@article {pmid42897293,
year = {2026},
author = {Lignon, VA and Jones, EE and Dhami, MK and Kaiser, C and Mas, F},
title = {Pollinator Species Identity, Behavioural Ecology and Life History Traits Shape Epibiont Bacterial Diversity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42897293},
issn = {1432-184X},
mesh = {Animals ; *Pollination ; Bees/microbiology/physiology ; *Bacteria/classification/genetics/isolation & purification ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Diptera/microbiology/physiology ; Flowers/microbiology ; Life History Traits ; Phylogeny ; *Microbiota ; },
abstract = {Pollinators interact with flowers partly through direct surface contact, yet the bacterial communities associated with their external surfaces (epibionts) remain poorly understood compared with their gut microbiomes. This study characterised the epibiont bacterial communities of four pollinator species associated with northern highbush blueberry (Vaccinium corymbosum 'Duke') in New Zealand: bumble bee (Bombus terrestris), honey bee (Apis mellifera), drone fly (Eristalis tenax), and a New Zealand native bee (Lasioglossum sordidum). Using 16 S rRNA gene sequencing, we detected distinct epibiont communities among pollinator species, with significant differences in alpha and beta diversity. Bumble bees consistently exhibited specialised and low‑diversity communities, whereas drone flies showed the highest bacterial diversity. Several pollinator gut‑associated core bacterial genera, including Gilliamella, Lactobacillus, and Snodgrassella, were detected across most species, representing the first reports of Snodgrassella on E. tenax and of Lactobacillus and Gilliamella on L. sordidum. Environmentally acquired taxa dominated the epibiont communities, consistent with pollinator exposure to floral and habitat‑specific bacterial sources. Differential abundance analysis identified species‑specific bacterial signatures and highlighted how pollinator identity, behavioural ecology, and life history traits shape epibiont composition.},
}

Animals
*Pollination
Bees/microbiology/physiology
*Bacteria/classification/genetics/isolation & purification
New Zealand
RNA, Ribosomal, 16S/genetics
*Biodiversity
*Diptera/microbiology/physiology
Flowers/microbiology
Life History Traits
Phylogeny
*Microbiota

@article {pmid42897351,
year = {2026},
author = {Vijande, C and Fuentes-González, C and Lazzari, M and Lema, JM and Balboa, S},
title = {Industrial WWTP Sludge as a Reservoir of Putative Plastic-Degrading Enzymes: Insights Into Microbial Community Structure.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42897351},
issn = {1432-184X},
support = {ED481A 2022/391//Xunta de Galicia/ ; ED431F2024/302//Xunta de Galicia/ ; RYC2021-031220-I//Agencia Estatal de Investigación/ ; },
mesh = {*Sewage/microbiology ; *Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Biodegradation, Environmental ; Metagenomics ; Biofilms/growth & development ; *Microbiota ; Proteobacteria/genetics/enzymology/isolation & purification ; *Wastewater/microbiology ; },
abstract = {Plastic pollution has emerged as a major environmental challenge. While various microorganisms and enzymatic mechanisms involved in plastic degradation have been described, the microbial communities present in wastewater treatment plants (WWTPs) - particularly those linked to the oil industry - remain largely underexplored as potential reservoirs of plastic-associated metabolic functions. This study evaluated the potential of microbial communities from an industrial WWTP located in an oil refinery complex to colonise different plastic polymers, as well as their genetic potential for plastic-associated transformations. Industrial sewage sludge was incubated with four polymeric substrates: low-density polyethylene, polyamide, polypropylene, and polystyrene. Metagenomic analysis of the inoculum was performed to assess its potential to harbour genes encoding proteins with sequence similarity to enzymes previously associated with plastic transformation or degradation. Additionally, 16S rRNA amplicon sequencing studied changes in microbial community composition during biofilm formation. Proteobacteria accounted for approximately 50% of the microbial relative abundance in the inoculum. Metagenomic screening identified 773 genes encoding proteins with homology to enzymes previously associated with plastic degradation. Biofilms developed on plastic surfaces were dominated by Proteobacteria and Bacteroidota, although differences in dominant classes and orders were observed depending on the polymer type. Correlation analyses further indicated associations between specific microbial taxa and individual plastic types. Overall, the results highlight industrial WWTP sludge as a potential reservoir of microorganisms associated with plastic colonisation, providing new insights into plastisphere community assembly in engineered environments.},
}

*Sewage/microbiology
*Plastics/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
Biodegradation, Environmental
Metagenomics
Biofilms/growth & development
*Microbiota
Proteobacteria/genetics/enzymology/isolation & purification
*Wastewater/microbiology

@article {pmid42897614,
year = {2026},
author = {Gattei, A and Vettorazzo, S and Pindo, M and Salmaso, N and Manghi, P and Larsen, S and Donati, C},
title = {Metagenomics identifies distinct functional and taxonomic profiles between freshwaters and associated sediments in alpine habitats.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42897614},
issn = {2524-6372},
support = {PNRR, Mission 4 Component 2, Investment 1.4, D.D. 1034 17/06/2022, Project CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
abstract = {BACKGROUND: Alpine freshwater habitats are biodiversity hotspots, home to uniquely adapted microbial communities. However, our understanding of how taxonomic composition and metabolic potential of microbial communities varies across habitat type and physiography remains limited.

RESULTS: Using metagenomic sequencing, we examined microbial diversity and functions in sediment and water habitats across a physiographic gradient, including deep and shallow lakes, pasture ponds, ponds and peat bogs. Overall, sediments supported more diverse and even microbial communities. Conversely, waters displayed higher heterogeneity across the physiographic gradient in both taxonomic and functional composition. Notably, water communities from small water bodies, especially peat bogs and ponds, showed comparable diversity to their respective sediment communities, with higher taxonomic richness than aquatic communities from larger water bodies. Sediment microbial communities showed higher functional potential for nitrogen and methane metabolism, a pattern related to the likely anoxic conditions. By contrast, water bodies favored higher potential for carbohydrate metabolism, carbon oxidation and photosynthesis. Lastly, we recovered 496 bacterial and archaeal metagenome-assembled genomes and found that 73% could not be assigned at the species level.

CONCLUSIONS: Our findings shed new light on the microbial diversity and metabolic potential of alpine freshwater ecosystems, highlighting the vast and unknown diversity harbored by these fragile alpine ecosystems.},
}

@article {pmid42899019,
year = {2026},
author = {Bhatti, M and Thalib, HI and Tayyebah, A and Zobairi, A and Dahan, N and Hassan, FE},
title = {The emerging role of CRISPR-Cas systems in helicobacter pylori and the gut microbiota as regulators of gastrointestinal cancer risk.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1889115},
pmid = {42899019},
issn = {1664-3224},
mesh = {Humans ; *CRISPR-Cas Systems ; *Helicobacter pylori/genetics/immunology/pathogenicity ; *Gastrointestinal Neoplasms/microbiology/etiology/diagnosis ; *Helicobacter Infections/microbiology/complications/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; Animals ; Host-Pathogen Interactions ; },
abstract = {Gastrointestinal cancers contribute to 26% of global cancer incidence and 35% of deaths, with major contributors such as Helicobacter pylori (H. pylori) infection, gut dysbiosis, and lifestyle factors. CRISPR-Cas systems, while best known for their role in bacterial adaptive immunity, also shape bacterial physiology and host-microbe interactions, yet their influence on gastrointestinal carcinogenesis is poorly understood. This review brings together current evidence on the functions of CRISPR-Cas systems in H. pylori and the gut microbiota, highlighting their potential impact on cancer risk, diagnostics, and therapy. Key themes synthesized in this review include their role in bacterial immunity, contributions to microbial imbalance and virulence regulation, and emerging applications in cancer detection, microbiome modulation, and precision oncology. CRISPR profiles are being explored as biomarkers, while engineered systems show promise in targeted editing, phage therapy, and highly sensitive diagnostic platforms such as Cas12a-based assays. Despite this progress, challenges remain, including the risk of off-target effects, technical difficulties in detecting CRISPR signatures within complex microbial communities, and a lack of longitudinal human studies. Overall, CRISPR-Cas systems are emerging as natural regulators of microbial ecology and as engineered tools with potential applications in gastrointestinal cancer research, diagnostics, and precision microbiome interventions.},
}

Humans
*CRISPR-Cas Systems
*Helicobacter pylori/genetics/immunology/pathogenicity
*Gastrointestinal Neoplasms/microbiology/etiology/diagnosis
*Helicobacter Infections/microbiology/complications/immunology
*Gastrointestinal Microbiome/immunology/genetics
Animals
Host-Pathogen Interactions

@article {pmid42899314,
year = {2026},
author = {Shidhaye, S and Chaudhary, A and Gautam, Y and Chafle, V and Patil, H and Umekar, M and Rudayni, HA and Trivedi, R},
title = {Live biotherapeutics in the post-antibiotic era: exploring the potential of probiotics to counter multidrug resistance.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/17460913.2026.2749225},
pmid = {42899314},
issn = {1746-0921},
abstract = {Antimicrobial resistance (AMR) is a major global health threat that compromises the effectiveness of existing antibiotics and highlights the urgent need for alternative and adjunctive therapeutic strategies. Probiotics have emerged as potential adjunctive strategies because of their ability to modulate host-microbe interactions and influence microbial ecology without promoting resistance. This review examines the current evidence on the potential role of probiotics in combating multidrug-resistant organisms, based on findings from in vitro studies, animal models, and clinical investigations. The review is based on a narrative literature search of the PubMed database, covering studies published between 2020 and 2025, with earlier landmark studies. The mechanisms discussed include competitive exclusion of pathogens, the production of antimicrobial compounds, the enhancement of intestinal barrier function, and the modulation of host immune responses. In addition, probiotics are evaluated for their capacity to interfere with quorum sensing and inhibit biofilm formation, thereby reducing pathogen virulence and colonization. The review also addresses key limitations, including strain-specific variability, safety concerns in vulnerable populations, and the lack of standardized clinical protocols. Current evidence suggests that probiotics may represent a useful adjunct to existing AMR management strategies. However, their broader clinical application requires larger research to establish their efficacy and safety.},
}

@article {pmid42899649,
year = {2026},
author = {Schäfer, RB and Backhaus, T and Filser, J and Gessner, MO and Liess, M and Roß-Nickoll, M and Rundlöf, M and Scheringer, M and Spurgeon, DJ and Tscharntke, T and Van den Brink, PJ and Schäffer, A},
title = {Insufficient Environmental Protection by the European Regulatory Framework for Pesticides.},
journal = {Environmental science & technology},
volume = {60},
number = {41},
pages = {29260-29272},
doi = {10.1021/acs.est.6c06604},
pmid = {42899649},
issn = {1520-5851},
support = {101057014//HORIZON EUROPE European Research Council/ ; },
mesh = {*Pesticides ; European Union ; Environmental Monitoring ; Europe ; Risk Assessment ; Ecosystem ; Biodiversity ; },
abstract = {Schriever et al. (2025) argue that environmental risk assessment of pesticides in the European Union is sufficiently protective and that regulatory thresholds are rarely exceeded. Here, we reexamine these claims based on existing evidence from monitoring, systematic reviews, and different types of field studies. The available evidence indicates that measured pesticide concentrations frequently exceed predicted concentrations and regulatory thresholds and are associated with adverse ecological impacts. The mechanisms driving this result include the joint action of pesticides applied in temporal and spatial proximity, varied environmental conditions, interactive effects of pesticides with additional stressors, and indirect ecological effects that propagate within biological communities. These neglected intricacies explain why current single-substance prospective assessments tend to underpredict real-world pesticide exposure and impact in field settings. The corollary is that the current regulatory framework in Europe proves to be insufficient to protect biodiversity and ecosystems. Priority regulatory reforms include strengthening postregistration monitoring, refining predictive exposure models, and explicitly considering landscape context, indirect and mixture effects, and interactions with nonchemical stressors.},
}

*Pesticides
European Union
Environmental Monitoring
Europe
Risk Assessment
Ecosystem
Biodiversity

@article {pmid42899707,
year = {2026},
author = {Luo, M and Dong, M and Qiao, H and Jin, D and Chang, S and Ullah, F and Yin, M and Shen, J and Yin, Y and Yan, S},
title = {Nanoscale pesticide delivery suppresses pathogens and enriches beneficial microbiomes for safer crop protection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag273},
pmid = {42899707},
issn = {1751-7370},
abstract = {Nanocarrier-based pesticide delivery platforms substantially boost agrochemical utilization efficiency, yet their cascading ecological repercussions for rhizosphere and soil microbial ecology remain insufficiently understood. Here, a star polycation (SPc) nanocarrier was employed to construct a matrine nano-formulation (MT@SPc) with typical nano-pesticide characteristics. MT@SPc and commercial matrine formulation (MT SL) were employed as representative systems to further evaluate their impacts on rhizosphere and soil microbial ecosystems. Compared with MT SL, MT@SPc reshaped rhizosphere microbial communities by suppressing phytopathogens and promoting the enrichment of beneficial bacteria. Further validation using four representative bacterial isolates obtained from soil demonstrated that MT@SPc significantly inhibited the growth of the phytopathogen Pectobacterium carotovorum, whereas enriched beneficial bacteria exhibited lower susceptibility to MT@SPc. Multi-scale mechanistic analyses revealed that MT@SPc could interact with bacterial cell surfaces through physicochemical interactions, resulting in pronounced surface deformation and structural damage in P. carotovorum. Multi-omics analyses associated with physiological and biochemical assays further demonstrated that MT@SPc disrupted cell wall and membrane integrity, leading to ionic imbalance, metabolite leakage and oxidative stress. However, beneficial bacteria maintained higher stability, and their enrichment was associated with microbial community shifts following pathogen suppression. Overall, this study reveals that nano-pesticides drive rhizosphere community restructuring through differential microbial responses, providing mechanistic insights into nano-pesticide-microbiome interactions in complex ecological systems.},
}

@article {pmid42900352,
year = {2026},
author = {Desvennes, C and Loranger-Merciris, G and Gourdine, JL and Montout, L and Moreau, F and Thouin, J and Pruneau, L},
title = {Impacts of farming practices on pig gut microbiota and their interactions with soil microbial communities in tropical agroecosystems.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {11},
pages = {},
pmid = {42900352},
issn = {1572-9699},
mesh = {Animals ; *Soil Microbiology ; Swine/microbiology ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Agroecology ; *Gastrointestinal Microbiome ; Tropical Climate ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Biodiversity ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; Ecosystem ; },
abstract = {Livestock farming systems are associated with differences microbial communities in both animals and soils, yet the ecological mechanisms linking these compartments remain poorly understood. This study investigated the effects of contrasting farming systems (intensive vs. agroecological) on the gut microbiota of Creole pigs and associated soil microbial communities in farms located in Guadeloupe (French West Indies). Fecal and soil samples were analyzed using 16S and 18S Ribosomal Ribonucleic Acid (rRNA) genes metabarcoding to characterize bacterial, archaeal and fungal diversity. Pig gut microbiota was dominated by Bacillota (63.44% and 67.55% for intensive and agroecological raised pigs respectively) and Bacteroidota (24.70% and 18.56% for intensive and agroecological raised pigs respectively), whereas soils were mainly dominated by Acidobacteriota (14.61% and 17.48% for plowed and unplowed soil respectively), Actinomycetota (7.61% and 9.05% for plowed and unplowed soil respectively), and Bacillota (6.62% and 9.87% for plowed and unplowed soil respectively), indicating limited taxonomic overlap. Agroecological management was associated with higher relative abundances of Bacillota and Euryarchaeota in pigs and greater fungal diversity in soils. A total of 234 operational taxonomic units (OTUs) were common to all four groups (pig gut-agroecological, pig gut-intensive, plowed soil and unplowed soil), representing the microbial taxa shared between gut and soil environments; however, these taxa were generally abundant in the gut and rare in soils. These results suggest an ecological link between pigs and soil microbial communities that may be mediated by environmental processes. This underscores the interconnectedness of animal and environmental health within a One Health framework.},
}

Animals
*Soil Microbiology
Swine/microbiology
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Agroecology
*Gastrointestinal Microbiome
Tropical Climate
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Biodiversity
Agriculture/methods
RNA, Ribosomal, 18S/genetics
Ecosystem

@article {pmid42900414,
year = {2026},
author = {Almeida, KA and Guimarães, RA and Porto, VBC and Góes, LFM and de Moreira, FMS and Quensen, J and Tiedje, J and de Medeiros, FHV},
title = {Effects of a three-year maize-soybean rotation on soil bacterial diversity and fumonisin-producing Fusarium spp. inoculum potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42900414},
issn = {1573-0972},
support = {152719/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CAG 03787/18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Zea mays/microbiology/growth & development ; *Soil Microbiology ; *Fusarium/metabolism/genetics ; *Glycine max/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Fumonisins/metabolism ; Seasons ; Rhizosphere ; Brazil ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Agriculture/methods ; },
abstract = {Maize-soybean succession dominates grain production in tropical Brazil, and rotation is often recommended to improve soil health. However, few field studies have followed both soil bacterial diversity and fumonisin-producing pathogens over several seasons in tropical no-till systems. We compared continuous maize, continuous soybean and maize-soybean rotation for three seasons (2016-2017 to 2018-2019). In a fourth season (2019-2020), maize was grown in all plots to test legacy effects. Bacterial communities were profiled by 16 S rRNA (V3-V4) amplicon sequencing. The fum1 gene of fumonisin-producing Fusarium spp. was quantified by qPCR in soil and in maize stalks left on the soil surface. In the first three seasons, rotation did not detectably increase bacterial diversity, although statistical power was low (n = 4 plots; post-hoc power 12-61%). Community composition differed among seasons and was associated with antecedent precipitation as Actinobacteria were most abundant in the driest season. In the fourth season, a continuous-soybean history was associated with higher bacterial richness and Shannon diversity in the maize rhizosphere at tasselling than a rotation history, whereas bulk-soil diversity did not differ among land uses. A rotation history was associated with lower fum1 abundance in bulk soil. In contrast, continuous maize was associated with lower fum1 in stalks (third season), less stalk rot and fewer infected grains. Soil and crop residues therefore responded differently to rotation. Given the single site and limited plot-level replication, these findings should be regarded as hypothesis-generating.},
}

*Zea mays/microbiology/growth & development
*Soil Microbiology
*Fusarium/metabolism/genetics
*Glycine max/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification/metabolism
*Fumonisins/metabolism
Seasons
Rhizosphere
Brazil
Biodiversity
RNA, Ribosomal, 16S/genetics
Soil/chemistry
Agriculture/methods

@article {pmid42900755,
year = {2026},
author = {Naeem, M},
title = {Reduced Crude Protein Nutrition in Poultry: Mechanistic Links Between Nitrogen Metabolism, Gut Microbial Ecology, and Intestinal Physiology.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70116},
pmid = {42900755},
issn = {1439-0396},
abstract = {Reducing dietary crude protein (CP) has emerged as an effective nutritional strategy to improve nitrogen utilisation efficiency and reduce environmental nitrogen losses in poultry production. Beyond these practical benefits, dietary protein concentration and digestibility influence nitrogen flow, microbial substrate availability, and metabolic interactions within the gastrointestinal tract, thereby shaping host-microbiota function. This review synthesises current evidence on the mechanistic links between reduced crude protein nutrition, nitrogen metabolism, gut microbial ecology, and intestinal physiology in poultry. Quantitative evidence indicates that responses depend strongly on the magnitude of CP reduction and dietary formulation. For example, a 2-percentage-point CP reduction with balanced lysine, methionine, and threonine improved growth and intestinal morphology, whereas a 3-percentage-point reduction has been associated with decreased duodenal and ileal villus height; in contrast, a 1.5-percentage-point reduction produced no significant morphological impairment. Recent evidence further shows that a 2% lower-protein diet can increase ileal microbial richness and diversity, while bacteriophage supplementation significantly improves nitrogen digestibility (p = 0.045), and dietary protein level itself affects nitrogen digestibility (p = 0.017). Collectively, moderate CP reduction supported by adequate digestible amino acids and highly digestible ingredients can decrease undigested nitrogen flow and proteolytic fermentation while maintaining intestinal function. However, excessive protein restriction, poor amino acid balance, or reduced ingredient digestibility may disrupt microbial metabolism and compromise intestinal integrity. These findings position reduced crude protein nutrition as a precision nutritional strategy in which the magnitude of protein reduction, amino acid adequacy, digestibility, and microbial substrate availability collectively determine productive, intestinal, and environmental outcomes.},
}

@article {pmid42902746,
year = {2026},
author = {Bhowmik, N and Stubbendieck, RM},
title = {Natural products shape microbial ecology and disease in the cystic fibrosis airway.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
pmid = {42902746},
issn = {1460-4752},
abstract = {Covering up to 2026Cystic fibrosis (CF) is a life-shortening autosomal recessive genetic disorder caused by mutation in the gene encoding the CF transmembrane conductance regulator (CFTR). Dysfunction in CFTR leads to the accumulation of thick and dehydrated mucus in the respiratory tract, which serves as a substrate for a complex microbiota that includes commensal oral and respiratory bacteria and opportunistic pathogenic bacteria and fungi. During chronic infections, these microbes persist in the airways and contribute to progressive lung tissue damage, ultimately leading to respiratory failure and premature death. Within this environment, microbes synthesize a diverse repertoire of natural products, including antimicrobials, siderophores and other metallophores, signaling molecules, toxins, and other virulence factors. In this review, we thoroughly discuss natural products produced by members of the CF airway microbiota, primarily the bacterial pathogens Burkholderia spp., Pseudomonas aeruginosa, and Staphylococcus aureus and the fungal pathogens Aspergillus fumigatus and Scedosporium spp. When known, we describe the biosynthesis and roles of these natural products in microbial persistence, interspecies interactions, and virulence in the CF airway. When these roles are unknown, we infer potential roles based on evidence from the literature in different disease contexts. Finally, we briefly highlight natural products produced by the CF microbiota as novel sources for developing new antimicrobials and as drug targets to treat disease.},
}

@article {pmid42903952,
year = {2025},
author = {Zhang, H and Yang Lee, BJ and Wang, T and Xiang, X and Tan, Y and Han, Y and Bi, Y and Zhi, F and Wang, X and He, F and Salminen, SJ and Zhu, B and Yang, R},
title = {Microbiota, chronic inflammation, and health: The promise of inflammatome and inflammatomics for precision medicine and health care.},
journal = {hLife},
volume = {3},
number = {7},
pages = {307-326},
pmid = {42903952},
issn = {2949-9283},
abstract = {The terms "inflammatome" (holistic inflammation networks) and "inflammatomics" (a novel omics field) were proposed to decode dysbiosis-driven chronic inflammation and its disease links. Inflammatomics explores microbiota-immune crosstalk, particularly innate immune interactions, revealing how dysregulated microbial communities trigger chronic inflammation underlying disorders like inflammatory bowel disease, metabolic diseases, and neurodegeneration. This discipline transcends traditional inflammation paradigms by dissecting molecular pathways connecting dysbiosis to systemic inflammation, enabling early detection and precision interventions. It integrates evolutionary perspectives on host-microbe interactions, emphasizing the human body as a stress-sensitive "organ". Challenges include standardizing inflammatome profiling, translating findings into clinical tools, and advancing multiomics technologies. By bridging microbial ecology, immunology, and systems medicine, inflammatomics holds a transformative potential to shift health care from reactive treatment to proactive, personalized prevention, targeting disease origins shaped by chronic inflammatome dysregulation.},
}

@article {pmid42883502,
year = {2026},
author = {Tsanasidou, C and Bosnea, L and Terpou, A},
title = {Rethinking Salt in Cheese: Advances, Challenges, and Strategies for Sodium Reduction.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
pmid = {42883502},
issn = {2304-8158},
abstract = {Sodium chloride (NaCl) is a multifunctional component of cheese manufacture that contributes to flavor, microbial control, moisture regulation, texture formation, product safety, and shelf stability. However, the association between excessive dietary sodium intake, elevated blood pressure, and cardiovascular disease has increased demand for reduced-sodium foods. Cheese reformulation is particularly challenging because reducing NaCl may simultaneously modify water activity, microbial ecology, acidification, proteolysis, lipolysis, texture, flavor development, and sensory acceptance. Accordingly, the purpose of this review is to critically evaluate the scientific evidence concerning direct NaCl reduction, partial replacement with mineral salts, flavor-enhancement approaches, modified salting and processing technologies, and complementary preservation strategies in cheese. Particular attention is given to the mechanisms through which these interventions affect microbial succession, ripening biochemistry, rheological properties, safety, shelf life, and consumer acceptance. The review also evaluates the limitations affecting industrial implementation, including process reproducibility, regulatory compliance, mineral accumulation in recirculated brines, ingredient costs, and environmental considerations. Current evidence indicates that no single strategy is universally applicable. Instead, safe and acceptable sodium reduction requires cheese-specific combinations of salt replacement, process control, microbial management, and sensory optimization.},
}

