@article {pmid42019623,
year = {2026},
author = {Sant'ana, AB and Tomich, T and Rotta, PP and Carvalho, D and Silva, LHR and Vieira, JVF and Junqueira, RVB and Zambon, RM and Silva, AL},
title = {Dietary tannins and compounds from fermentation of saccharomyces cerevisiae effects on intake, productive performance, enteric methane emission, and rumen microbial diversity of lactating dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27817},
pmid = {42019623},
issn = {1525-3198},
abstract = {The reduction of enteric methane emissions from ruminants is a central topic in research on sustainable livestock research. Feed additives targeting the rumen microbiome are among the strategies being explored to reduce methane emissions and improve nutrient efficiency. In this context, the aim of this study was to investigate the effects of an additive composed by condensed tannins and Saccharomyces cerevisiae yeast compounds on intake, productive performance, nitrogen metabolism, methane emission, and rumen microbial biodiversity of lactating Holstein and Holstein × Gyr dairy cows. Sixteen dairy cows (8 Holstein and 8 Holstein × Gyr) were allocated to 2 treatments following a randomized block design according to milk yield and DIM: a control treatment (CON; without additive) and an additive treatment (ADT), in which the diet contained 2.7 g/kg DM of a commercial feed additive composed of condensed tannins from Acacia mearnsii and yeast compounds derived from Saccharomyces cerevisiae (Muucare Nature®). The trial lasted 84 d, including a 24-d adaptation period. The animals were housed in tie stalls and kept under identical conditions. Between d 17-19 and 47-49, samples of orts and feeds offered to the animals were collected. On d 18 and 19, as well as 48 and 49, spot collections of feces and urine were performed. Rumen fluid was collected via an esophagus on d 22 and 52, and the microbial composition was later analyzed by 16S rRNA sequencing. The VFA concentrations and rumen ammonia nitrogen were also quantified. Methane emission was measured using the sulfur hexafluoride tracer technique. The additive increased the apparent digestibility of DM and OM by about 6% without affecting feed intake, milk yield, and feed efficiency. Methane emission per ECM (g/kg) was reduced by almost 30%, and methane emission per milk yield (g/kg) showed a similar trend. The ADT cows showed higher propionate production and a lower acetate-to-propionate ratio. The microbial diversity in the rumen was altered, with a reduced α diversity and a different community composition, including an increased abundance of Prevotella ruminicola. The total amount of methanogens was unchanged, although one species, Methanobrevibacter smithii, tended to be less abundant. The additive reduced methane emission and improved nutrient digestibility, rumen fermentation, and nitrogen efficiency. These results indicate that the additive based on Acacia tannins and Saccharomyces cerevisiae yeast is a sustainable tool to reduce methane emissions in dairy production systems without compromising milk production.},
}

@article {pmid42019697,
year = {2026},
author = {Gao, Y and Liu, Y and Hussain, I and Wang, L and Cheng, F and Zheng, Z and Cai, Y and Wang, X},
title = {Integrated microbiome-metabolomics profiling reveals substrate-dependent variation in agricultural Jiaosu from fruit waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134668},
doi = {10.1016/j.biortech.2026.134668},
pmid = {42019697},
issn = {1873-2976},
abstract = {Agricultural Jiaosu (AJ), a novel biotechnology, is used to stably obtain beneficial microbiome and metabolites from organic waste. It is widely applied in agriculture and environmental remediation and is particularly suitable for the efficient treatment of fruit waste. However, the characteristics and differences in the microbiome and metabolome of AJ prepared from different substrates remain unclear. Herein, the substrate-dependent variations in microbial consortia and metabolomic profiles across six types of AJ prepared from different substrates were revealed through integrated microbiome and metabolomics analyses. Metabolomics analysis identified a total of 3,159 metabolites, and random forest machine learning analysis of differentially expressed metabolites indicated that 50% of the top 20 marker metabolites across the six AJ samples belonged to organoheterocyclic compounds, organic acids and derivatives, shikimates and phenylpropanoids. Microbial analysis revealed that Lactobacillus and Lentilactobacillus constituted the core microbiome in all six AJ, and that mixed fruit waste AJ exhibited the highest microbial diversity. Carbohydrate metabolism genes (19.57% of total metabolic genes) were predominant. Notably, genes encoding enzymes involved in pyruvate, propanoate, and butanoate metabolic pathways exhibited high expression in the mixed fruit waste AJ. Correlation and co-occurrence network analyses revealed robust interconnections among physicochemical properties, differential metabolites, and significant microorganisms within the AJ system. This study demonstrates how substrate selection shapes the functional microbiome and metabolic landscape of AJ through integrated multi-omics analysis, offering mechanistic insights for the engineered production of AJ.},
}

