@article {pmid42252506,
year = {2026},
author = {Galtier, A and Warinner, C and Velsko, IM},
title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag136},
pmid = {42252506},
issn = {1759-6653},
abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.},
}

@article {pmid42252693,
year = {2026},
author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W},
title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag145},
pmid = {42252693},
issn = {1751-7370},
abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.},
}

@article {pmid42252762,
year = {2026},
author = {Ahsan, M and Afzoon, S and Nandni, and Ahmed, A and Mubashirah, and Priyanka, and Rahman, HU and Arif, AR and Faiz, A and Mirza, I and Bhatt, N},
title = {Chronic Kidney Disease and the Gut Microbiota: An Expanding Confluence in the Development of the Disease.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70192},
doi = {10.1002/cph4.70192},
pmid = {42252762},
issn = {2040-4603},
abstract = {PURPOSE: Chronic kidney disease (CKD) remains a major global health burden despite advances in conventional therapies. This review synthesizes current clinical and experimental evidence on the bidirectional relationship between CKD and gut microbial dysbiosis, emphasizing mechanisms, measurable outcomes, and therapeutic interventions.

METHODS: A narrative review of recent clinical and experimental studies was conducted to explore alterations in gut microbial composition, generation of uremic toxins, and the impact of CKD therapies on microbial balance. Emerging microbiota-targeted interventions were also examined.

RESULTS: Studies consistently report reduced microbial diversity, loss of short-chain fatty acid (SCFA)-producing taxa, and enrichment of proteolytic, toxin-producing bacteria in CKD. Gut-derived metabolites such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and trimethylamine N-oxide (TMAO) are linked to oxidative stress, RAAS activation, and fibrogenesis. In human trials, microbiota-directed therapies show modest biochemical benefits: a meta-analysis of 21 randomized studies reported mean reductions in serum BUN (8.5 mg/dL) and CRP (1.4 mg/L) with probiotic or synbiotic supplementation, while inulin (10 g/day) in stage 3-4 CKD reduced serum pCS by 25% and increased fecal butyrate by 40%. However, most mechanistic data derive from animal and in vitro models, and human evidence remains heterogeneous and underpowered. Stage-specific differences are evident-early CKD shows subtler dysbiosis, while advanced CKD and dialysis populations exhibit profound microbial shifts and variable responsiveness.

CONCLUSION: The gut microbiota is a promising, modifiable contributor to CKD pathophysiology. Stage-stratified longitudinal studies are needed to establish causality and therapeutic efficacy.},
}

@article {pmid42252802,
year = {2026},
author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M},
title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {3},
pages = {e70324},
doi = {10.1002/jcsm.70324},
pmid = {42252802},
issn = {2190-6009},
support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; },
abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).},
}

@article {pmid42252976,
year = {2026},
author = {Unno, T},
title = {16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {5},
pages = {e2603014},
doi = {10.71150/jm.2603014},
pmid = {42252976},
issn = {1976-3794},
support = {RS-2025-02633155//Rural Development Administration/ ; },
abstract = {16S rRNA gene amplicon sequencing is the most widely used approach for characterizing microbial communities, yet analyzing such data requires navigating a fragmented landscape of bioinformatics tools with distinct installation requirements, parameter settings, and data formats. Here we present 16S-Pipeline, an open-source, web-based platform that provides a complete workflow from raw FASTQ files to publication-ready statistical analyses. 16S-Pipeline automatically detects sequencing type (paired-end, single-end, long-read), variable region, and sequencing platform (Illumina, PacBio HiFi, Nanopore), then performs quality filtering, primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy assignment against SILVA v138.1, phylogenetic tree construction, and optional functional prediction via PICRUSt2. Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping. Built-in NCBI SRA integration enables downloading public datasets for re-analysis and generates submission metadata spreadsheets for data deposition. The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License.},
}

@article {pmid42253015,
year = {2026},
author = {Wang, Z and Pu, R and Gao, B and Cai, W and Yang, G},
title = {Oral microbiota associated with tooth loss and cognitive function in older adults: Evidence from NHANES.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70154},
pmid = {42253015},
issn = {1943-3670},
support = {82271001//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The aim of this study is to investigate the association between tooth loss and cognitive decline and to explore the potential role of salivary microbial genera in this relationship in a nationally representative population.

METHODS: Data from 1,413 adults aged ≥ 60 years in NHANES 2011-2012 were analyzed. Cognitive function was assessed using the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) Word Learning Tests, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test (DSST). Salivary microbiome profiles were obtained from a subsample of 661 participants using 16S rRNA sequencing. Complex survey regression, PERMANOVA, and multivariable microbial association analyses were applied. Mediation analyses were conducted as exploratory analyses to evaluate potential microbial pathways linking tooth loss with cognitive outcomes.

RESULTS: Moderate tooth loss was associated with higher odds of low global cognition (OR = 2.91, 95%CI: 2.01-4.23), low AFT (OR = 1.57, 95%CI: 1.03-2.39), and low DSST (OR = 2.15, 95%CI: 1.47-3.16) after adjustment. Sixteen genera were associated with at least one cognitive metric, including Prevotellaceae_NA, Phocaeicola, and Lactobacillus. In exploratory mediation analyses, three organic acid-producing genera (Lactobacillus, Lachnospiraceae_NA, and Leptotrichiaceae_NA) were identified as potential contributors to the association between tooth loss and cognition.

CONCLUSION: Tooth loss was associated with cognitive decline in older adults, and both conditions were accompanied by differences in salivary microbial composition. Exploratory mediation analyses suggested that certain organic acid-producing taxa may contribute to the observed association.

PLAIN LANGUAGE SUMMARY: Tooth loss is common in older adults and has been linked to problems with memory and thinking, but the reasons for this connection are not fully understood. In this study, we used data from a large national health survey of adults aged 60 years and older to examine tooth loss, results from several cognitive tests, and the types of bacteria found in saliva. We found that older adults with more missing teeth were more likely to perform poorly on tests measuring memory, attention, and processing speed. We also observed that some types of oral bacteria were related to both tooth loss and cognitive performance. In exploratory analyses, several groups of bacteria that produce organic acids were linked to the relationship between tooth loss and cognitive outcomes. These findings suggest that differences in the oral microbial community may be one of several biological pathways connecting oral health and cognitive function. Understanding how oral health, diet, and oral bacteria interact may help researchers better understand factors related to cognitive aging and to identify potential targets for future research and prevention strategies.},
}

@article {pmid42253256,
year = {2026},
author = {Suchday, P and Dhabuwala, A and Adrejiya, P and Bajpai, P and Shingala, TS and Prajapati, K and Patel, V and Nunna, K and Desai, R},
title = {The Role of Firmicutes in Coronary Artery Disease: A Taxonomic-Level Meta-Analysis of Mendelian Randomization Studies.},
journal = {Current cardiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/011573403X432303260316044935},
pmid = {42253256},
issn = {1875-6557},
abstract = {INTRODUCTION/OBJECTIVE: The Gut Microbiome (GM) plays a critical role in cholesterol metabolism through the production of metabolites such as trimethylamine N-oxide and shortchain fatty acids, contributing to inflammation, endothelial dysfunction, and host gene regulation. This study aims to taxonomically characterize gut microbial profiles, evaluate their association with coronary artery disease, and explore the potential therapeutic implications of microbiome- mediated cardiometabolic pathways.

METHODS: We pooled data from six Mendelian Randomization studies that utilized the MiBio- Gen consortium and CAD, and cardiovascular risk GWAS data from CARDIoGRAMplusC4D, FinnGen, and UK Biobank databases. Within the phylum Firmicutes, inverse variance weighted analysis was used to estimate the association between: (1) protective effects of Clostridiales vadinBB60 group, Genus Butyricicoccus, Genus Ruminococcus UCG010, Coprococcus 1, Intestinibacter, Ruminiclostridium 6, Anaerotruncus, and Family Acidaminococcaceae; and (2) causative effects of Clostridium innocuum group, Genus Turicibacter, Eisenbergiella, Holdemanella, Eubacterium, Coprostanoligenes group, Ruminococcaceae UCG005, and Genus Catenibacterium on CAD.

RESULTS: Higher levels of phylum Firmicutes exhibit a statistically significant protective effect on CAD (OR: 0.880, 95% CI: 0.853-0.907), with low heterogeneity (I² = 20%, P = 0.857). Conversely, an increased abundance of Firmicutes also correlates with a higher risk of CAD (OR: 1.10, 95% CI: 1.06-1.14), showing low heterogeneity (I² = 20%, P = 0.90). Leave-one-out sensitivity analyses confirmed the robustness of these results.

DISCUSSION: The findings highlight a significant relationship between gut microbiome dysbiosis and adverse cardiometabolic outcomes, potentially mediated through inflammatory pathways, metabolic signaling, and microbial metabolite production. These results support the growing role of microbiome-targeted interventions as emerging strategies for cardiometabolic risk modification.

CONCLUSION: Firmicutes exhibit both protective and causative effects on CAD. These findings highlight the complexity of the gut microbiome's role in cardiovascular diseases. Further detailed research on the mechanisms by which specific bacteria at the lower taxonomic levels exert this effect is imperative to understand this complex relationship and its clinical implications.},
}

@article {pmid42253936,
year = {2026},
author = {Wetzel, S and Kohnert, E and Huber, R and Müller, A and Knott, A and Kousoulas, L and Kreutz, C and Badr, MT and Lederer, AK},
title = {Divergent Resilience of Bacterial and Fungal Gut Microbiota After Colorectal Surgery: Insights From a Prospective Longitudinal Cohort Study.},
journal = {MedComm},
volume = {7},
number = {6},
pages = {e70781},
pmid = {42253936},
issn = {2688-2663},
abstract = {The composition of the gut microbiota changes throughout life and is shaped by various external influences, particularly major physiological stressors such as surgery. The extent of these changes and their impact remain poorly understood. This prospective cohort study aimed to investigate changes in the gut microbiota following colorectal surgery and to identify factors that modify these alterations. Paired pre- and postoperative stool samples from 59 patients at the University Medical Centre Freiburg were analyzed using 16S rRNA and ITS2 gene sequencing. Analyses included alpha and beta diversity, LEfSe differential feature analysis, network analysis with Louvain clustering, KEGG pathway annotation, and correlation with clinical parameters. Bacterial diversity significantly decreased postoperatively (Shannon index: p < 0.001), while fungal diversity remained largely unchanged (p > 0.05). Beta diversity revealed increased inter-patient variability in bacterial communities after surgery (PERMANOVA p = 0.001). Preoperative network analyses identified 18 microbial network clusters and interkingdom associations between bacteria and fungi. KEGG pathway mapping showed cluster-specific metabolic profiles, including enrichment in degradation pathways, antimicrobial resistance mechanisms, and bacterial secretion systems. The contrasting responses of bacterial and fungal communities highlight the importance of considering the entire gut microbiome in perioperative care and suggest a central role for interkingdom interactions in maintaining gut homeostasis during surgical recovery.},
}

@article {pmid42253941,
year = {2026},
author = {Yu, R and Zhang, M and Meng, Y and Zhu, C and Zhang, W and Zhang, H and Cao, Z and Du, M and Zhao, Z and Bai, J and Han, Y and Tang, Y and Kang, W and To, KF and Jiao, S and An, L and Zhou, Z},
title = {Gastric Cancer: Pathobiology and Therapeutics.},
journal = {MedComm},
volume = {7},
number = {6},
pages = {e70772},
pmid = {42253941},
issn = {2688-2663},
abstract = {Gastric cancer (GC) remains a formidable global health challenge, characterized by pronounced molecular heterogeneity, late-stage diagnosis, and limited durable responses to existing therapies. This review synthesizes recent advances in GC research through an integrated, multidisciplinary lens, spanning tumor biology, microenvironmental dynamics, and therapeutic innovation. We first consolidate updated histopathological and molecular classification systems, highlighting oncogenic programs that underpin GC development, including Hippo-YAP signaling and emerging neural-stem cell interactions. We then examine the immunosuppressive tumor microenvironment, emphasizing the dynamic crosstalk among tumor-associated macrophages, regulatory T cells, tertiary lymphoid structures, and cancer-associated fibroblasts that collectively drive metastatic dissemination and therapeutic resistance. Emerging biomarker-guided strategies, including CLDN18.2-targeted therapies, dual immune checkpoint blockade, and engineered cellular therapies, are critically discussed alongside rational combination approaches designed to overcome resistance. Beyond canonical paradigms, we highlight transformative frontiers, such as cancer neuroscience, microbiome-driven immune modulation, and spatially resolved multiomics technologies, that enable high-resolution mapping of cellular interactions. Finally, we critically assess translational barriers, including organ-specific metastatic tropism and resistance evolution, and propose that the convergence of deep molecular profiling, neural-immune modulation, and AI-enabled computational oncology will be central to advancing precision medicine for GC. This integrated framework aims to accelerate the development of mechanism-based combination therapies.},
}

@article {pmid42253950,
year = {2026},
author = {Han, X and Guo, XL and Qiu, J},
title = {From gut-reproductive microbiota to ferroptosis: a comprehensive insight into the molecular-pathogenicity of endometriosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1762013},
pmid = {42253950},
issn = {1664-3224},
abstract = {Endometriosis (EMS) is a highly heterogeneous chronic gynecological disease characterized by pain, infertility, and relapse, with its etiology and pathogenesis not yet fully elucidated. Traditional theories, including "retrograde menstruation," "implantation theory," and "abnormalities in immune tolerance," struggle to adequately explain the complex lesion behavior, diverse phenotypic characteristics, and accompanying immune-metabolic disorders. In recent years, the key roles of imbalances in the gut and reproductive microbiomes, abnormal iron metabolism, and the newly proposed ferroptosis in the occurrence and development of EMS have gradually gained attention, suggesting that this disease may be a systemic condition involving the interplay of microbial ecology, iron metabolism, and cell death. Existing studies indicate that the gut-reproductive microbiome profoundly influences the body's iron homeostasis and iron load by regulating mucosal immunity, systemic inflammatory responses, and metabolic environments. This, in turn, activates the ferroptosis pathway through iron-dependent lipid peroxidation and cell membrane damage, participating in the formation, maintenance, and inflammatory microenvironment shaping of ectopic lesions. Based on these findings, this article systematically reviews the interactions between gut-reproductive microbiome imbalance and iron metabolism disorders, integrating multi-omics evidence such as microbiome analysis, metabolomics, and iron metabolism/ferroptosis-related molecular markers. It proposes a new pathological mechanism framework of "dysbiosis-iron overload-ferroptosis" incorporating microecological imbalance and ferroptosis into a unified picture of the pathogenesis of EMS. Furthermore, this article discusses potential therapeutic strategies and application prospects surrounding microbiome remodeling (such as probiotics, fecal microbiota transplantation, dietary and lifestyle interventions) and pharmacological targeting of key ferroptosis-related molecules. Through a comprehensive and critical analysis of existing evidence, this review aims to provide a more systematic theoretical framework for the mechanistic research of EMS and offer ideas and directions for future clinical translation of precise classification, individualized intervention, and novel treatment plans.},
}

@article {pmid42253968,
year = {2026},
author = {Feng, P and Zhang, W and Zhao, Y and Zhao, P and Li, E},
title = {Synthetic microbial communities: a novel emerging models for dissecting gut microbiota-host interactions in neurodegenerative diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1822743},
pmid = {42253968},
issn = {1664-3224},
abstract = {The gut-brain axis (GBA) has emerged as a critical regulatory pathway underlying the pathogenesis of neurodegenerative diseases (NDs) such as Alzheimer's disease and Parkinson's disease. However, the high complexity and individual variability of native gut microbiotas hinder the precise elucidation of causal relationships between specific microbial taxa, their metabolites, and host neuroinflammatory or neurodegenerative processes. Synthetic microbial communities (SynComs), consisting of defined and reproducible bacterial strains, have recently emerged as powerful experimental models to overcome these limitations. This review summarizes the applications of SynComs in dissecting GBA crosstalk in NDs, highlighting their utility in validating key microbial mediators, deciphering molecular signaling pathways (e.g., microbial metabolite-brain barrier interactions, immune cell activation), and evaluating therapeutic strategies targeting the gut microbiota. By reducing community complexity while retaining core functional traits, SynComs enable controlled in vitro and in vivo studies that bridge the gap between observational microbiome profiling and mechanistic insights. Furthermore, the customization of SynComs allows for mimicking disease-specific microbial dysbiosis, facilitating the identification of novel therapeutic targets for NDs. Collectively, SynComs represent an innovative and standardized tool to advance our understanding of gut microbiota-host interactions in neurodegeneration and accelerate the development of microbiome-based interventions.},
}

@article {pmid42254101,
year = {2026},
author = {Khan, SA and Qamar, MA and Ali, T and Omer, MH and Tahir, A},
title = {Reconsidering immunotherapy resistance: the emerging role of the tumor microbiome in head and neck and lung cancers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3812-3814},
pmid = {42254101},
issn = {2049-0801},
abstract = {Immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized treatment for non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC), yet resistance limits durable responses in many patients. Emerging evidence implicates the intratumoral microbiome - comprising bacteria, fungi, and viruses within tumor tissues - as a key modulator of tumor biology, immune infiltration, and ICI sensitivity, beyond traditional tumor-intrinsic and immune factors. In HNSCC, human papillomavirus (HPV)-negative tumors exhibit higher oncobacteria abundance than HPV-positive ones, with elevated levels linked to worse survival in HPV-positive oropharyngeal cases, suggesting an immunosuppressive tumor microenvironment that may influence ICI outcomes. In NSCLC, intratumoral taxa such as Fusobacterium nucleatum and Bacteroides fragilis promote progression and evasion via immune checkpoint modulation (PD-1/PD-L1), pro-inflammatory pathways (toll-like receptors and cytokines like interleukin-6/tumour necrosis factor-alpha), metabolic reprogramming (PI3K/AKT), and recruitment of suppressive cells (neutrophils and myeloid-derived suppressor cells). Pan-cancer studies show microbial enrichments and compositional shifts in responders versus non-responders to ICI, with metabolites (e.g., lactate and succinic acid) driving M2 macrophage polarization, T-cell suppression, and resistance. The gut-tumor axis further exacerbates refractoriness through systemic dysbiosis and immune alterations. Preclinical models indicate that targeted microbiome interventions - such as fecal microbiota transplantation, specific probiotics (e.g., Bifidobacterium spp. and Akkermansia muciniphila), or selective antibiotics - can restore antitumor immunity, enhance ICI efficacy, and minimize broad dysbiosis risks. Integrating intratumoral microbial profiling into HNSCC and NSCLC clinical trials could refine patient stratification, uncover predictive biomarkers, and accelerate microbiome-directed adjunct therapies, advancing precision oncology and expanding immunotherapy benefits.},
}

@article {pmid42254119,
year = {2026},
author = {Sanan, A and Bibi, F and Sadat, SH},
title = {Rare co-existence of rodent-borne arenavirus patterns and autoimmune-like systemic flares: novel microbiome markers for public health risk stratification.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3901-3902},
pmid = {42254119},
issn = {2049-0801},
}

@article {pmid42254157,
year = {2026},
author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A},
title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3348-3359},
pmid = {42254157},
issn = {2049-0801},
abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.},
}

@article {pmid42254190,
year = {2026},
author = {Wu, X and Cai, S and Bai, Z and Li, P and Jia, Y and Li, J},
title = {Association between the oral microbiota and hyperlipidemia: evidence from a national cross-sectional study.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3129-3141},
pmid = {42254190},
issn = {2049-0801},
abstract = {BACKGROUND: Oral and gut microbiota interact in the pathogenesis of metabolic diseases. However, the associations between the oral microbiome and host lipid metabolism remain unclear. This study aimed to explore the relationship between metabolic syndrome and the oral microbiome.