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42884597,
year = {2026},
author = {Kamalakar, K and Akerele, C and Lafont, E and Koralnik, LR and Gilman, C and Litran, JC and Lee, J and Robinson-Papp, J and Malaspina, D},
title = {Gut Microbiome-Mediated Neuroprotective Effect of the Mediterranean Diet: A Narrative Review of Cognitive Aging, Alzheimer's Disease, and Parkinson's Disease.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
pmid = {42884597},
issn = {2072-6643},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/prevention & control ; *Alzheimer Disease/prevention & control/microbiology ; *Cognitive Aging/physiology ; *Neuroprotection ; Animals ; },
abstract = {Background: Alzheimer's disease (AD) and Parkinson's disease (PD) are major neurodegenerative disorders for which disease-modifying therapies are limited. Increasingly, evidence suggests that diet influences neurodegenerative risk through interactions among the gut microbiome, immune system, and brain. The Mediterranean diet (MD) is associated with improved cognitive health, but the mechanisms underlying its potential neuroprotective effects remain incompletely understood. Objective: In this narrative review, evidence on microbiome-mediated mechanisms linking MD adherence to neuroprotection was synthesized, and how Mediterranean dietary components influence microbial ecology, metabolites, immune regulation, and neuroinflammation relevant to cognitive aging, AD, and PD was evaluated. Methods: Evidence from experimental, observational, and clinical studies was reviewed, focusing on microbial metabolites, intestinal barrier integrity, immune regulation, and inflammatory pathways. Discussion: Mediterranean dietary components, including fiber, polyphenols, whole grains, legumes, nuts, extra-virgin olive oil, and omega-3 fatty acids, may promote beneficial microbial communities and metabolite production. Short-chain fatty acids, secondary bile acids, indole derivatives, and phenolic metabolites may strengthen the intestinal and blood-brain barriers, regulate immune responses, and suppress neuroinflammation. Conversely, dysbiosis may increase intestinal permeability, lipopolysaccharide translocation, systemic inflammation, and microglial activation. However, evidence remains heterogeneous and largely observational or experimental. Conclusions: The MD may promote neuroprotection through interconnected diet-microbiome-immune pathways. Longitudinal and intervention studies integrating microbiome, metabolomic, inflammatory, neuroimaging, and cognitive measures are needed to establish causality and advance precision nutrition strategies to prevent neurodegenerative disease.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/prevention & control
*Alzheimer Disease/prevention & control/microbiology
*Cognitive Aging/physiology
*Neuroprotection
Animals

@article {pmid42885316,
year = {2026},
author = {Jin, C and Wang, Y},
title = {Gut microbiota in patients receiving dialysis: Mechanisms, complications and the road to personalized microbiome‑based care (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {6},
pages = {},
doi = {10.3892/mmr.2026.14044},
pmid = {42885316},
issn = {1791-3004},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Dialysis/adverse effects ; *Dysbiosis/microbiology/etiology ; *Precision Medicine/methods ; },
abstract = {Gut dysbiosis is increasingly recognized as a potential contributor to poor outcomes in patients receiving dialysis, yet its mechanistic complexity and therapeutic implications remain incompletely understood in clinical practice. The uremic environment, dietary restrictions, polypharmacy and dialysis modality‑specific factors collectively reshape the gut microbial ecology, promoting the overproduction of deleterious metabolites such as indoxyl sulfate, p‑cresyl sulfate and trimethylamine N‑oxide while depleting protective short‑chain fatty acids. These alterations compromise intestinal barrier integrity, fuel systemic inflammation through endotoxemia and NOD‑like receptor family pyrin domain containing 3 inflammasome activation and have been associated with cardiovascular disease, immune dysfunction, peritonitis, protein‑energy wasting and cognitive impairment. Although probiotic, prebiotic, synbiotic and dietary interventions show promise, heterogeneous responses across trials underscore the inadequacy of one‑size‑fits‑all strategies. Multi‑omics profiling has revealed substantial interindividual variability in microbial composition and metabolic capacity, providing a rationale for personalized approaches. The present review synthesizes current evidence on the mechanisms underlying dysbiosis and complications in patients receiving dialysis and proposes a roadmap toward personalized microbiome‑based care to improve clinical outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Renal Dialysis/adverse effects
*Dysbiosis/microbiology/etiology
*Precision Medicine/methods

@article {pmid42887297,
year = {2026},
author = {Mendes-Oliveira, F and Belisário, AR and Martins, ML and Martins, RCR and Franco, LAM and Scaccia, N and Fonseca, JVDS and Moura, ICG and de Souza, VR and Costa, SF and Valença, I and Bolina-Santos, E and Mendes, FG and Moreno, EC and Timponi, A and Coelho Dos Reis, JGA and Martins-Filho, OA and Carneiro-Proietti, AB and Sabino, EC},
title = {Microbial diversity in leg ulcer and skin in Sickle Cell disease.},
journal = {Hematology, transfusion and cell therapy},
volume = {48},
number = {4},
pages = {108550},
doi = {10.1016/j.htct.2026.108550},
pmid = {42887297},
issn = {2531-1387},
abstract = {INTRODUCTION: Leg ulcers are a common, painful, and difficult-to-treat complication of sickle cell disease due to their prolonged healing process. The microbial composition of these wounds remains poorly understood. This study investigated the microbiota diversity in sickle cell disease leg ulcers and associations with laboratory parameters.

METHODS: Samples were collected from leg ulcers, intact skin adjacent to the ulcers, and intact skin from healthy controls. Microbiome profiling was performed by sequencing the V4 region of the 16S ribosomal RNA (rRNA) gene. The laboratory results of patients with sickle cell disease leg ulcers were analyzed alongside the identified taxa using correlation-based analyses.

RESULTS: Microbial diversity was significantly lower in sickle cell disease leg ulcers compared to intact skin. Additionally, leukocytes and mean corpuscular volume were statistically associated with the relative abundance of bacteria of the genera Pseudomonas and Aeromonas. Staphylococcus spp. was the predominant genus identified in leg ulcers and was negatively associated with Pseudomonas spp., reflecting a dysbiotic microbial profile characterized by taxa commonly associated with chronic wounds.

CONCLUSIONS: The observed associations between bacterial taxa and laboratory parameters are exploratory, do not imply causality, and contribute to the characterization of the microbial ecology of sickle cell disease leg ulcers.},
}

@article {pmid42889337,
year = {2026},
author = {Maghembe, RS and Damian, D and Bahati, S and Makaranga, A},
title = {Microbiome-Endocannabinoidome Crosstalk as an Immunometabolic Rheostat in Inflammatory Disease.},
journal = {FASEB bioAdvances},
volume = {8},
number = {10},
pages = {e70163},
pmid = {42889337},
issn = {2573-9832},
abstract = {Chronic inflammatory diseases reflect disrupted coordination among microbial ecology, epithelial barriers, lipid signaling, and immunity. The microbiome-endocannabinoidome (eCBome) axis is already recognized as a regulator of metabolism, permeability, and inflammatory tone; the unresolved issue is how to distinguish direct crosstalk from parallel or associative changes. This review therefore operationalizes the axis as an immunometabolic rheostat defined by five measurable domains: microbial functions and metabolites, compartment-specific eCBome ligands and enzymes, barrier integrity and microbial translocation, immune-cell programming, and tissue or clinical outcomes. We distinguish classical endocannabinoids (anandamide and 2-arachidonoylglycerol) from the endocannabinoid-related N-acylethanolamines palmitoylethanolamide and oleoylethanolamide, which act prominently through PPARα, TRPV1, GPR119, and related pathways. Evidence is appraised as direct causal, mechanistically supportive, associative, or hypothesis-generating. The strongest causal foundation links microbiota manipulation to intestinal eCBome tone, permeability, and metabolic endotoxemia, while disease-specific evidence is most developed in obesity-associated inflammation and inflammatory bowel disease. Engineered Lactobacillus paracasei platforms that produce PEA or OEA in situ provide particularly informative proof-of-concept because they couple a defined microbial perturbation to lipid-mediator release, receptor-dependent barrier effects, and inflammatory or metabolic outcomes. By contrast, evidence in MASLD/MASH, neuroinflammation, and systemic autoimmunity remains more compartment-dependent and heterogeneous. Clinical translation must account for the psychiatric toxicity that ended centrally active CB1 antagonism with rimonabant, the target and off-target complexity of FAAH/MAGL inhibition, and limitations of surrogate barrier biomarkers. A causal roadmap should combine gnotobiotic and loss-of-function models, isotope tracing, organoids, and gut-on-chip systems with tissue-resolved lipidomics and longitudinal, biomarker-enriched human trials.},
}

@article {pmid42892979,
year = {2026},
author = {Wang, W and He, Z and Chen, J and Ding, R and Wang, L and Chen, M and Kang, J and Tong, L and Du, T},
title = {Revolutionizing drought defense: The water-plant-microbe synergy in climate-smart agriculture.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117422},
pmid = {42892979},
issn = {2589-0042},
abstract = {Global warming-induced water scarcity threatens agricultural sustainability. While precision irrigation and microbial inoculants are recognized as effective individual strategies, their synergistic potential remains under-explored. This review synthesizes recent advances in the "water-plant-microbe" synergy to propose a bidirectional regulatory mechanism for climate-smart agriculture. We demonstrate that irrigation regimes function as a primary filter for rhizosphere microbial assembly, thereby defining the hydraulic niche for colonization. Conversely, functional microbes actively engineer the soil environment via exopolysaccharide production and hormonal modulation, thereby enhancing plant hydraulic status and water use efficiency (WUE). In contrast to previous reviews focusing on single factors, this review constructs an integrated framework linking soil hydrology with microbial ecology, supported by emerging comparative evidence. We conclude that future agricultural water management must shift from solely regulating water supply to managing the holobiont's hydrological interactions, offering a promising systems-level strategy to safeguard food security under climate stress.},
}

@article {pmid42893235,
year = {2026},
author = {Mousavi, SQ and Amiri, A and Bandani, AR},
title = {16S rRNA gene amplicon data from four composite gut-region samples of Microcerotermes diversus workers.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113302},
pmid = {42893235},
issn = {2352-3409},
abstract = {This data article describes bacterial V3-V4 16S rRNA gene amplicon data from four anatomically defined composite gut preparations of Microcerotermes diversus workers. Termites were collected from infested Morus nigra branches in Shush, Khuzestan Province, southwestern Iran. Guts from 400 workers were dissected into four anatomical categories, and corresponding tissues were pooled to generate one composite DNA sample and one sequencing library per category. The amplicons were sequenced on an Illumina MiSeq platform using a 2 × 300-bp paired-end configuration. Public resources comprise quality-filtered paired-end FASTQ files in the NCBI Sequence Read Archive under BioProject PRJNA1328141, 82 representative partial 16S rRNA gene sequences in GenBank under accessions PX349529-PX349610, and processed OTU, taxonomic, diversity, and rarefaction records in Figshare, together with four pH records reported in this article. Sample identifiers T1-T4 link the anatomical definitions, sequence runs, processed outputs, tables, and figures. The archived reads and processed files can be used for sample-level reanalysis, taxonomic reclassification, workflow benchmarking, and harmonized comparison with independently generated termite microbiome data.},
}

@article {pmid42895087,
year = {2026},
author = {Aranda, M and Pariente, JA and Terrón, MP and González-Flores, D and Aranda, E and Ruiz-Moyano, S and Velázquez, R and Martín, A},
title = {Comparative dietary profiling of smoked and non-smoked paprika (Capsicum annuum L.) in Wistar rats: metabolomic, biochemical and gut microbiota responses in a healthy animal model.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo03991j},
pmid = {42895087},
issn = {2042-650X},
abstract = {Paprika (Capsicum annuum L.) is a widely consumed spice whose bioactive composition is substantially influenced by processing conditions. Traditional smoking, as applied in the production of PDO Pimentón de la Vera, enriches paprika with wood smoke-derived phenolics while also introducing polycyclic aromatic hydrocarbons (PAHs), warranting an integrated evaluation of processing-related biological responses and safety considerations. This study compared physiological, biochemical, metabolomic, and cecal microbiota responses to dietary supplementation with smoked and non-smoked paprika in healthy Wistar rats. Thirty animals of both sexes (16 females and 14 males) received a control diet or diets supplemented with 5% smoked or non-smoked paprika for 30 days. Histological examination revealed no treatment-related alterations in the organs evaluated. Hematological and biochemical analyses showed diet- and sex-associated differences in hematocrit, plasma glucose, total antioxidant capacity, and lipid-related parameters, although all values remained within normal physiological ranges. Untargeted urinary metabolomics, restricted to males because of insufficient urine volume in females, identified features tentatively annotated as phenolic conjugates and other metabolites associated with paprika intake, with several signals showing higher abundance in the smoked paprika group. Cecal metagenomic analyses showed sex-dependent changes across taxon-level abundance, alpha diversity, and beta diversity. In females receiving smoked paprika, lower TC and LDL-C coincided with higher alpha diversity and lower cecal lipid content, suggesting a potential link between intestinal microbial ecology and lipid handling. Overall, paprika processing was associated with distinct biochemical, metabolomic, and cecal microbiota response patterns in this healthy animal model.},
}

@article {pmid42895354,
year = {2026},
author = {Goethals, V and Vanwinsen, N and Mermans, F and De Gand, S and Boon, N and Van de Wiele, T and De Paepe, K},
title = {An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting, and extraction bias in sorted microbial communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0071226},
doi = {10.1128/spectrum.00712-26},
pmid = {42895354},
issn = {2165-0497},
abstract = {Fluorescence-activated cell sorting (FACS) followed by metataxonomics is commonly used to probe the composition of microbial subpopulations with a functionality of interest. Metataxonomic analysis of sorted low-microbial-biomass samples is prone to contamination and bias introduced during sorting and DNA extraction. To improve metataxonomic accuracy, the DNA yield obtained by the DNeasy PowerSoil Pro kit was first maximized. FACS-sequencing using the optimized DNA extraction method distorted the composition of sorted microbiota by introducing sheath fluid contaminants, termed the FACSome. Since FACSome contaminants were experiment-specific, a standardized, applicable in silico decontamination method was developed to characterize and remove FACSome contamination in PacBio and Illumina metataxonomic sequencing data based on carefully selected controls. The optimized DNA extraction and decontamination methods were validated in soil, water, feces, saliva, gut reactor, and mock microbial communities. Metataxonomic profiles of non-selectively sorted and unsorted samples derived from these ecosystems did not perfectly match due to relic DNA depletion during FACS. Effective (97%) relic DNA depletion was confirmed with a spike-in experiment and is desirable since naturally present relic DNA can interfere with function-driven FACS-sequencing. A nuclease-based digest further enhanced relic DNA depletion. Since FACS depleted relic DNA, the preservation of intact cells prior to sorting is essential for activity- or viability-targeted FACS. Intact cells were best preserved during long-term -80°C storage of fecal samples that were not amended with glycerol-1× Tris-EDTA cryoprotectant.IMPORTANCEBulk meta-omics fail to provide sufficient resolution to gain mechanistic insights in microbial ecosystems. Function-driven microbiome research requires high-throughput profiling of active microbial subpopulations. These can be singled out through fluorescence-activated cell sorting (FACS) combined with function-, activity-, or viability-based labeling. The resulting low-biomass sorted samples present a currently overlooked challenge for accurate 16S rRNA gene profiling. We systematically identified all potential sources of interference to enable decontamination of 16S rRNA gene sequences from sorted microbiota. While this study focused on metataxonomic read-outs, our optimized extraction and decontamination workflow can advance other sequencing-based omics analyses of sorted microbial communities. Our optimized FACS-sequencing workflow is thus imperative to unlock the full potential of single-cell labeling and FACS, in turn enabling mode-of-action studies that will broaden our understanding of microbe-environment interactions.},
}

@article {pmid42883395,
year = {2026},
author = {Meo, SR and Ravikumar, A and Noppe, C and De Clercq, P and Defoirdt, T},
title = {Mucin Increases the Virulence of Enterotoxigenic Escherichia coli.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
pmid = {42883395},
issn = {2079-7737},
support = {//Higher Education Commission Pakistan/ ; //Bijzonder Onderzoeksfonds UGent/ ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important pathogen of humans and other mammals (such as piglets and calves). Mucin, a glycoprotein that forms the major fraction of the intestinal mucus layer, is a key host substance that ETEC encounters in the host environment. This study investigated whether physiologically relevant concentrations of mucin modulate virulence-related phenotypes in ETEC. Growth of ETEC remained unaffected across mucin concentrations ranging from 50 mg/L to 1000 mg/L. Mucin increased swimming motility in a concentration-dependent manner, with motility doubling at the highest concentrations tested relative to the mucin-free control. Further, mucin also increased biofilm formation in a dose-dependent manner, with approximately 4.5-fold higher biofilm levels at the highest concentration. Finally, mucin increased the virulence of ETEC in the invertebrate infection model Galleria mellonella, resulting in a 1.5- to 3.3-fold increase in larval mortality caused by mucin-treated ETEC compared with the untreated ETEC group. These findings indicate that ETEC responds to mucin as a host-derived cue, promoting virulence-associated traits linked to colonization and infection. Understanding this host-pathogen interaction may lead to the development of novel control strategies against ETEC, which is an urgent societal challenge in the context of rising antibiotic resistance.},
}

@article {pmid42883490,
year = {2026},
author = {Méndez-Hernández, A and Muñoz-Yáñez, C and González-Galarza, FF and Prieto-Hinojosa, AI and Guangorena-Gómez, JO},
title = {Dietary Gradient, Blastocystis Colonisation, and Gut Microbiota Ecology in Mexican University Students: An Exploratory Cross-Sectional Study.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
pmid = {42883490},
issn = {2304-8158},
support = {//Science and Technology council of the state of Durango./ ; },
abstract = {Gut microbiota is shaped by interactions among diet, host characteristics, and microbial colonisation. This exploratory cross-sectional study examined associations between a dietary gradient, Blastocystis colonisation, and gut microbiota in 41 university students, seven (17.1%) of whom were colonised with Blastocystis. Dietary intake was assessed using a validated food frequency questionnaire, and a diet-ratio was derived from the relative energy contribution of industrialised and non-industrialised foods. Gut microbiota was characterised by 16S rRNA gene sequencing. The multivariable model including diet-ratio, age, and body mass index was associated with microbiota structure in the primary genus-level analysis (PERMANOVA: R[2] = 0.090, p = 0.041), although this association was attenuated after adjustment for abdominal pain and was not retained using the de novo DADA2 ASV table. Blastocystis colonisation was not associated with overall microbiota composition but was associated with greater alpha diversity (Shannon: p = 0.033; Gini-Simpson: p = 0.043). These alpha-diversity associations remained statistically significant after additional adjustment for abdominal pain and genus-level rarefaction, although they were less consistent in other sensitivity analyses. Genus-level associations with the dietary gradient did not remain significant after false discovery rate correction. No statistically significant diet-ratio × Blastocystis interaction was detected, although the small number of colonised participants limited assessment of effect modification. Overall, these findings suggest that dietary and Blastocystis-related associations may involve different ecological dimensions of the gut microbiota and warrant confirmation in larger studies.},
}

@article {pmid42881005,
year = {2026},
author = {Gionchetta, G and Borrego, CM and Manaia, CM and Hernando-Amado, S and Laso-Pérez, R and Villaverde, J and Subirats, J},
title = {When does environmental antimicrobial resistance become a health risk?.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.005},
pmid = {42881005},
issn = {1878-4380},
abstract = {Environmental antimicrobial resistance (AMR) only constitutes a meaningful risk when resistant bacteria overcome key ecological and transmission barriers to reach, persist in, and colonize susceptible hosts. By linking exposure, evolution, transmission, and ecology, our framework provides a realistic basis for assessing AMR risks across One Health compartments.},
}

@article {pmid42883044,
year = {2026},
author = {Qin, J and Li, T and Li, X and Han, P and Jin, M and Qiao, L},
title = {Gut Microbiota-Mucosal Immune Interactions Underlying Intestinal Homeostasis in Weaned Piglets.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193075},
pmid = {42883044},
issn = {2076-2615},
support = {LZ25C170001, LD26C170001//Zhejiang Provincial Natural Science Foundation/ ; 2025M770268//China Postdoctoral Science Foundation/ ; },
abstract = {The gut microbiota and mucosal immune system undergo extensive remodeling after weaning and jointly influence intestinal homeostasis, resistance to enteric pathogens, and growth performance in piglets. This developmental transition is particularly vulnerable to dietary changes, the loss of maternally derived factors, environmental stressors, and pathogen exposure, all of which can disrupt microbial ecology and mucosal immune regulation. This review examines the reciprocal interactions between the gut microbiota and mucosal immunity in weaned piglets. It describes how microbial communities and their metabolites regulate epithelial barrier integrity, innate and adaptive immune responses, B-cell differentiation, and secretory immunoglobulin A (sIgA) production, with particular emphasis on short-chain fatty acids, tryptophan-derived metabolites, and bile acids. Conversely, host-derived factors, including mucins, antimicrobial peptides, sIgA, cytokines, and inflammation-associated changes in the intestinal microenvironment, are discussed in relation to microbial colonization, spatial distribution, and functional activity. Disruption of these interactions can impair epithelial barrier function, promote excessive inflammation, weaken colonization resistance, and increase susceptibility to enteric infection and post-weaning diarrhea. Finally, this review evaluates nutritional and microbiota-targeted strategies for modulating microbiota-immune interactions and improving intestinal health in weaned piglets.},
}

@article {pmid42880829,
year = {2026},
author = {Saha, S and Shah, AS and Burgess, TI and Bayliss, KL},
title = {Core and Keystone Epiphytic and Endophytic Bacteria Associated With Potato Leaves Are Driven by Cultivar and Site.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70446},
pmid = {42880829},
issn = {1462-2920},
support = {AS19004//Hort Innovation/ ; },
mesh = {*Solanum tuberosum/microbiology ; *Endophytes/classification/isolation & purification/genetics ; *Plant Leaves/microbiology ; *Bacteria/classification/isolation & purification/genetics ; Australia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bacteria that colonise leaf surfaces and internal tissues benefit potato health and productivity. Whether these bacteria are present across potato cultivars and production fields is unknown. Leaf samples were collected from field-grown potatoes (Imperial Blue, Innovator, Nicola, and Royal Blue) at 12 commercial farms across three production regions in Australia. Epiphytic and endophytic bacteria were analysed by amplicon sequencing. Both cultivar and site influenced the bacterial community composition, with endophytes strongly influenced by cultivar, while epiphytes were less consistent. Site-specific bacteria varied with climate, with limited influence from location. Endophytic bacteria identified across cultivars and sites were a Delftia sp., Acinetobacter sp., and Caldalkalibacillus thermarum. The same Delftia sp. and C. thermarum were also cultivar-specific core endophytes in cvs. Imperial Blue, Innovator, and Royal Blue. A Pantoea sp. was the only core epiphyte. The relative abundance of reproducible core taxa was not significantly different between cultivars. The Delftia sp. was the only putative keystone taxon in both endophyte and epiphyte communities in multiple cultivars. The results suggest that potato leaf bacterial communities are influenced by cultivar and site, but also have a shared core. These findings support isolation and further investigation of the roles of core bacterial taxa in potatoes.},
}