@article {pmid42019703,
year = {2026},
author = {Burch, K and Sahyoun, AM and Abutineh, S and Munkhsaikhan, U and Alipour, M and Zahran, G and Ait-Aissa, K and Wang, Q and Samy, S and Kassan, A and Ishrat, T and Abidi, AH and Kassan, M},
title = {From mouth to mind: Investigating oral microbial contributions to autism spectrum disorder.},
journal = {Neuroscience and biobehavioral reviews},
volume = {186},
number = {},
pages = {106702},
doi = {10.1016/j.neubiorev.2026.106702},
pmid = {42019703},
issn = {1873-7528},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by persistent social communication challenges and restricted, repetitive patterns of behavior. ASD arises from both genetic and environmental influences. Growing evidence also points to microbial dysbiosis, especially in the gut and mouth, as a potential contributor to neurodevelopment and symptom patterns. While gut microbiome alterations have been well documented in ASD, the oral microbiota has received comparatively less attention, despite its established roles in systemic inflammation, immune regulation, and even neurological function. Understanding these microbial shifts may help identify early biomarkers and guide oral health interventions to improve outcomes in ASD populations. This narrative review synthesizes current knowledge on the relationship between oral microbiota dysbiosis and ASD, with three primary objectives: (1) to characterize oral microbiome alterations observed in individuals with ASD compared to neurotypical controls; (2) to explore potential mechanisms linking oral dysbiosis to core and comorbid ASD symptoms; and (3) to evaluate therapeutic strategies targeting the oral microbiome as potential interventions for ASD.},
}

@article {pmid42019706,
year = {2026},
author = {Li, G and Wu, M and Yang, X and Song, Y and Zhao, T and Zeng, Z},
title = {Disruption of the core intestinal microbiota contributes to fluoride-induced neurotoxicity in the host organisms.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110547},
doi = {10.1016/j.cbpc.2026.110547},
pmid = {42019706},
issn = {1532-0456},
abstract = {Fluoride is a potential environmental toxic substance associated with dental fluorosis, skeletal fluorosis, and neurotoxic effects. However, the underlying mechanisms remain poorly understood, especially concerning the potential role of fluoride-induced intestinal microbiota dysbiosis in modulating the nervous system via the gut-neuraxis. In this study, an interspecies insect model of fluoride-induced neuronal damage was established to investigate the underlying mechanisms. The results showed markedly elevated malondialdehyde levels, along with reduced glutathione content and decreased catalase and acetylcholinesterase activity in the hemolymph, while histopathological analysis further confirmed the extent of oxidative damage in the nervous tissues caused by fluoride exposure. Using 16S rRNA amplicon sequencing, we found that fluoride decreased the relative abundance of core intestinal microbiota such as Enterococcus, Staphylococcus, and Delftia, while increasing the abundance of unclassified norank_o_Chloroplast and norank_f_Mitochondria taxa. Additionally, the intestinal microbiome exhibited significant heterogeneity, a reduced gut microbiome health index, and an elevated microbial dysbiosis index under fluoride exposure. Metabolomics results indicated that metabolic pathways such as D-amino acid metabolism, aminoacyl-tRNA biosynthesis, ABC transporters, and purine metabolism were enriched following fluoride treatment. Fluoride exposure also significantly altered the levels of several neurotransmitter-related metabolites, including L-glutamate, L-glutamic acid, N-acetyl-L-glutamic acid, L-glycine, spermidine, and serotonin (P < 0.05). Pearson's correlation analysis revealed a relationship between intestinal microbiota dysbiosis and disruptions in neurotransmitter metabolites. These findings provide new insights into the mechanisms of fluoride-induced neurotoxicity, improving the understanding of neurological pathology in fluorosis-endemic areas.},
}