METHODS: Participants from the 2009-2012 National Health and Nutrition Examination Survey database were analyzed. Correlations between alpha diversity and hyperlipidemia, as well as blood lipid levels, were examined. Principal coordinate analysis and permutational multivariate analysis of variance were used to determine differences in microbial composition between groups. Linear discriminant analysis effect size (LEfSe) analysis identified key microbial taxa associated with hyperlipidemia. Cox regression and Kaplan‒Meier methods were applied for survival analyses. Functional Annotation of Prokaryotic Taxa and mediation analyses were used to explore the role of microbial functions in microbiome-mediated hyperlipidemia risk.

RESULTS: A total of 3104 participants were included, with 2215 diagnosed with hyperlipidemia. Multivariate linear regression revealed significant correlations between alpha diversity and total cholesterol and low-density lipoprotein levels (P < 0.017). Cox regression indicated that higher oral microbial alpha diversity was associated with a lower risk of cardiovascular mortality (P < 0.017). Beta diversity analysis revealed distinct oral microbial profiles between hyperlipidemic and non-hyperlipidemic individuals (P < 0.017). LEfSe analysis identified Prevotella and Parvimonas as key genera enriched in the oral microbiota of hyperlipidemic participants. Sulfur metabolism partially mediated the association between Parvimonas and hyperlipidemia.

CONCLUSION: The oral microbiota is closely associated with host lipid metabolism. Prevotella and Parvimonas exhibit higher oral abundances in hyperlipidemic individuals, with Parvimonas abundance directly correlated with blood lipids. Parvimonas may increase hyperlipidemia risk via sulfur metabolism. Further studies are needed to elucidate the underlying mechanisms, which could serve as effective targets for hyperlipidemia management.},
}

@article {pmid42254217,
year = {2026},
author = {Saad Ibrahim Abdelghany Elbeshbishy, R and Khatak, A},
title = {The skin microbiome: the overlooked axis in modern dermatology.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3045-3047},
pmid = {42254217},
issn = {2049-0801},
abstract = {The skin microbiome plays a critical role in maintaining cutaneous barrier integrity, modulating immune responses, and influencing the expression of dermatologic disease, yet its integration into clinical practice remains limited. Microbial alterations have been described in conditions such as atopic dermatitis, acne vulgaris, psoriasis, and chronic wounds; however, uncertainty regarding causality, interindividual variability, and lack of methodological standardization have hindered clinical translation. Current diagnostic frameworks rarely incorporate microbial metrics, while antimicrobial therapies remain central to management, often without consistent consideration of their ecological impact. Emerging microbiome-directed strategies, including topical probiotics, bacteriophage therapy, and microbiome-preserving approaches, show early promise but lack robust clinical validation. Advancing the role of the skin microbiome in dermatology will require standardized research methodologies, integration of multi-omics approaches, and well-designed clinical trials with clinically meaningful outcomes. This editorial highlights the need for a balanced and evidence-based framework that incorporates microbial perspectives into dermatology without overstating current evidence, advocating for a gradual integration that complements established immunologic and barrier-focused paradigms.},
}

@article {pmid42254258,
year = {2026},
author = {Panhwar, H and Panhwar, DM and Mudasir, M and Mahato, AK},
title = {Microbiome-derived metabolites as novel placental functional markers: predictive role in vasa previa.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3859-3860},
pmid = {42254258},
issn = {2049-0801},
}

@article {pmid42254377,
year = {2026},
author = {Storck-Thy, C and Krogfelt, KA and Jønsson, R},
title = {The overlooked role of the seminovaginal microbiota in infertility: a narrative mini review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1784130},
pmid = {42254377},
issn = {2296-858X},
abstract = {Infertility affects up to 15% of couples worldwide and is influenced by complex biological, immunological, and environmental factors. While reproductive microbiome research has expanded rapidly, the majority of published studies remain largely descriptive, focusing on taxonomic profiling rather than functional or mechanistic insight. Findings from vaginal microbiome studies have been heterogeneous and strongly influenced by methodological variation, and the male genital microbiome has received comparatively less attention, particularly in a couple context. This narrative mini review provides a synthesis of studies investigating paired male and female reproductive microbiomes, emphasizing observational evidence of partner- associated microbial patterns in relation to fertility outcomes. The term 'seminovaginal' microbiota is discussed as a hypothesis describing the transient and dynamic interface arising during sexual activity. Current evidence is limited, largely associative, and constrained by insufficient standardization of sampling, sample handling and processing, data analysis, restricting causal interpretation. Addressing these gaps through coupled, longitudinal, and mechanistic study designs is essential for advancing biologically meaningful conclusions in infertility research and reproductive treatments.},
}

@article {pmid42254439,
year = {2026},
author = {Rahimah, S and Tallei, TE and Savitri, M and Yamada, C and Kim, HJ and Choi, M and Park, MN and Ophinni, Y and Kim, B},
title = {Nutraceutical Interventions in Stunting: Advances, Challenges, and Prospects.},
journal = {Food science & nutrition},
volume = {14},
number = {5},
pages = {e71910},
pmid = {42254439},
issn = {2048-7177},
abstract = {Childhood stunting remains a major global health challenge, reflecting the cumulative effects of inadequate nutrition, recurrent infection, and chronic intestinal dysfunction during early life. Beyond conventional micronutrient supplementation, nutraceutical interventions have emerged as complementary strategies to address the complex biological pathways underlying impaired linear growth. This review synthesizes current evidence on nutraceutical approaches to stunting, including improvements in macronutrient quality, bioactive food components, and microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, postbiotics, and microbiota-directed foods. Evidence from clinical and preclinical studies indicates that nutraceutical effects on growth are generally modest and heterogeneous, with more consistent effects on weight gain than on height-for-age (HAZ). Variability in efficacy is strongly influenced by baseline nutritional status, environmental enteric dysfunction (EED), infection burden, dietary quality, and water, sanitation, and hygiene (WASH) conditions. Mechanistically, nutraceuticals may act through modulation of gut barrier integrity, inflammatory tone, microbial metabolism, and endocrine signaling pathways, particularly those involving the growth hormone-insulin-like growth factor-1 (GH-IGF-1) axis. Recent microbiota-directed food trials provide proof-of-concept that targeted correction of microbiome immaturity and gut dysfunction can support linear growth. Looking forward, advances in nutrigenomics, microbiome science, and epigenetics support a shift toward precision nutrition strategies that tailor interventions to biological responsiveness and context. Systems biology approaches integrating multi-omics data, network pharmacology, and interpretable artificial intelligence are expected to refine mechanistic understanding and guide intervention design. Effective translation will require rigorous trial designs, regulatory clarity, and integration of nutraceuticals within broader stunting reduction frameworks in low- and middle-income countries.},
}

@article {pmid42254500,
year = {2026},
author = {Kubota, A and Zang, L and Shinkai, T and Nakai, M and Tajima, A and Shimada, Y},
title = {Systems-level investigation of the anxiolytic gut-brain interactions induced by paraprobiotic Lactobacillus brevis SBC8803 in zebrafish.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1804536},
pmid = {42254500},
issn = {1664-302X},
abstract = {INTRODUCTION: Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics-live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis-is increasing. Heat killed Lactobacillus brevis SBC8803 enhances serotonin (5 hydroxytryptamine; 5 HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish.

METHODS: Adult male AB-strain zebrafish were fed a diet containing heat killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. To explore the underlying mechanisms, we performed brain RNA sequencing and V3-V4 region of 16S rRNA amplicon sequencing of intestinal contents, followed by integrative multi omics analyses, including Gene Set Variation Analysis (GSVA) combined with DIABLO-based data integration and residual correlation analysis.

RESULTS: SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent entries into this region, consistent with reduced anxiety-like behavior. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. GSVA combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of the SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism.

DISCUSSION: These findings support the biological validity of the SBC8803 administration-associated interactions observed in the multi-omics analyses. These findings suggest that the paraprobiotic SBC8803 may exert anxiolytic-like effects in zebrafish and reshape gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a potential mechanistic framework for considering heat killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.},
}

@article {pmid42254513,
year = {2026},
author = {Zhang, H and He, R and Xu, L and Zhou, H and Yu, R and Huang, P},
title = {A multi-omics case-control study identifying oropharyngeal microbiome-metabolite patterns that characterize secondary bacterial pneumonia among influenza patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824965},
pmid = {42254513},
issn = {1664-302X},
abstract = {Secondary bacterial pneumonia is a severe complication of influenza;howeve the biological determinants that distinguish progression from uncomplicated infection remain poorly understood. We investigated the oropharyngeal microbiome and plasma metabolome as potential discriminators of pneumonia development. In this study, we report a cross-sectional case-control study conducted during the 2022-2023 influenza season to identify and internally validate a microbiome-metabolite profile that characterizes pneumonia cases from uncomplicated influenza. We enrolled 236 consecutive influenza patients from Jiangsu Province, China (October 2023-December 2024): 59 with secondary pneumonia and 177 uncomplicated controls. Oropharyngeal swabs were subjected to 16S rRNA V3-V4 sequencing; plasma metabolomics was performed by UPLC-MS/MS in both ion modes. Seven machine-learning algorithms were compared; Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression was selected because it yielded the highest cross-validated discrimination. Microbial composition distinguished groups, not richness. Pneumonia cases showed enrichment of Synergistota and Bifidobacteriaceae with depletion of Bacillaceae (β-diversity p = 0.057). Controls exhibited enriched glycolysis and lipid metabolism pathways; pneumonia cases showed elevated degradation pathways (GLUCARDEG and GALLATE-DEGRADATION). Plasma metabolomics revealed a lipid depletion signature: phospholipids PC(O-16:0/0:0) and PS(14:0/18:3(9Z,12Z,15Z)) were significantly reduced (area under the (receiver operating characteristic) curves (AUCs) = 0.69-0.71). Small Molecule Pathway Database (SMPDB) pathway analysis demonstrated suppressed anabolic (tyrosine, steroid, and purine metabolism) and enhanced catabolic (beta-oxidation of very long-chain fatty acids) pathways. Machine learning identified Peptococcus as the top indicator (LASSO AUC = 0.65); Shapley Additive Explanation (SHAP) analysis revealed a monotonic risk increase with abundance. Oropharyngeal dysbiosis and systemic metabolic reprogramming characterize influenza cases that progress to secondary pneumonia. Peptococcus and four metabolites form an internally validated exploratory profile associated with secondary pneumonia; external validation and performance optimization are warranted.},
}

@article {pmid42254515,
year = {2026},
author = {Chen, H and Montero-Vale, M and Owusu-Kyei, K and Lara-Muñoz, A and Rubio-Garcia, E and de Pedro-Jové, R and Guiral, E and Chileshe, MN and Williams, J and Bofill, A and Samai, M and Casals-Pascual, C and Vila, J and Menéndez, C},
title = {Early-life carriage and antibiotic resistance of Streptococcus pneumoniae in infants from Sierra Leone.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822296},
pmid = {42254515},
issn = {1664-302X},
abstract = {Streptococcus pneumoniae remains a major cause of child morbidity and mortality in sub-Saharan Africa, with increasing macrolide resistance mediated by erm(B) and mef(A/E/I). Integrating phenotypic and sequencing-based approaches may improve antimicrobial resistance surveillance accuracy. This study assessed nasopharyngeal carriage and macrolide resistance of S. pneumoniae among young infants in Sierra Leone (November 2022-February 2023), nested within the ICARIA trial (NCT04235816) which evaluated azithromycin for child mortality reduction. Infants aged 6-10 weeks presenting for Penta-1 immunization before trial recruitment were enrolled. Two nasopharyngeal swabs were collected per infant. S. pneumoniae was detected by lytA PCR, azithromycin minimal inhibitory concentrations (MICs) were determined by E-test, and erm(B) and mef(A/E) were identified by PCR in isolates. A subset of paired samples underwent targeted amplicon sequencing for microbiome and resistome profiling. Carriage prevalence was 17.3% (162/936; 95% CI: 14.9-19.9%), with 45.7% (74/162) of isolates resistant to azithromycin (MIC ≥ 2 μg/mL). High-level resistance (MIC ≥ 64 μg/mL) was mainly mediated by erm(B) alone (53.8%) or in combination with mef(A/E) (38.5%), whereas all 22 moderately resistant isolates (MIC 2-48 μg/mL) carried mef(A/E) only. Among susceptible isolates, 3.8% (2/52) harbored mef(A/E) despite low MICs. Microbiome sequencing showed 96% concordance with lytA PCR for S. pneumoniae detection. Normalized resistome read counts for erm(B) and mef(A/E) were significantly higher in PCR-positive samples (p = 1.98 × 10[-9] and p = 8.14 × 10[-7]). These findings provide the first estimates of nasopharyngeal S. pneumoniae carriage and macrolide resistance among infants in Sierra Leone, revealing a high prevalence of resistance. The results underscore the need to strengthen antibiotic stewardship, particularly in child survival programs with azithromycin. Large and longitudinal studies are also needed. Clinical Trial Registration: ClinicalTrials.gov, NCT04235816.},
}

@article {pmid42244577,
year = {2026},
author = {Ettinger, CL and Eisen, JA},
title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.28.596327},
pmid = {42244577},
issn = {2692-8205},
abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.},
}

@article {pmid42244628,
year = {2026},
author = {Getange, D and Mukaratirwa, S and Chebet, D and Kabii, J and Khogali, R and Villinger, J},
title = {Ehrlichia ruminantium infection is associated with tissue-specific microbial community shifts in Amblyomma gemma ticks from cattle in Kenya.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.727963},
pmid = {42244628},
issn = {2692-8205},
abstract = {UNLABELLED: Tick-borne pathogens can reshape vector microbiomes in ways that influence pathogen colonisation and transmission, yet the interplay between Ehrlichia ruminantium and the microbiota of its tick vectors remains uncharacterised. We profiled bacterial communities in haemolymph, midgut, and salivary glands of infected (n = 11) and uninfected (n = 12) Am. gemma ticks, a vector of E. ruminantium in East Africa, collected from cattle in Kajiado County, Kenya, using near-full-length 16S rRNA gene amplicon sequencing on the Oxford Nanopore platform. Community composition, alpha and beta diversity, co-occurrence networks, keystone taxa, and PICRUSt2-inferred functional profiles were compared across tissue-infection status groups. We identified 226 bacterial genera dominated by Coxiella , Pseudomonas , Acinetobacter , Proteus , and Rickettsia . Infection was associated with tissue-specific shifts in community composition (PERMANOVA R [2] = 0.14, p < 0.001) and co-occurrence network structure, with midgut networks showing complete hub taxon turnover (Jaccard = 0.000, p = 0.043). Haemolymph communities converged around Luteimonas as a keystone taxon, while opportunistic Proteobacteria, including Acinetobacter and Serratia , emerged as keystones in infected midgut. Endosymbiotic Rickettsia was near-absent in infected tissues (0.3% vs 9.3% mean relative abundance in midgut), consistent with competitive exclusion. Functional inference identified FDR-significant enrichment of predicted aerobactin siderophore biosynthesis, antimicrobial efflux, and oxidative stress response gene families in infected microbiota. These findings show tissue-specific restructuring of the Am. gemma microbiome associated with E. ruminantium infection and point to candidate targets for microbiome-based interventions against heartwater.

IMPORTANCE: Heartwater, caused by the bacterium Ehrlichia ruminantium and transmitted by Amblyomma ticks, kills up to 90% of susceptible ruminants and is one of the most devastating tick-borne diseases in sub-Saharan Africa. Controlling heartwater requires understanding how the pathogen interacts with the microbial communities living inside its tick vector. In this exploratory study, we show that E. ruminantium infection is associated with tissue-specific shifts in the Amblyomma tick microbiome, including reduced abundance of beneficial symbionts, elevated representation of opportunistic bacteria among community hubs, and enrichment of iron acquisition and antimicrobial resistance functions. The midgut, the first tissue colonised during infection, showed the most marked structural reorganisation. These tissue-resolved microbiome signatures point to potential targets for novel control strategies, such as anti-microbiota vaccines or approaches that reinforce natural colonisation resistance, offering new strategies to reduce heartwater transmission and protect livestock livelihoods across Africa.},
}

@article {pmid42244638,
year = {2026},
author = {Zeng, X and Meng, X and Weakley, AM and Jarrett, KE and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Lai, R and Brearley-Sholto, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and de Aguiar Vallim, TQ and Fischbach, MA},
title = {Ecology and engineering to modify the bile acid output of a defined microbial community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.23.727444},
pmid = {42244638},
issn = {2692-8205},
abstract = {The bile acid pool, which is synthesized collaboratively by the host and its microbiome, impacts metabolism, immunity, and disease risk. Targeted microbiome interventions could in principle reshape the bile acid pool for therapeutic benefit, but practical strategies remain elusive. In the course of screening a complex defined community for metabolic phenotypes by dropping out individual strains, we observed that several of the single-strain dropout communities had markedly increased deoxycholic and lithocholic acid levels and a larger bile acid pool. In each of these communities, a second strain- Lactobacillus plantarum- had bloomed. The bile salt hydrolase activity of L. plantarum was necessary and sufficient to expand the size of the bile acid pool. An engineered community in which the bsh gene is overexpressed in multiple Lactobacillus strains confers on mice increased levels of secondary bile acid levels and a larger pool size. By overexpressing a different pair of bile acid metabolic genes in multiple strains of Lactobacillus -7α- and 7β-hydroxysteroid dehydrogenase-we changed the composition of the bile acid pool, enlarging it and redirecting it toward ursodeoxycholic acid. Together, these results demonstrate that fine details of the microbiome's strain composition can have a substantial effect on bile acid metabolism, and that rational manipulation of the microbiome can alter the size and composition of the bile acid pool.},
}

@article {pmid42244647,
year = {2026},
author = {Zeng, X and Meng, X and Weakley, AM and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and Fischbach, MA},
title = {A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.23.727446},
pmid = {42244647},
issn = {2692-8205},
abstract = {The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the community's metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H 2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.},
}

@article {pmid42244659,
year = {2026},
author = {De Silva, GLSN and Vinzelj, J and Miller, SL and Jemmett, AM and Elshahed, MS and Youssef, NH},
title = {Diversity and community structure of anaerobic gut fungi in camels.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.28.728439},
pmid = {42244659},
issn = {2692-8205},
abstract = {Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius , Camelus bactrianus , and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genera identified. However, this diversity was unevenly distributed, with three genera (Neocallimastix , Caecomyces , and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 genera exceeding 1% relative abundance in the entire dataset. While several of the genera identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, such as Oontomyces, Aestipascuomyces , Liebetanzomyces , and the yet uncultured genera NY09, NY03, and JV-2025d are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae . Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae , elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in psuedoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.},
}

@article {pmid42244690,
year = {2026},
author = {Tao, J and Gomez, D and Abu, YF and Rojas, K and Roy, S},
title = {Short-term oxycodone exposure produces delayed and persistent gut microbiome disruption in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.727957},
pmid = {42244690},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome is a critical part of host homeostasis, yet its resilience following opioid exposure remains poorly understood. While opioid-induced short-term dysbiosis is well documented, the long-term recovery dynamics following oxycodone remain unclear. This study characterized the temporal dynamics of the fecal microbiota in male C57BL/6J mice following a brief 3-day oxycodone regimen (5mg/kg, BID). 16S rRNA gene sequencing was performed at baseline, day 3, 10, 17, and 70. While acute post-treatment phases (day 3 to 10) showed subtle taxonomic shifts in Clostridium_sensu_stricto_1 and Romboutsia , significant community disruption emerged later. By day 17, beta diversity significantly differed from saline controls (P =0.002). At day 70, both alpha diversity (p=0.02) and beta diversity (P=0.007) remained significantly altered, characterized by enriched Akkermansia and Marvinbryantia alongside depleted Eubacterium_xylanophilum . These findings demonstrate that even brief oxycodone exposure triggers persistent, non-recovering dysbiosis that became detectable only after treatment cessation and persisted through day 70. This suggests that the window for microbiome recovery exceeds two months in mice (equivalent to several human years), highlighting a potential long-term risk for patients prescribed short-term opioid courses.