*Solanum tuberosum/microbiology
*Endophytes/classification/isolation & purification/genetics
*Plant Leaves/microbiology
*Bacteria/classification/isolation & purification/genetics
Australia
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid42875136,
year = {2026},
author = {Ge, W and Han, Y and Dong, C and Gui, Y and Zhu, G and Huang, W and Li, B and Liu, H and Gong, G and Lu, Y and Liu, H},
title = {Exogenous substances promote the formation of Phallus dongsun primordia by remodeling the mycosphere microenvironment.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101869},
doi = {10.1016/j.funbio.2026.101869},
pmid = {42875136},
issn = {1878-6146},
mesh = {*Mycelium/growth & development/drug effects/metabolism ; Culture Media/chemistry ; Biomass ; },
abstract = {Exogenous substance application (ESA) directly influences subterranean processes through the action of macrofungal mycelia, garnering considerable attention for its role in enhancing crop yields and resource utilization. However, the intricate mechanisms of mycosphere metabolite-microbe interactions governing macrofungal development remain unclear. This study employed Phallus dongsun for plate culture and pot experiments, integrating multi-omics analysis to investigate the regulatory mechanisms governing the growth and development of this macrofungus through functional interactions between the macrofungus, metabolites, and microorganisms under ESA. Single-factor plate cultures revealed that 60 mg/L ZnSO4·7H2O exhibited the most pronounced effect on promoting mycelial growth and biomass in all three P. dongsun strains, while 1.5 g/L MgSO4 demonstrated a slightly weaker yet still significant effect. To verify the performance of each ESA under natural conditions, single-factor pot experiments were conducted. Pot experiments showed that 1.5 g/L MgSO4 was optimal for primordia formation and earliness. Furthermore, triacontanol (TRIA, 6 mg/L), vitamin B6 (VB6, 6 mg/L) and ZnSO4·7H2O (60 mg/L) also exhibited promotional effects on primordia formation and earliness, respectively. ESA significantly altered the mycosphere metabolite composition and microbial community structure, enhancing metabolite chemodiversity and keystone taxa diversity (P < 0.05). Moreover, ESA significantly enhanced the accumulation of the keystone taxa Paraburkholderia and major metabolites-such as lipids and organic acids-within the mycosphere. Notably, ESA promoted coupling of carbon (C) and phosphorus (P) cycling, while decoupling nitrogen (N) cycling in the mycosphere. Partial least squares modeling (PLS-PM) further indicated that ESA-induced N cycling constraints significantly stimulated P. dongsun primordia formation and P uptake. Furthermore, ESA indirectly enhanced P. dongsun primordia number by increasing keystone taxa diversity. This finding provided new theoretical insights into understanding the interaction mechanisms between macrofungi and their microenvironments, as well as their microbial ecology.},
}

*Mycelium/growth & development/drug effects/metabolism
Culture Media/chemistry
Biomass

@article {pmid42876392,
year = {2026},
author = {Götze, S and Decker, T and Balluff, S and Beemelmanns, C},
title = {γ-Amino acid-containing natural products of bacterial origin: structure, biosynthesis, and bioactivity.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00072j},
pmid = {42876392},
issn = {1460-4752},
abstract = {Covering: 1966 to 2026γ-Amino acids are structurally diverse non-proteinogenic building blocks that endow bacterial natural products with unique conformational, physicochemical, and biological properties. Although individual γ-amino acid-containing metabolites have been extensively investigated, their structural diversity, biosynthetic origins, and functional significance have rarely been considered from a unified perspective. Here, we review nearly six decades of research on bacterial γ-amino acid-containing natural products, covering from 1966 and the discovery of bleomycin to genome-guided discoveries in 2026. We discuss the major structural classes of γ-amino acids, including GABA-derived, β-keto, statine-type, vinylogous, fully reduced, and masked amino acid-derived motifs, and highlight how these building blocks are generated through primary metabolism, hybrid NRPS-PKS assembly lines, and specialized tailoring reactions. Particular emphasis is placed on the relationships between γ-amino acid structure, biosynthetic logic, and biological function, including their roles in protease inhibition, covalent target engagement, metallophore activity, and microbial ecology. Finally, we discuss emerging opportunities for genome mining and biosynthetic engineering that are expected to accelerate the discovery and exploitation of γ-amino acid-containing natural products.},
}

@article {pmid42876830,
year = {2026},
author = {Carella, S and De Angelis, B and Nardi, B and Branda, F and Ceci, D and Borghetti, C and Mercuri, A and Cordellini, M and Maglio, C and Gonnelli, M and Garcea, R and Ceccarelli, G},
title = {Recommendations for microbiological sampling in infected hard-to-heal wounds: an Italian association for cutaneous ulcers (AIUC) perspective.},
journal = {Frontiers in surgery},
volume = {13},
number = {},
pages = {1908843},
pmid = {42876830},
issn = {2296-875X},
abstract = {Chronic and hard-to-heal wounds represent a significant and growing healthcare burden, frequently complicated by infection and impaired healing. Despite the availability of international guidelines, microbiological assessment in clinical practice remains highly heterogeneous, with substantial variability in sampling techniques, timing, and interpretation of results. This variability occurs within a broader One Health context, where antimicrobial resistance and microbial ecology are shaped by interconnected human, environmental, and healthcare factors. The present recommendations, developed by the Italian Association for Cutaneous Ulcers (AIUC), aim to provide a structured and operational framework for microbiological sampling in infected hard-to-heal wounds. A multidisciplinary expert panel conducted a structured review of the literature and developed consensus-based recommendations through iterative discussion. The resulting framework addresses key aspects of the diagnostic pathway, including indications for sampling, selection of techniques (swab, tissue biopsy, and fine needle aspiration), standard operating procedures, and principles for the interpretation of microbiological findings. The recommendations emphasise a context-driven approach to sampling, recognising the complementary roles of different techniques according to clinical presentation and depth of infection. Particular attention is given to the distinction between colonisation and infection, the limitations of quantitative thresholds, and the impact of biofilm, polymicrobial interactions, and host-related factors on diagnostic accuracy and antimicrobial response. The document also highlights the importance of integrating microbiological data with clinical assessment to support appropriate antimicrobial stewardship. By translating existing evidence into practical and reproducible procedures, these recommendations aim to reduce variability in clinical practice and improve the quality of microbiological diagnostics in wound care. Within a One Health perspective, standardised and reliable microbiological data may also support surveillance of antimicrobial resistance and inform more integrated infection control strategies. The proposed framework supports more consistent clinical decision-making and may contribute to optimising antimicrobial use and patient outcomes across diverse healthcare settings.},
}

@article {pmid42877438,
year = {2026},
author = {Liu, X and Li, W and Deng, C and Fernandez, Z and Gao, Y and Ma, S and Qian, C},
title = {Effects of Low-Intensity Pulsed Ultrasound on the Gut-Brain Axis.},
journal = {Medical devices (Auckland, N.Z.)},
volume = {19},
number = {},
pages = {609488},
pmid = {42877438},
issn = {1179-1470},
abstract = {The gut-brain axis is a bidirectional communication network involved in inflammatory, metabolic, and neurobehavioural homeostasis. Low-intensity pulsed ultrasound (LIPUS) is a non-invasive biophysical modality that may influence this axis through acoustic mechanotransduction and downstream changes in inflammatory signalling, epithelial barrier function, microbial ecology, and neuroimmune activity. This mini review synthesizes predominantly preclinical evidence on abdominal and brain-directed LIPUS. Current rodent studies indicate that abdominal stimulation can produce coordinated intestinal, systemic, microbial, and central responses, whereas brain-directed stimulation can be accompanied by improvement in both cerebral inflammation and intestinal pathology. Mechanistic studies outside the gut-brain axis further suggest that mechanosensitive ion channels, focal-adhesion signalling, cytoskeletal remodelling, NF-κB, and inflammasome-related pathways may connect acoustic forces to biological responses. However, no single study has established the complete causal sequence from acoustic stimulation to gut-brain communication. Direct human evidence for LIPUS efficacy in gut-brain axis-related disorders is currently lacking. LIPUS should therefore be regarded as a promising preclinical approach requiring standardized acoustic reporting, independent replication, causal pathway validation, and disease-specific optimization before clinical translation.},
}

@article {pmid42878485,
year = {2026},
author = {Mavrodi, O and Panchenko, A and Dykhovychnyi, O and Leslie, I and Barannyk, L and Thomashow, L and Weller, D and Mavrodi, D},
title = {Environmental determinants of phenazine- and 2,4-diacetylphloroglucinol-producing Pseudomonas in the wheat rhizosphere across a precipitation gradient.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418825},
doi = {10.1128/spectrum.04188-25},
pmid = {42878485},
issn = {2165-0497},
abstract = {The Columbia Plateau of the Inland Pacific Northwest (IPNW) encompasses one of North America's largest dryland wheat production regions, where soil moisture strongly influences plant growth, health, and rhizosphere microbial communities. Two ecologically and genetically distinct groups of the Pseudomonas fluorescens complex naturally suppress soilborne wheat pathogens in IPNW fields by producing either phenazine-1-carboxylic acid (Phz+) or 2,4-diacetylphloroglucinol (Phl+). To determine how precipitation and associated soil factors shape the abundance of these bacteria, we analyzed wheat root samples from commercial fields spanning a precipitation gradient across the Columbia Plateau. We quantified pairwise relationships among environmental variables using Spearman correlations and constructed a correlation network to visualize patterns of association. Network analysis revealed that precipitation influences soil properties indirectly, with organic matter, clay content, cation exchange capacity, and pH forming an interconnected cluster of correlated variables. Wheat rhizosphere colonization frequency by Phz+ pseudomonads was primarily associated with soil pH, which correlated with precipitation through its effects on weathering and organic matter accumulation, whereas colonization frequency of Phl+ pseudomonads showed weaker associations with abiotic variables. Phz+ pseudomonads were favored in neutral to alkaline, coarse soils typical of the low-precipitation zone, whereas Phl+ populations thrived in wetter, organic-rich soils with lower pH. These findings highlight soil pH as a key environmental filter mediating precipitation-driven differences in Pseudomonas populations and suggest that biotic interactions and plant selection further modulate root colonization. Understanding how these agriculturally important microbial functional groups respond to moisture regimes provides insight into the sustainability of disease-suppressive microbiomes in the IPNW.IMPORTANCEDryland wheat-based production systems of the Inland Pacific Northwest are highly vulnerable to changing precipitation patterns that affect crop productivity, soilborne pathogens, and soil microbial ecology. This study reveals how long-term rainfall gradients influence the balance between two groups of beneficial Pseudomonas that protect wheat from root diseases. We show that soil pH, closely linked to rainfall, organic matter, and mineral weathering, is a key abiotic factor controlling the presence of phenazine-producing bacteria in dryland wheat grown in low-precipitation zone soils. In contrast, 2,4-diacetylphloroglucinol producers dominate in wetter, organic-rich environments. These insights help explain how beneficial microbiomes adapt to environmental constraints and identify soil conditions that promote natural disease suppression. Understanding these mechanisms will aid in predicting microbiome resilience and guiding management strategies to maintain wheat productivity under changing weather conditions.},
}

@article {pmid42878492,
year = {2026},
author = {Khocht, A and Rams, TE and Chen, T and Suzuki, JB},
title = {Diagnostic Accuracy of Salivary Thiols Point-of-Care Test for Detecting Subgingival Dysbiosis in Adults: A Cross-Sectional Study.},
journal = {Clinical and experimental dental research},
volume = {12},
number = {5},
pages = {e70485},
doi = {10.1002/cre2.70485},
pmid = {42878492},
issn = {2057-4347},
support = {//ALT BioScience, Lexington, Kentucky/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Saliva/chemistry/microbiology ; *Sulfhydryl Compounds/analysis ; Adult ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; *Periodontitis/microbiology/diagnosis ; Dental Plaque/microbiology ; *Gingivitis/microbiology/diagnosis ; Middle Aged ; *Point-of-Care Testing ; Bacteria/isolation & purification ; },
abstract = {OBJECTIVES: Many bacteria implicated in the pathogenesis of periodontitis produce thiol compounds containing sulfhydryl (-SH) groups. This cross-sectional study used a prototype chromogenic test strip to investigate the relationship between whole saliva -SH levels and subgingival bacterial species in subjects with and without periodontal disease.

MATERIALS AND METHODS: Ninety-six subjects were enrolled. Full-mouth comprehensive clinical periodontal evaluations were performed. Subjects were divided into 3 groups: periodontally healthy, gingivitis, and periodontitis. Subgingival plaque samples were collected and analyzed for their content of 40 bacterial species using checkerboard DNA-DNA hybridization. Subgingival dysbiosis severity was determined with a modified Subgingival Microbial Dysbiosis Index (mSMDI). Salivary thiol levels were determined semi-quantitatively with a chromogenic strip dipped in pooled saliva on the tongue surface.

RESULTS: Low and high strip scores were uniquely associated with contrasting groups of subgingival bacteria. Individuals with high strip scores harbored increased levels of P. gingivalis, P. intermedia, T. forsythia, P. nigrescens, E. nodatum, and T. denticola as well as higher mSMDI scores than individuals with low strip scores. Furthermore, strip scores showed high specificity (93%) in correctly identifying individuals with normobiotic subgingival microbiota.

CONCLUSIONS: Low salivary thiol levels are useful indicators of subgingival normobiosis.},
}

Humans
Cross-Sectional Studies
*Saliva/chemistry/microbiology
*Sulfhydryl Compounds/analysis
Adult
*Dysbiosis/diagnosis/microbiology
Female
Male
*Periodontitis/microbiology/diagnosis
Dental Plaque/microbiology
*Gingivitis/microbiology/diagnosis
Middle Aged
*Point-of-Care Testing
Bacteria/isolation & purification

@article {pmid42879486,
year = {2026},
author = {McCoy, D and Sun, X and Buchanan, PJ and Zakem, EJ},
title = {Microbial niche partitioning explains N2O distributions and cycling in marine oxygen minimum zones.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {42},
pages = {e2612813123},
doi = {10.1073/pnas.2612813123},
pmid = {42879486},
issn = {1091-6490},
support = {LS-FMME-00871981//Simons Foundation (SF)/ ; 2125142//National Science Foundation (NSF)/ ; 101167445//EC | European Research Council (ERC)/ ; },
mesh = {*Nitrous Oxide/metabolism ; *Oxygen/metabolism ; Ecosystem ; *Seawater/microbiology/chemistry ; Oxidation-Reduction ; Nitrogen Cycle ; Bacteria/metabolism ; Models, Biological ; },
abstract = {Oxygen minimum zones (OMZs) are marine hotspots for cycling and emission of the powerful greenhouse gas nitrous oxide (N2O). Steep redox gradients host diverse microbial communities that produce and consume N2O, generating a characteristic vertical distribution, with low concentrations in anoxic cores and supersaturated accumulation in surrounding oxyclines. Although the accumulation is commonly attributed to stronger O2 inhibition of N2O consumption than production, this differential inhibition is not consistently observed, suggesting that interactions among nitrogen-cycling metabolisms may provide additional mechanisms. To evaluate the ecological controls on the N2O profile, we embed a trait-based ecosystem model into an eddy-resolving simulation of the Eastern Tropical South Pacific OMZ. In this framework, redox energetics, metabolite exchange, competition, and grazing structure microbial growth, setting emergent niches of microbial functional types, particularly aerobic ammonia oxidizers and diverse anaerobic denitrifiers that mediate N2O cycling. In the anoxic core, cross-feeding tightly couples denitrifiers that produce and consume N2O, maintaining low concentrations. As O2 increases in the oxycline, competition with aerobic metabolisms and intensified grazing gradually exclude denitrifiers. However, because they draw on more abundant substrates, N2O-producing denitrifiers persist to higher O2 than N2O consumers, reflecting the vulnerability of populations dependent on intermediate metabolites. This ecological decoupling drives N2O accumulation and captures the characteristic double-peaked vertical structure without imposing physiological O2 intolerance thresholds. More broadly, by revealing how niche partitioning and producer-consumer coupling shape other features of OMZ biogeochemistry, these results provide a basis for projecting future shifts in marine nitrogen loss and N2O emissions.},
}

*Nitrous Oxide/metabolism
*Oxygen/metabolism
Ecosystem
*Seawater/microbiology/chemistry
Oxidation-Reduction
Nitrogen Cycle
Bacteria/metabolism
Models, Biological

@article {pmid42879603,
year = {2026},
author = {Passarini, MRZ and Benegas, GRS and Flores, GAN and Lacerda Júnior, GV and Ottoni, JR and Câmara, PEAS and Rosa, LH},
title = {Fungal community in the soil of Punta Hannequim, Antarctica, assessed by environmental DNA metabarcoding.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {98},
number = {4},
pages = {e20250057},
doi = {10.1590/0001-3765202620250057},
pmid = {42879603},
issn = {1678-2690},
mesh = {Antarctic Regions ; *Soil Microbiology ; *DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification/isolation & purification ; *DNA, Fungal/genetics ; Biodiversity ; },
abstract = {The fungal community present in soil collected from Punta Hannequim on King George Island, Antarctica, was evaluated using DNA metabarcoding through high-throughput sequencing. A total of 123 fungal amplicon sequence variants (ASVs) were detected, belonging to the phyla Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, and Rozellomycota. The most dominant ASVs were from the genera Trichoderma, Gorgomyces, and Neobulgaria. In addition, many unassigned ASVs were identified and may represent previously unknown fungal diversity in Antarctic microbial ecology. The observed ASV richness rarefaction curve showed that all diversity of the sample was recovered. The taxonomic groups observed in the sampled region included endemic, cosmopolitan, and opportunistic plant pathogenic taxa. The results presented expand knowledge of the fungal community in the soil of King George Island, aiming to guide the development of selective culture media capable of recovering greater microbial diversity from this environment and consequently, broadening perspectives in the field of Antarctic mycology.},
}

Antarctic Regions
*Soil Microbiology
*DNA Barcoding, Taxonomic/methods
*Fungi/genetics/classification/isolation & purification
*DNA, Fungal/genetics
Biodiversity

@article {pmid42696758,
year = {2026},
author = {Royle, J and Applebaum, I and Wasan, J and Asselin, S and Bennett, J},
title = {Host-specific soil oomycete communities are spatially repeatable across natural grasslands.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-13},
doi = {10.1139/cjm-2026-0106},
pmid = {42696758},
issn = {1480-3275},
mesh = {*Oomycetes/classification/genetics/isolation & purification/physiology ; *Grassland ; *Soil Microbiology ; Rhizosphere ; Canada ; Plants/microbiology ; Soil/parasitology ; Microbiota ; },
abstract = {Soil oomycetes contain some of the most devastating plant pathogens, and are widespread within the soil microbiome, yet how individual plant species structure oomycete communities in natural soils, and whether any such structuring is consistent across space, remains poorly resolved. Because host-specific pathogen accumulation is a central prediction of plant-soil feedback theory but is rarely tested outside greenhouse conditions, we focused on whether the host-specific fraction of these communities is preferentially pathogenic. Using oomycete-specific internal transcribed spacer amplicons, we sequenced rhizosphere-associated and paired bulk soils from four grassland species across 25 sites on the Canadian Prairies spanning more than 200 000 km[2], totalling 1800 samples. Each host supported a distinctive core of taxa, with two species more likely to host pathogenic taxa unique to their rhizosphere. This enrichment was decoupled from richness of oomycete taxa in the rhizosphere, indicating selective accumulation rather than a by-product of resource-rich environments. Community composition also differed among hosts after accounting for site level edaphic variation. Host plant identity therefore leaves a detectable, spatially repeatable imprint on soil oomycete communities, one expressed most strongly through the selective accumulation of pathogenic taxa.},
}

*Oomycetes/classification/genetics/isolation & purification/physiology
*Grassland
*Soil Microbiology
Rhizosphere
Canada
Plants/microbiology
Soil/parasitology
Microbiota

@article {pmid42864608,
year = {2026},
author = {Dörr, A and Dekić Rozman, S and Duncker, LV and Kehrmann, J and Buer, J and Virta, M and Meyer, F and Kraiselburd, I},
title = {ERMA: a harmonizing epicPCR data analysis tool.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42864608},
issn = {1471-2164},
support = {grant no. ZMII2-2523COR10A-E//WBEready consortium, German Federal Ministry for Health (Bundesministerium für Gesundheit, BMG/ ; 01ZZ2013//SMITH-Medizininformatik-Konsortium-Nachwuchsgruppe Vorhersage von Sepsis auf Basis von Mikrobiomsequenzdaten, German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF)/ ; 01ZZ2013//SMITH-Medizininformatik-Konsortium-Nachwuchsgruppe Vorhersage von Sepsis auf Basis von Mikrobiomsequenzdaten, German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF)/ ; },
mesh = {*Polymerase Chain Reaction/methods ; *Software ; Reproducibility of Results ; Data Analysis ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: EpicPCR links functional genes to taxonomic markers at the single-cell level and has become an important method in microbial ecology and antimicrobial resistance research. However, the lack of missing standardized data analysis workflows limits reproducibility and comparability across studies. Existing analyses are often based on custom, unpublished scripts, complicating cross-study benchmarking and reuse.

RESULTS: We present ERMA, an open-source, Snakemake-based pipeline that enables an automated, standardized, reproducible, and scalable epicPCR data analysis with minimal user input. ERMA supports both Illumina and ONT sequencing data and integrates quality control, database preparation, dual similarity searches against taxonomic and functional reference databases, results integration, filtering, and visualization. The pipeline is adaptable to a broad range of research questions beyond AMR due to modular database preparation and integration of specific UniRef queries. We evaluated ERMA using five publicly available epicPCR datasets covering diverse sample sources and sequencing depths. Across these datasets, ERMA achieved mean concordance rates of approximately 70-83% with the taxonomic results reported in the respective publications. In addition, validation using a defined five-member mock community spiked into clinical wastewater demonstrated full recovery of mock genera, with 85% of ERMA-detected genera also detected by independent 16S rDNA gene analysis of the same wastewater sample. Attrition analysis showed inconsistent filtering patterns across studies, reflecting dataset-specific quality differences.

CONCLUSION: While large-scale reference datasets for epicPCR remain limited, validation using both publicly available studies and a defined mock community shows strong, interpretable performance across heterogeneous datasets. By providing a transparent, modular, and reproducible workflow, ERMA contributes toward harmonized epicPCR data analysis and establishes a foundation for future methodological standardization and benchmarking efforts as reference datasets improve.},
}

*Polymerase Chain Reaction/methods
*Software
Reproducibility of Results
Data Analysis
High-Throughput Nucleotide Sequencing

@article {pmid42865466,
year = {2026},
author = {Sandak, A and Pajerski, W and Gubenšek, A and Butina Ogorelec, K and Černoša, A},
title = {The archibiome: extending engineered living materials to multiscale built environments.},
journal = {Frontiers in systems biology},
volume = {6},
number = {},
pages = {1943876},
pmid = {42865466},
issn = {2674-0702},
abstract = {The integration of living systems into architecture is advancing rapidly through developments in biotechnology, materials science, and design approaches grounded in regenerative principles. Engineered Living Materials (ELMs) and living artefacts demonstrate how microbial systems can be embedded within materials to enable responsiveness, metabolic activity, and adaptive functionality. However, current applications remain largely confined to discrete material components, overlooking the complex and dynamic microbial ecosystems already present within buildings. This opinion paper introduces the concept of the archibiome as a framework for extending ELMs from isolated systems to interconnected architectural environments. The archibiome conceptualizes buildings as dynamic microbial ecosystems in which engineered systems, material interfaces, and native microbial communities interact across spatial and temporal scales. While this shift offers opportunities for adaptive and regenerative design, it also introduces challenges related to system stability, environmental variability, biosafety, and regulatory constraints. Addressing these challenges requires interdisciplinary approaches that integrate microbial ecology, materials engineering, architectural design, and regulatory science. Ultimately, the archibiome positions microbial life as a design variable, enabling a transition toward predictive, systems-level strategies for living architecture.},
}

@article {pmid42865545,
year = {2026},
author = {Chen, Z and Gan, W and Cao, F and Yu, F and Lin, W and Wang, X and Hong, Y and Yang, M and Hong, L and Chen, C and Wu, J and Liu, X and Zhang, W and Lian, Y},
title = {Intratumoral microbiota-host gene associations characterize stage-associated microecological patterns in colorectal cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934580},
pmid = {42865545},
issn = {1664-302X},
abstract = {INTRODUCTION: Intratumoral microbiota are emerging as important ecological components of the colorectal cancer (CRC) microenvironment. However, their stage-associated patterns and coordination with host gene expression remain poorly understood. This study aimed to characterize stage-associated associations between intratumoral microbiota and the host transcriptome in CRC.

