = {Reytor-González, C and Román-Galeano, NM and Aules-Curicama, LS and Cevallos-Villacis, CD and González, E and Jima Gavilanes, D and Horowitz, R and Simancas-Racines, D},
title = {The Oral-Gut-Immune-Nutrition Axis in Rheumatoid Arthritis: Molecular Mechanisms and Therapeutic Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828603},
issn = {1422-0067},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Diet ; Animals ; *Mouth/microbiology/immunology ; },
abstract = {Rheumatoid arthritis is a chronic systemic autoimmune disease that arises from complex interactions among genetic susceptibility, environmental factors, and immune dysregulation. Growing evidence indicates that microorganisms residing in the oral cavity and gastrointestinal tract, together with dietary factors, play a central role in shaping inflammatory and autoimmune responses in rheumatoid arthritis, forming an interconnected microbiome-immune-nutrition axis. Alterations in the composition and function of oral and intestinal microbial communities are associated with disruption of mucosal barrier integrity, activation of innate and adaptive immune pathways, increased differentiation of proinflammatory T lymphocyte subsets, and loss of immune tolerance that promotes autoantibody production. In addition, microbially derived metabolites, particularly short-chain fatty acids, provide a mechanistic link between microbial ecology, immune regulation, and bone metabolism. Diet represents a key upstream modulator of this axis. Dietary patterns rich in anti-inflammatory nutrients support microbial diversity and immunoregulatory metabolite production, whereas diets high in processed foods and saturated fats favor proinflammatory microbial profiles. Accumulating clinical evidence suggests that nutritional strategies and microbiome-targeted dietary interventions may reduce systemic inflammation and disease-related comorbidities when used alongside standard pharmacological treatments. Taken together, the microbiome-immune-nutrition axis represents a modifiable and clinically meaningful target in rheumatoid arthritis, emphasizing the need for interdisciplinary research and well-designed clinical trials to translate these insights into personalized approaches for disease management. The aim of this review is to integrate current mechanistic and clinical evidence on the interactions between the microbiome, immune system, and nutrition in rheumatoid arthritis, with a focus on their pathogenic relevance, therapeutic potential, and implications for personalized, diet-based interventions.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/therapy
*Gastrointestinal Microbiome/immunology
Diet
Animals
*Mouth/microbiology/immunology

@article {pmid41832088,
year = {2026},
author = {Schwalbe, M and Bosch, T and El Aidy, S},
title = {Gut motility as a driver of microbial community architecture and host-microbe evolution.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.12.016},
pmid = {41832088},
issn = {1878-4380},
abstract = {Digestive systems are dynamic, contractile ecosystems that continually shape the physical and chemical niches inhabited by gut microbes. Patterns of mixing and propulsion generate flow, shear, and nutrient gradients that select for microbial traits such as adhesion, biofilm formation, and metabolic timing. Microbial metabolites, in turn, influence smooth muscle excitability and enteric neural circuits, creating bidirectional feedback that structures microbial communities and affects host physiology. We argue that gastrointestinal motility, an ancient and nearly universal feature of metazoan digestive systems, functions as an evolutionary scaffold, linking microbial spatial organization with host neuromuscular diversification. Comparative evidence from cnidarians to mammals highlights how these interactions have shaped both microbial ecology and host adaptation, with relevance for understanding modern dysmotility-microbiome disorders.},
}