IMPORTANCE: Short-term opioid exposure is generally assumed to cause only transient disruption of the gut microbiome. However, the duration of microbiome recovery following clinically relevant opioid treatment remains poorly defined. In this study, we show that a brief three-day course of oxycodone in mice resulted in delayed and persistent alterations in gut microbial community structure that remained detectable for at least 70 days after treatment cessation. Notably, significant divergence in microbial composition emerged weeks after exposure rather than immediately following treatment, suggesting that short-term opioid use may initiate longer-lasting remodeling of the gut microbiome than previously appreciated. These findings highlight the importance of considering extended recovery timelines when evaluating the microbiological consequences of opioid exposure.},
}

@article {pmid42244733,
year = {2026},
author = {Grossman, A and Weng, J and Silverman, AD and Bor, B},
title = {Resolving Host-Episymbiont Interaction Dynamics through Continuous Cultivation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.01.722272},
pmid = {42244733},
issn = {2692-8205},
abstract = {UNLABELLED: Patescibacteria are an elusive linage of "microbial dark matter" bacteria predicted to represent ∼25% of total bacterial diversity. Despite this abundance and ubiquity, these organisms are challenging to cultivate, resulting from their specialized episymbiotic lifestyle. All cultivated representatives to date, predominantly composed of Saccharibacteria from the oral microbiome, depend on cognate prokaryotic hosts for growth and reproduction. Studying the growth dynamics of episymbiotic bacteria and their hosts in batch cultures has suggested that many episymbionts initially reduce host populations, and that hosts eventually adapt to episymbiont stress after serial passaging. However, discontinuous batch cultures do not reflect natural interactions between these organisms due to their drastically different growth rates. An episymbiont requires several (∼2-4) serial passages alongside its host to reach the high cell densities needed to impact host growth, which complicates investigation of host inhibition and adaptation to episymbiont stress. To describe these dynamics accurately, we utilized continuous culture via small-scale Raspberry Pi powered bioreactors, called Pioreactors. Within a bioreactor, host bacteria can be cultivated at a consistent growth rate indefinitely, providing the perfect substrate for cultivation of model Saccharibacteria. Quantification of time until host crash, crash severity, time until recovery, and stable co-culture density provides mechanistic ways to describe episymbiont-host interactions. First, we used these techniques to compare episymbiont infection by three different episymbionts, revealing distinct infection patterns ranging from mild inhibition with rapid host adaptation, to rapid host collapse followed by "arms race" oscillation dynamics. Then, bioreactors were used to quantify the episymbiotic role played by a known host-binding type 4 pili (T4P-2), demonstrating that loss of long-distance host binding significantly delayed the host crash without altering general crash dynamics. These experiments reveal that episymbionts can have drastically different effects on bacterial communities and provide the tools necessary to describe strain/species differences and molecular interactions.

IMPORTANCE: Episymbiotic Patescibacteria represent one of the largest branches of life on Earth, as well as one of the least understood. Furthermore, because Patescibacteria can manipulate their hosts growth and morphology they have immense ecological potential to be shaping the communities they occupy, both environmental and microbiome-associated. Our study highlights for the first time the potential of small-scale continuous cultivation for studying episymbiotic interactions that cannot be captured in discontinuous cultures. Herein we used these techniques to interrogate inter-species variation in host inhibition potential and to determine how loss of a long-distance episymbiosis factor mechanistically alters the cycle of episymbiont infection; however, this cultivation platform will enable researchers to answer many new questions about these ubiquitous host-episymbiont interactions.},
}

@article {pmid42244821,
year = {2026},
author = {Gao, X and Zou, Y and Fang, J and Wu, X and Zheng, W and Zhang, Y and Hao, W},
title = {The association between tongue features and tongue coating microbiota and gastrointestinal cancer: a systematic review and meta-analysis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2681268},
pmid = {42244821},
issn = {2000-2297},
abstract = {BACKGROUND: Gastrointestinal (GI) cancers pose a significant health burden, highlighting the need for non-invasive biomarkers. Tongue inspection, a traditional diagnostic method in Chinese medicine, has been increasingly quantified via imaging and microbiome analysis.

OBJECTIVE: This review synthesizes evidence on tongue features and coating microbiota in GI cancer detection.

DESIGN: We systematically searched PubMed, EMBASE, Cochrane and Chinese databases until July 2025 for case-control or cohort studies comparing tongue characteristics or microbiota between GI cancer patients and healthy controls. Data were pooled using fixed- or random-effects models.

RESULTS: Sixteen studies (n = 4,994) were included. GI cancer patients showed significantly higher rates of abnormal tongue body morphology (OR = 5.33, 95% CI 3.26-8.72), abnormal tongue body color (OR = 17.85, 95% CI 7.01-45.54), abnormal tongue coating texture (OR = 5.98, 95% CI 4.02-8.91) and abnormal tongue coating color (OR = 3.24, 95% CI 2.00-5.26) versus controls. Although α-diversity did not differ, certain taxa (e.g. Actinobacteria, Prevotella_7) were reduced in cancer patients. Subgroup analyses by cancer type showed generally consistent directions of association for abnormal tongue manifestations in gastric, colorectal and esophageal cancers, despite significant heterogeneity.

CONCLUSION: Abnormal tongue features and specific microbial shifts are associated with GI cancers, suggesting potential non-invasive tools for early detection. However, due to heterogeneity and methodological limitations, further large-scale prospective studies are needed for validation.},
}

@article {pmid42245041,
year = {2026},
author = {Hu, S and Cheng, H and Gillenwater, L and Manpearl, K and Mandava, A and Wang, Y and Pividori, M and Stranger, B and Krishnan, A and Greene, CS and Gao, Y},
title = {Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph Integration.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.26354182},
pmid = {42245041},
abstract = {OBJECTIVE: Biomedical knowledge graphs (KGs) such as PrimeKG, Hetionet, UMLS, and PharmGKB are increasingly used as the substrate for downstream machine-learning, retrieval-augmented generation, drug-repurposing, and electronic health record (EHR) augmentation pipelines. The dominant assumption in published work is that integrating two or more such KGs is a tractable engineering step solved by identifier (ID) matching. This paper interrogates that assumption empirically. We quantify how much concept overlap survives realistic alignment, and we characterize the new failure modes introduced by the methods that practitioners reach for when ID matching is insufficient.

MATERIALS AND METHODS: We compared four widely used biomedical KGs (PrimeKG, Hetionet v1.0, the full UMLS Metathesaurus, and PharmGKB) across eleven node types using a tiered alignment pipeline: (1) direct ID matching for nodes sharing a primary vocabulary; (2) cross-ontology bridging using standard mappings (e.g., MONDO↔DOID, HPO↔UMLS, HPO↔UMLS↔MeSH for side effects, NCBI Gene↔HGNC↔UMLS, UBERON↔FMA/SNOMEDCT_US/NCI/MeSH for anatomy); (3) ClinicalBERT cosine-similarity grouping at threshold ≥ 0.98 for over-segmented disease nodes, with a deterministic suffix-stripping canonicalizer; (4) exact name matching for ontology-poor types (anatomy, REACTOME pathways); and (5) embedding-based fuzzy matching with UMLS lookup (SapBERT and ClinicalBERT) for free-text microbiome concepts. We applied the pipeline to a 698-concept gut-microbiome benchmark spanning taxa, pathways, and disease labels, validated grouping decisions against the curated SSSOM mappings released by the MONDO project, and audited the ClinicalBERT consolidation against five clinical-genetics case studies drawn from the literature.

RESULTS: Per-type pairwise coverage was strikingly asymmetric. Genes/proteins and the three Gene Ontology categories aligned cleanly across PrimeKG and Hetionet (mutual coverage 94-99%), but disease overlap was sparse: only 0.7% of PrimeKG individual disease nodes mapped to Hetionet, rising to 2.0% after MONDO grouping (versus 78.7% and 18.4% from the Hetionet side). PrimeKG-to-UMLS coverage spanned 100% (effect/phenotype via HPO) down to 20.8% (REACTOME pathways), with drugs at 73.7% and anatomy at 58.8%. PrimeKG-to-PharmGKB drug coverage required up to two bridging hops (DrugBank → UMLS → RxNorm/ATC/MeSH). Bigger was not uniformly more complete: on a 698-concept microbiome drug benchmark, Hetionet missed 0 concepts while PrimeKG missed 16. ClinicalBERT-based grouping consolidated 22,205 raw MONDO disease nodes into 17,080 groups but introduced three reproducible failure modes documented in case studies: (i) peer over-merging: for example, all 22 osteogenesis imperfecta subtypes collapsed into a single node despite distinct severity classes; (ii) parent-child collapse: e.g. acute myeloid leukemia merged with myeloid leukemia, erasing the acute/chronic distinction that drives clinical management; and (iii) lexical false positives: neurofibromatosis and schwannomatosis grouped together despite cellular-pathology differences.

DISCUSSION: Identifier matching alone is a weak baseline for biomedical KG integration. Cross-ontology bridges and embedding-based consolidation expand coverage but do so at the cost of clinically meaningful resolution, and the resulting failures are systematic rather than random. Reporting only aggregate coverage statistics obscures these losses, which propagate silently into downstream tasks.

CONCLUSION: We provide reusable per-type coverage tables, a taxonomy of three integration failure modes, and concrete recommendations for downstream studies that depend on a unified biomedical KG. We argue that future KG integration work should report per-type coverage and per-cluster confidence rather than aggregate match rates.},
}

@article {pmid42245388,
year = {2026},
author = {Benjelloun, J and Hnini, M and Bouzroud, S and El Attar, I and Mghazli, N and Hami, A and Talbi, C and Aurag, J and Smouni, A and Guedira, A and Taha, K},
title = {Bioprospecting Cycas revoluta-associated bacterial endophytes for tomato (Solanum lycopersicum L.) growth promotion under salt stress.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {253},
pmid = {42245388},
issn = {2190-572X},
abstract = {UNLABELLED: Twenty endophytic bacterial strains isolated from Cycas revoluta coralloid roots were characterized for their salt stress tolerance and phyto-beneficial properties, mainly indole-3-acetic acid production, siderophore secretion and phosphate solubilization under both optimal and stressful conditions. Their genetic diversity was assessed through 16 S rRNA gene sequencing. Results demonstrated a significant diversity of genera, including Agrobacterium, Pseudomonas, Pantoea, Bacillus, Peribacillus, Ochrobactrum, and Stenotrophomonas. Salt tolerance assays and PGP screening revealed the high tolerance threshold and PGP potential of two of isolated bacteria (Pantoea sp. LMR-C62 and Bacillus sp. LMR-C11). Tomato (Solanum lycopersicum L. cv Campbell 33) seeds bio-priming with these strains significantly improved germination rate (up to 75.3% at 150 mM NaCl) and decreased the mean germination time compared to non-inoculated seeds. In greenhouse trials, plantlet inoculation with these two strains led to significant improvements in root length (up to +55%), shoot dry weight (+72%), leaf area (+33%), and relative water content (+92%) under salt stress conditions. Indeed, tomato inoculation improved root development, leaf area, and plant height. At the physiological level, the results indicated positive effects of the inoculation on chlorophyll and anthocyanin contents. These findings demonstrate that Cycas revoluta-associated bacterial endophytes, particularly Panteoa sp. LMR-C62 and Bacillus sp. LMR-C11, hold robust potential as biofertilizer candidates for enhancing tomato growth and resilience under saline conditions. To our knowledge, this is the first report prospecting the unique coralloid root microbiome of Cycas revoluta for agricultural purposes, revealing novel halotolerant endophytes with notable biofertilizer potential.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material at 10.1007/s13205-026-04861-5.},
}

@article {pmid42245391,
year = {2026},
author = {Kumari, J and Das, S and Ranjan, S and Singh, S},
title = {From intake to impact: dietary modulation of the gut-brain axis across health and neurological disease.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {247},
pmid = {42245391},
issn = {2190-572X},
abstract = {The gut-brain axis (GBA) is an intricate, bidirectional communication network linking the gastrointestinal microbiota to the central nervous system. Mounting evidence underscores its critical role in the pathogenesis of neurological and neurodegenerative disorders. Diet serves as a primary modulator of this axis, possessing the capacity to profoundly reshape microbial diversity, metabolic output, and host-microbiota interactions. This review highlights the modulatory effects of distinct dietary patterns-specifically the Western, Mediterranean, and Ketogenic diets-on GBA signaling and overall neurological health. We comprehensively analyzed how these diets alter gut microbiota composition, influence the production of neuroactive microbial metabolites, and regulate neuroimmune signaling pathways. Furthermore, the mechanistic correlations between diet-driven microbiota alterations and the pathophysiology of neurodegenerative diseases were explored. By evaluating preclinical data on the neuroprotective potential of specific dietary components, this review underscores the therapeutic promise of microbiome-targeted dietary interventions while critically addressing the translational challenges for clinical application.},
}

@article {pmid42245491,
year = {2026},
author = {León, ED and Francino, MP},
title = {Correction: Roles of secretory immunoglobulin A in host-microbiota interactions in the gut ecosystem.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868593},
doi = {10.3389/fmicb.2026.1868593},
pmid = {42245491},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.880484.].},
}

@article {pmid42245495,
year = {2026},
author = {Kuźniar, A and Das, AP and Goraj, W},
title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820854},
doi = {10.3389/fmicb.2026.1820854},
pmid = {42245495},
issn = {1664-302X},
}

@article {pmid42245499,
year = {2026},
author = {Wang, X and Wang, S and Chang, Z and Zhao, M and Zhang, X and Fayzullo, N and Bunyod, E and Li, S and Wang, J},
title = {A transformer based deep learning framework for accurate single nucleotide variant correction in heterogeneous samples.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1838029},
pmid = {42245499},
issn = {1664-302X},
abstract = {Profiling host genetic variations in heterogeneous host-microbiome mixtures is crucial for understanding cross-species interactions and microenvironmental dynamics. However, the variable host DNA fraction (purity) in bulk sequencing data severely compromises the performance of standard variant callers, leading to significant systematic biases in quantifying single nucleotide variants (SNVs). To address this, we developed a Transformer-based computational framework designed to model sequence context and technical artifacts in low-purity samples. The architecture employs a group-encoding mechanism to process multidimensional features-including variant allele frequency (VAF) distributions, base-level purity estimates, sequencing depth, and local genomic context (such as repeat regions and chromatin accessibility). By capturing long-range dependencies among these diverse signals, the model effectively neutralizes purity-induced biases to accurately recover the true host SNV count. We evaluated the framework using simulated sequencing data across a broad purity gradient (0.2-1.0). Our approach significantly reduced quantification errors, achieving high concordance between the corrected and actual ground-truth SNV counts. Benchmarking the corrected counts against the raw outputs of conventional callers (Mutect, Freebayes, LoFreq, and Platypus) demonstrated substantial performance gains, particularly in ultra-low purity conditions (0.2-0.3) where traditional statistical priors typically fail to provide reliable quantifications. Feature ablation and residual analyses further validated the independence of the multidimensional inputs and the unbiased, zero-centered nature of the count corrections. This deep learning pipeline provides a robust solution for the accurate quantification of host SNVs in complex biological mixtures, facilitating reliable downstream genetic analyses in highly heterogeneous microenvironments.},
}

@article {pmid42245500,
year = {2026},
author = {Dinh-Hung, N and Mohammed, H and Linh, NV and Tran, NT},
title = {Editorial: Probiotics in aquaculture: enhancing health and sustainability.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1864753},
pmid = {42245500},
issn = {1664-302X},
}

@article {pmid42245502,
year = {2026},
author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M},
title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825173},
pmid = {42245502},
issn = {1664-302X},
abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.},
}

@article {pmid42245509,
year = {2026},
author = {Wang, Z and Li, L and Dong, Y and Zhang, Y},
title = {The microbiota-tryptophan-brain axis in neurodegenerative diseases: pathogenic mechanisms, disease-specific roles, and translational therapeutics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820111},
pmid = {42245509},
issn = {1664-302X},
abstract = {The pathogenesis of neurodegenerative diseases (NDDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD) is very complex. Recent studies have shown that gut microbiota and their metabolites play a key role in the progression of these diseases. Tryptophan (Trp) is an essential amino acid, which mainly produces a variety of biologically active compounds in the intestine through the metabolism of indole pathway, Kynurenine pathway (KP) and serotonin pathway, including indole derivatives, Kynurenine (KYN) and serotonin (5-HT). These metabolites affect the central nervous system (CNS) through the Microbiota-gut-brain axis (MGBA) and affect CNS in a variety of mechanisms, including immune regulation, neuroprotection and maintenance of intestinal barrier function. They are involved in key pathological processes such as neuroinflammation, oxidative stress and pathological protein aggregation. This paper systematically reviews the mechanism of the role of Trp metabolites derived from gut microbiota in NDDs, and explores their specific roles in AD, PD, Amyotrophic Lateral Sclerosis (ALS) and Huntington's disease (HD), and summarizes the potential therapeutic value of the current pathway strategy. These strategies include nutritional intervention, targeted microbiome therapy [such as probiotic and fecal microbiota transplantation (FMT)], and metabolite-derived drugs. Future research must clarify its dynamic mechanism in the human body, develop relevant biomarkers, and promote personalized prevention and treatment strategies through clinical transformation, so as to provide a new direction for early intervention and treatment of NDDs.},
}

@article {pmid42245510,
year = {2026},
author = {Patel, M and Ijoma, GN and Ziarno, M},
title = {Editorial: Bifidobacteria: exploring the roles of these microbiome guardians and their effects on human health.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861676},
doi = {10.3389/fmicb.2026.1861676},
pmid = {42245510},
issn = {1664-302X},
}

@article {pmid42245514,
year = {2026},
author = {Shen, X and Yu, FXD and Xie, S and Hsu, CD and Domingos, JA and Gibson-Kueh, S},
title = {Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1739391},
pmid = {42245514},
issn = {1664-302X},
abstract = {INTRODUCTION: Aquarium systems are engineered yet biologically dynamic ecosystems where microbial communities underpin nutrient cycling, organic matter decomposition and water quality regulation. These processes directly affect aquatic animal health.

METHODS: This study conducted a two-month time series analysis of waterborne microbiomes across six freshwater exhibits at River Wonders, Singapore, using 16S rRNA gene sequencing. Exhibits were categorized as "Healthy" (LM, MJ, EE) or "Stressed" (P, MJR, RG) based on fish health, and as indoor or semi-indoor/outdoor by system design.

RESULTS AND DISCUSSION: Temporal fluctuations in microbial composition and diversity were evident over time, with distinct profiles between indoor and semi-indoor/outdoor. Potential opportunistic or pathogenic genera, including Edwardsiella, Flavobacterium, Aeromonas, Pseudomonas and Mycobacterium, were consistently among the 30 most abundant taxa. The most severe dysbiosis occurred in exhibit P, characterized by a transient Pseudomonas bloom (51.4%), loss of nitrifiers (Nitrosomonas, Nitrospira) and concurrent fish health issues. MJR and RG harbored persistent polymicrobial risks, while "Healthy" exhibits maintained relatively more balanced microbial communities with lower pathogen loads. Routine husbandry interventions (e.g., partial water changes, substrate cleaning) coincided with improved microbial evenness and reductions in opportunistic taxa. These findings highlight diagnostic potential of microbiome profiling to detect early dysbiosis and support evidence-based husbandry in managed aquatic systems.},
}

@article {pmid42245662,
year = {2026},
author = {Cabanero-Navalon, MD and Carda-Diéguez, M and Mira, A and Moral Moral, P and Diaz Luna, MM and Balastegui-Martín, H and Salavert Lletí, M and Garcia-Bustos, V},
title = {Multiniche mycobiome profiling identifies distinctive fungal dysbiosis in common variable immunodeficiency.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804724},
pmid = {42245662},
issn = {1664-3224},
abstract = {BACKGROUND: Common variable immunodeficiency (CVID) is associated with bacterial dysbiosis, particularly in patients with immune dysregulation, but the contribution of the fungal microbiome (mycobiome) remains poorly understood.