METHODS: We profiled 73 regional tumor specimens from 30 independent, treatment-naïve CRC patients using full-length 16S rRNA gene sequencing and mRNA sequencing. Microbial diversity, predicted functional profiles, co-occurrence networks, differential abundance, and microbiota-host transcriptome associations were analyzed. Regularized canonical correlation analysis and machine-learning modeling with SHAP-based feature interpretation were performed to identify stage-discriminative features. Candidate associations were evaluated in two independent public microbiome datasets. Mendelian randomization and immune-infiltration analyses were further conducted to explore the potential biological relevance of representative microbiota-gene associations.

RESULTS: Disease stage was a major factor shaping intratumoral microbial composition. Advanced-stage CRC exhibited increased microbial α-diversity, distinct predicted functional profiles, and altered microbial co-occurrence patterns. Integrated microbiota-transcriptome analysis identified ten genus-level and six species-level candidate microbiota-gene association pairs. Core genera showed reproducible stage-discriminative signals in two independent public microbiome datasets. SHAP analysis identified the principal microbial and host transcriptomic features contributing to stage classification. Integrating microbial and host gene signatures improved classification performance, with the combined model achieving an AUROC greater than 0.90. The Alloprevotella-MDH1 pair was selected as a representative association axis. Alloprevotella abundance was negatively correlated with MDH1 expression, while low MDH1 expression was associated with poorer survival and distinct metabolic-immune states in CRC. Exploratory Mendelian randomization analysis provided preliminary genetic epidemiological support for an association between Alloprevotella abundance and CRC risk.

DISCUSSION: Intratumoral microbiota and host transcriptional profiles exhibit coordinated, stage-associated alterations in CRC. The identified microbiota-gene associations, particularly the Alloprevotella-MDH1 axis, provide potential biological links between tumor microbial ecology, host metabolism, immune states, and CRC progression. These findings support the value of integrated microbiome-transcriptome analysis for characterizing the intratumoral microenvironment and identifying candidate microbial-host regulatory relationships.},
}

@article {pmid42866007,
year = {2026},
author = {Ni, FX and Pan, CF and Chen, HH and Huang, DH and Jiang, ZB},
title = {From gut to lung: the microbiome-directed causal mechanisms and therapeutic horizons in asthma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1935791},
pmid = {42866007},
issn = {1664-3224},
mesh = {Humans ; *Asthma/therapy/microbiology/immunology/metabolism/etiology ; Animals ; *Lung/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/immunology ; Probiotics/therapeutic use ; },
abstract = {The gut-lung axis represents a predominantly gut-to-lung communication network through which gut microbiota and their metabolites influence pulmonary immunity. In asthma, gut dysbiosis-characterized by reduced microbial diversity, depletion of short-chain fatty acid (SCFA)-producing taxa, and expansion of pro-inflammatory pathobionts-has been consistently associated with disease severity and type 2 inflammation. While the axis is conceptually bidirectional, the vast majority of mechanistic evidence to date describes unidirectional gut to lung regulation. This review critically synthesizes evidence on the gut-lung axis in asthma. We evaluate multi-kingdom microbial ecology, evaluating contributions from bacterial, fungal, protozoan, and phage. We examine metabolite-specific immune reprogramming via SCFAs, bile acids, and tryptophan derivatives, explicitly acknowledging unresolved controversies including the SCFA concentration paradox. We integrate causal inference frameworks that combine Mendelian randomization, gnotobiotic models, and experimental triangulation. We also present precision therapeutic pipelines with evidence-based grading of interventions ranging from probiotics to engineered live biotherapeutics. We propose that targeting the gut-lung axis represents a foundational strategy for asthma modification and outline a roadmap from multi-omics discovery to biomarker-guided clinical trials. Distinguishing this review from prior work, we explicitly separate established mechanisms from speculative pathways and provide actionable criteria for clinical translation. We also critically identify the reverse (lung to gut) pathway as a major knowledge gap requiring urgent investigation.},
}

Humans
*Asthma/therapy/microbiology/immunology/metabolism/etiology
Animals
*Lung/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
Dysbiosis/immunology
Probiotics/therapeutic use

@article {pmid42866813,
year = {2026},
author = {Amedorme, D and Addy, H and Osei-Poku, P and Kwarteng, A},
title = {Inferred functional potential of microbial communities in traditional African fermented dairy products using 16S rRNA.},
journal = {Access microbiology},
volume = {8},
number = {10},
pages = {},
pmid = {42866813},
issn = {2516-8290},
abstract = {Background. Africa is home to several indigenous dairy products that span the continent. These dairy products are widely consumed and cherished for their rich nutritional profile and distinctive taste, shaped by microbial fermentation. However, their microbiome remains largely unexplored, thus limiting knowledge of microbial composition, diversity and functional inference. These limitations have implications for product quality and safety and scientific documentation. Methods. The 16S rRNA dataset on five popularly consumed dairy products, Nono, Wara, Kwerionik, Ghee and Nunu, with the SRA accession number PRJNA532858, was collected for taxonomic classification and diversity analysis using the Quantitative Insights into Microbial Ecology 2 pipeline. Functional inference was conducted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 version 2. Results. In this dataset, an average of 12 phyla were observed, including Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. At the genus level, lactic acid bacteria, particularly Lactobacillus and Streptococcus, were predominant in Nono, Wara and Nunu, with relative abundances: 57.7, 33.5 and 39.3% for Lactobacillus and 16.6, 36.7 and 39.5% for Streptococcus. Functional predictions revealed both shared and product-specific metabolic capabilities, with varying taxonomic contributions to key pathways across samples. Conclusion. Across the analysed samples, the products exhibit both conserved and distinct predicted functional signatures inferred from the 16S rRNA gene data. Particularly, those related to ATP-binding cassette transporters, amino acid metabolism, sugar utilization and biosynthetic pathways. Streptococcus dominated in the purine-rich environments of Nono and Nunu; Wara displayed lactic acid bacteria co-dominance, with a focus on peptidoglycan metabolism; Kwerionik exhibited broader microbial diversity, with a three-way taxonomic distribution; and Ghee stood out with Acetobacter-driven lipid and oxidative metabolism, showcasing the community's adaptive plasticity to distinct environmental and processing conditions. These findings suggest that traditional dairy fermentations function as complex microbial ecosystems and highlight their potential importance in food systems and microbial ecology.},
}

@article {pmid42869381,
year = {2026},
author = {Kanca, MF and Pazarcı, Ö and Karaali, E and Çiloğlu, O and Uluöz, M and Gökmen, MY and Çetintaş, E},
title = {Impact of Earthquake-Related Mass Casualty Burden on Hospital Microbial Ecology and Surgical Site Infections After Elective Orthopaedic Surgery: A Retrospective Cohort Study.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2026.09.030},
pmid = {42869381},
issn = {1532-2939},
abstract = {OBJECTIVES: The aim of this study was to compare surgical site infections (SSIs) developing after primary elective orthopaedic procedures before and after the February 6, 2023 earthquakes and to investigate the incidence, causative pathogen distribution, and antimicrobial resistance patterns.

MATERIALS AND METHODS: This single-center retrospective cohort study included patients undergoing primary total or partial hip arthroplasty, total knee arthroplasty, or open reduction and internal fixation. The Patients were divided into pre-earthquake (June 1, 2018-February 5, 2023) and post-earthquake (June 1, 2023-November 1, 2025) periods. The SSI cases were defined according to periprosthetic joint infection (ICM 2025) and fracture-related infection (FRI 2018) criteria. Microbiological profiles, resistance patterns, and clinical outcomes were compared between groups.

RESULTS: A total of 99 and 118 SSI cases were identified in the pre- and post-earthquake cohorts, respectively. Overall SSI rates were similar between groups (0.98% vs. 1.19%; p=0.143). However, post-earthquake infections were associated with significantly longer hospital stays (28 vs. 22 days; p=0.025) and increased debridement procedures (2.0 vs. 1.0; p=0.006). Polymicrobial infections increased significantly (12.1% vs. 23.7%; p=0.028). A marked microbiological shift was observed, with Gram-negative organisms becoming predominant (67.7% vs. 47.6%; p=0.004), while Gram-positive organisms decreased. Staphylococcus aureus isolation significantly declined (35.4% vs. 17.2%; p=0.008). Meticillin resistance among Gram-positive isolates increased (34.9% vs. 60.0%; p=0.022), whereas no significant change in Gram-negative carbapenem resistance was observed.

CONCLUSION: Our study results showed that the rates of polymicrobial infections and meticillin resistance among Gram-positive isolates increased significantly. This microbiological shift was also associated with clinically relevant outcomes, including prolonged hospital stay and an increased number of debridement procedures. Taken together, in centers exposed to a high burden of mass casualty patients, the infection dynamics of routine elective surgical cases may continue to evolve even months after the disaster. Reassessment of existing empirical treatment protocols is warranted in such settings.},
}

@article {pmid42870310,
year = {2026},
author = {Ren, G and Yang, T and Sheng, Z and Chen, Y and Chen, L and Wang, Y and He, P and Luo, H},
title = {Multi-omics reveals that dietary Piper sarmentosum Roxb. extract improves goat meat quality via the microbiota-muscle amino acid metabolic axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42870310},
issn = {1674-9782},
support = {2023YFD1600102//National Key R&D Program of China/ ; GHYF2022004//Key Research and Development Program of Hainan Province/ ; },
abstract = {BACKGROUND: Improving meat quality through nutritional regulation is an important approach in ruminant production. Growing evidence suggests that rumen microbiota influences host metabolism via microbial metabolites, thereby affecting meat quality. However, whether Piper sarmentosum Roxb. extract (PSE), a medicinal and edible plant-derived extract, improves meat quality through rumen microbiota-host metabolic interactions remains unclear. Thirty-six weaned male Hainan black goats (approximately 3 months old) were randomly assigned to four dietary treatments supplemented with 0, 200, 400, or 600 mg/kg PSE (dry matter basis), respectively. After a 90-day feeding trial, goats were fasted for 12 h before slaughter, and rumen and longissimus lumborum muscle samples were collected for subsequent analyses.

RESULTS: Supplementation with 600 mg/kg PSE significantly enhanced meat quality traits, including higher ultimate pH, improved color stability, and increased water-holding capacity, without affecting growth performance or carcass traits. Transcriptomic and metabolomic analyses revealed that PSE supplementation was associated with remodeling of amino acid and energy metabolism in muscle, particularly glutamate-related pathways. These metabolic changes were accompanied by increased expression of key metabolic genes, including BCAT2, IDH1, and IDH3A, alongside alterations in energy-related metabolites, such as the downregulation of carnitine and upregulation of creatinine. Concomitant shifts in rumen microbial composition were observed, with PSE supplementation increasing the abundance of genera like Weissella and Ruminococcus, while reducing potentially opportunistic genera, such as Acinetobacter and Klebsiella. Weissella showed strong positive correlations with elevated rumen metabolites like serine, threonine, choline, and hypoxanthine. Metagenome-assembled genome analysis of Weissella cibaria revealed an enrichment of genes related to amino acid metabolism and glycosyltransferase families. Correlation and mediation analyses further revealed associations among Weissella abundance, rumen metabolites, and muscle metabolic traits, supporting a potential microbiota-metabolite-host metabolic relationship.

CONCLUSIONS: Collectively, this study provides new insights into the association network linking PSE-induced alterations in rumen microbiota, microbial metabolites, and host muscle metabolism in relation to goat meat quality. These findings suggest that PSE supplementation may improve meat quality through coordinated changes in rumen microbial ecology and muscle metabolic profiles.},
}

@article {pmid42874540,
year = {2026},
author = {Dara, M and Calabrisotto, LS and Bisanti, L and Torreagrossa, N and La Corte, C and Bertini, F and Catania, V and Quatrini, P and Parrinello, D and Piazzese, D and Cammarata, M and Banni, M and Parisi, MG},
title = {Integrated assessment of bioplastic materials effects on microbial communities and macroinvertebrate model, Mytilus galloprovincialis, in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120459},
doi = {10.1016/j.marpolbul.2026.120459},
pmid = {42874540},
issn = {1879-3363},
abstract = {The increasing use of biopolymer derivatives raises concerns about their actual environmental sustainability, which remains insufficiently understood. In this study, we adopted an integrated approach combining microbial and ecotoxicological perspectives to evaluate their impact in marine ecosystems. We investigated the plastisphere composition of conventional petroleum-based High Density Polyethylene (HDPE) and polyhydroxyalkanoates (PHA), polyhydroxybutyric acid (PHB), and polylactic acid (PLLA) scaffolds after 60 days of exposition in marine ecosystem or microcosm, by high throughput metagenomics 16S rRNA gene sequencing and culture dependent approach. A variation in terms of composition and abundance of plastisphere, between petroleum-derived and bio-based degradable scaffolds, was observed. A high abundance of Proteobacteria was detected in all polymers, with Alpha and Gamma Proteobacteria dominant. At the genera level, high abundance of sequences assigned to hydrocarbon-degrading bacteria (i.e. Oleibacter, Labrenzia, Alcanivorax) was detected in biopolymeric plastic compared to petroleum-based plastic. To link microbial colonization and material degradation with biological effects on marine fauna, the impact of biopolymer-derived micro- and nanoparticles on the mussel Mytilus galloprovincialis was assessed. Both in vitro and in vivo assays demonstrated immune system activation through phagocytosis and encapsulation, while in vivo exposures influenced several biomarkers (phagocytosis, haemocyte density, lysozyme, glutathione peroxidase, phenoloxidase, alkaline phosphatase, esterase), suggesting potential detrimental effects after 72 h. By bridging microbial ecology with immunological responses in a bioindicator species, this multidisciplinary study provides novel insights into the complex ecological footprint of biodegradable plastics in marine environments.},
}

@article {pmid42874808,
year = {2026},
author = {Jiang, B and Liu, T and Duan, W and Xue, Y},
title = {Multikingdom Gut Microbiome and Immune Aging: A Host-Microbial Signaling Perspective.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103414},
doi = {10.1016/j.arr.2026.103414},
pmid = {42874808},
issn = {1872-9649},
abstract = {Immune aging comprises heterogeneous changes in hematopoietic output, immune-cell function, inflammatory regulation, and tissue-specific immune states. In parallel, the gut microbiome undergoes ecological and functional remodeling across the bacteriome, mycobiome, virome, and archaeome, but these changes do not define a single "aged microbiome" and vary with host health, frailty, diet, medication exposure, and environmental context. Here, we examine how multikingdom gut microbiome remodeling intersects with distinct trajectories of immune aging. Rather than treating dysbiosis as a uniform upstream cause of immunosenescence, we organize the evidence around four interconnected processes: microbial signal generation, tissue access and compartmentalization, host sensing, and cell-specific interpretation. Age-associated changes in microbial metabolites and immunostimulatory products can influence epithelial barrier function, inflammatory signaling, immunometabolism, hematopoiesis, and lymphoid and myeloid cell states, but evidence strength varies substantially across pathways and microbial kingdoms. Causal support is most developed for selected bacteriome-associated mechanisms in experimental models, whereas aging-specific mechanistic evidence for the mycobiome, virome, and archaeome remains comparatively limited. Importantly, this relationship is reciprocal, because intrinsic immune and tissue aging can also reshape microbial ecology and functional capacity. We therefore view the gut microbiome as a dynamic and potentially modifiable component of immune aging rather than an autonomous driver of immunosenescence. This perspective shifts the translational focus from restoring a youthful microbiome toward targeting microbiome-associated functions and host-response pathways linked to specific immune-aging phenotypes.},
}

@article {pmid42858922,
year = {2026},
author = {Eftekharian, S and Rastkar, S},
title = {The Oral Microbiome in the Biological and Clinical Response to Photobiomodulation During Cancer Supportive Care: A Critical Mechanistic and Translational Review.},
journal = {Photodiagnosis and photodynamic therapy},
volume = {},
number = {},
pages = {105682},
doi = {10.1016/j.pdpdt.2026.105682},
pmid = {42858922},
issn = {1873-1597},
abstract = {Cancer therapy can disrupt the oral microbial ecosystem through mucosal injury, salivary dysfunction, immune suppression, antimicrobial exposure, dietary change, and altered oral hygiene. Photobiomodulation therapy (PBMT) is guideline-supported for prevention of oral mucositis in selected oncologic settings, but whether the oral microbiome contributes to PBMT response remains uncertain. This critical narrative review reframes the question from whether PBMT changes the oral microbiome to what role, if any, microbial ecology plays in the biological and clinical response to PBMT during cancer supportive care. Evidence is organized as direct clinical evidence, indirect clinical evidence, experimental microbial evidence, and mechanistic hypothesis. Direct clinical evidence is sparse and internally mixed: a four-patient uncontrolled pilot reported concurrent cytokine and microbiome shifts after PBMT, whereas a 2023 head-and-neck cancer case series reported clinical improvement in mucositis without significant pre-post changes in salivary bacterial community structure. The strongest current rationale therefore supports a host-first model in which PBMT modifies epithelial integrity, inflammatory and redox signaling, tissue repair, and possibly salivary physiology, thereby changing the ecological conditions experienced by oral microorganisms. Direct microbial photobiological effects remain plausible but are highly dependent on wavelength, irradiance, radiant exposure, oxygen availability, organism, and biofilm state, and should not be conflated with antimicrobial photodynamic therapy. We propose four non-equivalent roles for microbiome change: mediator, modifier, biomarker, or consequence of treatment response. Oral mucositis is the most informative clinical model, but causal interpretation requires longitudinal sampling, functional microbial assays, complete PBMT dosimetry, validated clinical and patient-reported outcomes, and rigorous control of antimicrobials, periodontal status, oral hygiene, diet, feeding support, and anticancer treatment. Microbiome modulation should currently be regarded as an emerging mechanistic hypothesis and research endpoint rather than an established mechanism of PBMT efficacy.},
}

@article {pmid42859577,
year = {2026},
author = {Manfredy Dedós, A and Carmona Beltrán, AG and Hanson, LR and Núñez Ortiz, AM and Santana Rivera, JN and Ríos Colón, N and Ramos Arroyo, JM and Sambolín-Pérez, CA},
title = {Culture-Dependent and Molecular Characterization of Bacteria Associated with Banana Fruits in Puerto Rico.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42859577},
issn = {2578-9430},
abstract = {The genus Musa spp. encompasses significant global food crops, including bananas and plantains, which play an essential role in the economies, nutrition, and culinary practices of developing countries. Nonetheless, Musa spp. face threats from abiotic and biotic stressors, including phytopathogens. Consequently, exploring cultivable bacteria on fruits is vital for understanding bacterial ecological dynamics. Isolates were characterized using culture-dependent techniques: 16S rDNA barcoding and functional prediction, phylogenetic analysis, and morphological approaches. This exploratory study identified three isolates associated with plants and the environment. Future research should conduct larger surveys and genomic analyses around the island to understand bacterial ecology in bananas.},
}

@article {pmid42859606,
year = {2026},
author = {Roy, G and Mutkule, SN and Selvi, PS and Datta, N},
title = {Off-flavors in fish: origins, detection, and mitigation strategies.},
journal = {Journal of food science and technology},
volume = {63},
number = {10},
pages = {1803-1816},
pmid = {42859606},
issn = {0022-1155},
abstract = {UNLABELLED: Off-flavors in farmed fish are a major sensory challenge, causing global losses over $1 billion annually. These undesirable taste and odor compounds compromise product quality and consumer acceptance, reducing competitiveness against wild-caught alternatives. Although many studies exist, few provide an integrated analysis of biochemical origins, molecular mechanisms, and practical mitigation strategies. This review synthesizes recent advances (2020-2025) in biochemical characterization, microbial ecology, and detection technologies. Emphasis is placed on muscle composition, lipid oxidation, and pH-dependent microbial metabolism in shaping sensory defects. Mitigation strategies including electrooxidation, bioaugmentation, and tissue-targeted depuration are critically assessed for sustainability and commercial relevance. Integrating sensory, instrumental, and molecular perspectives, the article identifies research gaps and proposes future directions for aquaculture producers, processors, and researchers.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13197-026-06788-4.},
}

@article {pmid42861577,
year = {2026},
author = {Samra, NA and Suliman, SGI and Al-Hadad, M and Boomsma, DI and Alhantoobi, F and Alsamahi, M and Abufarajallah, H and Al Tikriti, A and Aung, Z and Richards, S and Sajini, A and Mousa, M and Sulaiman, F and Osman, W},
title = {Toward "Obesityomics": Domain-Specific Omics in Precision Obesity Medicine with a Brief AI Perspective.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70226},
doi = {10.1111/obr.70226},
pmid = {42861577},
issn = {1467-789X},
support = {RIG-2024-017//Khalifa University of Science, Technology and Research/ ; },
abstract = {BACKGROUND: Obesity's global rise has outpaced the effectiveness of "one-size-fits-all" prevention and treatment strategies. The promise of precision medicine lies in addressing the etiological and biological diversity of obesity and transforming it into actionable endotypes.

OBJECTIVES: In a narrative review, we analyze "obesityomics," looking at the contributions each omics layer makes to understanding and managing obesity. The areas we evaluate are genomics (heritability, polygenic risk, and monogenic forms), epigenomics (development and environment imprinting), transcriptomics (tissue-specific programs of adipose, liver, muscle, and hypothalamus), proteomics (signaling networks and adipokines), metabolomics and lipidomics (fuel partitioning, lipotoxicity, and metabolic inflection points), and microbiome science (metabolites, host-microbe interactions, and microbial ecology). Our domain-by-domain (single-omics) approach demonstrates how disease taxonomy, causal pathways, and biomarkers can be refined and targeted therapeutically.

DISCUSSION: We argue that "obesityomics" is a pragmatic approach to aligning omics modalities to the right questions at the right time, not a wholesale merger of datasets. Artificial intelligence (AI)-including machine learning and deep learning-should be used in conjunction with quality control, feature selection, modest data integration, and obesity intervention prediction. Among the key challenges in managing sensitive multilayer data are harmonization, standardization, reproducibility, equitable representation, and governance. The translation priorities include prospective studies related to patient-centered outcomes, biomarker panels that are clinic-ready, interoperability standards, and cost-effectiveness evaluations.

CONCLUSION: The review maps concrete steps to assist people with obesity in making better choices by identifying what each omics domain excels at and introducing a brief AI perspective.},
}

@article {pmid42853603,
year = {2026},
author = {Pessoa, P and Slayton, CY and Tashev, SA and Kruithoff, R and Shepherd, DP and Presse, S},
title = {Obtaining maximum information from colony counts with REPOP.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {42853603},
issn = {2050-084X},
support = {R35 GM148237/GM/NIGMS NIH HHS/United States ; W911NF-23-1-0304//Army Research Office/ ; 2310610//National Science Foundation/ ; 35GM148237/NH/NIH HHS/United States ; },
mesh = {Animals ; Colony Count, Microbial/methods ; Caenorhabditis elegans/microbiology ; Bayes Theorem ; *Bacteria/growth & development ; },
abstract = {Bacterial counts from native environments, such as soil or the animal gut, often show substantial variability across replicate samples. This heterogeneity is typically attributed to genetic or environmental factors. A common approach to estimating bacterial populations involves successive dilution and plating, followed by multiplying colony counts by dilution factors. This method, however, overestimates the heterogeneity in bacterial population because it conflates the inherent uncertainty in drawing a subsample from the total population with the uncertainty in the sample arising from biological origins. In other words, this approach may obscure features that may otherwise be present in the data, hinting at the presence of genuine subpopulations. For example, in plate counting applied to Caenorhabditis elegans gut microbiota, observed multimodality is often interpreted as large host-to-host variance, while the randomness introduced by measurement is frequently ignored. To explicitly account for the uncertainty introduced by dilution and plating randomness, we introduce REPOP, a PyTorch-based library to REconstruct POpulations from Plates within a Bayesian framework. Beyond simple cases, REPOP addresses more complex scenarios, including multimodal populations and correcting the mathematically subtle, but experimentally relevant, bias introduced by excluding plates deemed too crowded to distinguish individual colonies. We demonstrate REPOP's ability to resolve distinct population peaks otherwise obscured by standard multiplication methods. Applications to both simulated and experimental datasets, including bacterial samples of different concentrations and ones from the gut microbiota of C. elegans, show that REPOP accurately recovers the underlying multimodality by properly accounting for error propagation, where naive multiplication fails. REPOP is available on GitHub: https://github.com/LabPresse/REPOP.},
}

Animals
Colony Count, Microbial/methods
Caenorhabditis elegans/microbiology
Bayes Theorem
*Bacteria/growth & development

@article {pmid42854152,
year = {2026},
author = {Baouche, Y and Guéneau, M and Kurzthaler, C},
title = {Active Brownian Dynamics in Channels: First-Passage and Spatiotemporal Properties via Siegmund Duality.},
journal = {Physical review letters},
volume = {137},
number = {13},
pages = {138301},
doi = {10.1103/g83n-r4hs},
pmid = {42854152},
issn = {1079-7114},
abstract = {Accumulation at boundaries represents a widely observed phenomenon in active systems with implications for microbial ecology and engineering applications. To rationalize the underlying physics, we study the first-passage properties and spatial distributions of an active Brownian particle (ABP) in a channel. Leveraging Siegmund duality, we establish a direct mapping between the propagators of ABPs with absorbing and hard-wall boundary conditions, yielding analytical results in both problems. We analyze the system across low and high activity regimes-quantifying persistent motion relative to diffusion-and show that active motion, together with a favorable initial orientation, typically lowers the mean first-passage time relative to passive diffusion. Notably, the full time-dependent propagator between hard walls approaches a wall-accumulated stationary state, given by the derivative of the splitting probability as a consequence of Siegmund duality.},
}

@article {pmid42854995,
year = {2026},
author = {Freudenthal, J and Bonkowski, M and Engelmann, NM and Schlegel, M and Dumack, K},
title = {Physiological diversity and adaptation of Rhizaria revealed by phylogenomics and comparative transcriptomics.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108750},
doi = {10.1016/j.ympev.2026.108750},
pmid = {42854995},
issn = {1095-9513},
abstract = {Protists are vastly diverse, forming over 20 supergroups of the eukaryotic diversity and fulfilling plentiful functions. Rhizaria is a widespread and highly abundant clade comprising important parasites and a huge diversity of free-living heterotrophic predators. Despite the diversity and biogeochemical importance of Rhizaria, our understanding of their physiology and metabolic capabilities remains limited, mainly due to limited genomic and transcriptomic data and methodological challenges associated with cross-species comparative transcriptome analyses. In this study, we assembled 15 transcriptomes of the bacterivorous Rhogostoma and their eukaryvorous relatives. By combining phylogenomic analyses and comparative analyses of population-level transcriptomes, we established an evolutionary framework to which we relate orthogroup similarity, orthogroup expression patterns, and functional annotations. The morphologically highly similar Rhogostoma strains formed two distinct phylogenetic clusters differing in orthogroups and orthogroup expression patterns related to cell adhesion and biofilm formation. Furthermore, we observed considerable intra-genus variation in amino acid and lipid metabolism in Rhogostoma, as well as lower completeness of these pathways compared to their eukaryvorous relatives. We hypothesize that the thecofilosean ancestor underwent a reduction in metabolic versatility, explained by increased specialization and reduced food spectra, which provided the foundation for subsequent metabolic radiation within Rhogostoma. Overall, our findings indicate that even closely related and morphologically similar species in Rhizaria may differ distinctly in their functional repertoire.},
}

@article {pmid42855413,
year = {2026},
author = {Nuijten, P and Pan, X and Staiano, I and Lidbury, I and Raaijmakers, JM and Carrión, VJ},
title = {Flavobacterium spp.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.004},
pmid = {42855413},
issn = {1878-4380},
}

@article {pmid42856507,
year = {2026},
author = {Din, MO and Brennan, C and Zhao, J and Oles, R and Patel, L and Birmingham, A and Sevilir, DM and Hansen, L and Wright, GM and Ambre, M and Tomita, M and Boyer, T and Gonzalez, A and Ackermann, G and McDonald, D and Kralicek, S and Hecht, G and Hasty, J and Smarr, L and Knight, R},
title = {Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.28.754546},
pmid = {42856507},
issn = {2692-8205},
abstract = {Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.},
}

@article {pmid42857515,
year = {2026},
author = {Karthick, V and Thamarai, R and Amalraj, S and Narayanasamy, K},
title = {Cytopathology of the microbiome-immune interface: Emerging applications of cytology in infectious, inflammatory, and neoplastic conditions.},
journal = {CytoJournal},
volume = {23},
number = {},
pages = {57},
pmid = {42857515},
issn = {0974-5963},
abstract = {OBJECTIVES: The objective of the study is to synthesize current evidence on the microbiome-immune interface as reflected in cytopathologic specimens and to explore the emerging diagnostic, prognostic, and translational applications of cytology in infectious, inflammatory, and neoplastic diseases.

MATERIAL AND METHODS: This narrative review integrates published literature on cytopathology, microbiome research, and immune profiling. Relevant studies examining cytologic specimens, including fine-needle aspiration, effusion cytology, liquid-based cytology, and lavage samples, were evaluated for their contributions to understanding host-microbe interactions. Emphasis was placed on studies incorporating molecular microbiome analysis (16S ribosomal ribonucleic acid sequencing, metagenomics), immunocytochemistry, cytokine profiling, and digital image analysis.

RESULTS: Cytologic specimens provide a minimally invasive platform that captures dynamic interactions between epithelial cells, immune infiltrates, and microbial communities. In infectious diseases, cytology enables direct pathogen visualization while reflecting immune activation patterns such as granuloma formation and neutrophilic inflammation. In chronic inflammatory disorders, cytologic features including lymphoid infiltrates and macrophage activation may correspond with microbiome-driven immune dysregulation. In oncology, tumor-associated microbiota detectable in cytology samples influence immune checkpoint expression, macrophage polarization, and tumor microenvironment remodeling. Integration of molecular assays, single-cell technologies, and artificial intelligence further enhances the ability of cytology to characterize microbiome-immune signatures within limited specimens.

CONCLUSION: Cytopathology is evolving from a purely morphologic discipline into an integrative platform that bridges microbial ecology and immune dynamics. Incorporating microbiome profiling and immune phenotyping into routine cytologic evaluation holds promise for improved disease stratification, early detection, and personalized therapeutic decision-making. Recognizing cytology as a window into the microbiome-immune interface may redefine its role in precision medicine across infectious, inflammatory, and neoplastic conditions.},
}

@article {pmid42853358,
year = {2026},
author = {Razzaq Meo, S and Noppe, C and De Clercq, P and Van de Wiele, T and Defoirdt, T},
title = {Indole decreases the virulence of enterotoxigenic Escherichia coli.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42853358},
issn = {1573-0972},
mesh = {*Enterotoxigenic Escherichia coli/drug effects/pathogenicity/genetics ; *Indoles/pharmacology ; Animals ; Virulence/drug effects ; Escherichia coli Proteins/genetics/metabolism ; Biofilms/drug effects/growth & development ; Gene Expression Regulation, Bacterial/drug effects ; Sigma Factor/genetics/metabolism ; Enterotoxins/metabolism/genetics ; Escherichia coli Infections/microbiology/drug therapy ; Bacterial Proteins/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Bacterial Toxins/genetics/metabolism ; },
abstract = {Indole signaling is being explored as one of the promising targets for anti-virulence therapy against antibiotic-resistant pathogens. Indole has been reported to influence key virulence-related phenotypes, particularly motility and biofilm formation, in various bacterial pathogens. This study aimed to investigate the impact of indole on enterotoxigenic Escherichia coli (ETEC). The results revealed that indole decreased both swimming motility and biofilm formation in ETEC across concentrations ranging from 0 to 1000 µM, with a maximum reduction of 75% in swimming motility and 47% in biofilm formation at the highest concentration. RT-qPCR analysis revealed that motility-related genes (i.e., flagellin fliC and flagellar transcription activator flhC) were downregulated by 5-fold and 2.5-fold, respectively. Additionally, the stress response sigma factor gene rpoS and the heat-stable enterotoxin gene estP were downregulated by 2-fold and 1.7-fold, respectively. Competitive ELISA showed that indole decreased secreted heat-stable enterotoxin levels by more than 10-fold, which is consistent with the decreased estP mRNA levels. Finally, indole decreased the virulence of ETEC towards the invertebrate infection model Galleria mellonella, resulting in a 1.8-fold increased survival after 5 days. These findings indicate that indole signaling controls ETEC virulence, making it an interesting target for anti-virulence therapy.},
}

*Enterotoxigenic Escherichia coli/drug effects/pathogenicity/genetics
*Indoles/pharmacology
Animals
Virulence/drug effects
Escherichia coli Proteins/genetics/metabolism
Biofilms/drug effects/growth & development
Gene Expression Regulation, Bacterial/drug effects
Sigma Factor/genetics/metabolism
Enterotoxins/metabolism/genetics
Escherichia coli Infections/microbiology/drug therapy
Bacterial Proteins/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Bacterial Toxins/genetics/metabolism

@article {pmid42851669,
year = {2026},
author = {Yang, K and Qin, J and Xue, X and Lin, G and Huang, K and Gu, D and Su, J and Wang, J and Cui, Y and Ma, X and Tian, Z and Yu, M and Liu, Z and Rong, T and Lu, Y and Zhong, R and Liu, X and Yang, P and Deng, D},
title = {Synthetic microbial community to enhance the fermentation and feed valorization of pineapple waste.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929714},
pmid = {42851669},
issn = {1664-302X},
abstract = {Global livestock industry is confronted with severe feed-supply pressure, and valorizing agro-industrial by-products has become a promising way to alleviate feed resource shortages. Large quantities of pineapple waste are produced annually during pineapple processing, but antinutritional factors greatly limit its direct application in pig diets. Pineapple waste (PW) is a promising agro-industrial by-product for feed production; however, its high levels of antinutritional factors and structural carbohydrates limit its utilization in monogastric animals. This study aimed to develop a synthetic microbial community (SysComs) for upgrading PW into a functional feed ingredient. Four functional strains were separately screened according to their dominant single degrading or metabolite-synthesizing traits, and further combined into a synthetic community owing to their complementary metabolic capacities, including tannin-degrading Lactiplantibacillus plantarum, xylan-degrading Pediococcus pentosaceus, phytase-producing Lactobacillus fermentum, and butyrate-producing Clostridium butyricum. Fermentation with SysComs markedly improved the nutritional and functional properties of PW. Compared with raw PW, fermented pineapple waste (FPW) showed substantial reductions in tannin and phytate contents, with removal rates reaching 80.65 and 89.62%, respectively. Total dietary fiber and insoluble dietary fiber were significantly decreased, whereas soluble dietary fiber increased from 5.60 to 8.18%. Meanwhile, butyrate concentration increased from 1.65 to 6.63%, accompanied by a decrease in pH from 6.10 to 4.87. Microbial community analysis showed that SysComs fermentation shifted PW from a contaminant-rich microbial community toward a lactic acid bacteria-dominated structure, with enrichment of Lactobacillus, Levilactobacillus, Enterococcus, Bacillus, and Weissella. Untargeted metabolomics further revealed that fermentation extensively remodeled the metabolite profile of PW, with 258 metabolites upregulated and 437 downregulated. Pathways related to flavonoid biosynthesis, flavone and flavonol biosynthesis, and secondary metabolite biosynthesis were significantly enriched. Luteolin, taxifolin, phlorizin, and gallocatechin were markedly increased. In pig experiment, dietary FPW supplementation significantly increased average daily gain by 13.10% and improved gross energy digestibility from 85.36 to 87.46% compared with the control group (p < 0.05). Moreover, FPW reshaped the colonic microbiota by increasing microbial richness and enriching beneficial fiber-degrading and short-chain fatty acid-associated taxa, including Christensenellaceae R-7 group, Lachnospiraceae NK4A136 group, and Monoglobus. These findings demonstrate that SysComs fermentation effectively reduced antinutritional factors, enhanced nutrient accessibility, enriched functional metabolites, and improved growth performance and gut microbial ecology in pigs. Targeted microbial fermentation is an effective strategy for converting pineapple waste into a high-value functional feed ingredient.},
}

@article {pmid42852572,
year = {2026},
author = {Post, A and Yadlapalli, A and Webb, T and Zhang, A and Yelampalli, A and Challa, K and Indugu, N and Pitta, DW},
title = {Core microbial populations drive longitudinal development of the hindgut bacterial microbiota in Jersey calve.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0187826},
doi = {10.1128/spectrum.01878-26},
pmid = {42852572},
issn = {2165-0497},
abstract = {The early-life gut microbiome represents a critical window during which microbial succession may exert lasting effects on host metabolism and productivity. While gut microbiome-host phenotypic associations have been extensively studied in Holstein calves, such relationships are rarely reported in alternative breeds, including Jersey calves. We hypothesized that Jersey calves would exhibit age-dependent community shifts characterized by core microbial populations and breed-associated bacterial networks that may contribute to metabolic phenotype. Fecal samples were collected from dams post-calving, and Jersey calves (n = 12) were sampled longitudinally at 24-48 h and weekly through 12 weeks. Bacterial communities were profiled using the V1-V2 region of the 16S rRNA gene. The number of observed ASVs and Shannon diversity increased with age (P < 0.001), and Beta diversity revealed age-dependent structuring (weighted R[2] =0.12, P = 0.023; unweighted R[2] =0.37, P = 0.001), with calf communities gradually converging toward dams. Taxonomic analyses revealed a conserved core microbiome comprising 34 taxa accounting for over 90% of total community abundance. Neonatal samples were dominated by facultative anaerobes, including Escherichia and Streptococcus, with early colonization by Blautia and Collinsella. Calves then exhibited transient enrichment of milk-glycan-associated taxa, including Lactobacillus and Bacteroides. Weeks 3-7 stages saw preeminence of acetogens (Blautia, Dorea, Collinsella), followed by later enrichment of adult-associated fiber-degrading taxa. Collectively, these findings demonstrate a consistent age-dependent pattern of hindgut microbiome maturation among Jersey calves. The taxonomic patterns provide a foundation for investigating potential links between early-life microbial ecology and breed-specific metabolic phenotypes.IMPORTANCEThe neonatal period represents a critical window for microbial community assembly and interaction with the host. While microbial succession in Holstein calves has been studied extensively, little is known about microbiome assembly in Jersey calves. Herein, we performed longitudinal profiling of the hindgut microbiome of Jersey calves from birth through twelve weeks of age. Microbial communities underwent a structured succession broadly resembling patterns reported previously in Holsteins, with network analyses revealing microbial assemblages that shift with diet throughout the pre- and postweaning periods. Jersey calves also exhibited a notably elevated abundance of several acetate-associated taxa during early life. These findings provide the first detailed characterization of hindgut microbiome assembly in Jersey calves and identify microbial community structures potentially linked to breed-specific metabolic phenotypes. Such information is critical for designing microbiome-targeted strategies to improve calf growth, health, and feed efficiency, and for influencing milk components.},
}

@article {pmid42852577,
year = {2026},
author = {Malaguarnera, L},
title = {The chitinase-microbiota axis: connecting innate immunity, microbial ecology, and mucosal homeostasis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {10},
pages = {},
doi = {10.1093/jleuko/qiag130},
pmid = {42852577},
issn = {1938-3673},
mesh = {*Immunity, Innate ; *Chitinases/metabolism/immunology ; Humans ; Animals ; *Homeostasis ; *Microbiota/immunology ; Chitinase-3-Like Protein 1 ; },
abstract = {Chitinases and chitinase-like proteins are evolutionarily conserved molecules increasingly recognized as components of biological networks linking environmental exposure, innate immunity, tissue organization, and host-microbial interactions. Mammalian chitinases include the catalytically active chitotriosidase (CHIT1) and acidic mammalian chitinase (CHIA/AMCase), alongside nonenzymatic chitinase-like proteins such as chitinase-3-like protein 1 (CHI3L1/YKL-40), which exert distinct but interconnected functions. Host chitinases and microbial chitinolytic systems may converge in environmental chitin processing, whereas CHI3L1 can influence epithelial-microbial interactions and mucus-associated microbial organization through nonenzymatic mechanisms. Environmental exposure and host genetic variability add further complexity: changes in exposure to microorganisms and chitin-containing organisms may modify chitinase-related pathways, while functional variants in CHIT1 and CHIA alter host chitinolytic capacity. However, their consequences for human microbial ecology remain incompletely defined. CHI3L1 also has established functions in neuroinflammatory and astroglial responses, raising the possibility of convergence with microbiota-dependent gut-brain communication, although a direct chitinase-microbiota-brain pathway has not been demonstrated. Here, we propose a multidimensional chitinase-microbiota axis integrating environmental chitin exposure, host and microbial chitinolytic activity, innate immune signaling, epithelial-microbial interactions, and tissue remodeling. We distinguish experimentally established mechanisms from emerging or hypothetical connections and identify critical gaps for testing causal relationships across mucosal, metabolic, and neuroimmune compartments. Reframing chitinases and chitinase-like proteins as context-dependent components of host-microbial ecosystems may provide a mechanistic framework for investigating inflammatory, metabolic, and neuroimmune diseases and defining future biomarker and therapeutic opportunities.},
}

*Immunity, Innate
*Chitinases/metabolism/immunology
Humans
Animals
*Homeostasis
*Microbiota/immunology
Chitinase-3-Like Protein 1

@article {pmid42852904,
year = {2026},
author = {Harrison, LB and Ahmed, JO and Coulibaly, GM and Veyrier, FJ},
title = {Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0044426},
doi = {10.1128/msystems.00444-26},
pmid = {42852904},
issn = {2379-5077},
abstract = {UNLABELLED: Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypotheses, which previously relied on PCR or culture. However, the problem of determining the presence/absence of a given species of interest is not trivial, particularly when closely related species are present in the reference database or metagenomic sample. Reference-based methods for detecting species-level taxa mostly rely on thresholding of aligned reads or mapped k-mers, or derivative metrics such as genomic coverage, creating a trade-off between recall/completeness and precision/purity. New methods for species-level profiling (YACHT, Metapresence, and sylph) have recently been published. Here, we test the performance of these methods, along with Kraken2/bracken and MetaPhlAn4, to detect related species of interest using simulated metagenomic samples from genomes in the families Mycobacteriaceae and Neisseriaceae, which contain closely related genomes. Among methods tested, Metapresence, when used with an alignment quality filter, and sylph offer the best overall performance. Sylph maintains high precision but requires a depth of coverage greater than approximately 0.1× to reliably detect a genome's presence. Metapresence has a lower limit of detection of hundreds of reads, but this is balanced against relatively lower precision. Both methods are relatively robust to the presence of reads from genomes outside the groups of interest. We demonstrate the application of these methods in two real-world data sets: a mycobacterial community in a drinking water system and the community of Neisseriaceae present in the human oral cavity.

IMPORTANCE: Detecting which bacterial species of interest are present in a given sample is fundamental to studies of microbial ecology and evolution and to applied microbiology (e.g., clinical diagnostics). Culture-dependent and culture-independent (e.g., PCR) approaches are increasingly complemented by metagenomic approaches, but methods to accurately identify specific low-abundance species-level genomes in a shotgun metagenomic sample are still being refined. Here, we comprehensively test YACHT, Kraken2/bracken, Metapresence, MetaPhlAn4, and sylph using two simulated data sets of bacterial families, Mycobacteriaceae and Neisseriaceae, that contain closely related species. Our simulations exploit natural genomic diversity to create a challenging benchmark. We demonstrate that Metapresence and sylph perform best, with the former being well suited to low-biomass host-associated data sets and the latter with environmental metagenomic samples. This study is the first extensive benchmark of these methods for this use case and demonstrates that these methods can accurately identify closely related species of interest.},
}

@article {pmid42852908,
year = {2026},
author = {Zhao, J and Lu, Z and Liu, Q and Liu, J and Wang, L and Huang, J and Yang, F and Yu, H},
title = {Multi-omics elucidate octapeptin mechanisms in alleviating intestinal injury in mice challenged with ETEC K88 via modulated microbial and host pathways.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103226},
doi = {10.1128/msystems.01032-26},
pmid = {42852908},
issn = {2379-5077},
abstract = {The mechanisms whereby antimicrobial peptides (AMPs) confer intestinal protection during enteric bacterial infection remain unclear. Here, we examined the protective effects and underlying mechanisms of the AMP, octapeptin, against intestinal infection induced by enterotoxigenic Escherichia coli K88 (ETEC K88) in mice. Octapeptin ameliorated intestinal injury by modulating gut microbiome-host interactions. When compared with ETEC K88 mice, octapeptin significantly attenuated growth retardation, systemic oxidative stress, pro-inflammatory cytokine elevation, and ileal morphological damage. Integrated cecal microbiome, metabolome, and ileal transcriptome analyses revealed that octapeptin reversed ETEC K88-induced dysbiosis, notably increasing beneficial genera abundance. Concomitantly, octapeptin altered microbial metabolite profiles and significantly influenced ileal gene expression in circadian rhythm regulation. Correlation analysis and variance partitioning further identified a coherent "microbiota-metabolite-transcriptome" axis underlying these phenotypic improvements. Thus, octapeptin alleviates ETEC K88-induced intestinal injury via multi-level interactions that restore microbial ecology and regulate host circadian and immune pathways, thereby highlighting host-directed AMP mechanisms.IMPORTANCEAntimicrobial peptides are promising alternatives to antibiotics, but how they work inside the body remains poorly understood. Using a multi-omics approach, this study shows that octapeptin, a natural cyclic lipopeptide, protects mice against intestinal infection by reshaping the gut microbiota, reprogramming gut metabolites, and stabilizing host circadian clock genes that are disrupted by infection. These findings reveal a previously unrecognized link between gut microbes and the intestinal circadian clock. This mechanistic framework could guide the development of peptide-based strategies to prevent enteric infections in animals.},
}

@article {pmid42841659,
year = {2026},
author = {Kovenskiy, A and Mukhanbetzhanov, N and Jarmukhanov, Z and Duisebayeva, A and Morenko, M and Kossumov, A and Chulenbayeva, L and Vinogradova, E and Popov, M and Kushugulova, A and Kozhakmetov, S},
title = {Escherichia coli-derived enterobactin is associated with delayed gut microbiome maturation in infants born to mothers with obesity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098626},
doi = {10.1128/msystems.00986-26},
pmid = {42841659},
issn = {2379-5077},
abstract = {Maternal obesity has been increasingly recognized as a factor influencing early-life microbiome development. However, its impact on the infant gut resistome and virulome remains insufficiently characterized. In this prospective longitudinal study, we investigated gut microbiome composition, antibiotic resistance genes (ARGs), and virulence factor profiles in infants born to mothers with obesity and normal weight during the first year of life. Shotgun metagenomic sequencing was performed on maternal and infant fecal samples collected at birth and at 1, 3, 6, and 12 months. Infants born to obese mothers exhibited delayed microbiome maturation characterized by early enrichment of Pseudomonadota, particularly Escherichia coli and Klebsiella pneumoniae, and reduced abundance of Bifidobacterium species. This compositional pattern was accompanied by a significantly higher ARG burden in early life, including enrichment of genes associated with antibiotic inactivation, efflux mechanisms, and β-lactam resistance. Although taxonomic differences between groups were no longer statistically detectable at the 12-month time point, where the sample size was smallest, functional disparities in the resistome persisted. Additionally, infants born to obese mothers demonstrated increased relative abundance of secretory virulence-associated genes and E. coli-derived enterobactin, suggesting enhanced iron-scavenging capacity and competitive potential of Enterobacteriaceae. Together, these findings suggest that maternal obesity is associated with altered early microbial ecological dynamics, promotes resistome expansion, and may delay transition toward a stable Bacteroidota- and Bacillota-dominated microbiome.IMPORTANCEThe first year of life is a critical window for gut microbiome development, during which early microbial disturbances may influence later health. This study shows that maternal obesity is associated not only with altered infant microbial succession but also with functional changes in the infant gut microbiome, including greater antibiotic resistance gene burden and enrichment of virulence-associated traits. The finding of increased Escherichia coli-derived enterobactin suggests that iron-scavenging mechanisms may help Enterobacteriaceae persist during early infancy and may contribute to delayed microbial maturation. By linking maternal obesity with infant microbiome development, resistome expansion, and virulence-related functions, this work provides new insight into how maternal metabolic status may shape early microbial ecology and potential microbiome-associated risks.},
}