METHODS: We conducted a cross-sectional, multi-compartment study in 41 adults with CVID (24 with immune dysregulation, dCVID; 17 with infectious-only manifestations, iCVID) and 15 matched healthy controls. Saliva, sputum and stool samples were analyzed using ITS1 amplicon sequencing with amplicon sequence variant-based taxonomic assignment, followed by α/β-diversity analyses, multivariate modeling, differential abundance testing and machine learning approaches for biomarker identification.

RESULTS: Across all three niches, mycobiome composition differed significantly between CVID and controls, whereas dCVID and iCVID did not separate. Fungal richness and evenness were reduced in CVID, most prominently in respiratory and oral samples. ANCOM-BC revealed a reproducible "Candida-skewed" configuration in both phenotypes, with marked enrichment of Candida albicans in sputum, stool and saliva, accompanied by increased abundance of other opportunistic yeasts such as Nakaseomyces glabratus. In contrast, environmental or putatively commensal taxa were consistently depleted. Random forest models based on fungal profiles accurately discriminated CVID from controls, with AUC up to 0.96 (95% CI 0.91-0.99) in saliva and 0.94 (95% CI 0.88-0.99) in stool, whereas classification of dCVID versus iCVID was modest.

CONCLUSION: Together, these findings provide the first integrated view of mycobiome alterations across multiple ecological niches in CVID, highlighting consistent enrichment of opportunistic yeasts over commensals. The expansion of C. albicans supports a potential pathobiont role, and the strong discriminatory performance of fungal signatures underscores their promise as non-invasive biomarkers in this immunodeficiency.},
}

@article {pmid42245783,
year = {2026},
author = {Edielu, A and Lo, CW and Mawa, PA and Webb, EL and Elliott, AM and Mugerwa, JK and Oduru, G and Nassuuna, J and Ayebazibwe, GK and Struebig, M and Friedman, JF and Bustinduy, AL and Holland, MJ},
title = {Schistosoma mansoni infection is associated with changes in gut microbiota in preschool age children in Albertine Region, Uganda.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9768290/v1},
pmid = {42245783},
issn = {2693-5015},
abstract = {Current understanding of gut microbiota alterations during helminthiasis is largely derived from experimental models, often focusing on a narrow range of metrics. This study investigates the structural and functional shifts in the gut microbiome associated with Schistosoma mansoni infection in a paediatric cohort. We conducted a cross-sectional study of preschool-aged children (12-47 months) comparing S. mansoni -infected individuals (56) to uninfected controls (57). Microbial DNA was extracted from stool samples and sequenced via the Illumina MiSeq v3 platform targeting the V4-16S rRNA region. Diversity was assessed through alpha (Chao1, Simpson, Shannon) and beta (UniFrac and Bray-Curtis distance) metrics. Functional potential was predicted using PICRUSt2 mapped against the KEGG database. The infected group (median age 36 months) exhibited significantly higher alpha diversity and species richness compared to uninfected peers (median age 26 months). Beta diversity analysis confirmed distinct microbial clustering between the two groups (p-value = 0.001). Notably, S. mansoni infection was characterized by the proliferation of pro-inflammatory taxa and a concomitant depletion of short-chain fatty acid (SCFA) producers. Functional modeling indicated a significant downregulation of metabolic pathways involved in energy metabolism and SCFA biosynthesis. S. mansoni infection is associated with profound structural and functional dysbiosis in preschool-aged children. The depletion of SCFA producers and altered metabolic pathways suggest that infection may impair host nutritional status and influence the parasite's lifecycle, necessitating further longitudinal investigation.},
}

@article {pmid42245806,
year = {2026},
author = {Cunningham, ME and Williams, MT and Spaine, KM and Marcinkowska, A and Matveyev, AV and Hur, BJ and Natterer, HO and Chatterjee, RB and Oldfield, CJ and Edupuganti, L and Zhu, B and Jefferson, KK and Iii, JFS and Olex, AL and Serrano, MG and Buck, GA},
title = {Differential Host Gene Expression Associated with Non-Lactobacillus-dominant Vaginal Microbiomes During Pregnancy.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9268667/v1},
pmid = {42245806},
issn = {2693-5015},
abstract = {Background The vaginal microbiome significantly influences gynecological and obstetric health, yet the interrelationship between host vaginal gene expression and the microbiota during pregnancy is understudied-particularly in racioethnically diverse cohorts. Here, we leveraged metatranscriptomic data from 123 participants from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI) cohort to perform a novel integrated analysis of human host gene expression and vaginal microbiota composition during pregnancy. We hypothesized that host gene expression at the vaginal-mucosal interface would exhibit distinct transcriptional profiles when colonized by bacteria commonly present in bacterial vaginosis (BV), termed BV-associated vagitypes, compared to Lactobacillus -dominated microbiomes. Such distinct host response would provide evidence linking vaginal inflammation to microbiome composition during pregnancy in a majority Black cohort. By profiling host expression with different BV-associated vagitypes, these host-microbiome signatures could inform clinically actionable biomarkers for microbiome-focused interventions during pregnancy in historically underrepresented populations. Results Host transcriptomic profiles differed significantly between BV-associated and Lactobacillus -dominated vagitypes, with this association remaining significant when analyses were restricted to Black participants. We identified 13 consistently differentially expressed genes in women with BV-associated vagitypes-vaginal microbiomes comprised of high relative abundance of either Gardnerella spp., Candidatus Lachnocurva vaginae, or a mixture of multiple anaerobic taxa-compared to women with Lactobacillus crispatus vagitypes. These differentially expressed genes are involved in host immune response (DKK1, H2BC21, ILRUN, S100A9), oxidative stress response and inflammasome activation (CSTB), transcription modulation (CLK1, PAX9), vesicle trafficking (EXPH5), ubiquitination (FBXO32), membrane integrity (PIEZO1), and ion transport (S100A16, SCNN1A, SLCO4A1). Conclusion BV-associated vagitypes are correlated with distinct host immunomodulatory gene expression profiles during pregnancy, independent of self-reported racioethnicity. We demonstrated novel molecular insights into microbiome-host interaction during pregnancy within the context of adverse cervicovaginal health.},
}

@article {pmid42245824,
year = {2026},
author = {de Azevedo-Lopes, A and Traulsen, A},
title = {Multilevel selection in multitype populations.},
journal = {PNAS nexus},
volume = {5},
number = {6},
pages = {pgag180},
pmid = {42245824},
issn = {2752-6542},
abstract = {Multilevel selection has important implications for understanding the origin, ecology, and evolution of host-associated microbiomes. Selection on the host-level can have a substantial impact on the evolution of microbial lineages, favoring microbes that are beneficial to the host. However, previous research has focused on the evolution of interactions among only two types. We alter this perspective by examining the role of multilevel selection in shaping the interaction dynamics of a population with many microbial types-a case of particular relevance for microbiomes. We ask how multilevel selection influences the selection of interactions among various microbial types, whether it promotes microbial diversity within the population, and whether it increases the likelihood of microbial lineages evolving beneficial interactions with their host and other microbes. To address these questions, we simulate a multitype population structured into groups, where individuals interact within groups through an evolutionary game that determines their fitness. We classify pairwise interactions by their dynamical outcomes: dominance, coexistence, or bistability. We find that multilevel selection reshapes interactions dynamics in complex ways, depending on the details of the population structure. We show the impact of the interaction patterns emerging in such a system.},
}

@article {pmid42246001,
year = {2026},
author = {Chen, S and Liu, J and Ni, H and Zhu, F and Liu, H and Lin, R},
title = {Gut microbiota and the kidney-gut-skin axis in chronic kidney disease-associated pruritus: mechanisms and therapeutic implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1811786},
pmid = {42246001},
issn = {2235-2988},
mesh = {Humans ; *Pruritus/therapy/etiology/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; *Kidney/microbiology ; Dysbiosis ; Probiotics/therapeutic use ; },
abstract = {Chronic kidney disease-associated pruritus (CKD-aP) is a highly prevalent and debilitating symptom in patients with chronic kidney disease (CKD) and end-stage kidney disease (ESKD), severely impairing quality of life, sleep quality, mental health, and clinical outcomes. Its pathogenesis is multifactorial and remains incompletely understood, involving chronic inflammation, immune imbalance, abnormal neuro-opioid pathways, mineral metabolism disorders and skin barrier damage. The kidney-gut-skin axis has attracted increasing attention as a novel theoretical framework to elucidate the roles of gut microbiota dysbiosis, gut-derived uremic toxins, intestinal barrier impairment and systemic inflammation in the development of CKD-aP. This review summarizes the traditional pathogenic mechanisms of CKD-aP, reviews recent advances linking gut microbial alterations to pruritus-related pathways, and systematically evaluates gut-targeted and metabolism-targeted interventions, including probiotics, prebiotics, synbiotics, AST-120, fecal microbiota transplantation, phytochemicals, Uremia Clearance Granules, and vitamin D-related strategies. Current evidence is mostly associative and is mainly derived from general CKD/ESKD populations, animal models, and in vitro studies; specific clinical validation in CKD-aP cohorts remains limited. Accordingly, gut microbiome-related mechanisms and interventions remain hypothetical and adjunctive, without established causal relationships or validated standard therapies for CKD-aP. Future studies are required to identify CKD-aP-specific pathological alterations, adopt longitudinal design and multi-omics analysis, conduct mechanistic verification, and perform randomized controlled trials with pruritus as a predefined primary endpoint.},
}

Humans
*Pruritus/therapy/etiology/microbiology
*Renal Insufficiency, Chronic/complications/microbiology/therapy
Animals
*Gastrointestinal Microbiome/physiology
*Skin/microbiology/pathology
*Kidney/microbiology
Dysbiosis
Probiotics/therapeutic use

@article {pmid42246005,
year = {2026},
author = {Orcel, E and Sentausa, E and Hage, H and Louis, K and Taha, M and Bellais, S and Villain, A and Beloeil, L and Sijmons, S and Devos, N and Saliou, A},
title = {UMI-guided single locus sequence typing method for phylotyping Cutibacterium acnes from skin samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1807759},
pmid = {42246005},
issn = {2235-2988},
mesh = {Humans ; *Skin/microbiology ; Skin Microbiome ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Molecular Typing/methods ; *Propionibacteriaceae/genetics/classification/isolation & purification ; *Bacterial Typing Techniques/methods ; },
abstract = {INTRODUCTION: Cutibacterium acnes is a dominant member of the human skin microbiota and displays substantial strain-level diversity with relevance for skin health and disease. However, accurate characterization of C. acnes lineages directly from skin samples remains challenging due to low biomass, host DNA contamination, and limitations of short-read sequencing.

METHODS: Here, we present SLST-Seq, a culture-independent approach based on single-locus sequence typing (SLST), enabling strain-level profiling of C. acnes from low-input skin-strip samples. SLST-Seq adapts the LUMI-Seq® synthetic long-read sequencing technology to the C. acnes SLST marker, combining unique molecular identifier barcoding with de novo assembly to reconstruct full-length SLST sequences with high accuracy.

RESULT: Method performance was validated using single-isolate controls, defined genomic DNA mixtures, spike-in dilution series, and run-specific controls, demonstrating high specificity, quantitative accuracy across a wide range of target-to-background DNA ratios, and strong run-to-run reproducibility. Applied to skin-strip samples from healthy volunteers, SLST-Seq generated robust SLST profiles and revealed marked inter-individual variability, with donor-specific community structures largely conserved between face and back skin sites.

DISCUSSION: Overall, SLST-Seq provides a sensitive and scalable framework for in situ analysis of C. acnes population structure and supports high-resolution studies of skin microbiome composition from challenging clinical samples.},
}

Humans
*Skin/microbiology
Skin Microbiome
DNA, Bacterial/genetics
Phylogeny
Sequence Analysis, DNA
*Molecular Typing/methods
*Propionibacteriaceae/genetics/classification/isolation & purification
*Bacterial Typing Techniques/methods

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

@article {pmid42246268,
year = {2026},
author = {Yun, S and Choi, KS and Min, H and Jo, YK and Jang, S},
title = {Development strategies for engineered live biotherapeutic products for metabolic diseases.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/07388551.2026.2653692},
pmid = {42246268},
issn = {1549-7801},
abstract = {Metabolic diseases, such as obesity and diabetes, have risen due to lifestyle changes. Traditional treatments, including dietary modifications and pharmacological interventions, are limited by low compliance and adverse effects, highlighting the need for alternative therapeutic approaches that offer improved patient compliance and long-term effectiveness. Engineered live biotherapeutic products (eLBPs) have emerged as a promising strategy that combines bacterial chassis with synthetic genetic circuits for precise and targeted disease treatment. Unlike conventional therapeutics, eLBPs can colonize the intestinal tract and enable localized and condition-responsive therapeutic activity while offering improved safety profiles through defined mechanisms of action. This review highlights key strategies for eLBP development, particularly chassis selection and genetic circuit design. Applications in metabolic diseases, including inherited disorders such as phenylketonuria (PKU), demonstrate how engineered gene circuits can modulate specific metabolic pathways. However, several challenges remain, including genetic stability, interindividual variability, biological safety, and production scalability. In addition, further research on host-microbiota interactions is required to improve therapeutic predictability and efficacy, supporting the development of safe and effective personalized eLBP-based therapies for metabolic diseases.},
}

@article {pmid42246374,
year = {2026},
author = {Pauwels, A and Devolder, L and Falony, G and D'haeseleer, M and Nagels, G and Van Remoortel, A and Derrien, M and D'hooghe, M and Raes, J},
title = {Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681876},
doi = {10.1080/19490976.2026.2681876},
pmid = {42246374},
issn = {1949-0984},
abstract = {Despite a wealth of gut microbiota studies in multiple sclerosis (MS), consistent results are lacking. Here, we study confounder effects and use of quantitative microbiome profiling (QMP) in 228 MS patients (103 untreated) and 2860 population controls (Flemish Gut Flora Project (FGFP)). Total bacterial load was lower in relapsing remitting (RR)MS, while strong fecal moisture effects, indicative of longer transit times, in MS vs. FGFP, were driven by primary progressive (PP)MS. Applying cell count and moisture in deconfounded QMP, we identified 21 differentially abundant genera in MS, with a.o. Lachnobacterium, Blautia enriched, and Clostridium, Bacteroides depleted. Deconfounded QMP across 10 published studies (1065 patients, 874 controls) did not confirm commonly detected markers (Akkermansia, Roseburia), yet lowered Bacteroides, and higher Blautia and Methanobrevibacter emerged as robust MS biomarkers. Lowered butyrate producers (Butyricicoccus, Butyricimonas) merit further investigation. Enterotype stratification linked the low cell count Bacteroides 2 enterotype to low-efficacy DMTs, and the Prevotella enterotype to lower disease severity. Serum glial fibrillary acidic protein (GFAP), a disease progression biomarker, was identified as a covariate of gut microbial variation and inversely correlated with Faecalibacterium and Roseburia abundance in PPMS. Overall, our study provides robust disease markers and emphasizes the importance of QMP and confounder control.},
}

@article {pmid42247160,
year = {2026},
author = {Palani Kumar, MK and Iyer, KS and Shahi, SK and Raygoza Garay, JA and Mangalam, A and Dayal, S},
title = {Age and sex dependent shift in murine gut microbiome reveals pathological links to host cardiovascular and metabolic pathways.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42247160},
issn = {2509-2723},
support = {HL168630/HL/NHLBI NIH HHS/United States ; HL007344/HL/NHLBI NIH HHS/United States ; BX007087//U.S. Department of Veterans Affairs/ ; AI162778//National Institute of Allergy and Infectious Diseases/ ; 18IPA4180014//American Heart Association/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; 1I01CX002212//Iowa City Veterans Affairs Medical Center/ ; },
abstract = {The gut microbiome undergoes dynamic, sex-dependent changes across the lifespan. However, comprehensive studies examining the combined effects of age and sex are limited. This study investigated both compositional and functional alterations in the gut microbiome of young (4 months, n = 14) and aged (20 months, n = 20) C57BL/6 J mice of both sexes using 16S rRNA gene (V3-V5) sequencing. Microbial community structure and predicted functional profiles were analyzed via QIIME2 and PICRUSt2, with pathway annotation based on MetaCyc. Compared to aged mice, young mice exhibited higher alpha diversity, with the highest increase observed in young females. This sex-specific difference was lost in aged mice. Aging was also associated with an increased Firmicutes-to-Bacteroidetes ratio, and distinct shifts in key taxa, including increased Lactobacillus and Roseburia and reduced Bacteroides and Lachnospiraceae. Functional prediction revealed substantial age-related metabolic shifts, especially in females showing alteration in 45 pathways including upregulation of branched-chain amino acid (BCAA) metabolism, uric acid metabolism, and lipopolysaccharide biosynthesis. To directly link alterations in microbial BCAA metabolism with host metabolic outcomes, fecal abundance of the bacterial BCAA aminotransferase gene (ilvE) was quantified and found to be significantly increased in aged mice. Concurrently, aged mice exhibited higher plasma levels of BCAA, insulin, and random glucose, indicating age-associated metabolic dysregulation. Fecal ilvE abundance associated positively with plasma BCAA levels, and negatively with blood glucose in aged mice, suggesting a link between microbial BCAA metabolism and host glucose homeostasis. Our findings demonstrate that gut microbiome composition and function are influenced by both age and sex. We also showed that these alterations in microbial BCAA metabolism are associated with host metabolic parameters during aging. Our findings underscore the importance of incorporating both age and sex as biological variables in microbiome research and may inform development of age- and sex-specific microbiome-targeted interventions.},
}

@article {pmid42247343,
year = {2026},
author = {Somboonna, N and Rujirawan, P and Promvaranon, T and Wongtada, C and Triwatcharikorn, J and Chottawornsak, N and Kantikosum, K and Wongsaroj, L and Parinyanitikul, N and Chongpison, Y and Chiewchengchol, D and Rerknimitr, P},
title = {Skin Barrier Dysfunction, Antimicrobial Peptide Alterations, and Microbiome Changes in Solid Cancer Patients Treated with Epidermal Growth Factor Receptor Inhibitors.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000551797},
pmid = {42247343},
issn = {1421-9832},
abstract = {INTRODUCTION: Epidermal growth factor receptor inhibitors (EGFRIs) are targeted therapies for solid cancers. Their use is associated with cutaneous adverse events (cAEs). This study aimed to investigate cAEs and changes in skin biophysics reflecting the skin barrier function, alterations in antimicrobial peptides (AMPs), and the skin microbiome in patients undergoing treatment with EGFRIs.

METHODS: A 2-year prospective cohort study was conducted involving patients receiving EGFRIs for solid cancers. cAEs and skin biophysical properties, including transepidermal water loss (TEWL), skin pH, elasticity, sebum, and pigmentation, were measured at baseline and follow-up visits up to 48 weeks. AMPs were assessed using a tape-stripping technique from the cheeks at months 0, 1, and 6, with protein assays and ELISA to determine the levels of human beta-defensin (hBD)-3 and ribonuclease (RNase)-7. Skin microbiome analysis was performed through 16S rRNA sequencing of cheek swabs collected at months 0, 1, and 6.

RESULTS: Eighty-four patients were enrolled. The cumulative incidence of cAEs was 94.05%. Skin biophysical properties showed significantly increased TEWL and pH, decreased pigmentation, and no significant changes in elasticity and sebum. AMP analysis from 15 patients revealed significant reduction of RNase-7 levels after 6 months into EGFRIs, while hBD-3 level change was insignificant. A microbiome study from 18 patients showed statistically increased Corynebacterium kroppenstedtii at months 1 and 6, while Cutibacterium acnes, Corynebacterium aurimucosum, Staphylococcus epidermidis, and Staphylococcus aureus were not significantly different among groups.