@article {pmid42842337,
year = {2026},
author = {Acar, A and Akin, N},
title = {Table Olive Fermentation: Microbial Ecology, Metabolite Transformation, and Emerging Non-Thermal and Omics-Based Technologies.},
journal = {Journal of food science},
volume = {91},
number = {10},
pages = {e71520},
doi = {10.1111/1750-3841.71520},
pmid = {42842337},
issn = {1750-3841},
mesh = {*Olea/microbiology/chemistry/metabolism ; *Fermentation ; *Food Microbiology ; Multiomics ; Phenols/metabolism ; Yeasts/metabolism ; Food Handling/methods ; Volatile Organic Compounds/metabolism ; Metabolomics ; },
abstract = {Table olive fermentation is a complex microbial process in which lactic acid bacteria and yeasts contribute to the transformation of phenolic compounds, organic acids, and volatile metabolites that influence product quality, safety, and functionality. Fermentation outcomes remain variable because of cultivar characteristics, spontaneous microbial succession, and limited control over microbial and biochemical dynamics. Recent research has therefore shifted toward a more mechanistic understanding of microbial-metabolite interactions and strategies for more reproducible fermentation control. This review critically examines the microbial ecology, phenolic bioconversion, volatile compounds and metabolite formation, and their relationships with table olive quality. Emerging non-thermal technologies, including ultrasound, high hydrostatic pressure, pulsed electric fields, cold plasma, and pulsed light, are evaluated according to their demonstrated and potential roles in microbial modulation, mass transfer, phenolic transformation, and process stability, with particular attention to the strength of table-olive-specific evidence. The review further examines omics and multi-omics approaches for functional microbial characterization and metabolite profiling, together with sensor-based monitoring, artificial intelligence, and machine learning as emerging tools for data-driven fermentation assessment. The evidence indicates that technological maturity varies substantially among emerging approaches and that most omics- and AI-based applications remain more advanced in characterization and classification than in real-time fermentation control. Further development will require integration of strain-resolved microbiology, quantitative metabolite analysis, process monitoring, predictive modelling, and sensory validation under independent pilot- and industrial-scale conditions. Such approaches may support a transition from empirical fermentation toward more reproducible and evidence-based table olive bioprocessing.},
}

*Olea/microbiology/chemistry/metabolism
*Fermentation
*Food Microbiology
Multiomics
Phenols/metabolism
Yeasts/metabolism
Food Handling/methods
Volatile Organic Compounds/metabolism
Metabolomics

@article {pmid42843892,
year = {2026},
author = {Hu, B and Liu, Y and Zhang, X and Manickam, S},
title = {Microbial Metabolic Messengers from Fermented Foods: Multi-Organ Regulation of Energy Homeostasis and Obesity.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag146},
pmid = {42843892},
issn = {1753-4887},
support = {2025S075//Ningbo Public Welfare Research/ ; Y202557618//General Scientific Research Project of Zhejiang Provincial Department of Education/ ; UTB/GSR/2/2025 (5)//Universiti Teknologi Brunei (UTB)/ ; },
abstract = {Mechanistic evidence was systematically reviewed on how major metabolites produced during fermentation of foods modulate obesity through gut microbiota remodeling and multiorgan metabolic regulation, with emphasis on the gut-brain axis, immunometabolic pathways, and epigenetic mechanisms. Obesity remains a major global public health challenge, and conventional management strategies are frequently limited by poor long-term efficacy, low adherence, and undesirable side effects. Increasing evidence positions the gut microbiome as a central metabolic organ that profoundly influences host energy homeostasis and adiposity. Individuals with obesity commonly have a disrupted intestinal microbial ecosystem characterized by reduced microbial diversity, depletion of health-promoting taxa, and enrichment of facultative pathogens, which compromise intestinal barrier function, promote chronic low-grade inflammation, and disturb systemic metabolic regulation. Fermented foods, integral to traditional diets, provide a rich source of live microorganisms and a diverse repertoire of bioactive metabolites produced through fermentation. A narrative review was conducted by synthesizing evidence from experimental, mechanistic, and preclinical studies on fermented foods, gut microbial ecology, fermentation-derived metabolites, and obesity-related metabolic pathways. Current evidence indicates that the anti-obesity effects of fermented foods are mediated not only by transient microbial colonization but, more importantly, by fermentation-derived metabolites such as short-chain fatty acids, conjugated linoleic acid, and indole derivatives (eg, indole-3-propionic acid). These metabolites exert multiorgan physiological effects through the gut-brain axis, immunometabolic pathways, and epigenetic regulation. Collectively, they modulate key processes, including enteroendocrine hormone secretion, hepatic glucose and lipid metabolism, browning of white adipose tissue, and central appetite control, ultimately contributing to metabolic restoration. This review provides a systematic and mechanistic evaluation of how major fermentation-derived metabolites counteract obesity by reshaping gut microbiota composition and functional activity across interconnected organ systems. The insights provide a strengthened conceptual framework for designing microbiota-directed nutritional strategies to sustain body-weight regulation.},
}

@article {pmid42845194,
year = {2026},
author = {Lee, B},
title = {Predatory Mechanisms of Myxobacteria and Their Potential in the Development of Biocontrol Agents.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2608010},
doi = {10.4014/jmb.2608.08010},
pmid = {42845194},
issn = {1738-8872},
mesh = {*Myxococcales/physiology ; *Biological Control Agents ; Animals ; *Pest Control, Biological/methods ; *Antibiosis ; Plant Diseases/prevention & control/microbiology ; },
abstract = {Climate change, environmental degradation, and the depletion of finite resources are intensifying the search for sustainable, bio-based solutions across agriculture, environmental management, and chemical production. Against this backdrop, myxobacteria have emerged as a valuable but still underused microbial resource, distinguished by their ecological versatility, multicellular behavior, predatory lifestyle, and biosynthetic capacity. This review integrates the mechanistic basis of myxobacterial predation with its translational potential in biocontrol, linking microbial ecology to applied biotechnology. The available evidence indicates that predation is not a single process but a coordinated program built from swarm behavior, gliding motility, contact-dependent killing, secreted hydrolytic enzymes, outer membrane vesicle (OMV)-mediated interference, nutrient competition, and specialized metabolites. Through these layers, myxobacteria antagonize phylogenetically diverse targets, including bacteria, fungi, oomycetes, and ciliates, with more limited evidence extending to cyanobacteria and nematodes. Unlike recent reviews that address either the cellular and genetic mechanisms of predation or antagonism against plant pathogens in isolation, this review connects mechanism with application and compares the maturity of the available evidence across target classes. Within this framework, selected bacterial and fungal plant-disease systems have field-level support; oomycetes are mechanistically well supported but have limited field validation; ciliates provide direct mechanistic predation evidence without biocontrol validation; cyanobacteria remain emerging with laboratory-based evidence; and nematodes remain preliminary, with evidence restricted to in vitro studies using Caenorhabditis elegans. Myxobacteria therefore merit continued investigation not only as model organisms for microbial ecology and natural product discovery but also as multifunctional platforms for sustainable biocontrol and broader biotechnological applications.},
}

*Myxococcales/physiology
*Biological Control Agents
Animals
*Pest Control, Biological/methods
*Antibiosis
Plant Diseases/prevention & control/microbiology

@article {pmid42845945,
year = {2026},
author = {Liang, W and Ma, X and Zhang, P and Zhang, W and Yu, C},
title = {Cross-kingdom synthetic microbial communities outperform single-kingdom consortia in promoting potato growth under continuous cropping.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1920336},
pmid = {42845945},
issn = {1664-302X},
abstract = {Continuous cropping obstacles, including soilborne plant pathogen accumulation and soil microbial community degradation, present a critical bottleneck limiting sustainable potato production worldwide. To tackle the prominent obstacles associated with potato continuous cropping, this study explored the potential of synthetic microbial communities (SynComs) in regulating soil microbial ecology and promoting potato growth. Three SynComs were constructed, including a single bacterial consortium (SB), a single fungal consortium (SF), and a bacteria-fungal mixed consortium (SBF), using four bacterial strains (Bacillus licheniformis, Streptomyces sp., Pseudomonas lundensis, and Microbacterium sp.) and three fungal strains (Penicillium sp., Aspergillus fumigatus, and Aspergillus terreus). These SynComs were then evaluated for their effectiveness to overcome continuous cropping obstacles for potato in potted experiments, with non-inoculated group set as the blank control (CK). Our results demonstrated that the SBF consortium exhibited the most pronounced growth-promoting effect throughout the entire potato growth season. Specifically, SBF inoculation increased plant height, stem diameter, root length, and total biomass by 16.24%, 40.84%, 25.84%, and 13.86%, respectively, at the seedling stage; and 27.71%, 22.27%, 28.73%, and 39.31%, respectively, at the flowering stage. SynCom inoculation significantly altered both alpha and beta diversity of soil microbial communities and showed pronounced temporal dynamics. Mantel test analysis suggested that SynCom and pivotal bacterial taxa were the core driving factors for biomass accumulation in potato plants (P < 0.05). Collectively, SynComs effectively increased the abundance of inoculate-related microbes and restructured rhizosphere microbiota to promote potato growth. This study provides a sustainable strategy for alleviating potato continuous cropping obstacles and improving potato productivity.},
}

@article {pmid42846731,
year = {2026},
author = {Chen, M and Su, Q and Sun, M and Zhang, H and Xu, J and Zhang, C and Wang, Y},
title = {Modulating the Gut-Ovarian Axis: Mechanistic Rationale and the Limits of Current Evidence for Probiotics in Female Reproductive Aging.},
journal = {Food science & nutrition},
volume = {14},
number = {10},
pages = {e72454},
pmid = {42846731},
issn = {2048-7177},
abstract = {Female reproductive aging is characterized by progressive follicular depletion, deterioration of oocyte quality, and endocrine decline, with oxidative stress, mitochondrial dysfunction, immune-inflammatory remodeling, and granulosa-cell loss contributing to ovarian functional deterioration. This critical narrative review, supported by a structured literature search, evaluates mechanistic, preclinical, and human evidence for probiotic and microbiota-targeted modulation of the gut-ovarian axis. The current evidence base remains predominantly preclinical. In premature ovarian insufficiency (POI), polycystic ovary syndrome (PCOS), chemotherapy-induced ovarian injury, and reproductive-aging models, selected interventions have modified intestinal microbial ecology, barrier function, microbial metabolites, and systemic immune-metabolic-endocrine signaling, with model-specific effects on ovarian redox homeostasis, granulosa-cell survival, follicular development, mitochondrial function, and oocyte-related outcomes. Mechanistic support is strongest where gut dependency, metabolite supplementation, or related causal approaches have been demonstrated, but responses remain highly strain-, model-, dose-, route-, and host-dependent. Human trials in PCOS and menopause-related or reproductive settings have reported changes in selected metabolic, hormonal, menstrual, symptom, quality-of-life, and fertility-related outcomes; however, our structured literature and trial-registry searches did not identify a randomized human trial specifically designed to test whether probiotic or microbiota-targeted intervention slows the longitudinal physiological loss of ovarian reserve or delays physiological ovarian aging. Findings from disease models, fecal microbiota transplantation, or other experimental interventions should therefore not be equated with the efficacy of oral probiotic foods or supplements. Current evidence supports biological plausibility and translational potential rather than established ovarian anti-aging efficacy. Future studies should evaluate well-characterized oral strains using prespecified ovarian-aging-relevant endpoints, mechanistic biomarkers, and standardized safety assessment.},
}

@article {pmid42847688,
year = {2026},
author = {Stroek, R and Gabriëls, M and Winkelhorst, M and van den Broek, M and Pabst, M and Jourdin, L and Daran, J-M and Bajic, D},
title = {Integrated multi-omics and metabolic modeling links structure to function in high-performing electrosynthetic biofilm communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0080326},
doi = {10.1128/msystems.00803-26},
pmid = {42847688},
issn = {2379-5077},
abstract = {Microbial electrosynthesis (MES) is a promising technology for the valorization of CO2 into industrially relevant building blocks. The high-performing MES systems in terms of production rates of acetate (12.5-19.7 mmol L[-1]catholyte day[-1]), butyrate (1.9-12.2 mmol L[-1]catholyte day[-1]), and caproate (0.6-0.9 mmol L[-1]catholyte day[-1]) discussed in this study consist of mixed microbial communities. However, the microbial community members, metabolic pathways, and interactions driving product formation in MES communities remain poorly understood. To overcome these challenges, we conducted a comprehensive characterization of three high-performing MES communities, combining multi-omics with metagenome-scale metabolic modeling. Using a high-resolution metagenomic pipeline, we reconstructed high-quality genomes of 25 metagenome-assembled genomes present in our reactors, including six fully circular genomes. We report the presence of Clostridium aromativorans for the first time in a gas-fermenting system. In particular, our findings identified three acetogenic species, Eubacterium limosum, Sporomusa sphaeroides, and C. aromativorans, as key contributors to the production of acetate, butyrate, and caproate via the Wood-Ljungdahl and the reverse β-oxidation pathways. In addition, we found genes related to lactate and ethanol production from acetyl-CoA, along with proteomic evidence of lactate production. This paves the way for investigating the role of cross-fed metabolites such as lactate and ethanol as electron donors in chain elongation. Finally, meta-genome-scale metabolic modeling suggests that the communities might be sustained by the cross-feeding of specific cofactors such as pyridoxine, pantothenate, biotin, and thiamin. This study provides key insights into the structure and function of electrosynthetic communities, bringing us closer to the rational engineering of MES systems.IMPORTANCEMicrobial electrosynthesis (MES) offers a promising route to transform CO2 and renewable electricity into valuable platform chemicals. However, the microbial ecology governing the assembly and function of these systems remains poorly understood, limiting our ability to engineer them. By integrating high-resolution multi-omics with metabolic modeling, this study provides a systems-level framework to dissect the structure and function of electrosynthetic microbial communities. Understanding which organisms drive carbon fixation and chain elongation, how electrons and intermediates are transferred within the biofilm, and how metabolic dependencies structure these communities is essential for improving productivity and product specificity in MES. More broadly, this work highlights how integrated multi-omics approaches can resolve the functional organization of complex microbial ecosystems and provides methodological advances that are broadly applicable to the study and engineering of microbial communities in autotrophic, electricity-driven biotechnologies.},
}

@article {pmid42849066,
year = {2026},
author = {Zhang, X and Yan, N and Zhang, F and Ji, T and Hu, H and Ma, Y and Fu, J and Brusseau, ML},
title = {Concurrent interactions between PFAS and bacteria during 6:2 fluorotelomer sulfonate transport in saturated and unsaturated porous media.},
journal = {Journal of contaminant hydrology},
volume = {284},
number = {},
pages = {105132},
doi = {10.1016/j.jconhyd.2026.105132},
pmid = {42849066},
issn = {1873-6009},
abstract = {The role of microbial communities in regulating the transport and retention of per- and polyfluoroalkyl substances (PFAS) in the subsurface environment, particularly under water-unsaturated conditions, remains poorly understood. Here, miscible-displacement experiments were conducted with saturated and unsaturated sand-packed columns to investigate the influence of biofilms on the transport of 6:2 fluorotelomer sulfonate (6:2 FTS), considering biofilm age, bacterial species, and flow rate. The underlying mechanisms were further elucidated through characterization of extracellular polymeric substances (EPS), zeta potential, and cell surface hydrophobicity, while microbial community responses to 6:2 FTS exposure were also evaluated. Compared with clean sand, biofilm-coated sand enhanced 6:2 FTS retention under both saturated and unsaturated conditions. Under saturated conditions, retention differences among bacterial species were primarily governed by EPS content and protein-to-polysaccharide ratios. In contrast, species-level effects became less pronounced under unsaturated conditions, indicating a shift from species dependent controls to coupled biofilm interface processes. Quantitative analysis of these specific experiments showed that biofilms-associated processes contributed 42% of the additional apparent retention observed upon transition from saturated to unsaturated conditions, compared with 58% attributed to air-water-interfacial adsorption. These results demonstrate that biofilm-associated processes constitute an important and previously overlooked retention domain contributing substantially to the enhanced retention of 6:2 FTS under unsaturated conditions. Biofilm maturation further increased retention through EPS accumulation and associated changes in surface physicochemical properties, including surface potential, roughness, and hydrophobicity. Moreover, 6:2 FTS exposure altered bacterial community composition, suggesting reciprocal interactions between PFAS transport and microbial ecology. These findings provide new mechanistic insights into PFAS fate in the subsurface and improve the basis for predicting PFAS transport and designing remediation strategies for PFAS-impacted sites.},
}

@article {pmid42849204,
year = {2026},
author = {Bedoya, K and Buetas, L and Rozès, N and Mas, A and Portillo, MC},
title = {Grape ripeness shapes microbial community dynamics and fermentation outcomes during modified pied de cuve wine fermentations.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112098},
doi = {10.1016/j.ijfoodmicro.2026.112098},
pmid = {42849204},
issn = {1879-3460},
abstract = {Pied de cuve (PdC) is a traditional inoculation strategy consisting of adding a small volume of actively fermenting must to initiate alcoholic fermentation (AF) in the main vat. In this study, we evaluated the effect of grape ripeness on microbial community composition, fermentation performance, and Saccharomyces cerevisiae strain diversity using a modified spontaneous PdC prepared with sulphur dioxide (SO2) and ethanol and fermented at 18 °C. PdC inoculation was compared with inoculation using the commercial S. cerevisiae strain QA23 and with spontaneous fermentation. Experiments were performed at three ripening stages corresponding to potential alcohol content (PAC) of 10%, 12% and 13% (v/v). Amplicon sequencing revealed that both early winemaking sampling point and grape ripeness significantly shaped bacterial and fungal community composition, whereas ripeness had a limited effect on fungal alpha diversity. Despite differences in PdC development among maturity levels, PdC inoculation consistently improved fermentation kinetics compared with spontaneous fermentation, particularly at 13% PAC. Interdelta-PCR analysis showed that PdC fermentations preserved higher S. cerevisiae strain diversity than commercial inoculation, while an indigenous strain recurrently detected across fermentations displayed strong competitive ability against QA23. Differences in inoculation strategy were also reflected in wine chemistry and sensory properties, with PdC wines showing controlled acetic acid concentrations and favourable sensory profiles. Overall, these results demonstrate that grape ripeness acts as an ecological driver of fermentation and that modified PdC inoculation represents a practical strategy for balancing fermentation reliability with the preservation of indigenous fermentative diversity.},
}

@article {pmid42849841,
year = {2026},
author = {Qi, YL and Yan, Y and Li, XM and Li, YL and Liao, LZ and Liu, J and Ma, JW and Ma, JH and Chen, H},
title = {Gut Microbiota and nutrition as Emerging Modulators of Immune Checkpoint Inhibitor Therapy: Current Evidence, Challenges, and Future Perspectives.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {105168},
doi = {10.1016/j.clnesp.2026.105168},
pmid = {42849841},
issn = {2405-4577},
abstract = {Immune checkpoint inhibitors (ICIs), a major class of cancer immunotherapies, have transformed the treatment of advanced cancers, yet durable benefit remains limited by primary or acquired resistance and immune-related adverse events (irAEs). Increasing evidence implicates the gut microbiome and nutritional state as modifiable host factors that may shape both therapeutic efficacy and toxicity. Here, we critically review the emerging evidence linking microbial ecology, dietary exposure, immunonutrition and ICI outcomes, with particular emphasis on the diet-microbiome-metabolite-immune axis. Clinical cohorts and preclinical models indicate that microbiome composition and, increasingly, microbial function and metabolic cross-talk are associated with ICI responsiveness, while microbiome perturbations may also influence susceptibility to irAEs. Dietary patterns and nutritional status likewise correlate with treatment outcomes, with dietary fibre and Mediterranean-style dietary patterns providing early clinical signals, whereas evidence for specific immunonutrients and restrictive dietary strategies remains inconsistent or insufficient. Mechanistically, dietary substrates can reshape microbial communities and metabolite production, thereby modulating immune-cell states and antitumour responses. However, these effects are highly context dependent and cannot be inferred from individual taxa or metabolites alone. We further examine emerging strategies that integrate nutritional optimization with microbiome modulation as a potential means of simultaneously improving efficacy and therapeutic tolerability. Despite substantial mechanistic progress, clinical evidence remains predominantly observational or early phase, and no microbiome-informed dietary intervention has yet established a reproducible benefit in prospective trials. Future studies should therefore move beyond descriptive associations towards evaluating causal, biomarker-guided and patient-stratified interventions integrating longitudinal dietary, microbiome, metabolomic and immune profiling.},
}

@article {pmid42851078,
year = {2026},
author = {Doumbia, B and Luo, S and Yang, S and Wang, C and Jia, Y and Kuprin, AV and Geng, A and Zhu, D and Sun, J and Ezenwanne, BC and Xie, R and Dar, MA},
title = {Harnessing bacterial symbionts of beetles for the valorization of lignin into value-added byproducts: Recent advances and future perspectives.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70378},
pmid = {42851078},
issn = {1744-7917},
support = {32250410285//National Natural Science Foundation of China/ ; 2023YFC3403600//National Key R&D Program of China/ ; WGXZ2023020L//Foreign Expert Program, of Ministry of Science and Technology (MoST) of China/ ; 124012400285-7//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Lignin is the most abundant renewable aromatic heteropolymer in nature and is highly recalcitrant due to its complex structure. The gut systems of beetles function as an evolutionarily optimized microreactor wherein mechanical pretreatment, physicochemical gradients, and selectively maintained microbial consortia act synergistically to transform, mineralize, and metabolize lignin as an energy source. Beetle-associated bacterial symbionts represent a promising yet underexploited resource for lignin valorization into value-added products. This review provides emerging evidence of lignin degradation by beetles in association with their gut symbionts and indicates the diversity of gut bacteria involved in lignin depolymerization. We further discuss the mechanisms by which beetles and their gut bacteria metabolize lignin, the lignin-transforming capacities of the bacterial symbionts and their potential application in the valorization of waste lignin into added-value byproducts. Finally, we assess the emerging research trends on the bioprospection of lignin-degrading bacteria from underexplored beetle species. Despite significant advantages, several key challenges remain unresolved, including difficulties in isolation and culturing of key gut bacteria in vitro, limited biochemical validation of candidate enzymes and the unresolved linking of specific genes or taxa to in situ lignin transformation. Future studies should integrate discovery-driven microbial ecology, multi-omics, predictive modeling and precision genome engineering to convert the complexity of beetle gut bacterial communities into a practical blueprint for scalable lignin valorization, and the biomanufacturing of high-value products from lignin-based waste.},
}

@article {pmid42851568,
year = {2026},
author = {Enwere, M and Bryan, NS and Onu, A and Neufeld, M and El-Hussein, MT and Yakub, I and Omale, C and Onyedike, O and Atim, T and Agbeyomi, O and Davies, E and Okeke, UE and Holmes, L},
title = {The microbiome-nitric oxide axis in cancer immunotherapy: a targeted qualitative systematic review of mechanistic and translational evidence.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1904698},
pmid = {42851568},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/therapy/immunology/metabolism/microbiology ; *Nitric Oxide/metabolism/immunology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Fecal Microbiota Transplantation ; Translational Research, Biomedical ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, but responses vary substantially among patients. Clinical studies have associated features of the gut microbiome with ICI outcomes, while experimental evidence suggests that microbial metabolites and nitric oxide (NO)-related pathways may influence antitumor immunity and tumor vascular biology. This qualitative systematic review evaluated the evidence supporting a proposed microbiome-NO-ICI framework.

METHODS: Five databases were searched for peer-reviewed studies published between January 2000 and August 2025. Fifty-four distinct primary studies met the eligibility criteria, comprising 21 clinical studies, 19 animal studies and 14 in vitro mechanistic studies. Evidence was synthesized narratively according to study type and thematic domain.

RESULTS: Several clinical cohorts associated enrichment of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium species and other short-chain fatty acid-producing taxa with favorable ICI outcomes; however, the reported microbial signatures varied across cohorts and analytical platforms. Microbial-transfer experiments and early non-randomized fecal microbiota transplantation studies provide proof-of-concept evidence that microbiome composition can influence antitumor immune responses, although the clinical intervention evidence remains preliminary. Animal and cellular studies indicate that microbial metabolites, host nitric oxide synthase pathways and reactive nitrogen signaling can affect immune-cell function, vascular regulation and tumor hypoxia. Direct clinical evidence linking microbiota-mediated nitrate reduction or dietary nitrate supplementation to improved ICI outcomes is lacking. Human dietary nitrate studies conducted outside oncology demonstrate increased circulating nitrate and nitrite and measurable vascular effects but do not establish anticancer or ICI efficacy.

CONCLUSION: The microbiome-NO-ICI axis should be regarded as a testable integrative model linking microbial ecology, immune regulation and tumor vascular biology. Current evidence supports biological plausibility but is insufficient to establish NO- or microbiome-directed interventions as effective adjuncts to ICI therapy. Prospective mechanistic studies and biomarker-driven clinical trials are required before therapeutic translation.},
}

Humans
*Neoplasms/therapy/immunology/metabolism/microbiology
*Nitric Oxide/metabolism/immunology
Animals
*Gastrointestinal Microbiome/immunology
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use
Fecal Microbiota Transplantation
Translational Research, Biomedical

@article {pmid42835729,
year = {2026},
author = {Coppola, F and Nazzaro, F and Fratianni, F and Polito, F and Ayala-Zavala, JF and De Feo, V and Coppola, R and Tremonte, P},
title = {Mixed-species biofilms in food systems: from community assembly to ecology-informed management.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1945500},
pmid = {42835729},
issn = {1664-302X},
abstract = {Biofilms in food-processing environments present multifaceted challenges for food safety, quality, and public health. These microbial communities, forming on a variety of surfaces within food-processing facilities, are responsible for persistent contamination, increased tolerance to cleaning and disinfection, and the transmission of spoilage organisms and pathogens. This review provides a comprehensive overview of current knowledge on the formation, ecological organization, persistence, and impact of mixed-species biofilms in food systems, emphasizing their central role in contamination control and food safety management. While recent advances in analytical technologies have improved our understanding of their complexity and resilience, significant knowledge gaps remain regarding their behavior under real-world industrial conditions. The review highlights the limitations of traditional eradication-based approaches and discusses innovative strategies for monitoring, controlling, and preventing biofilm-associated risks in modern food production systems.},
}

@article {pmid42836075,
year = {2026},
author = {Rosado, AS},
title = {Extreme microbes for a changing planet and beyond.},
journal = {Sustainable microbiology},
volume = {3},
number = {4},
pages = {qvag041},
pmid = {42836075},
issn = {2755-1970},
}

@article {pmid42836172,
year = {2026},
author = {Raab, M and Behr, JH and Vasileiadis, S and Neumann, G and Smalla, K and Grosch, R and Geistlinger, J and Rozhon, W and Babin, D and Kampouris, ID},
title = {Positive effects of reduced tillage intensity on soil organic matter are linked to shifts of K-/r-strategists in soil bacterial community composition.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag251},
pmid = {42836172},
issn = {2730-6151},
abstract = {Compared to conventional ploughing, reduced tillage intensity (e.g. cultivator tillage) benefits soil organic matter (SOM) accumulation, which has been attributed to lower disruption of soil aggregates under reduced tillage intensity. While soil microorganisms have been known to contribute to SOM accumulation, the contribution of microbial processes to SOM content has been overlooked, with the underlying mechanisms remaining unclear. We here estimated how cultivator tillage shifts soil bacterial community composition toward slower-growing K-strategists, in contrast to faster-growing r-strategists, by analyzing previously generated data from a long-term field trial in loess chernozem soil. We annotated the 16S rRNA genes from the whole amplicon sequence variant dataset through sequence alignment and identified publicly available genomes phylogenetically related to them with at least 97% sequence identity. Next, we computationally inferred traits such as growth rate, genome size, and the number of carbohydrate catabolism-related genes. These traits were strongly associated with positive responders to cultivator or mouldboard-plough tillage in the bulk soil bacterial communities. Moreover, mouldboard-plough tillage showed a lower ratio of slower- to faster-growing bacterial taxa compared to cultivator tillage in the bulk soil. While this relationship was absent in rhizosphere bacterial communities, these communities showed an overall lower ratio of slower- to faster-growing bacterial taxa than the bulk soil bacterial communities. Moreover, this ratio was negatively correlated with SOM only under mouldboard-plough tillage in bulk soil bacterial communities. Overall, our results indicate that tillage intensity influences the relationship of bacterial K-/r-strategists with SOM.},
}

@article {pmid42836487,
year = {2026},
author = {Falcón, LI and Acosta-González, A and Antúnez, K and Daille, LK and Dorador, C and Duchicela, J and García-Amado, MA and Godoy-Vitorino, F and Mejía, LC and Mendonca-Hagler, LC and Piccini, C and Pinto-Tomás, AA and Rojas-Badía, MM and Schiaffino, MR and Servín-Garcidueñas, LE and Solano-Arguedas, AF and Vásquez, M and Wall, LG and Zambrano, MM},
title = {Microbial ecology in Latin America: underexplored opportunities of a transformative science.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag129},
pmid = {42836487},
issn = {1751-7370},
}

@article {pmid42838399,
year = {2026},
author = {Naeem, M and Pacheco, WJ},
title = {Gut health as a determinant of nutrient use efficiency in poultry: biological basis and nutritional optimization.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101860},
doi = {10.1016/j.tjnut.2026.101860},
pmid = {42838399},
issn = {1541-6100},
abstract = {Efficient nutrient use is fundamental to sustainable poultry production because it influences productive performance, feed costs, animal welfare, and environmental nutrient losses. Although improvements in nutrient utilization have traditionally focused on diet formulation and feed additives, increasing evidence demonstrates that gut health is a central biological determinant governing digestion, absorption, and retention of nutrients. Gut health encompasses the coordinated interaction among intestinal morphology, digestive physiology, epithelial barrier integrity, gut microbiota, and mucosal immune homeostasis, all of which collectively regulate nutrient use efficiency. Disruption of these components by nutritional imbalances, enteric pathogens, heat stress, mycotoxins, and management-related stressors impairs digestive and absorptive function, increases intestinal permeability, alters microbial ecology, and redirects nutrients from productive processes toward immune activation and tissue repair. Consequently, maintaining intestinal homeostasis has become a major objective of modern poultry nutrition. This review synthesizes current knowledge on the biological mechanisms linking gut health with nutrient use efficiency and examines how intestinal development, digestive function, nutrient transport, barrier integrity, microbial metabolism, and immune regulation interact to determine productive performance. Major nutritional, environmental, and pathological factors compromising gut function are discussed, together with current nutritional strategies including precision diet formulation, microbiota modulation, feed enzymes, functional amino acids, phytogenic compounds, antioxidants, and trace minerals that improve intestinal function and nutrient utilization. Collectively, the evidence synthesized in this review demonstrates that maintaining gut health is fundamental to maximizing nutrient use efficiency and provides a biological foundation for improving productive efficiency while reducing nutrient losses and supporting more sustainable poultry production.},
}

@article {pmid42840080,
year = {2026},
author = {Raghunatha Reddy, L and Jehmlich, N and Fiskal, A and Fischer, CB and Ternes, T and Meier, J and Wick, A},
title = {Comparative proteomics reveals hydrogenase-centered steel-dependent growth and corrosion in Desulfovibrio vulgaris and Desulfovibrio ferrophilus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1944645},
pmid = {42840080},
issn = {1664-302X},
abstract = {Comparative proteomic analyses including ecologically distinct sulfate-reducing strains and different cellular fractions are scarce, limiting our understanding of corrosion-related mechanisms under anoxic conditions and the identification of protein signatures relevant to microbiologically influenced corrosion (MIC). To capture both freshwater and marine adaptations, we investigated the well-established SRB model strains Desulfovibrio vulgaris and Desulfovibrio ferrophilus. We compared energy metabolism, electron transport pathways, and growth patterns in both strains cultivated with lactate, H2, or steel as electron donor. Time-dependent biophysicochemical measurements, SEM/EDX, and shotgun proteomics were performed. We explored cellular proteins in planktonic and biofilm fractions, as well as potential extracellular enzymes in the supernatant. In both the strains, growth with steel revealed energy metabolisms more similar to H2-dependent metabolism instead of direct iron-to-microbe electron transfer (DIMET). Increased abundances of periplasmic hydrogenases and c-type cytochromes served as proteomic signatures supporting H2-mediated iron-to-microbe electron transfer (HIMET). Concomitant to bacterial growth and biofilm formation, mineral deposits of carbonates, phosphates and FeS were formed, the latter especially in saltwater treatments. The close association of D. ferrophilus cells with FeS particles supports the possibility of the role of FeS in electron transfer in addition to H2 as well as formate mediated electron transfer which may have contributed to the high corrosion levels with D. ferrophilus. Neither strain exhibited increased abundances of redox proteins known to be involved in extracellular electron transfer, supporting that DIMET may have not been a dominant mechanism under the given conditions. This interpretation is also in line with the observation that only a small proportion of the total cells were associated with the steel surface, and that direct cell-to-steel contact was not observed. These findings show that SRB can be metabolically flexible and that hydrogenase-based systems are sufficient for steel-dependent growth leading to corrosion. This is especially relevant in natural environments, where more than one type of electron donor is available and different modes of extracellular electron transfer exist.},
}

@article {pmid42840879,
year = {2026},
author = {Cheng, J and Zhang, X and Zhou, J and Liu, L and Feng, J and Zhao, L},
title = {Periodontitis and Parkinson's disease: a narrative review of associations, proposed mechanisms, and clinical considerations.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1926663},
pmid = {42840879},
issn = {2673-4842},
abstract = {Periodontitis is a common chronic inflammatory disease, and oral health problems are frequent in people with Parkinson's disease (PD). Observational studies consistently indicate poorer periodontal status in PD, but evidence that periodontitis increases the incidence or progression of PD is inconsistent and does not establish causality. This narrative review summarizes current evidence on epidemiological associations, biologically plausible mechanisms, and dental management considerations. Human data support an association between PD and greater periodontal disease burden, plausibly related to motor impairment, reduced self-care capacity, salivary dysfunction, and altered oral microbial ecology. By contrast, proposed pathways from periodontitis to PD, including systemic inflammation, blood-brain barrier disruption, microbial products, and the oral-gut-brain axis, are supported mainly by preclinical, indirect, or low-level human evidence and should be regarded as hypotheses rather than established mechanisms. Observational reports of lower PD incidence among individuals receiving dental scaling do not demonstrate a preventive effect of periodontal treatment. In clinical practice, periodontal care should therefore be justified by established oral-health needs and individualized for PD-related motor, swallowing, cognitive, medication, and device-related considerations, rather than presented as a strategy to prevent or modify PD. Better longitudinal studies and interventional trials are needed to clarify temporality, mechanisms, and any neurological effects of periodontal treatment.},
}

@article {pmid42840990,
year = {2026},
author = {Mahajan, GB},
title = {Gut microbiome modulation by diet and lifestyle in kidney stone disease and autism spectrum disorder: emerging mechanisms and translational prospects.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1901989},
pmid = {42840990},
issn = {2813-4338},
abstract = {BACKGROUND: The gut microbiome occupies a central position in mediating the physiological consequences of diet, lifestyle, and physical activity. While this interplay is broadly recognized, its mechanistic consequences in two clinically underserved conditions-urolithiasis (kidney stone disease) and autism spectrum disorder (ASD)-remain poorly explained. Both conditions share convergent pathophysiology rooted in metabolic dysregulation, impaired epithelial barrier function, immune dysregulation, and altered microbial metabolite profiles, all of which are modifiable through dietary and behavioral interventions.

METHODS: This minireview synthesizes current evidence from clinical, epidemiological, and mechanistic studies to evaluate the bidirectional relationship between gut microbial ecology and disease pathogenesis in urolithiasis and ASD, with emphasis on dietary compounds, fermented foods, probiotics, and lifestyle behaviors as modulatory factors.

RESULTS: In urolithiasis, evidence implicates reduced abundance of oxalate-degrading taxa (notably Oxalobacter formigenes), dysbiotic short-chain fatty acid (SCFA) profiles, and urinary microbiome perturbations in stone formation and recurrence. In ASD, microbial alterations in gastrointestinal-symptomatic individuals converge on reduced butyrate-producing taxa, elevated pro-inflammatory species, and altered serotonin and gamma-aminobutyric acid (GABA) biosynthetic pathways.

CONCLUSION: Dietary interventions-particularly high-fiber regimens, polyphenol-rich foods, fermented products, and targeted probiotic formulations-show mechanistic plausibility for microbiome restoration in both conditions. However, clinical translation is constrained by methodological heterogeneity, confounding lifestyle variables, and a paucity of longitudinal, mechanistically anchored trials. We outline a research agenda prioritizing standardized multi-omics, paired gut-urine sampling protocols, and rigorously controlled dietary interventions to bridge this gap.},
}

@article {pmid42831621,
year = {2026},
author = {Espinoza, JL and Phillips, AJ and Dupont, CL},
title = {Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/msystems.00970-26},
pmid = {42831621},
issn = {2379-5077},
abstract = {Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing resource requirements, while translated searches in protein space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics data set analyzing metabolic shifts between early and mature biofilm communities, and a dental caries metatranscriptomics data set where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.IMPORTANCEUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy, with lower resource requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.},
}

@article {pmid42832251,
year = {2026},
author = {Pu, J and Ding, Y and Chen, G and Chen, W and Yu, B and Liu, C},
title = {Curcumin in inflammatory bowel disease: highlighting gut microbiota-metabolite-host interactions.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo03442j},
pmid = {42832251},
issn = {2042-650X},
abstract = {Inflammatory bowel disease (IBD) is driven by a complex interplay among epithelial barrier breakdown, immune dysregulation, microbial dysbiosis, and redox imbalance. Curcumin, a major curcuminoid from turmeric (Curcuma longa L.) and a widely used food ingredient, has attracted sustained interest as a dietary bioactive for IBD prevention and adjunct management. Notably, curcumin shows low systemic bioavailability, allowing a substantial fraction to reach the distal gut, where it can be biotransformed by the gut microbiota and act locally on the mucosa. This review synthesises recent evidence on: (i) curcumin's gastrointestinal fate, including host conjugation and microbial reduction to more stable metabolites; (ii) the bidirectional curcumin-microbiota relationship, whereby baseline microbial functions shape curcumin metabolism and response, while curcumin remodels microbial ecology and metabolite outputs (short-chain fatty acids, bile acids and tryptophan-derived indoles); and (iii) downstream host pathways linked to barrier integrity, NF-κB and MAPK signalling, immune cell polarisation, and redox-sensitive programmes (Nrf2 and ferroptosis susceptibility). We further discuss food-grade formulation and delivery strategies that tune colonic exposure and microbiota engagement, and outline research priorities for evidence mapping, responder stratification and standardised biomarkers to accelerate translation of curcumin-based functional foods for IBD.},
}

@article {pmid42832669,
year = {2026},
author = {Saha, A and Jones, JM and Plummer, A and Larkin, JW},
title = {Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {41},
pages = {e2608188123},
doi = {10.1073/pnas.2608188123},
pmid = {42832669},
issn = {1091-6490},
support = {R35GM142584//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; CASI//Burroughs Wellcome Fund (BWF)/ ; },
mesh = {*Bacillus subtilis/physiology ; *Biofilms/growth & development ; Polyglutamic Acid/analogs & derivatives/metabolism/chemistry ; Gels/chemistry ; Polysaccharides, Bacterial/metabolism/chemistry ; Phase Transition ; Rheology ; },
abstract = {Microbes across diverse species and environments form biofilms, living materials composed of cells and extracellular polymers. Biofilm-dwelling cells benefit from emergent soft matter physics, which sculpts three-dimensional morphologies and facilitates osmotic nutrient uptake. Although biofilms are modeled as viscoelastic gels, the physical origins of the phase transition underlying their conversion from groups of cells to living gels have not been systematically investigated. Here, we show that Bacillus subtilis biofilms use polymer composition to tune their physical properties and drive gel formation. Using imaging, water immersion experiments, and rheological measurements with matrix knockout strains, we demonstrate the complementary roles of two polymers in this developmental transition: hydrophilic poly-γ-glutamic acid swells colonies by absorbing water while exopolysaccharides serve as effective cross-linkers, causing a sol-gel-like phase transition that imparts structural integrity. With matrix knockout coculture biofilms, we independently modulate the production of each polymer and reveal a phase space of biofilm morphologies. Colonies that produce both polymers develop macroscopic wrinkles. A thin-film model predicts biofilm wrinkling from swelling-induced internal strain coupled with elasticity. The model reproduces the shape of our observed morphological phase diagram. Our results demonstrate that bacteria leverage gelation to vary their material properties and morphologies, with implications for microbial ecology and engineering living matter.},
}

*Bacillus subtilis/physiology
*Biofilms/growth & development
Polyglutamic Acid/analogs & derivatives/metabolism/chemistry
Gels/chemistry
Polysaccharides, Bacterial/metabolism/chemistry
Phase Transition
Rheology

@article {pmid42833009,
year = {2026},
author = {Raut, R and Tushar, ZH and Shrestha, R and Mostafa, MS and Adhikari, A and Basnet, U and Rahman, FA},
title = {Post-slaughter poultry meat preservation for sustainable food systems: Mechanisms, microbial safety, shelf-life extension, and emerging preservation strategies.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107869},
doi = {10.1016/j.psj.2026.107869},
pmid = {42833009},
issn = {1525-3171},
abstract = {Post-slaughter handling plays a critical role in determining the quality, microbial safety, and shelf life of poultry meat, yet spoilage and contamination remain persistent challenges for the poultry industry, contributing to food loss and reduced sustainability across the food supply chain. This review synthesizes current knowledge on post-slaughter factors influencing poultry meat deterioration, with emphasis on microbial ecology, spoilage mechanisms, and preservation strategies that enhance food safety and support sustainable food systems. Key processing steps, including scalding, defeathering, evisceration, chilling, packaging, and transport, are identified as major contamination points, where cold-chain integrity strongly governs microbial growth and quality loss. Major spoilage organisms, including Pseudomonas spp., lactic acid bacteria, Enterobacteriaceae, Brochothrix thermosphacta, Campylobacter, and Salmonella, are discussed in relation to psychrotrophic growth, enzymatic degradation, lipid oxidation, biofilm formation, and volatile compound production. Shelf-life assessment is evaluated using integrated microbiological, chemical (TBARS, TVB-N, VOCs), and sensory indicators, each with inherent limitations, to support effective quality management and minimize product losses. Preservation strategies are categorized into conventional (refrigeration, freezing), biological (lactic acid bacteria, bacteriocins, plant extracts), and advanced systems such as modified atmosphere packaging, vacuum packaging, active and intelligent packaging, and nanotechnology-based approaches. Evidence indicates that multi-hurdle strategies combining complementary interventions provide superior shelf-life extension through synergistic effects on microbial and oxidative stability. Collectively, these preservation strategies have the potential to reduce food loss and waste, improve resource efficiency, and enhance the sustainability of poultry production and food systems while maintaining product quality and safety.},
}

@article {pmid42833514,
year = {2026},
author = {Perendeci, NA and Mohamadnia, S and Zacharopoulos, I and Gesicka, A and Baniamerian, H and Ghofrani-Isfahani, P and Yılmaz, F and Angelidaki, I},
title = {Decarbonizing waste: Building tomorrow's biorefinery beyond biogas.},
journal = {Biotechnology advances},
volume = {94},
number = {},
pages = {109067},
doi = {10.1016/j.biotechadv.2026.109067},
pmid = {42833514},
issn = {1873-1899},
abstract = {Anaerobic digestion (AD) is increasingly recognized as a foundational process in the global shift toward sustainable, circular, and low-carbon systems. Long established for its capacity to convert organic waste into biogas and nutrient-rich digestate, AD now plays a pivotal role in climate-smart production, decentralized energy generation, and resource recovery. Yet its full potential extends far beyond these traditional outputs. Advances in microbial ecology and process engineering are transforming AD into a modular biomanufacturing platform capable of producing high-value compounds. These biomolecules offer renewable pathways for the synthesis of biofuels, single-cell protein (SCP), methanol, microalgal products, and other speciality chemicals, positioning AD at the heart of emerging bioeconomies. This dual capacity, addressing today's urgent need for sustainability and enabling tomorrow's bio-based production system, positions AD as an important technology in future biorefineries. This article appeals to a broad readership seeking to understand AD, which is one of the most mature yet dynamically evolving processes for biological resource recovery. Increasingly positioned as a central platform for future circular bioeconomies and sustainable biomanufacturing, this review specifically focuses on pivotal aspects of next-generation biorefineries, including biomethanation, SCP and methanol production, microalgal-based products, and integrated resource recovery strategies.},
}

@article {pmid42835245,
year = {2026},
author = {Mujahid, W and Safdar, S and Aftab, A and Tabassum, S and Bakhtiar, SM},
title = {Integrative Metagenomic Analysis Reveals Human Gut Microbiome-Derived Candidate Non-invasive Biomarkers for Type II Diabetes Mellitus.},
journal = {Iranian journal of medical sciences},
volume = {51},
number = {9},
pages = {617-629},
pmid = {42835245},
issn = {1735-3688},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/diagnosis ; Biomarkers/analysis ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics/physiology ; Case-Control Studies ; Bacteroides/genetics ; Dysbiosis/diagnosis ; },
abstract = {BACKGROUND: Type II Diabetes Mellitus (T2DM) is increasingly associated with alterations in the gut microbiome, which influences host metabolism, inflammation, and insulin sensitivity. Metagenomic profiling has emerged as a promising non-invasive strategy for identifying disease-associated microbial signatures. However, distinguishing disease-specific biomarkers from general dysbiosis remains a major challenge. This study aimed to develop an integrative subtractive metagenomic framework to identify candidate disease-specific gut microbial biomarkers.

METHODS: This in silico case-control study used publicly available metagenomics datasets from healthy controls and individuals with T2DM. Assembly-based and read-based taxonomic profiling approaches were integrated. Differential abundance analysis using the Wilcoxon rank-sum test identified key microbial taxa significantly associated with T2DM.

RESULTS: Potential microbial biomarkers were identified as Bacteroides dorei, Bacteroides gracilis, Bacteroides stercoris, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Eggerthella lenta, Escherichia coli, Faecalibacterium prausnitzii, Parabacteroides distasonis, Ruminococcus torques, and Subdoligranulum. These taxa are involved in gut metabolic homeostasis and may serve as candidate non-invasive biomarkers for T2DM.