CONCLUSION: Treatment with EGFRIs compromises skin barrier function and AMP production, leading to skin microbiota changes.},
}

@article {pmid42247989,
year = {2026},
author = {Tang, Y and Qi, F and Yu, Y and Fu, Y and Zhu, P},
title = {Knowledge mapping of cholestatic liver disease and TGR5 research: A bibliometric study of trends and frontiers.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 1},
pages = {109158},
doi = {10.1016/j.compbiolchem.2026.109158},
pmid = {42247989},
issn = {1476-928X},
abstract = {OBJECTIVE: This study aims to provide a comprehensive bibliometric analysis of global research trends surrounding TGR5 in cholestatic liver diseases from 2006 to 2025, with the objective of elucidating publication outputs, geographic and institutional contributions, collaborative networks, journal co-citation analysis and reference co-citation mapping, key research themes, and emerging frontiers.

METHODS: Bibliographic data were retrieved from the Web of Science Core Collection (WoSCC) and supplemented by validation against Scopus and PubMed to mitigate database selection bias.Analyses were performed using CiteSpace (version 6.2.R2), VOSviewer (version 1.6.20), and the bibliometrix R package. Performance analysis was employed to evaluate productivity and impact across countries, institutions, and authors. Advanced science mapping techniques, including Thematic Map analysis, network topology metrics, and citation burst detection, were conducted to provide deeper computational and systems-level biological insights.

RESULTS: A total of 418 publications were included. Annual publications showed a steady upward trend, with the United States leading in productivity (n = 138), total citations (n = 14,638), and H-index (59), followed by China with high output but relatively lower citation impact. European countries, notably Italy and Germany, demonstrated strong collaborative networks and influence relative to output volume. Keyword and thematic analyses revealed a shift from molecular mechanisms to clinical applications and, more recently, to gut microbiota and metabolic interactions. Major research clusters encompassed bile acid receptors, gut-liver axis mechanisms, and metabolic disorders. Quantitative network analysis revealed a modularity of 0.8238 and mean silhouette of 0.96, indicating well-defined cluster structures. Although prominent research groups were identified, international collaboration remained limited.

CONCLUSION: The study illustrates the dynamic and evolving nature of TGR5 research, marked by a transition from basic science to translational and systems-level approaches. As the first comprehensive bibliometric and systems-level mapping analysis of TGR5 research in cholestatic liver diseases, this study uniquely integrates computational network analysis with microbiome-host interaction frameworks.While research productivity continues to grow, future efforts would benefit from enhanced international collaboration, microbiome engineering, systems medicine, biomarker discovery, and AI-integrated hepatology research. These findings provide valuable insights for researchers and policymakers aiming to navigate and advance this promising field.},
}

@article {pmid42248042,
year = {2026},
author = {Wang, L and Gong, X and Rao, S and Huang, L and Cheng, H and Cheng, S and Luo, J and Li, Q and Wei, Y and Xu, H},
title = {Biological effects of selenium on Hypnum plumaeforme and the underlying mechanisms mediated by physiology and microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120341},
doi = {10.1016/j.ecoenv.2026.120341},
pmid = {42248042},
issn = {1090-2414},
abstract = {Bryophytes provide vital ecosystem services, yet the biological effects of selenium (Se) on them remain largely unknown. This study simulated ecological scenarios with different selenite exposure levels to investigate the response patterns of growth, physiology, and symbiotic bacterial communities in Hypnum plumaeforme. Overall, its inorganic, organic, and total Se content increased with increasing selenite exposure levels. At 2 mg/L, H. plumaeforme accumulated more biomass, carotenoids and selenomethionine (SeMet), but less lipid and phosphorus (P). Enhanced methylselenocysteine (MeSeCys) biosynthesis facilitated its Se detoxification. At 4 mg/L, H. plumaeforme had more photosynthetic pigments, carbohydrates and protein, but fewer chloroplasts and less P. H2O2 accumulation did not result in elevated malondialdehyde (MDA) content and growth inhibition, which was attributed to the activation of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), as well as increased SeMet biosynthesis for Se detoxification. The enrichment of Variovorax and TM7a might support its starch accumulation and Se tolerance. At 8 mg/L, H. plumaeforme had more photosynthetic pigments and protein, but fewer chloroplasts and less P. Excessive SeMet synthesis induced Se toxicity. Although SOD, CAT and GPX were activated, H2O2 and MDA accumulation occurred in this bryophyte, resulting in reduced biomass and impaired nitrogen (N) uptake. The enrichment of bacterial taxa, including Alphaproteobacteria, might facilitate its antioxidant defense. This study identifies the growth-promoting, neutral, and inhibitory effects of Se on H. plumaeforme, and illustrates the underlying physiological and microbial regulatory mechanisms. These findings provide important theoretical support for bryophyte conservation and Se ecological risk assessment.},
}

@article {pmid42248044,
year = {2026},
author = {Wang, X and Yin, S and Zheng, Y and Yu, X and Li, Y and Zhang, B and Liu, J and Zhang, Y and You, X},
title = {Hydrochar decreased the enantioselective bioaccumulation of prothioconazole-desthio in the tobacco through rhizosphere soil metabolic regulation.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120333},
doi = {10.1016/j.ecoenv.2026.120333},
pmid = {42248044},
issn = {1090-2414},
abstract = {Pollution of soil environments by pesticides is a serious global issue. Char amendments (pyrochar and hydrochar) have been widely used to remediate contaminated soils. However, the rhizosphere soil metabolic mechanisms underlying the hydrochar remediated prothioconazole pollution in the soil-plant ecosystem are poorly understood. Therefore, cattle manure derived hydrochar (CHC) and pyrochar (CPC), and reed straw derived hydrochar (RHC) and pyrochar (RPC) were prepared to investigate their effect on mitigating plant enantioselective bioaccumulation of prothioconazole and metabolites using the 30-day tobacco bioassay, and to clarify the remediation mechanisms underlying hydrochar-remediated prothioconazole-polluted soil-tobacco ecosystem via rhizosphere soil microbiome and metabolite analysis. Char amendments had little effect on prothioconazole bioaccumulation in tobacco tissues, whereas primarily decreased bioaccumulation of prothioconazole-desthio in tobacco roots, following inhibition order of S-enantiomer (63.8-73.4%) > R-enantiomer (67.3-75.6%). Pyrochar efficiently inhibited transfer of prothioconazole-desthio from soils to tobacco roots than hydrochar, with the order of RPC (67.5-71.1%) ≈ CPC (62.7-68.6%) > CHC (48.1-56.4%) ≈ RHC (34.0-47.5%). Hydrochar efficiently weakened the prothioconazole abiotic degradation in the soils could account for decreased bioaccumulation of prothioconazole-desthio in the tobacco roots. The promoted prothioconazole microbially hydroxylated and recruited prothioconazole-degrading bacteria due to enhanced secretion of root exudates (e.g., phenolic acids) were the rhizosphere metabolic mechanisms on prothioconazole enantioselective degradation in the hydrochar-amended soils. These findings provide the basis for developing char-based remediation measures to mitigate prothioconazole pollution.},
}

@article {pmid42248217,
year = {2026},
author = {Steininger, HM and McCauley, KE and Braga, GE and Morin, A and Lee, KE and Visness, CM and Fadrosh, DW and Dapas, M and O'Connor, GT and Bacharier, LB and Rivera-Spoljaric, K and Kattan, M and Lemanske, RF and Zoratti, EM and Martinez, FD and Gold, DR and Hartert, TV and Johnson, CC and Miller, RL and Seroogy, CM and Wood, RA and Togias, A and Jackson, DJ and Gern, JE and Ober, C and Lynch, SV and , },
title = {Upper Airway Microbiome Interacts with GSDMB and ORMDL3 Asthma Risk SNPs to Influence Early-Life Wheeze Risk.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.05.021},
pmid = {42248217},
issn = {1097-6825},
abstract = {BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus increase risk of chronic wheeze and asthma development.

OBJECTIVE: Determine if 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk.

METHODS: Nasal wash samples from 12-month-old infants in two birth cohorts, Childhood Origins of Asthma (COAST; n = 180) and Urban Environment and Childhood Asthma (URECA; n = 139), underwent 16S rRNA V4 sequencing. Nasal microbiota dominated by Moraxella, Streptococcus or Haemophilus (MSH) or Corynebacterium, Dolosigranulum, Staphylococcus or Bacillus (CDSB) were assessed. Paired blood was genotyped for nine 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first three years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389[TT]) were compared to the heterozygous (rs7216389[CT]) line using bulk RNA sequencing.

RESULTS: SNPs, particularly those in the Orsomucoid-like sphingolipid biosynthesis regulator 3 (rs8076131; OR = 1.72, CI = 1.09-2.71, Pint = 0.031) and Gasdermin B (rs2305480, OR = 1.72, CI = 1.09-2.71, Pint = 0.042 and rs7216389, OR = 1.73, CI = 1.09-2.70, Pint = 0.047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate [FDR] Pint = 0.016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389[TT] exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line.

CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.

CLINICAL IMPLICATION: Interventions aimed at decreasing pathogenic bacterial colonization of the airways may reduce wheeze burden in genetically susceptible children.

CAPSULE SUMMARY: Upper airway microbiota interact with asthma-risk genetic variants to influence early-life wheeze risk.},
}

@article {pmid42248250,
year = {2026},
author = {Ortega-Reyes, D and Asami, S and Suda, W and Ohno, H},
title = {Host genetics, diet, and the gut microbiome: Addressing methodological and reproducibility challenges in human studies.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101646},
doi = {10.1016/j.tjnut.2026.101646},
pmid = {42248250},
issn = {1541-6100},
abstract = {The interplay between host genetics, diet, and the gut microbiome is a key focus in human health research. However, progress has been slowed by substantial methodological differences and limited reproducibility across studies. This narrative review examines major sources of variability throughout the research process, with a focus on design, measurement, and analysis. It highlights how factors such as cohort structure, confounder control, dietary assessment, sample collection and preservation, DNA extraction, sequencing methods, and statistical approaches can significantly influence microbiome taxonomic assignments and abundances, and hinder the replication of host-microbiome-diet associations. We discuss how these issues complicate the interpretation of microbiome heritability estimates, genome-wide association signals, and reported gene-diet-microbiome links, which often have small effects and depend heavily on context. We then review ongoing efforts to improve reproducibility and harmonization, including consensus reporting standards, protocol harmonization, and validation techniques such as standardized workflows, mock communities, controls, and absolute quantification methods. Finally, we outline key priorities to enhance cross-study comparability and meta-analyses, including thorough confounder assessment, transparent reporting, and diverse, longitudinal study designs to advance the application of precision nutrition and microbiome-based public health strategies.},
}

@article {pmid42248727,
year = {2026},
author = {Hudson, J and Taylor, N and Coffey, MJ and Pushpakumara, BLDU and Prentice, B and Jaffe, A and Visser, S and Sivam, S and Day, AS and Oliver, M and Ranganathan, S and Selvadurai, H and Wainwright, C and Ooi, CY and van Dorst, J},
title = {Is the gut a reservoir of non-tuberculous mycobacteria in people with cystic fibrosis?.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.06.001},
pmid = {42248727},
issn = {1873-5010},
abstract = {Non-tuberculous mycobacteria (NTM) represent a significant disease burden in the cystic fibrosis (CF) population. Whilst the acquisition of NTM to the respiratory tract is predominantly attributed to environmental exposures, the contribution of the gut-lung axis to NTM pulmonary disease remains poorly understood. In this study, we retrospectively examined 1285 stool microbiomes from 121 children and 52 adults with CF, and 135 healthy control (HC) children, in order to assess the prevalence, abundance and clinical significance of NTM in the gut. We detected various species of low clinical concern in the stool of 2% of people with CF and 1% of HC sampled, with longitudinal sampling revealing their occurrence to be sporadic and transient. Of the participants studied, only 11 had a history of prior clinical NTM respiratory colonisation or infection, but there was limited evidence to support ongoing persistence in the intestinal tract. This study suggests that the gut is not a meaningful reservoir for pulmonary NTM infections and it is unlikely to serve as a transmission route within the CF population.},
}

@article {pmid42248728,
year = {2026},
author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY},
title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.05.016},
pmid = {42248728},
issn = {1873-5010},
abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.

METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.

RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.

CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.},
}

@article {pmid42248767,
year = {2026},
author = {Grant, JM and Tu, C and Roberts, KE and Souza-Fonseca-Guimaraes, F},
title = {Pseudomyxoma peritonei and the microbiome: Emerging observations and unanswered questions.},
journal = {Trends in cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trecan.2026.05.004},
pmid = {42248767},
issn = {2405-8025},
abstract = {Pseudomyxoma peritonei is a rare, heterogeneous appendiceal cancer characterized by mucus-secreting tumor cells. Evidence suggests a microbial association, though its significance remains unclear. This forum article synthesizes links among microbial communities, mucin biology, and tumor behavior, highlighting key research challenges and how spatial multiomics may clarify disease mechanisms and therapeutic opportunities.},
}

@article {pmid42248895,
year = {2026},
author = {Ma, J and Li, Q and Xia, G and Zhang, J and Usman, S and Guo, X},
title = {Lactiplantibacillus plantarum-inoculated silage improves milk fat in dairy goats by reprogramming rumen microbiota to promote pyruvate metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01031-6},
pmid = {42248895},
issn = {2055-5008},
support = {2022YFD130100202//National Key Research and Development Program of China/ ; },
abstract = {Silage inoculated with homofermentative lactic acid bacteria exhibits superior nutritional quality and improves ruminant production performance. However, the mechanisms by which the inoculated silage modulates microbial and metabolic alterations along the rumen-mammary gland axis remain unclear. Here, Lactiplantibacillus plantarum BX62 inoculation enhanced silage quality and flavonoid content through reshaping the microbiome, which promotes carbohydrate-active enzyme secretion. Feeding the silage to dairy goats modulated ruminal microbiota through changes in silage flavonoid, fiber, and crude protein contents. Notably, increased flavonoid intake enriched ruminal flavonoid-degrading bacteria, leading to enhanced flavonoid transformation, fiber degradation, and pyruvate-centered carbohydrate metabolism, promoting acetate production. The increased ruminal acetate and upregulated expression of mammary lipogenic genes ultimately improved milk fat synthesis. Our findings reveal how L. plantarum links silage quality to rumen function and mammary gland metabolism, offering a mechanistic basis for improving lactation performance of dairy goats via modulating silage fermentation.},
}

@article {pmid42248917,
year = {2026},
author = {Yan, W and Huang, C and Li, D and Feng, J and Feng, G and Ma, H and Jansa, J and Klironomos, J and Zhuang, M and Zhang, F and Zhang, L},
title = {The precisely regulated keystone taxa facilitate microbial mineralization of soil organic phosphorus via niche partitioning.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01036-1},
pmid = {42248917},
issn = {2055-5008},
support = {32130094//the National Natural Science Foundation of China/ ; 2022YFD1901304 and 2024YFE0105000//the National Key Research and Development Program of China/ ; MOE, #00975101//the Disciplinary Breakthrough Project of Ministry of Education/ ; PC2024B02003//Pinduoduo-China Agricultural University Research Fund/ ; },
abstract = {Rhizosphere keystone taxa critically drive microbial community stability and soil biogeochemical cycles. However, the manipulation of such taxa remains a challenge. This study simulated plant-mediated modulation of keystone taxa via simplified synthetic root exudates to track their compositional shifts. The combination of luteolin, myristic acid, and glucose enhanced rhizosphere phosphatase activity, significantly enriched Domibacillus indicus D99, and converted it into a keystone taxon. This precise regulation was driven by transcriptional upregulation of C metabolism and an unusual fatty acid assimilation pathway. Additionally, metabolites produced by D. indicus D99 (such as bergapten and lactate) were preferentially utilized by phosphate-mineralizing bacteria, Bacillus sp. C67 and Domibacillus sp. C94. These partner bacteria exhibited less substrate overlap and pronounced resource partitioning, forming an efficient synergistic relationship with D. indicus D99 that amplified rhizosphere phosphatase activity and plant growth. This study highlights opportunities to utilize the ecological roles of keystone taxa in manipulating the microbiome.},
}

@article {pmid42249248,
year = {2026},
author = {Dave, AM and Chatrizeh, M and Wolf, MS and Morowitz, MJ and Simon, DW},
title = {The Role of Microbiome-Associated Metabolites and Their Clinical Implications in Traumatic Brain Injury: A Scoping Review.},
journal = {Neurocritical care},
volume = {},
number = {},
pages = {},
pmid = {42249248},
issn = {1556-0961},
support = {5T32HD040686//Foundation for the National Institutes of Health/ ; NINDS R21 NS115173/NS/NINDS NIH HHS/United States ; NINDS R01 NS127372/NS/NINDS NIH HHS/United States ; },
abstract = {Traumatic brain injury (TBI) is a major public health challenge, with heterogeneous mechanisms and limited targeted therapies. Despite advances in neurocritical care, interventions to meaningfully alter long-term outcomes have been elusive, and treatment remains largely supportive. Parallel to this, increasing evidence from both preclinical models and human studies implicates the gut microbiome as a dynamic modulator of neurologic injury and recovery through the microbiome-gut-brain axis, a bidirectional network linking the central nervous system, gastrointestinal tract, and intestinal microbiota. TBI and neurointensive care including mechanical ventilation, sedation, dietary modification, and antibiotics contribute to the development of dysbiosis and altered production of microbial metabolites. These bioactive molecules, such as short-chain fatty acids, tryptophan metabolites, bile acids, and polyamines, play critical roles in regulating blood-barrier integrity, immune activation, neurotransmission, and energy metabolism. In TBI, emerging preclinical and clinical data suggest that altered levels of these metabolites may influence secondary injury cascades and shape recovery. In this review, we synthesize current TBI-specific preclinical and clinical data on microbiome alterations and microbiome-associated metabolite signaling following TBI, and we place these findings in the broader context of microbiome-gut-brain research. Understanding these pathways could inform future strategies to optimize treatment, including targeted microbiome modulation, dietary interventions, or metabolite supplementation. We identify key knowledge gaps and outline priorities for translational research needed to determine whether monitoring and therapeutic manipulation of the microbiome-gut-brain axis can enhance patients' recovery trajectory.},
}

@article {pmid42249250,
year = {2026},
author = {Xie, J and Yang, Y and Chen, W and Wang, L and Weng, S and Lyu, Q and Cao, G},
title = {Synergistic Intervention for Obesity: Integrating Central Appetite Regulation and Peripheral Energy Expenditure.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {42249250},
issn = {2162-4968},
mesh = {Humans ; *Energy Metabolism/drug effects/physiology ; *Obesity/therapy/physiopathology/metabolism ; *Appetite Regulation/physiology/drug effects ; *Anti-Obesity Agents/therapeutic use/pharmacology ; Animals ; Weight Loss ; Energy Intake ; },
abstract = {PURPOSE OF REVIEW: Obesity stems from a chronic imbalance between energy intake and expenditure. Current therapeutic strategies primarily focus on reducing caloric intake, yet their long-term efficacy is often limited by compensatory metabolic adaptations that lead to weight regain. This review outlines the neural mechanisms through which the central nervous system regulates appetite and the peripheral metabolic pathways that drive adipose thermogenesis. Furthermore, it examines how integrated approaches-spanning from approved to preclinical and clinical-stage investigational agents (e.g., dual- or multi-target agonists), microbiome-targeted interventions (e.g., probiotics), and exercise therapy-can synergistically overcome the limitations of single-pathway strategies. Ultimately, this review provides a theoretical foundation for designing next-generation, personalized, multimodal obesity management regimens.