CONCLUSION: The results of this study advance understanding of microbiome-disease crosstalk and form the basis for further in vitro and in vivo validation and microbiome-targeted therapeutic approaches. Overall, this integrative metagenomic study supports alteration of microbial ecology in T2DM, validating the use of gut microbiome profiling as a diagnostic and therapeutic tool in metabolic disease research.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/diagnosis
Biomarkers/analysis
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics/physiology
Case-Control Studies
Bacteroides/genetics
Dysbiosis/diagnosis

@article {pmid42820982,
year = {2026},
author = {Gomez-Gomez, E and García-Hernández, J and Heredia, A and Calvo-Lerma, J and Andrés, A},
title = {Exploratory Associations Between Height-for-Age and Gut Microbiota Composition in Healthy School-Aged Children.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42820982},
issn = {1432-0991},
support = {AGROALNEXT/2022/030//Generalitat Valenciana/ ; },
mesh = {Humans ; Child ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Body Mass Index ; Female ; *Bacteria/classification/genetics/isolation & purification ; *Body Height ; Spain ; },
abstract = {Body mass index (BMI) is frequently used to investigate associations between gut microbiota and nutritional status in children, although it primarily reflects adiposity and may not fully capture broader aspects of physiological development. Height-for-age z-score (HAZ), an indicator of linear growth, may provide complementary information on microbiota-host interactions during childhood. This exploratory cross-sectional study investigated associations between anthropometric indicators and gut microbiota composition in a cohort of healthy Spanish school-aged children. Forty-five children aged 8-12 years were included. Faecal microbiota composition was analysed by 16S rRNA gene sequencing, and associations with anthropometric variables were evaluated using correlation and multivariable regression analyses. The gut microbiota was dominated by Bacillota and Bacteroidota, with limited variability in overall community structure across the cohort. BMI-for-age was not associated with microbial diversity, taxonomic composition or the Bacillota/Bacteroidota ratio. In contrast, HAZ was negatively associated with the Bacillota/Bacteroidota ratio, and this association remained significant after adjustment for BMI-for-age. No significant differences in alpha or beta diversity were detected according to anthropometric indicators. These findings suggest a possible relationship between linear growth and gut microbiota composition in healthy children. Given the limited sample size and cross-sectional design, the results should be considered exploratory and hypothesis-generating. Further studies are needed to confirm these observations and clarify the potential role of gut microbial ecology in childhood growth.},
}

Humans
Child
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Male
*Gastrointestinal Microbiome
Feces/microbiology
Body Mass Index
Female
*Bacteria/classification/genetics/isolation & purification
*Body Height
Spain

@article {pmid42821345,
year = {2026},
author = {Oporto, CI and Saona, LA and Quintrel, P and Urbina, K and Benavides-Parra, J and Grene, F and Villarreal, P and Vianna, JA and Piper, FI and Nespolo, RF and Cubillos, FA},
title = {Climate-driven adaptive microevolution in wild yeasts.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {40},
pages = {e2618715123},
doi = {10.1073/pnas.2618715123},
pmid = {42821345},
issn = {1091-6490},
support = {1260075//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; NCN2024_040//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1261724//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; 21231009//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 3240351//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; FB210008//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; ICN17_022//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; },
mesh = {*Climate ; *Saccharomyces/genetics/physiology/classification ; Chile ; *Adaptation, Physiological/genetics ; *Biological Evolution ; Genetic Variation ; Genome, Fungal ; Phylogeny ; Phenotype ; },
abstract = {Environmental variation imposes strong selection on microbial populations, yet linking ecological gradients to genomic and phenotypic diversification remains challenging due to limited sampling of wild microbes. Here, we leveraged the exceptional abundance of the cold-adapted yeast Saccharomyces eubayanus throughout Patagonian Nothofagus forests to investigate how climatic gradients shape natural microbial diversity. Using systematic sampling across ~1,000 km of Chilean Patagonia, spanning multiple seasons, altitudes, and thermal regimes, we integrated environmental, genomic, and phenotypic analyses of wild populations inhabiting Nothofagus forests. Whole-genome sequencing of 117 isolates identified three major Patagonian lineages that show strong latitudinal structuring and contrasting levels of nucleotide diversity, with colder, wetter southern populations harboring the greatest diversity. Multivariate and permutation-based analyses consistently identified latitude, temperature, and precipitation as the primary correlates of genomic variation, together explaining over half of the observed patterns of nucleotide diversity. Notably, S. eubayanus exhibited an inverse latitudinal diversity gradient, contrasting with patterns commonly reported in Northern Hemisphere populations. Climatic structuring was mirrored by pronounced phenotypic differentiation: Southern populations exhibited lower thermal optima, enhanced cold fitness, and increased sporulation capacity, whereas northern populations displayed greater growth performance under nutrient-rich and hyperosmotic conditions. Sporulation capacity closely paralleled nucleotide diversity along the same environmental gradient, linking climate, reproductive investment, and population diversification. Together, our results indicate that climatic gradients simultaneously shape demographic history, physiological performance, metabolic strategies, and life-history traits in natural yeast populations. More broadly, Patagonia emerges as a powerful natural system for understanding how environmental heterogeneity drives microbial diversification across heterogeneous landscapes.},
}

*Climate
*Saccharomyces/genetics/physiology/classification
Chile
*Adaptation, Physiological/genetics
*Biological Evolution
Genetic Variation
Genome, Fungal
Phylogeny
Phenotype

@article {pmid42823524,
year = {2026},
author = {Karwautz, C and Griebler, C},
title = {Microbial ecology of shallow groundwater ecosystems.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42823524},
issn = {1740-1534},
abstract = {Below every step we take there is groundwater. Out-competing rivers, lakes and wetlands in terms of water quantity and quality, shallow aquifers are an essential reservoir of freshwater for the human population. At the same time, they represent the largest freshwater biome on earth, forming a responsive but vulnerable interface between the highly dynamic surface aquatic and terrestrial ecosystems and the environmentally static deeper zones of the subsurface. Shallow aquifers are home to a vast phylogenetic and functional microbial diversity, regularly surpassing those of surface environments. Predominantly colonized by microorganisms, key drivers of community composition and biogeochemical cycles are the hydrogeological settings, availability of energy and prevailing redox conditions, as well as climate and local to regional anthropogenic activities. Although there is steadily growing knowledge on microbial biodiversity and their potential functions, quantitative data on active key processes, such as carbon cycling, are scarce. We do have a very incomplete idea of the abundances and distribution of viruses, protists and fungi and their ecological role in groundwater. In this Review, we discuss current and future pressures to shallow groundwater ecosystems in terms of microbial community dynamics particularly in light of global and climate change, that is, groundwater pollution and warming.},
}

@article {pmid42828194,
year = {2026},
author = {Chen, Y and Li, S and Lin, H and Zou, F and Wang, W},
title = {The oral-amplifier hypothesis: linking oral inflammation to intestinal microbial activity in autism spectrum disorder.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1940902},
pmid = {42828194},
issn = {1664-302X},
abstract = {The oral-amplifier hypothesis proposes a testable sequence linking oral inflammation to intestinal microbial activity. Gingival or periodontal inflammation may alter the identity and quantity of strains released into saliva. Gastrointestinal conditions may then clear those strains, permit repeated passage, or support local activity. A participant-matched strain is an oral and intestinal population from the same person that meets prespecified genomic, coverage, and contamination criteria. The hypothesis predicts that greater inflammation-associated oral strain output will precede increased abundance or activity of the genomically matched intestinal strain. The lag is calibrated to the participant's measured gastrointestinal transit time. The first proposed study tests this lagged within-person relationship, termed source-to-activity coupling. It asks whether community resistance, mucosal immunity, and local resources modify the relationship's magnitude, delay, or persistence. The second proposed study is a controlled oral-health intervention in which reduced gingival inflammation must accompany a verified reduction in candidate-strain salivary output. It then tests whether matched intestinal activity declines after that verified source reduction. ASD is methodologically informative because oral-care needs, diet, medication exposure, gastrointestinal symptoms, immune state, and transit time may vary together within individuals. This variation provides measurable contrasts for testing oral output and gastrointestinal filtering but does not make the mechanism ASD-specific or causal in ASD. Together, the two proposed studies test whether increased oral output precedes transit-calibrated matched intestinal activity and verified source reduction produces downstream decline. Concordance would support a reversible, strain-specific oral contribution, whereas failure of either temporal pattern would constrain or refute the hypothesis.},
}

@article {pmid42828306,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {From predicted bacteriocins to ecological function.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100662},
pmid = {42828306},
issn = {2666-5174},
abstract = {Genome and metagenome mining have uncovered large repertoires of predicted bacteriocin loci, but ecological interpretation has lagged behind discovery. This review uses bacteriocins as a focused model for a broader problem in antimicrobial gene prediction: sequence identifies encoded potential, but it does not establish expression, product deployment, target engagement, or community-level consequence. We distinguish four forms of bacteriocin "silence": transcriptional silence, where loci are not detectably expressed under tested conditions; conditional silence, where expression or activity emerges only under specific environmental or social cues; phenotypic silence, where expression or product formation does not yield detectable activity in routine assays; and ecological silence, where activity is observed but its consequences for coexistence, exclusion, colonization, or community assembly remain unresolved. We also clarify how this framework extends previous reviews of bacteriocin diversity and microbiome-shaping roles by providing an inference-centered taxonomy that separates encoded potential from demonstrated ecological function. Finally, we propose a function-first roadmap for bacteriocin research, including condition-resolved transcriptomics and proteomics, promoter and cue-dissection experiments, expanded target panels, spatially structured assays, defined consortia and microcosms, producer/non-producer comparisons, and explicit tests of resistance, immunity, and fitness consequences. Treating predicted bacteriocin loci as hypotheses rather than conclusions will improve how the field moves from gene catalogs to causal ecological understanding.},
}

@article {pmid42828642,
year = {2026},
author = {Balabat, MTJ and Loquero, EJ and Amer, NB and Coñado, JC and Cabolbol, HJB and Romarate, RA and Mabuhay-Omar, J and Watanabe, K and Chien, MF and Bacosa, HP},
title = {Urban Road Dust as a Microbial Hotspot: Spatial Variation of Bacterial Communities and Metal Associations in the Philippines.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828642},
issn = {1573-0972},
mesh = {*Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Philippines ; *Dust/analysis ; Cities ; *Metals/analysis ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; Environmental Monitoring ; Phylogeny ; Soil Microbiology ; },
abstract = {Urban road dust is a reservoir and transport medium for diverse microorganisms, yet its bacterial communities in tropical environments remain poorly understood. This study examined the spatial variation of road dust bacterial communities across three Philippine metropolitan areas: Metro Manila, Metro Cebu, and Metro Cagayan de Oro, spanning the country's three principal island groups. Dust from nine sites was analyzed using 16 S rRNA gene metabarcoding (V3-V4), with community composition, diversity, predicted functional potential (PICRUSt2), and metal associations evaluated; contamination was assessed using pollution indices (PLI, degree of contamination, and ecological risk). Proteobacteria and Actinobacteria dominated all sites, and a small core of genera: Paracoccus, Acinetobacter, Kocuria, and Deinococcus, was consistently detected. Alpha diversity did not differ among cities (Kruskal-Wallis, p > 0.05), whereas community composition did (PERMANOVA: R[2] = 0.466, p = 0.004), with distinct metropolitan clustering. This decoupling indicates that local conditions shape which taxa dominate rather than overall diversity, consistent with environmental filtering of a shared regional pool. Alkanindiges reached its highest relative abundance at Metro Cebu's commercial core. In Metro Cagayan de Oro, Paracoccus increased toward the most trace-metal-laden site (D3) and correlated positively with cobalt and nickel; with elevated predicted denitrification in this area, this points to a possible pollution-responsive signal. Metro Cagayan de Oro also showed a pronounced higher relative abundance of Chloroflexi, marking it as a distinctive, transitional urban environment. Pollution indices indicated baseline-to-moderate contamination across the sampled roadsides. Predicted function paralleled taxonomy (R[2] = 0.467). These findings establish a baseline for tropical road-dust microbiota and support integrating microbial assessment into urban environmental monitoring.},
}

*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Philippines
*Dust/analysis
Cities
*Metals/analysis
*Microbiota
Biodiversity
DNA, Bacterial/genetics
Environmental Monitoring
Phylogeny
Soil Microbiology

@article {pmid42813815,
year = {2026},
author = {Schloss, PD},
title = {Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093026},
doi = {10.1128/msystems.00930-26},
pmid = {42813815},
issn = {2379-5077},
abstract = {UNLABELLED: Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial ecology literature. Historically, rarefaction has been used in ecology and this practice was adopted by microbial ecologists. However, rarefaction has been strongly criticized, leading to the development of compositional data analysis and normalization methods. Therefore, I reassessed the benchmarking data that were generated by the developers of one such method, robust Aitchison PCA. I found numerous problems in the Python code that led to the support of robust Aitchison PCA. These problems extended to the creation of simulated data sets, implementation of machine learning methods, and choice of analysis parameters. Furthermore, the analysis of the simulated and case study data sets was done in a manner that was foreign to standard microbiome analyses. I corrected the problems in the original code, added data sets with smaller effect sizes, and expanded the collection of methods that purport to correct for uneven sequencing effort. Contrary to the claims of the original analysis, robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. In fact, even using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods, and other normalization methods. Rarefaction remains the preferred method of controlling for uneven sampling effort in amplicon sequence studies.

IMPORTANCE: Efforts to connect the structure of microbial communities with environmental processes and host health have captured widespread interest among scientists and the general public. The methods used to generate the sequencing data that are fundamental to these efforts result in wide variation in the number of sequences per sample. This variation and how to account for it can have detrimental effects on the ability to draw valid conclusions. Compositional data analysis methods, including robust Aitchison principal component analysis (PCA), have grown in popularity for mitigating these effects and have been proposed as alternatives to rarefaction. In this study, I reviewed and fixed the code that was used to benchmark robust Aitchison PCA and expanded the analysis. With this improved and expanded analysis, I found that rarefaction was still superior to robust Aitchison PCA and other methods of controlling for uneven sequencing effort.},
}

@article {pmid42813894,
year = {2026},
author = {Usmani, MW and Shakir, MZ and Khan, MA and Usman, M and Ullah, I and Mengjie, Y and Wang, N and Liu, X},
title = {Microglial State Reprogramming Across the Gut-Brain-Immune Axis: Limitations and Therapeutic Prospects of Traditional Chinese Medicine.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70060},
doi = {10.1002/dneu.70060},
pmid = {42813894},
issn = {1932-846X},
support = {2023AA503//NGHJG project of Xinjiang Production and Construction Crops/ ; 215-432094250//Ningbo Top Talent Project/ ; H2024000279//Health Fund of Translational Biomedicine/ ; },
mesh = {Humans ; Animals ; *Microglia/immunology/drug effects/physiology ; *Medicine, Chinese Traditional/methods ; *Brain/immunology/drug effects ; *Gastrointestinal Microbiome/physiology ; *Neuroimmunomodulation/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Bidirectional communication among the gut microbiota, immune system, and central nervous system shapes microglial maturation and responsiveness. This review evaluates microglia as context-dependent neuroimmune integrators rather than fixed M1/M2 populations. It organizes the literature into three linked layers: gut-derived signals and barrier physiology, microglial state transitions, and therapeutic modulation by Traditional Chinese Medicine (TCM). Experimental depletion, colonization, and metabolite studies provide causal evidence that the microbiota can modify microglial biology in animals; however, human evidence remains predominantly associative. Herbal formulations, isolated constituents, and acupuncture may alter microbial ecology, intestinal permeability, metabolite production, systemic inflammation, and microglial signaling. Yet most intervention studies measure only selected links in this chain and rely on rodent behavior, bulk cytokines, or limited polarization markers rather than direct, state-resolved microglial profiling. Therefore, improvements in cognition or inflammatory markers cannot by themselves, establish microbiota-mediated microglial reprogramming. We critically distinguish direct from indirect evidence, replace binary polarization language with state-specific terminology, and evaluate formulation standardization, bioavailability, safety, experimental confounding, and clinical generalizability. A credible translational program will require chemically defined interventions, causal perturbation of candidate microbes or metabolites, microglia-resolved multi-omics, preregistered clinical trials, and mediation analyses that connect target engagement to patient-relevant outcomes. TCM is thus best regarded as a testable source of multicomponent interventions, not yet a validated systems-level therapy for the gut-brain-immune axis.},
}

Humans
Animals
*Microglia/immunology/drug effects/physiology
*Medicine, Chinese Traditional/methods
*Brain/immunology/drug effects
*Gastrointestinal Microbiome/physiology
*Neuroimmunomodulation/physiology
*Brain-Gut Axis/physiology

@article {pmid42816582,
year = {2026},
author = {Chang, J and Wang, D and Yao, Z and Pang, Y and Zhang, H and Wang, C and Xie, Y and Sun, Y and Zhang, J and Li, W and Liang, A and Li, X and Chen, D and Chen, H and Chen, X and Wang, E and Tran, LP and Wang, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42816582},
issn = {2058-5276},
support = {32401436//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024YFD1501004//National Natural Science Foundation of China (National Science Foundation of China)/ ; U22A20593//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M753212//China Postdoctoral Science Foundation/ ; },
abstract = {Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.},
}

@article {pmid42818759,
year = {2026},
author = {Lu, Y and Zhang, M and Jiang, S and Zhang, S and Chen, Z and Wang, J and Liu, L and Wang, P and Gao, X},
title = {Qijiao Shengbai capsule ameliorates ulcerative colitis in mice by modulating gut microbiota and protecting the intestinal barrier, associated with suppression of the TLR4/MyD88/NF-κB pathway.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875650},
pmid = {42818759},
issn = {1664-302X},
abstract = {BACKGROUND: Qijiao Shengbai capsule (QJSB) is a classic traditional Chinese compound formulation composed of seven herbal ingredients, primarily used clinically to treat leukopenia. Individual herbs and their active components within QJSB demonstrate favorable efficacy against ulcerative colitis (UC). Nevertheless, no evidence exists of QJSB being a full-form prescription for treating UC.

METHODS: This study identified the chemical composition of QJSB using UHPLC-ESI-Q-Exactive Plus Orbitrap-MS. At the same time, a mouse model of ulcerative colitis (UC) was established using DSS to examine the effects of QJSB on disease symptoms, inflammatory factors, intestinal barrier function, and colonic histopathological changes. Furthermore, metabolomics, 16S rRNA sequencing, and network pharmacology were combined to analyze the potential mechanisms underlying the effects of QJSB intervention in UC-affected mice, and key pathways predicted by network pharmacology were validated using Western blot analysis.

RESULTS: The results showed that QJSB treatment significantly alleviated DSS-induced colitis symptoms in UC mice, as evidenced by weight recovery, a decrease in the disease activity index (DAI), improvement in colonic shortening, and reduced tissue damage. Gut microbiota analysis indicated that QJSB modulates the composition of the gut microbiota by upregulating the abundance of Akkermansia and Lactobacillus and downregulating the abundance of Bacteroides. Metabolomics results suggest that QJSB may help correct metabolic disturbances involving amino acids, linoleic acid, arachidonic acid, and alpha-linolenic acid. Furthermore, QJSB was associated with reduced levels of pro-inflammatory factors (TNF-α, IL-6, IL-1β), lipopolysaccharide (LPS), and myeloperoxidase (MPO), as well as improved intestinal barrier function. Western blot results suggest that QJSB intervention may be associated with the suppression of TLR4/MyD88/NF-κB signaling pathway activation.

CONCLUSION: The present findings suggest that QJSB may exert therapeutic effects against UC, potentially through mechanisms involving the inhibition of inflammatory responses, protection of intestinal barrier function, regulation of metabolic homeostasis, and restoration of gut microbial ecology. These results imply that QJSB could serve as a potential therapeutic candidate for UC and provide a new basis for its clinical application.},
}

@article {pmid42820214,
year = {2026},
author = {Sola, M and Paravel, A and Auger, S and Chatel, JM and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Veiga, P and Frioux, C and Mariadassou, M and Berland, M},
title = {NeighborFinder: an R package inferring local microbial network around a species of interest.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag201},
pmid = {42820214},
issn = {2635-0041},
abstract = {MOTIVATION: Understanding interactions from microbiome data is a central aspect in microbial ecology, as it provides insights into ecosystem stability, disease mechanisms, and can be used to design synthetic communities. Current network inference tools reconstruct global networks from co-abundance data, which means they capture the overall correlation structure for the entire set of taxa considered. These approaches are computationally intensive and suboptimal when the focus is on the local neighborhood of one or a few taxa of interest.

RESULTS: We introduce NeighborFinder, a local network inference method that enables the targeted discovery of direct neighbors around a species of interest. Using cross-validated multiple linear regression with ℓ 1 penalty and microbiome-specific filters, our approach infers interpretable species-centered interactions, with F1 score ≥ 0.95 on simulated cohorts ranging from 250 to 1000 samples. This method is well-suited for large metagenomic datasets and is particularly valuable for exploratory studies where the targeted hypotheses outweigh the need for global community structure. The approach complements existing methods by being biologically intuitive and computationally efficient.

The R package is available on CRAN https://CRAN.R-project.org/package=NeighborFinder. The data and source code used to calculate performances and produce the use case example can be found respectively at: https://doi.org/10.57745/UPITJ0 and https://doi.org/10.57745/HJLWW4.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}

@article {pmid42807077,
year = {2026},
author = {Wojciechowska, D and Salamon, S and Banachewicz, P and Przemieniecki, S and Kosewska, O and Błaszczyk, L and Szczapa, T and Wróblewska-Seniuk, K},
title = {Fungal DNA profiles across maternal and neonatal biological sites: findings from an exploratory pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869806},
pmid = {42807077},
issn = {1664-302X},
abstract = {BACKGROUND: The neonatal mycobiome remains an underexplored component of early-life microbial ecology. Although fungi may contribute to immune maturation and host-microbe interactions, fungal DNA profiles across maternal and neonatal body sites are poorly characterized. This exploratory pilot study aimed to characterize fungal DNA profiles across multiple maternal and neonatal biological compartments during early life.

MATERIALS AND METHODS: Ten mother-infant dyads were enrolled at ≥37 weeks' gestation. Three focal dyads (one complete and two near complete) were selected for detailed mycobiome sequencing, while additional breast milk samples expanded the dataset to 30 analyzed specimens. Maternal (vaginal, rectal, breast milk) and neonatal (skin, oral cavity, stool) samples were collected at 48-72 h after delivery and 6 weeks postpartum. Fungal DNA was analyzed using Oxford Nanopore long-read 18S rRNA sequencing. Taxonomic classification was performed with Kraken2 using the NCBI RefSeq Targeted Loci fungal 18S rRNA database. Alpha- and beta-diversity analyses were conducted in R using the phyloseq package.

RESULTS: A total of 428,555 fungal reads representing 107 genus-level operational taxonomic features were retained. Fungal DNA profiles differed across biological sites, with a greater relative abundance of Malassezia in neonatal skin and more heterogeneous profiles in gastrointestinal-associated samples. Alpha diversity did not differ significantly between sampling sites, whereas beta diversity suggested exploratory site-associated differences in community composition. Richness-based metrics were higher at 6 weeks than during early sampling, although this trend was not robust after accounting for sequencing depth, and beta-diversity analyses showed no clear temporal shift. Because negative controls were not sequenced, contamination from laboratory or reagent-derived fungal DNA cannot be excluded, and the findings should not be interpreted as evidence of viable fungi or stable colonization.

CONCLUSION: This exploratory pilot study suggests that fungal DNA profiles differ across maternal and neonatal body sites and that detectable fungal richness may increase by 6 weeks postpartum, although this finding was not robust to sequencing depth. Larger longitudinal studies incorporating ITS-based sequencing, strain-level analyses, sequenced technical controls, and functional profiling are needed to validate these observations and clarify the biological significance of early-life fungal communities.},
}

@article {pmid42809046,
year = {2026},
author = {Dwivedi, S and Kumar, A and Upreti, D},
title = {Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42809046},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Multiomics ; Biomarkers ; *Cattle Diseases/genetics/diagnosis ; Genomics ; },
abstract = {Bovine diseases arise from dynamic interactions among genetic susceptibility, regulatory responses, immune activity, metabolism, microbial ecology and tissue function. Although individual omics studies have identified numerous disease-associated molecular signatures, many remain context-dependent and poorly reproducible across animals, breeds, disease stages and biological matrices. Integrative multi-omics extends beyond parallel profiling of individual molecular layers by connecting genomic variation with epigenetic regulation, transcriptional activity, protein and metabolite states, and microbial ecology to reconstruct coordinated mechanisms underlying disease development and recovery. This review synthesizes integrative multi-omics data across a trajectory from pre-disease vulnerability through active disease to persistence or functional recovery, while examining ecological destabilization as a process that may arise at different points along this continuum. Across diseases, integration of multiple molecular layers identifies recurrent associations among genetic regulation of disease-response pathways, inflammatory activation, immune-metabolic and redox imbalance, tissue-barrier dysfunction and microbiome-metabolite feedback. These interacting processes have the potential to provide greater biological and predictive information than isolated molecular alterations. We therefore propose that robust biomarker development should prioritize reproducible cross-omics signals and compact panels integrating three complementary components: disease burden or causal trigger, host-response state and functional consequence. Such biomarkers require validation across independent populations, breeds, disease stages and field conditions before clinical deployment. By linking molecular layers rather than cataloguing individual signatures, multi-omics can support more reliable disease prediction, mechanistically informed diagnostics, targeted intervention and selection for improved disease resistance and resilience in cattle.},
}

Animals
Cattle
*Multiomics
Biomarkers
*Cattle Diseases/genetics/diagnosis
Genomics