RECENT FINDINGS: Traditional weight-loss drugs primarily act by centrally suppressing appetite, reducing food intake through modulation of neural circuits in regions such as the hypothalamus. However, studies show that relying on appetite suppression often triggers compensatory metabolic adaptation, ultimately leading to weight regain. Current anti-obesity drug development is therefore shifting toward integrated central-peripheral dual mechanisms. GLP‑1/glucagon dual-receptor agonists and triple-receptor agonists (such as retatrutide) have exhibited unprecedented weight-loss efficacy in clinical trials. These novel agents overcome the limitations of single-target appetite suppression by synergistically integrating central anorexigenic signaling with peripherally mediated increases in energy expenditure, thereby achieving more potent and durable weight reduction. The sustainability of obesity treatment relies on a dual-pronged intervention strategy: suppressing appetite to reduce energy intake while actively promoting energy expenditure, thereby overcoming the metabolic adaptation and weight rebound associated with monotherapy.},
}

Humans
*Energy Metabolism/drug effects/physiology
*Obesity/therapy/physiopathology/metabolism
*Appetite Regulation/physiology/drug effects
*Anti-Obesity Agents/therapeutic use/pharmacology
Animals
Weight Loss
Energy Intake

@article {pmid42249284,
year = {2026},
author = {Wang, L and Li, Y and Zhang, W and Zhao, Y and Lu, Y and Song, J and Guan, W},
title = {Melatonin-mediated dual regulation of physiological-biochemical traits and rhizosphere microbial communities alleviates drought stress in Bougainvillea.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09179-1},
pmid = {42249284},
issn = {1471-2229},
support = {202507AB040003//the Central Guidance for Local Science and Technology Development Fund Project/ ; 202302AE090018//the Key Technologies Research for the Germplasm of Important Woody Flowers in Yunnan Province/ ; },
abstract = {BACKGROUND: Drought conditions limit the distribution of Bougainvillea varieties, reduce their ornamental value, and increase maintenance costs. Although the rhizospheric melatonin-mediated mechanisms of plant drought resistance have been extensively documented. its role in the drought stress response of Bougainvillea, especially the regulatory effect on rhizosphere microorganisms, remains unclear. Using Bougainvillea glabra 'Cypheri' as plant material, this study employed a pot-based natural drought experiment combined with physiological indicator measurement, rhizosphere microbiome high-throughput sequencing, microbial network analysis, PICRUSt2 functional prediction, and redundancy analysis (RDA) to systematically investigate the regulatory mechanisms of melatonin on aboveground-belowground synergistic drought resistance.

RESULTS: Compared with the control group, drought stress significantly enhanced the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as the proline (Pro) content in Bougainvillea, while increasing malondialdehyde (MDA) accumulation. Conversely, leaf relative water content (RWC) and chlorophyll (Chl) content were markedly reduced. Simultaneously, the rhizosphere microbial community balance was disrupted, bacterial network robustness diminished, and carbon metabolic pathways were suppressed. Exogenous melatonin application further significantly enhanced antioxidant enzyme activities and Pro accumulation under drought stress, reduced MDA content, and improved the physiological status of plants. Simultaneously, it promoted the enrichment of Proteobacteria, modulated the abundance balance of Ascomycota, enhanced microbial network stability, and optimized carbon, nitrogen, and energy metabolic pathways. Collectively, these results demonstrate that melatonin enhances drought tolerance in Bougainvillea by regulating the structure and network stability of rhizosphere microbial communities, synergistically improving aboveground drought resistance physiology, and mediating aboveground-belowground synergistic interactions.

CONCLUSION: This study provides a theoretical foundation for the application of melatonin in drought-resistant cultivation practices for Bougainvillea species.},
}

@article {pmid42249293,
year = {2026},
author = {Tang, F and Zhao, C and Cao, Y and Liu, C and Mi, G and Cao, J and Li, Y and Wang, C},
title = {Unraveling microbial signatures in the comorbidity of autoimmune diseases and depression.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05223-0},
pmid = {42249293},
issn = {1471-2180},
support = {tsqn202408369//Taishan Scholars Program of Shandong Province-Young Taishan Scholars/ ; 202328057//Science and Technology Plan Project of Jinan/ ; 82304247//National Natural Science Foundation of China/ ; ZR2022QB152//Natural Science Foundation of Shandong Province/ ; 2021ZD0201808//National Key Research and Development Program of China/ ; 21320082164070//Young Scholars Program of Shandong University/ ; },
abstract = {BACKGROUND: Depression is a common comorbidity in autoimmune diseases (ADs), including inflammatory bowel disease (IBD), a well-characterized AD with prominent gut involvement and strong host-microbiome interactions. Yet, its underlying microbial associations remain insufficiently understood. This study aimed to explore the gut microbial composition and function in patients with ADs comorbid depression, including a subgroup with IBD comorbid depression, and to identify potential microbial and metabolic signatures associated with this comorbidity.

METHODS: We analyzed two curated cohorts from the American Gut Project: an AD cohort (n = 344; AD with depression: n = 115, AD without depression: n = 120, healthy controls: n = 109), and an IBD subgroup (n = 75; IBD with depression: n = 25, IBD without depression: n = 30, healthy controls: n = 20). Gut microbial profiles were evaluated using 16S rRNA gene sequencing (V4 region). Microbial diversity was assessed via α- and β-diversity indices. Differential abundance analysis was conducted using Linear Discriminative Analysis Effect Size (LEfSe) and Linear Discriminant Analysis (LDA) methods. Functional predictions were performed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology inference. Microbial co-occurrence networks were also constructed to explore taxonomic interaction patterns.

RESULTS: In the AD cohort, β-diversity was significantly reduced in patients with comorbid depression compared to those without, whereas α-diversity did not show statistically significant differences. A total of 40 microbial taxa were significantly different between patients with AD comorbid depression and AD without depression. In the IBD subgroup, 12 taxa were differentially abundant between patients with and without depression. Functional pathway predictions suggested disruptions in carbohydrate metabolism, energy metabolism, and glycan biosynthesis in patients with AD and comorbid depression compared to those without depression. Microbial network analysis revealed distinct co-occurrence structures in patients with comorbid depression.

CONCLUSIONS: This exploratory study suggests that individuals with ADs or IBD and comorbid depression exhibit distinct gut microbiome compositions and functional potentials compared to non-depressed counterparts. These associations may offer insights into gut-brain interactions in autoimmunity and mental health. However, due to the cross-sectional design, mechanistic and clinical inferences remain speculative and require validation in future studies.},
}

@article {pmid42249511,
year = {2026},
author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H},
title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42249511},
issn = {2049-2618},
support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.

RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.

CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.},
}

@article {pmid42249581,
year = {2026},
author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W},
title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.},
journal = {Microbial biotechnology},
volume = {19},
number = {6},
pages = {e70397},
pmid = {42249581},
issn = {1751-7915},
support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; },
abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.},
}

@article {pmid42249636,
year = {2026},
author = {Zhang, B and Yue, H and Skalse, A and Sangfuang, N and Shorthouse, D and Gaisford, S and Basit, AW},
title = {High-throughput identification of bacterial β-glucuronidase inhibitors using machine learning.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681789},
doi = {10.1080/19490976.2026.2681789},
pmid = {42249636},
issn = {1949-0984},
abstract = {The human gut microbiome plays a vital role in regulating host physiological functions and influencing the pharmacokinetics of interventions, particularly drug metabolism, which in turn affects pharmacodynamics. Gut microbial β-glucuronidase (GUS) is a key bacterial enzyme that modulates drug therapeutic outcome and gastrointestinal toxicity through deconjugating glucuronidated drug metabolites. Despite this, systematic high-throughput prediction of GUS inhibitors remains limited by sparse experimental data and the translational shortcomings of known compounds. Here, machine learning is applied as a powerful tool to identify potential GUS inhibitors from more than 10,000 FDA-approved drugs, food additives, and excipients. In this study, both unsupervised and supervised machine learning models were trained on literature-derived data describing the inhibitory potency of 122 compounds against Escherichia coli GUS (EcGUS). These models were compared with a newly developed SMILES-based 1D feature-embedded, self-attention classification model (IC-tf) designed for high-throughput screening. To improve interpretability, a dual-level analysis that combines SHAP attribution of handcrafted descriptors with branch-level transformer attention was applied to the IC-tf model. All models demonstrated strong predictive performance, with ROC-AUC values of 85.9%-89.3% under 3-fold cross-validation, with the IC-tf model showing the highest predictive power. In vitro validation with an external set of 20 compounds confirmed strong predictive accuracy for the Random Forest and IC-tf models. This work establishes a scalable computational framework for high-throughput discovery of gut microbial GUS inhibitors, facilitating efficient screening of co-administered drugs and excipients with the translational potential to improve drug bioavailability and reduce gastrointestinal toxicity.},
}

@article {pmid42249801,
year = {2026},
author = {Bivens, E and Atiq, O and Evans, T and Bimali, M and Brown, G and Crane, J and Darwish, N and Faulkner, JL and Govindarajan, R and Johnson, A and Kurilung, A and Lazarenko, O and Lu, YW and Marsh, K and Moreno, M and Nookaew, I and Robeson, M and Sunde, J and Ussery, D and Vural, E and Wilman, M and Nakagawa, M},
title = {A randomized double-blind placebo-controlled phase I/II clinical trial of a human papillomavirus therapeutic vaccine, PepCan, for reducing head and neck squamous cell carcinoma recurrence.},
journal = {Oncotarget},
volume = {17},
number = {1},
pages = {291-305},
doi = {10.18632/oncotarget.28892},
pmid = {42249801},
issn = {1949-2553},
abstract = {UNLABELLED: Copyright: &copy; 2026 Bivens et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

OBJECTIVES: The main goals were to assess safety and efficacy (i.e., recurrence reduction).

RESULTS: Seventeen patients were enrolled. The most common adverse events were grades 1 and 2 injection site reactions, and they occurred more frequently in the PepCan group (p < 0.0001). Two patients had allergic reactions (grade 2 and grade 3), at the 6th vaccination, which were considered to be a dose-limiting toxicity. No serious adverse events were reported. In the intention-to-treat analyses, 45% (5/11) had non-recurrence in the PepCan group while 80% (4/5) had non-recurrence in the placebo group (p = not significant). Those who received PepCan and experienced non-recurrence showed a trend of having higher new peripheral T cell immune responses to human papillomavirus type 16 E6 (p = 0.05). Pre-vaccination T helper type 1 cells were higher in the PepCan non-recurrence group compared to the PepCan recurrence group (p = 0.01).

METHODS: PepCan consists of four human papillomavirus type16 E6 peptides and a Candida skin testing reagent. Patients with head and neck squamous cell carcinoma who had no evidence of disease after standard of care treatments were randomized at 3:1 to PepCan versus placebo (saline). Seven intradermal injections were given followed with two observational visits. Safety was assessed using CTCAE version 5, and efficacy was assessed based on not having recurrence within 2 years. In addition, immune responses and oral and gut microbiome were assessed.

CONCLUSIONS: PepCan was well tolerated. PepCan does not seem to be effective in reducing recurrence; however, the results are inconclusive given the small patient numbers.},
}

@article {pmid42249994,
year = {2026},
author = {Faridi, U and Mir, R and Algehainy, NA and Alharbi, ZM and Tayeb, FJ and Barnawi, J and Jalal, MM and Altayar, MA and Moawadh, M and Mustafa, SK and Mir, MM and Alfaifi, J and Almazni, IA},
title = {Understanding the mechanisms underlying obesity induced tumorigenesis: therapeutic perspectives to manage dysregulated lipid metabolism.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-05200-z},
pmid = {42249994},
issn = {2730-6011},
abstract = {Obesity has emerged as one of the most significant global public health challenges of the twenty-first century and is now firmly established as a major risk factor for multiple cancer types. Hypertrophic adipose tissue generates chronic low-grade inflammation, adipose hypoxia, and fibrosis, which leads to activation of IL-6/STAT3, NF-κB, and PI3K/Akt/mTOR signaling. Hyperinsulinemia and insulin resistance increase oncogenic pathways, while dysregulated adipokines by elevated leptin and reduced adiponectin enhance proliferation, angiogenesis, epithelial mesenchymal transition, and immune evasion. Obesity further remodels the tumor microenvironment by promoting extracellular matrix deposition, angiogenesis, immunosuppressive cell expansion, and metabolic competition that impairs antitumor immunity. Emerging evidence also implicates obesity-driven epigenetic reprogramming, altered microbiome composition, and metabolic heterogeneity as key determinants of tumor aggressiveness and treatment response. Conventional oncologic therapies rarely account for host metabolic status, which may contribute to variable therapeutic efficacy in obese patients. This review integrates mechanistic and translational evidence to define actionable vulnerabilities within obesity-induced tumorigenic pathways. We evaluate targeted metabolic interventions, cytokine blockade, adipokine modulation, immune checkpoint optimization, microbiome-directed strategies, and precision stratification frameworks. The present review outlines a multidimensional therapeutic roadmap to improve prevention, treatment response, and long-term outcomes in obesity-associated malignancies.},
}

@article {pmid42250036,
year = {2026},
author = {Prajapati, KK and Pandey, R and Pandey, V and Upadhyay, KM and Singh, S and Pandey, VS and Pandey, VN},
title = {Unveiling the Nutraceutical Potential of Yam Dioscorea alata L.: A Comprehensive Review.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {81},
number = {2},
pages = {},
pmid = {42250036},
issn = {1573-9104},
abstract = {Dioscorea alata L. (water yam and purple yam) is a traditionally important food and medicinal plant widely used in Asia and the Pacific Islands. It has long been utilized in traditional medicine for treating weakness, inflammation, menstrual disorders, wound healing, and gastrointestinal ailments. The dual role as a dietary and therapeutic resource highlights its ethnopharmacological importance and supports the need for scientific validation. This review evaluates existing knowledge on the nutraceutical potential of D. alata. Recent studies report diverse biological activities, including antioxidant, anti-inflammatory, antidiabetic, anticancer, antihypertensive, cardioprotective, and gut microbiome-modulatory effects. These activities are largely attributed to bioactive compounds such as saponins and anthocyanins. The species shows considerable promise as a functional food and natural therapeutic resource. Moreover, its cultivation and utilization may contribute to food security and public health (SDG 2 and 3). Further, phytochemical and clinical studies are required to fully establish its nutraceutical value.},
}

@article {pmid42250066,
year = {2026},
author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W},
title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42250066},
issn = {1559-0291},
support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; },
abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.},
}

@article {pmid42250132,
year = {2026},
author = {Dweh, TJ and Taye, M and Deka, D and Samanta, SK and Talukdar, NC},
title = {Fusobacterium nucleatum in oral squamous cell carcinoma: molecular mechanisms, tumor microenvironment and translational implications.},
journal = {Archives of microbiology},
volume = {208},
number = {8},
pages = {},
pmid = {42250132},
issn = {1432-072X},
abstract = {Fusobacterium nucleatum has increasingly emerged as a microorganism of major interest in microbial dysbiosis-associated carcinogenesis, particularly in oral squamous cell carcinoma (OSCC), where chronic inflammatory remodeling, immune dysfunction, and epithelial plasticity contribute to aggressive tumor behavior and poor clinical outcomes. Recent experimental findings suggests that F. nucleatum may participate in multiple biologic processes linked to OSCC progression, including activation of inflammatory signaling pathways, disruption of epithelial integrity, metabolic adaptation, immune checkpoint-associated suppression, and resistance-related phenotypes. In this review, we critically evaluate current evidence regarding the molecular and cellular interactions of F. nucleatum within the OSCC tumor microenvironment, with particular emphasis on FadA- and Fap2-associated signaling, β-catenin-, NF-κB-, and STAT3-mediated pathways, epithelial-mesenchymal transition (EMT), stromal remodeling, and immune exhaustion signatures. We additionally examine the growing application of spatial transcriptomics, single-cell sequencing, and integrated multi-omics approaches for host-microbe characterization in OSCC. Importantly, current findings remain heterogeneous and context-dependent, varying according to tumor site, HPV status, microbial burden, host immune composition, and methodological variability across studies. Although microbiome-informed biomarkers and therapeutic strategies are increasingly being explored, most remain at early experimental stages and require robust OSCC-specific mechanistic and clinical validation before translational implementation.},
}

@article {pmid42250135,
year = {2026},
author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M},
title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42250135},
issn = {1573-0972},
abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.},
}

@article {pmid42250251,
year = {2026},
author = {Mirzai, M and Eslami, M and Azizi, AH and Lotfi, P and Alavi Khoshhall, SA and Mirzaei, A and Habibi, MA},
title = {Interplay Between the Ketogenic Diet and the Gut Microbiome in Glioblastoma: A Comprehensive Review of Mechanisms and Clinical Implications.},
journal = {Nutrition and cancer},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/01635581.2026.2684070},
pmid = {42250251},
issn = {1532-7914},
abstract = {Glioblastoma (GBM) is an aggressive glioma associated with poor prognosis and a median survival of under one year. Standard therapies-surgery, radiotherapy, and temozolomide-impose substantial financial burdens and reduce quality of life, driving interest in less invasive adjunctive approaches. The ketogenic diet (KD) has shown promise by targeting tumor metabolic vulnerabilities, as GBM cells rely heavily on glucose and exhibit limited capacity for ketone metabolism. Although KD is well-validated in epilepsy and diabetic ketoacidosis, its application in GBM yields inconsistent results due to small trials, low adherence, and variability in study designs. Emerging evidence suggests that interindividual differences in gut microbiota (GM) composition may significantly contribute to this inconsistency. GM modulates host metabolism, influences KD efficacy, and exhibits bidirectional interactions with tumor progression. Notably, glioma patients display distinct GM profiles that may alter therapeutic responses. This comprehensive review synthesizes current literature on the interplay between KD and GM in GBM, highlighting mechanisms by which GM variability affects metabolic outcomes. Understanding these interactions is essential to reconcile discrepant findings and optimize patient selection for KD-based interventions, ultimately advancing personalized metabolic strategies in neuro-oncology.},
}

@article {pmid42250371,
year = {2026},
author = {Maerten, P and Wolthuis, A and D'Hoore, A and Bislenghi, G and De Hertogh, G and Sagaert, X and Dresen, R and Broeckhoven, V and Rasschaert, G and Tejpar, S and Van Herpe, F and Van Cutsem, E and Dekervel, J and Haustermans, K},
title = {Multi-omic biomarkers of neoadjuvant treatment response in rectal cancer: A narrative review.},
journal = {European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology},
volume = {52},
number = {8},
pages = {111910},
doi = {10.1016/j.ejso.2026.111910},
pmid = {42250371},
issn = {1532-2157},
abstract = {BACKGROUND: Neoadjuvant treatment response in rectal cancer is highly heterogeneous, complicating patient selection for organ-preservation strategies. Robust biomarkers capable of accurately predicting treatment response are needed to improve personalized treatment decisions.

METHODS: We conducted a narrative review of studies published since 2015 evaluating predictors of response to neoadjuvant therapy in rectal cancer. A comprehensive PubMed/MEDLINE search identified evidence across six domains: (1) genomic and molecular biomarkers, (2) imaging-based biomarkers, (3) histopathological and digital pathology biomarkers, (4) liquid biopsy biomarkers (cfDNA and ctDNA), (5) patient-derived tumor models and (6) microbiome-associated biomarkers.

RESULTS: Treatment response in rectal cancer reflects a complex interplay between tumor-intrinsic, immune microenvironment and stromal features. Immune-enriched tumors, characterized by high intratumoral CD8[+] T-cell infiltration, CMS1/iCMS3 subtype and high Immunoscore, consistently demonstrate higher rates of pathological and clinical complete response. Conversely, KRAS, TP53, BRAF and SMAD4 mutations, fibroblast activation, TGFβ signaling, inflammatory cancer-associated fibroblasts and epithelial-mesenchymal transition programs are associated with treatment resistance. Artificial intelligence applied to MRI, endoscopy and digital pathology enables accurate response prediction, particularly when incorporating longitudinal features. Emerging technologies including ctDNA monitoring, patient-derived tumor models and microbiome profiling provide additional insight into treatment sensitivity and show promise for predicting treatment response.

CONCLUSIONS: Neoadjuvant treatment response in rectal cancer is dependent on genomic alterations, immune activation and stromal interactions. AI-driven biomarkers hold promise for personalized treatment and organ-preservation. Prospective, multicenter validation is essential to enable further clinical implementation.},
}

@article {pmid42250690,
year = {2026},
author = {Chao, Z and Zhang, Q and Pang, L and Sheng, Y and Zhang, J and Feng, T and Yu, L and Shi, W and Xu, Z and Huang, J and Chen, J},
title = {Copper-based nanoparticles trigger fitness decline in parasitoid wasps via gut microbiota-induced fatty acid dysregulation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128501},
doi = {10.1016/j.envpol.2026.128501},
pmid = {42250690},
issn = {1873-6424},
abstract = {The application of copper-based nanoparticles (Cu-based NPs, e.g., CuO-NPs and Cu-NPs) as nanopesticides represents a promising avenue for sustainable agriculture. However, their potential ecotoxicological effects on beneficial arthropods, particularly parasitoid wasps which are crucial for biological pest control, remain poorly understood. Here, we investigated the chronic toxicity of CuO-NPs and Cu-NPs to the endoparasitoid wasp Asobara japonica and elucidated the underlying mechanisms. We found that dietary exposure induced concentration-dependent lethality, primarily driven by released copper ions rather than the particles themselves. Sublethal exposure severely impaired wasp fitness, with reduced host-searching locomotion thereby mediating a decline in parasitism efficiency. Mechanistically, integrated transcriptomic and metabolomic analyses revealed a coordinated downregulation of some key genes in fatty acid homeostasis pathways and a consequent decline in free fatty acid levels. This disruption in energy mobilization likely compromised the energy supply necessary for sustained activity, thereby explaining the observed locomotion behavioral deficits. Furthermore, Cu-based NPs exposure selectively altered the rare gut microbiota, and shifts in specific bacterial genera correlated with the suppression of host fatty acid metabolism genes. Our results demonstrate that Cu-based NPs impair parasitoid wasp fitness through the disruption of gut microbiome homeostasis and energy metabolism, highlighting the need to consider these impacts in nanomaterial risk assessment for sustainable agriculture.},
}

@article {pmid42250808,
year = {2026},
author = {Sabina, R and Kharmawphlang, IM and Charan, K and Hussain, N},
title = {Per- and polyfluoroalkyl substances stress in soil ecosystems: decoding microbial dysbiosis mechanisms and advanced remediation strategies.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135036},
doi = {10.1016/j.biortech.2026.135036},
pmid = {42250808},
issn = {1873-2976},
abstract = {Per- and polyfluoroalkyl substances (PFAS), the so-called "forever chemicals," are emerging contaminants that severely disrupt soil ecosystems by rewiring microbial networks that sustain biogeochemical processes. This review deciphers the mechanisms underlying PFAS-induced microbial dysbiosis, revealing how these contaminants reconfigure community architecture, metabolic functions, and enzyme-mediated processes critical for biogeochemical cycling. It further integrates multi-omics approaches, spanning genomics to metabolomics, to elucidate molecular signatures and adaptive responses that govern microbial resilience and vulnerability across trophic hierarchies. Furthermore, the review examines PFAS biotransformation pathways, emphasising oxidoreductase-mediated mechanisms, kinetic bottlenecks, and catalytic constraints within complex soil matrices. By bridging microbial ecology with advanced material science, the review introduces a transformative paradigm of hybrid catalytic systems, including nanozyme-enabled transformations, engineered enzymes, and photocatalytic assemblies for targeted PFAS degradation. Thus, by linking microbial dysfunction with engineered catalytic innovation, the review offers a systems-level blueprint for sustainable and efficient strategies to restore PFAS-contaminated soils. Notably, this review highlights the urgent need for integrated multidisciplinary approaches to mitigate PFAS-induced ecological risks and advance sustainable soil restoration technologies.},
}

@article {pmid42250809,
year = {2026},
author = {Xia, X and Babar, S and Wang, J and Yan, B and Jiang, C},
title = {Nitric acid-modified biochar ameliorates saline-alkali soil and promotes cotton growth by regulating microbiomes and metabolites.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135087},
doi = {10.1016/j.biortech.2026.135087},
pmid = {42250809},
issn = {1873-2976},
abstract = {Biochar is extensively utilized for saline-alkali soil remediation; however, the effects of feedstock origin on its performance remain unclear. Moreover, there is a growing need to develop modified biochar with improved efficiency in saline-alkali soil. Therefore, cotton straw biochars derived from saline-alkali soil (SBC) and non-saline-alkali (NBC), along with their nitric acid-modified forms (HSBC and HNBC), were prepared and assessed via a cotton pot experiment. The results showed that the pH and total soluble salts (TSS) of SBC were significantly higher than those of NBC by 0.33 units and 306.80%, respectively. Nitric acid modification significantly reduced the pH value, salt and alkaline mineral content of biochar, and enriched acidic oxygen-containing functional groups. Meanwhile, SBC treatment increased the contents of Na[+], HCO3[-] and CO3[2-] in soil and showed no promoting effect on cotton growth. In contrast, the acid-modified biochar treatment reduced soil pH by 0.25-0.32 units, decreased TSS by 9.81%-12.11%, and significantly increased cotton dry biomass by 3.63-3.88 times. In addition, acid-modified biochar increased the complexity of the soil microbial network and promoted the enrichment of acid-producing microorganisms as well as stress-resistant microbial groups, such as Actinobacteria and Nocardioides. Simultaneously, it significantly induced the production of metabolites that enhance plant tolerance to saline-alkali stress, such as flavonoids and betalamic acid. In summary, acid-modified biochar enhances its beneficial effects on soil improvement and cotton growth through the coordinated regulation of rhizosphere acid-producing microorganisms and stress-responsive metabolites. This work highlights the scientific significance of biochar modification for advancing sustainable agriculture in saline-alkali regions.},
}

@article {pmid42250830,
year = {2026},
author = {Chen, L and Yuan, S and Wang, R and Chen, L and Zhang, B and Zhang, Z and Zhao, Y and Feng, W and Zheng, X and Li, K and Zhou, N},
title = {Revealing the enhancing mechanism and material basis of bile-processed Coptidis Rhizoma in anti-anxiety from perspective of cross organ regulation.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121969},
doi = {10.1016/j.jep.2026.121969},
pmid = {42250830},
issn = {1872-7573},
abstract = {Coptidis Rhizoma (CR) is a typical cold-attribute herb with potential anti-anxiety properties. Bile is of cold nature and can also interfere with the central nervous system. Bile-processed CR (BCR) exhibits synergistically enhanced anti-anxiety performance. However, the underlying mechanism and material basis for this synergism are not clear.

AIM OF THE STUDY: To decipher the enhanced anti-anxiety mechanism and material basis of BCR from the perspective of cross-organ regulation.

METHODS: A rat model of anxiety with sthenic heat syndrome was established to systematically evaluate the enhanced anti-anxiety efficacy of BCR in terms of anxiety behaviour, liver metabolism, and histopathology. Subsequently, the gut microbiome sequencing and untargeted metabolomics of the brain, liver, and serum were performed to explore the mechanism of BCR and CR in regulating the gut-liver-brain axis. In vivo and in vitro molecular biology experiments were performed to further clarify the mechanisms underlying the differential efficacy of BCR and CR. Finally, supramolecular self-assembly simulation and tissue distribution in target organs were carried out to predict the material basis for the enhanced efficacy of BCR.

RESULTS: BCR performed better than CR in improving the anxiety behaviour and liver metabolism and in alleviating cerebral injury in the rat model of anxiety. The results of gut microbiome and metabolomic analyses indicated that BCR was superior to CR in reshaping the gut microbiota composition and correcting the metabolic disorders in the brain, liver, and serum. Mechanistically, multiomic analysis revealed that BCR and CR (especially BCR) could block the TLR4/NF-κB pathway in the colon, attenuate hepatic inflammation, improve the integrity of the intestinal mucosa and blood-brain barrier, and inhibit the NLRP3/Caspase-1/IL-1β pathway in the brain, thereby blocking the transmission of inflammation along the gut-liver-brain axis and exerting anti-anxiety effects. BCR and CR (particularly BCR) could suppress the overactivation of ammonia-induced MAPK/NF-κB/iNOS pathway and overexpression of glutamine synthetase in the brain, consequently maintaining the normal morphology and glutamate uptake function (GLAST and GLT-1 activities) of astrocytes, alleviating neuronal apoptosis caused by glutamate excitotoxicity (GluN2B), and ultimately blocking the transmission of neurotoxicity along the gut-liver-brain axis to relieve anxiety. The alkaloid-bile acid supramolecules assembled during the decoction of BCR enabled more alkaloids and bile acids to be distributed in the brain and liver, providing material support for the enhanced effect of BCR.

CONCLUSIONS: BCR was superior to CR in blocking the transmission of inflammation and neurotoxic substances along the gut-liver-brain axis and, hence, exerted stronger efficacy in alleviating neuroinflammation and improving neuronal survival in the rat model of anxiety. The alkaloid-bile acid supramolecules may provide the material foundation. This study fully considers the characteristic of traditional Chinese medicine being able to exert therapeutic effects through multiple pathways, providing novel avenues for research on the processing mechanism.},
}

@article {pmid42251030,
year = {2026},
author = {Yang, J and Qin, K and Wang, Q and Guo, W and Yang, X},
title = {Gut commensal Parabacteroides goldsteinii-derived CDCA mediates FXR signalling to improve mucosal barrier function.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01035-2},
pmid = {42251030},
issn = {2055-5008},
support = {32502961//National Natural Science Foundation of China/ ; 32272916//National Natural Science Foundation of China/ ; 2023YFD1301400//National Key Research and Development Program of China/ ; },
abstract = {The gut microbiome plays a crucial role in maintaining barrier integrity. However, it remains urgently needed to mining the gut microbiota that contribute to intestinal mucus barrier and to understand their biological mechanisms. In this study, the Lueyang black-boned chicken (LBC, a Chinese native breed) exhibited higher abundances of Bacteroidetes and Parabacteroides and stronger intestinal barrier function than Arbor Acres (AA, a commercial breed) broilers. Microbiota transplantation from LBC to AA broilers improved the intestinal barrier function. Bacteroides expanded the exclusive metabolic niche of Parabacteroides goldsteinii by producing small metabolites, thereby increasing P. goldsteinii abundance within the gut. P. goldsteinii was identified as the main contributor to the enhanced intestinal mucosal barrier. P. goldsteinii bio-transformed the taurochenodeoxycholic acid into chenodeoxycholic acid, promoting mucin production via farnesoid X receptor activation. Collectively, these findings highlight that the gut microbiota of LBC creates an exclusive metabolic niche for P. goldsteinii through cross-feeding, and reveal the critical role of P. goldsteinii-mediated bile acid biotransformation in enhancing intestinal mucosal barrier function.},
}

@article {pmid42251226,
year = {2026},
author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR},
title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.},
journal = {Journal of natural medicines},
volume = {},
number = {},
pages = {},
pmid = {42251226},
issn = {1861-0293},
support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; },
abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.},
}

@article {pmid42251237,
year = {2026},
author = {Zheng, W and He, XR and Zheng, JW and Zhu, ZY and Ye, DY and Jia, XY and Xu, QC and Jiang, MZ},
title = {Effects of Helicobacter pylori infection on gastric mucosal microbiota.},
journal = {World journal of pediatrics : WJP},
volume = {},
number = {},
pages = {},
pmid = {42251237},
issn = {1867-0687},
support = {2023YFC2706504//Key Technologies Research and Development Program/ ; 2023YFC2706500//Key Technologies Research and Development Program/ ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) is a Gram-negative obligate pathogen that colonizes the human gastric environment. Its identification fundamentally altered the historical perception of the stomach as sterile, marking a pivotal shift in gastric microbial research. For 30 years, the dynamic interplay between this bacterium and the gastric lining has been a key research focus.

DATA SOURCES: The development of next-generation sequencing and advanced bioinformatics has provided powerful, culture-independent tools for probing the intricate diversity of the gastric microbiome. Current investigations extensively cover microbe-microbe interactions within the stomach, the relationship between the resident microbiota and H. pylori, and the dialogue between the microbiome and the host.

RESULTS: This article reviews current evidence detailing how H. pylori infection reshapes the microbial community on the human gastric mucosa.

CONCLUSION: Future research employing integrated multi-omics strategies is essential to unravel the long-term consequences of H. pylori on the mucosal ecosystem and host physiology.},
}

@article {pmid42251252,
year = {2026},
author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE},
title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13715-7},
pmid = {42251252},
issn = {1471-2334},
support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; },
abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.

METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.

RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n = 24; n = 8 previously diagnosed) and rhinovirus (n = 18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.

CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.},
}

@article {pmid42251273,
year = {2026},
author = {Li, L and Xu, M and Liu, M and Mao, J and Xiong, P and Li, R and Chen, J and Wu, X},
title = {Metatranscriptomic analysis of upper and lower respiratory tract microbiomes in patients with tuberculosis and community-acquired pneumonia.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13614-x},
pmid = {42251273},
issn = {1471-2334},
support = {31970174//National Natural Science Foundation of China/ ; 2023YFC260550//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Although changes in the lung microbiome have been observed in many respiratory diseases, the lung microbiome of patients with tuberculosis (TB) remains largely undefined. The aim of this study was to determine and compare the composition of upper and lower respiratory microbial communities, changes in host gene expression, and functional pathway activation in patients with TB and community-acquired pneumonia using a Metatranscriptomic approach.

METHODS: From November 2020 to November 2021, 42 bronchoalveolar lavage fluid samples, 10 oropharyngeal swabs, and 10 nasopharyngeal swabs were collected from patients hospitalized with TB or community-acquired pneumonia for RNA-sequencing, within 72 h of admission. Data from 28 healthy controls were downloaded from the National Center for Biotechnology Information database.

RESULTS: The most common microorganisms in the samples from patients with TB were Prevotella, Escherichia, Mycobacterium, and Verrucoccus. Notable differences in microorganism diversity were observed between the TB and community-acquired pneumonia groups as well as between the upper and lower respiratory tracts compared to that in healthy controls. Altered microbial interactions were also observed. Rothia and Mycobacterium were identified as marker microorganisms in the TB group, which exhibited increased expression of SNAP25, MGAM2, CNTN4, MMP12, and GPR174, in parallel to IL36A, RHCG, and CYP2B6 downregulation relative to the community-acquired pneumonia group. The pathways enriched for differential genes were similar among all patient groups, particularly involving neuroactive ligand receptor interaction and Ca[2+] signaling. Patients with TB differed from those with community-acquired pneumonia, particularly with regard to the cytokine-cytokine receptor interaction pathway. The most commonly detected antibiotic resistance genes conferred resistance against β-lactams and macrolides. Antibiotic resistance genes were more abundant in oropharyngeal than in nasopharyngeal samples.

CONCLUSIONS: The composition of microbial communities and host expression landscapes differs between TB and community-acquired pneumonia as well as between different respiratory tract sites. These changes in lung microbiota may impact lung disease development and prognosis.},
}

@article {pmid42251288,
year = {2026},
author = {Ramirez, SC and Lewis, ZJ and Hale, VL and Coffey, EL},
title = {Impact of sample processing method and volume on 16 S rRNA profiling of the urobiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05274-3},
pmid = {42251288},
issn = {1471-2180},
support = {T35OD011118/NH/NIH HHS/United States ; 1K08ES034821-01A1/NH/NIH HHS/United States ; K12TR004373/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The urinary microbiome (urobiome) plays important roles in both human and animal urogenital tract health. Characterization of these microbial communities presents several technical challenges, largely due to the low microbial biomass of urine. Whereas other low biomass liquid systems, such as aquatic samples, frequently employ small-pore vacuum filtration for microbial DNA concentration, urobiome studies have traditionally relied on centrifugation and pelleting of smaller volumes. Therefore, this study compared the effects of processing method (vacuum filtration versus pelleting) and sample volume on bacterial DNA yield, contaminant burden, and microbial diversity in canine urine.

RESULTS: A total of 50 urine aliquots were obtained across samples. Urine from 15 healthy dogs was pooled into five unique batches and divided into duplicate aliquots at volumes of 1, 3, 10, 30, and 50 mL. One aliquot was pelleted and one filtered (0.2 μm pore filter) prior to DNA extraction of the pellet or filter, respectively, and 16 S rRNA gene (V4) sequencing. Three aliquots ≥ 30 mL could not be filtered due to clogging. Sequence depth, DNA recovery, contaminant abundance, and microbial diversity were similar across urine volumes. Filtered samples contained a higher proportion of reads classified as contaminants (𝑃 = 0.002). Although beta diversity differed between methods (Bray-Curtis PERMANOVA, P = 0.007), the effect size was small (R[2] = 0.03) relative to the influence of urine batch (𝑃 = 0.001, R[2] = 0.65).

CONCLUSIONS: These findings indicate that interindividual variation predominates over methodological effects. Higher urine volumes (≥ 30 mL) were associated with technical challenges in filtered samples, whereas moderate urine volumes (1-10 mL) appear sufficient for urobiome characterization. Similar microbial recovery, increased contaminant signal, and occasional clogging with filtration suggests that pelleting remains an appropriate approach for urobiome characterization.},
}

@article {pmid42251420,
year = {2026},
author = {Helmbrecht, H and Ardalan, M and Kelly, L and Robinson, S and Fleiss, B and Doherty, DG and Gressens, P and Mallard, C and Molloy, EJ and Jantzie, LL},
title = {The role of persistent inflammation in failed recovery after perinatal brain injury: is resolution the cure?.},
journal = {Journal of neuroinflammation},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12974-026-03900-5},
pmid = {42251420},
issn = {1742-2094},
abstract = {Perinatal brain injury (PBI) is a major predictor of neurological disability. Commonly associated with prematurity, infection, stroke, hypoxia-ischemia, hemorrhage, and/or toxin exposure, PBI triggers acute and persistent systemic inflammation. There are many stages of vulnerability to PBI during development including pregnancy, birth - term and preterm, and neonatal age. The vulnerable stages can compound inflammation through injury to the placental-fetal-brain axis, adaptive and innate immune system development, neural-immune communication, and central nervous system maturation. Neonates exhibit unique inflammatory signatures and lasting neural-immune responses to various etiologies. Chronic immune dysregulation and priming to a secondary, later-in-life immune challenge defines different forms of PBI while shaping the neonatal and adult immune response with long-term changes. Immunomodulated changes impact regulatory, helper and innate T cells, neutrophils, natural killer cells and immune responsiveness. The major routes of persistent and compounding inflammation in PBI are perinatal neural-immune interactions, cytokine influx, and glial crosstalk. Most treatments are not administered long enough or in the optimal time window to combat sustained inflammation in tertiary and quaternary phases of PBI pathophysiology and are ineffective in reducing neonatal mortality and morbidity and promoting functional recovery. Indeed, persistent systemic and central inflammation is a likely explanation for failed recovery of PBI after the resolution of acute insults. We propose attenuating persistent inflammation and normalizing systemic immune reactivity as key to reducing the functional impact of PBI throughout the lifespan through various avenues including therapeutic treatment, gut microbiome modulation, and novel immunomodulation from preclinical research.},
}

@article {pmid42251450,
year = {2026},
author = {Tan, L and Liu, X and Ma, Y and Yang, J and Zhang, Q and Zhang, J and Bai, B and Ma, H and Meng, R and Degen, A and Palevich, N and Shi, P and Hao, L},
title = {The price of survival: comparative adaptation to high altitudes between yaks and cattle.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00584-3},
pmid = {42251450},
issn = {2524-4671},
support = {2024-ZJ-905//Qinghai Provincial Natural Science Fund for Distinguished Young Scholars/ ; 2025KTST04//Qinghai University Research Ability Enhancement Project/ ; 2022YFD1302103//the National Key R&D Sub-project/ ; 2025, L.Z.H.//Qinghai University Graduate Supervisor Innovation Team/ ; 2019QZKK0606//Special Topics of the Second Comprehensive Scientific Expedition of the Qinghai-Tibet Plateau/ ; QHKLYC-GDCXCY-2024-071, L.Z.H.//Leading talent of "Kunlun Talents High-level Innovation and Entrepreneurial Talents" in Qinghai Province/ ; },
abstract = {The yak (Bos grunniens) serves as an exceptional model for studying high-altitude adaptation mechanisms due to its evolutionary success in the hypoxic environment of the Qinghai-Tibet Plateau. Previous research has largely focused on genetic and physiological traits of yaks; however, the interactions between rumen microbiota and host physiology under hypoxic conditions are poorly understood. As the largest digestive organ in ruminants, the rumen and its microbiota play a central role in digestion and host nutrition. In this study, a comparative analysis of digestive metabolism and rumen microbiota was carried out in yaks and cattle (Bos taurus) under two distinct atmospheric oxygen scenarios: baseline (2,200 m) and hypoxic (3,800 m). Our findings reveal that yaks have developed unique microbial strategies to cope with energy deficits in hypoxic stress. These strategies include a shift in rumen microbiota toward amino acid degradation, providing more available energy substrates for host utilization, and enhanced long-chain fatty acid biosynthesis, enabling more efficient energy storage and utilization. This improves energy acquisition in yaks despite their reduced nutritional intake. However, this metabolic adaptation comes at a physiological cost - reduced microbial crude protein (MCP) synthesis, leading to elevated ruminal NH3-N levels, and increased fatty acid metabolism and urea cycle activity contributing to hepatic stress. Our results showed that under high-altitude conditions, yak MCP synthesis decreased by 47.3%; and ruminal NH3-N and serum ALT (a hepatic stress marker) increased by 147.2 and 19.7%, respectively. This study presents evidence of potential metabolic trade-offs in high-altitude adaptation, indicating that yaks may optimize microbially mediated energy production at the cost of liver health. These insights deepen our understanding of host-microbiome coevolution mechanisms in extreme environments and highlight biological costs associated with adaptation to high altitudes.},
}

@article {pmid42251689,
year = {2026},
author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X},
title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag090},
pmid = {42251689},
issn = {1536-4844},
support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; },
abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.

METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.

RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P = .040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P < .05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.

CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.},
}

@article {pmid42251779,
year = {2026},
author = {Leiva-Soto, S and Rubilar, O and Fincheira, P and Fernández-Baldo, M and Fernández-Triana, and Schoebitz, M and Larama, G and Rodriguez, R and López-Mena, E and Tortella, GR},
title = {Soil microbial functional recovery and community resilience driven by biogenic magnetite nanoparticles under carbendazim stress.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128573},
doi = {10.1016/j.micres.2026.128573},
pmid = {42251779},
issn = {1618-0623},
abstract = {The persistence of fungicides in agricultural soils poses a major threat to soil health, as these compounds disrupt microbial communities and compromise key ecosystem functions. Carbendazim, a commonly used systemic fungicide, is known for its ability to inhibit microbial activity and nutrient cycling. This study assessed the capacity of biogenic magnetite nanoparticles to mitigate carbendazim-induced disturbance and facilitate the recovery of soil microbial function. Citrate-stabilized magnetite nanoparticles were applied to an agricultural Andisol intentionally contaminated with carbendazim (10 mg kg[-1]) under controlled microcosm conditions. Soil enzyme activities related to carbon, nitrogen, and phosphorus cycling (β-glucosidase, urease, acid phosphatase), microbial gene abundances (16S rRNA, amoA, amoB copy number), community structure, and pesticide dissipation kinetics were measured for a 30-day period. Magnetite nanoparticles significantly accelerated carbendazim dissipation, reducing their half-life by approximately 50% compared to pesticide-only treatments. Nanoparticle application partially mitigated the inhibitory effects of carbendazim on soil enzymes. It showed trends towards the recovery of bacterial and nitrifier abundances, with community composition and diversity patterns aligning more closely with those of untreated soils. Co-occurrence network and multivariate analyses of the soil bacterial community, assessed through 16S rRNA amplicon sequencing, revealed patterns indicative of a partial restoration of bacterial interaction structure, with Carb/FeNPs-EC treatments showing increased network connectivity and modularity compared to carbendazim-only soils, approaching the interaction patterns characteristic of undisturbed bacterial assemblages. These findings offer preliminary evidence that biogenic magnetite nanoparticles may reduce pesticide pressure in agricultural soils while supporting microbial functional trends indicative of recovery. The use of onion peel waste as an eco-friendly precursor further highlights the circular potential of this approach. Onion peel is a widely generated agro-industrial by-product particularly rich in polyphenolic compounds, especially quercetin and its derivatives, which act as natural reducing and stabilizing agents during nanoparticle biosynthesis, eliminating the need for toxic chemical reagents and contributing to a lower environmental footprint. This dual role as both a waste valorization strategy and a source of bioactive capping agents warrants further evaluation of this approach as a sustainable soil amendment strategy.},
}

@article {pmid42251923,
year = {2026},
author = {Alum, EU and Emeruwa, AP and Obasi, DC and Okoroh, PN and Aniokete, UC and Akwari, AA and Uzor, S and Eji, MO and Amadi, EB},
title = {Gut microbiome-derived metabolites as predictors of bariatric surgery outcomes.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {591},
number = {},
pages = {121153},
doi = {10.1016/j.cca.2026.121153},
pmid = {42251923},
issn = {1873-3492},
abstract = {BACKGROUND: Bariatric surgery remains the most effective treatment for severe obesity and obesity-associated metabolic disorders. However, substantial interindividual variability exists in postoperative weight loss and type 2 diabetes mellitus remission. Increasing evidence suggests that gut microbiome-derived metabolites may influence metabolic responses after bariatric surgery.

OBJECTIVE: This narrative review synthesizes current evidence regarding the predictive role of gut microbiome-derived metabolites, particularly short-chain fatty acids, bile acids, and tryptophan-derived metabolites, in bariatric surgery outcomes.

METHODS: A narrative literature review was conducted using PubMed, Web of Science, Embase, and ClinicalTrials.gov to identify studies published through May 2026. Studies examining associations between microbiome-derived metabolites and postoperative bariatric outcomes were reviewed and narratively synthesized.

RESULTS: Available evidence suggests that higher preoperative levels of beneficial microbiome-derived metabolites are associated with improved postoperative weight loss, enhanced insulin sensitivity, and greater likelihood of type 2 diabetes mellitus remission. Short-chain fatty acids appear to influence satiety and glucose metabolism, bile acids regulate metabolic signaling through farnesoid X receptor and Takeda G protein receptor 5 pathways, and tryptophan metabolites modulate inflammation and gut-brain communication. Nevertheless, findings remain inconsistent because of methodological heterogeneity, limited cohort sizes, and differences in metabolomic profiling techniques.

CONCLUSION: Gut microbiome-derived metabolites represent promising candidate biomarkers for predicting bariatric surgery outcomes. However, large-scale longitudinal studies using standardized metabolomic approaches are required before clinical implementation can be achieved.},
}

@article {pmid42251996,
year = {2026},
author = {da Cruz, LL and Shlisky, J and Bellando, BJ and Chen, JR and Edwards, T and Fiecke, C and Larson-Prior, LJ and McCorkle, L and Moore, MB and Slaton, C and Sobik, S and Thakali, K and Whiteside, M and Andres, A},
title = {Longitudinal evaluation from birth to adolescence of soy-protein based infant formula compared to cow's-milk based formula and breastfeeding: A comprehensive summary of findings.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100669},
doi = {10.1016/j.advnut.2026.100669},
pmid = {42251996},
issn = {2156-5376},
abstract = {Breastfeeding is widely recognized as the gold standard food for infants. However, many families use infant formulas, including soy-based products, which have not been studied for their long-term safety and developmental effects. The Beginnings Study and the Beginnings Follow Up Study represent one of the most comprehensive prospective cohorts designed to examine how early infant feeding is related to growth, body composition, cardiovascular, microbiome, and skeletal outcomes, neurodevelopment, and reproductive maturation through adolescence. Conducted in Arkansas, U.S., the study enrolled 600 healthy, term infants fed soy-based infant formula, cow's milk-based infant formula, or human milk during infancy (200 per group). Of these, 385 participants (73.2%) completed the 6-year visit, and 190 (31.7% of enrolled and 49.4% of 6-year visit completers) participated in the 14-year Follow Up Study. Breastfeeding was associated with slower weight gain velocity during infancy, and consistent lower body mass index, fat mass index, and waist circumference extending into adolescence, compared to formula feeding. Formula-fed infants had comparable results to breastfed infants for skeletal mineralization, most neurocognitive parameters, and reproductive organ development. However, cardiovascular autonomic measures, including heart rate and vagal tone, differed by feeding group, with some sex-specific effects. Novel contributions included analyses of the gut microbiome and metabolomics profiles in early life, which revealed distinct dietary signatures, as well as neurodevelopmental assessments using electroencephalography, which highlighted transient differences in language-related brain responses among feeding groups. Together, these results demonstrate more similarities than differences between soy-based infant formula and cow's milk-based infant formula in health outcomes and supports the lasting benefits of breastfeeding. This evidence can help guide healthcare professionals in infant feeding recommendations and highlight critical windows to prevent obesity and promote lifelong health.},
}

@article {pmid42252003,
year = {2026},
author = {Júnior, AMCA and da Silva, AH and Buroxid, RP and Padovan, JR and Nunes, AT and Poleti, MD and Fukumasu, H and Gobesso, AAO},
title = {Impact of collagen supplementation on the fecal microbiome of young horses in training.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {106047},
doi = {10.1016/j.jevs.2026.106047},
pmid = {42252003},
issn = {0737-0806},
abstract = {BACKGROUND: Intense training in athletic foals may alter fecal microbiota, highlighting the need for nutritional strategies such as hydrolyzed collagen supplementation.

AIMS/OBJECTIVES: This study aimed to evaluate the effects of dietary hydrolyzed collagen on the fecal microbiome of weanlings in training.

METHODS: Twenty Mangalarga Marchador foals (206 ± 18 kg; 7 ± 1 mo age) were assigned to two groups: a supplemented group (50 g/day of hydrolyzed collagen for 180 days) and a control group. A completely randomized design with repeated measures over time was used. Foals were exercised five consecutive days per week. Fecal samples (10 g) were collected every 90 days (D0, D90 and D180) and analyzed by next-generation sequencing of the 16S rRNA gene. Alpha diversity was assessed using Chao1, Shannon, and Simpson indices, while beta diversity was evaluated by Principal Coordinate Analysis. Beta diversity differences were tested using PERMANOVA, and differential abundance at the phylum and genus levels was analyzed using the Wilcoxon rank-sum test.

RESULTS: A significant treatment effect (P < 0.05) was observed on D180 at the phylum level, with a higher abundance of Fibrobacterota in control foals. At the genus level in D180, Saccharofermentans, Lachnospiraceae UCG-009, and Fibrobacter were more abundant in the control group, whereas Intestinimonas, Lachnospiraceae UCG-010, and Phascolarctobacterium were more abundant in the supplemented group. There was no effect (P > 0.05) between groups on alpha diversity.

CONCLUSION: These results indicate that hydrolyzed collagen supplementation modulates the fecal microbiome of training young horses, reducing fibrolytic bacteria over time.},
}

@article {pmid42252139,
year = {2026},
author = {Barbé, A and Boland, L and Kanaan, N and Darius, T and Buemi, A and France, Y and Ronsyn, MA and Rahal, S and Lingurski, M and Van Bambeke, F and Bindels, LB and Haufroid, V and Devresse, A and Elens, L},
title = {ElucidatiNg Immunosuppressant pharmacokinetic variabilities by investigating Gut Microbiome modulations After kidney transplantation (ENIGMA): study protocol of a prospective longitudinal trial.},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e106623},
doi = {10.1136/bmjopen-2025-106623},
pmid = {42252139},
issn = {2044-6055},
abstract = {INTRODUCTION: In kidney transplantation, immunosuppressive therapy is essential to control alloimmune reactions, prevent graft rejection and improve patient survival rates. However, commonly used drugs like tacrolimus (TAC) and mycophenolate mofetil (MMF) have a narrow therapeutic window and exhibit significant inter- and intra-individual variability in pharmacokinetics (PK) and dose-response relationships. Recent pilot studies suggest that the gut microbiome may influence this variability.

METHODS AND ANALYSIS: ElucidatiNg Immunosuppressant pharmacokinetic variabilities by investigating Gut Microbiome modulations After kidney transplantation (ENIGMA) is a prospective, low-interventional, naturalistic longitudinal trial designed to identify biomarkers of TAC and MMF PK variability by examining gut microbiome changes and modulations after kidney transplantation and their link with TAC and MMF PK. Biological samples from 50 patients will be collected at nine specific timepoints pre- and post-transplantation using a rich PK and biological sampling strategy. This approach will enable the derivation of PK parameters for the investigated drugs and the creation of a biobank for future hypothesis testing.

ETHICS AND DISSEMINATION: The ENIGMA trial has received ethical approval from the European Medicines Agency (EMA). The reference number of our project is R&D/1325226 and is registered on the Clinical Trial Information System (CTIS) platform with European Union Clinical Trial number 2023-5 08 335-31-00. Results of the trial will be published in scientific journals and presented at different (inter)national conferences.

TRIAL REGISTRATION NUMBER: 2023-5 08 335-31-00 EMA.},
}

@article {pmid42252320,
year = {2026},
author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W},
title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55351-w},
pmid = {42252320},
issn = {2045-2322},
support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; },
abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.},
}

@article {pmid42252383,
year = {2026},
author = {Pichon, V and De Vrieze, M and Bellameche, F and Cristea, R and L'Haridon, F and Falquet, L and Weisskopf, L},
title = {Potato foliar infection with Phytophthora infestans drives strong, cultivar-specific shifts in rhizosphere communities.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00910-x},
pmid = {42252383},
issn = {2524-6372},
support = {207917/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {BACKGROUND: Potato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating plant microbiota members to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight.

RESULTS: Controlled foliar infection triggered substantial, cultivar-specific shifts in rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were involved in the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly upon infection than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates through sequence alignment. Their inhibition potential against P. infestans sporangia and zoospores was assessed through biological assays. These revealed the biocontrol potential of genera otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one.

CONCLUSION: Taken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains that are able to inhibit pathogen development and possibly contribute to its higher resistance against P. infestans.},
}

@article {pmid42252406,
year = {2026},
author = {Zhang, J and Wang, Y and Duan, X and Wang, R and Wang, Y and Lou, F},
title = {Comparative analysis of morphology and gut microbiome underlying trophic niche differentiation in three stomatopod species.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05258-3},
pmid = {42252406},
issn = {1471-2180},
support = {ZR2024MD076//Shandong Provincial Natural Science Foundation Committee/ ; BH202401//Observation and Research Station of Bohai Strait Eco-Corridor, MNR/ ; },
abstract = {Given that predatory strategies and trophic niche in stomatopods vary with raptorial appendage differentiation, a comparative analysis was conducted on three species (Odontodactylus japonicus, Lysiosquilla sulcirostris, and Oratosquilla oratoria) exhibiting distinct habitats and morphologies. The study measured their raptorial appendage morphology, digestive tract morphology, and gut microbiota. The results revealed significant differences in the raptorial appendages and digestive tract morphology among the three stomatopod species. O. japonicus has the significantly largest merus length, merus width, merus height and, L. sulcirostris has the significantly largest propodus length, dactylus length, hepatopancreas length and midgut length, while O. oratoria has the significantly largest hindgut length, cardiac stomach length and pyloric stomach length. Regarding digestive tract morphology, O. japonicus possessed the widest villus and tallest villus, in contrast to O. oratoria, which displayed the smallest values for these features. A total of 8,273 operational taxonomic units (OTUs) were obtained from all 16S rRNA sequences. The OTU numbers for O. oratoria, L. sulcirostris, and O. japonicus were 344, 113, and 82, respectively, with only 17 OTUs shared among all three species. The gut microbiota of O. japonicus was dominated by the phylum Pseudomonadota (88.90%), primarily comprised of the genus Cupriavidus (68.40%). In contrast, the dominant phylum in both L. sulcirostris and O. oratoria was Bacillota, with Mycoplasma being the dominant genus in each, respectively. Furthermore, O. oratoria exhibited the highest gut microbial diversity, whereas L. sulcirostris had the lowest. Functional profiling revealed that the relative abundance of gut microbiota associated with amino acid, lipid, and carbohydrate metabolism was significantly higher in O. japonicus than in both O. oratoria and L. sulcirostris. In conclusion, our findings provide further evidence for feeding habit differentiation and associated regulatory mechanisms among the three stomatopod species. The high gut microbial diversity in O. oratoria may contribute to its adaptability to the dynamic, heterogeneous habitats it occupies. Although the microbial abundance in O. japonicus is intermediate between that of O. oratoria and L. sulcirostris, its microbiota appears to be more efficient in digestive function, particularly in the metabolism of key nutrients. This study systematically elucidates the regulatory mechanisms underlying trophic niche differentiation in stomatopods from integrated morphological and physiological perspectives. Our findings provide a valuable foundation for future research on the evolution of higher taxonomic groups within Stomatopoda based on nutritional ecology.},
}

@article {pmid42252471,
year = {2026},
author = {Horton, DB and Verma, C and Rege, S and Crystal, S and Gerhard, T and Iizuka, A and Iozzio, M and Koffman, D and Parlett, LE and Varga, J and Rose, CD and Strom, BL},
title = {Recent antibiotic exposure and response to treatment of juvenile idiopathic arthritis: a retrospective cohort study.},
journal = {Arthritis research & therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13075-026-03842-6},
pmid = {42252471},
issn = {1478-6362},
support = {R01AR074436/AR/NIAMS NIH HHS/United States ; R01HD109335//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; UL1TR003017, UM1TR004789/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Juvenile idiopathic arthritis (JIA) has been tied to microbiome disruption and antibiotic exposure. Gut microbiota may affect how adults with rheumatoid arthritis respond to methotrexate. We tested if exposure to antibiotics was associated with response to methotrexate for JIA.

METHODS: We conducted a retrospective cohort study using national US public and private insurance claims data (2001-2023). We included children ages 1-17 continuously enrolled for ≥ 10 months and diagnosed with JIA who initiated methotrexate monotherapy or, for comparison, tumor necrosis factor inhibitor (TNFi) monotherapy without prior disease-modifying antirheumatic drug (DMARD) exposure. Antibiotic exposure during the 10-month baseline period was characterized by number of courses, timing, and type. The primary outcome was initiation of a second DMARD after ≥ 30 days (proxy of treatment ineffectiveness). Associations between antibiotic exposure and treatment change were estimated using Cox regression, adjusting for database and baseline demographic, disease, treatment, and health utilization covariates, and represented by adjusted hazard ratios (HRs) with 95% confidence intervals (CIs). In additional analyses, we examined differences based on JIA category (juvenile spondyloarthritis vs. others), outcome specification, and follow-up starting up to 90 days after initial DMARD exposure.

RESULTS: We identified 6,135 new methotrexate users (54.4% antibiotic-exposed) and 1,554 new TNFi users (49.5% antibiotic-exposed), among whom approximately 20% experienced the primary outcome over 10 months of follow-up. No relationships were observed between pre-DMARD antibiotic exposure and DMARD changes in methotrexate users (aHR 1.01, 95% CI 0.90, 1.13) or TNFi users (aHR 1.10, 95% CI 0.86, 1.40). Number of antibiotic courses, antibiotic timing, and type of antibiotic exposure, as well as nonbacterial antimicrobial drug exposure, were also not associated with treatment changes in methotrexate or TNFi users. Findings based on JIA category, alternative outcome definitions, and delayed start of follow-up were consistent.

CONCLUSIONS: Recent antibiotic exposure is not associated with changes in DMARD treatment in children with JIA. This finding is reassuring for a population with higher risks for serious infections than other children and with high rates of antibiotic exposure.},
}

@article {pmid42243719,
year = {2026},
author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS},
title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09123-3},
pmid = {42243719},
issn = {1471-2229},
support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; },
abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.

RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.

CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).},
}