@article {pmid42019707,
year = {2026},
author = {Guo, W and Jin, B and Pang, L and Liu, Y and Liu, D and Dong, Z and Chen, G},
title = {Unraveling olanzapine toxicity in planarian: Multi-omics reveals mechanisms of behavioral and regenerative deficits.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {306},
number = {},
pages = {110548},
doi = {10.1016/j.cbpc.2026.110548},
pmid = {42019707},
issn = {1532-0456},
abstract = {The pervasive release of antipsychotic pharmaceuticals into aquatic environments poses significant ecotoxicological risks. An integrated multi-omics framework was employed to comprehensively elucidate the toxicological effects and underlying mechanisms of olanzapine (OLA) on the freshwater planarian Dugesia constrictiva. Exposure to environmentally relevant (0.5 μg L[-1]) and elevated (5 μg L[-1]) concentrations of OLA induced significant morphological alterations and behavioral deficits. Pronounced neurotoxicity was evidenced by severe damage to the central nervous system, culminating in the complete loss of neural structures at higher concentrations. OLA exposure significantly impaired planarian regeneration, accompanied by alterations in stem cell proliferation and differentiation. Transcriptomic analysis revealed that OLA exposure dysregulated key cellular pathways, enhancing autophagy while suppressing neurodevelopment, immune function, and apoptosis. Metabolomic profiling further confirmed profound disruptions in energy metabolism and biosynthetic pathways, including the downregulation of steroid hormone biosynthesis and diverse amino acid metabolism. Moreover, OLA exposure induced significant shifts in the planarian microbiome, characterized by reduced alpha diversity, the emergence of opportunistic pathogens (Legionella), and a marked depletion of dominant taxa (Rhodoferax), indicating OLA-induced microbial dysbiosis. Collectively, our results provide novel mechanistic insights into the complex, cascading ecotoxicological effects of OLA on a representative aquatic invertebrate and underscore the significant environmental hazards posed by pharmaceutical contaminants in aquatic ecosystems.},
}

@article {pmid42019863,
year = {2026},
author = {Kim, T and Nguyen, I and Thomas, N and Picker, M and Clemente, JC and Agrawal, M and , },
title = {Intestinal inflammation impacts gestational weight gain in women with inflammatory bowel disease and growth in offspring.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2026.04.013},
pmid = {42019863},
issn = {1542-7714},
}

@article {pmid42020064,
year = {2026},
author = {Peters, BA},
title = {Evidence grows for the gut-kidney axis, but questions still remain.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {832-834},
doi = {10.1016/j.kint.2026.02.015},
pmid = {42020064},
issn = {1523-1755},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; },
abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.},
}

Humans
*Gastrointestinal Microbiome
*Kidney/microbiology/metabolism
Metabolomics
Cross-Sectional Studies
Metagenomics

@article {pmid42020126,
year = {2026},
author = {Ticlla, MR and Dumbaugh, M and Condori-Catachura, S and Kenfack, J and Hattendorf, J and Van Der Donck, L and Arista, KM and Arora, N and Gebert, S and Ackermann, L and Ahannach, S and Riveros, M and Blas, MM and Kenmoe, S and Barrière, FY and Shea, AA and Pinedo-Cancino, V and Rivas-Ruiz, R and Di Cecco, V and Esemu, L and Ochoa, TJ and Lebeer, S and Martin Hilber, A and Merten, S},
title = {Improving menstrual and vaginal health for all (IMVAHA): protocol for a randomised cross-over trial assessing the impact of menstrual products on the vaginal microbiome of women aged 18-35 years in Cameroon, Peru and Switzerland.},
journal = {BMJ open},
volume = {16},
number = {4},
pages = {e108568},
doi = {10.1136/bmjopen-2025-108568},
pmid = {42020126},
issn = {2044-6055},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Menstrual Hygiene Products ; Adult ; *Microbiota ; Young Adult ; Adolescent ; Cross-Over Studies ; Cameroon ; *Menstruation ; Switzerland ; Peru ; Randomized Controlled Trials as Topic ; Cross-Sectional Studies ; Health Surveys ; },
abstract = {INTRODUCTION: Menstrual health is critical to achieving gender equity and reaching the 2030 Sustainable Development Goals, yet evidence on the health impacts of menstrual products-particularly on the vaginal microbiota-is limited. The Improving Menstrual and Vaginal Health for All (IMVAHA) project aims to address this knowledge gap through qualitative exploration, a health survey and clinical trial embedded in three sister projects: Laura (Peru), Leke (Cameroon) and Marie (Switzerland). This paper outlines the protocol for the IMVAHA health survey and clinical trial studies, which aim to (1) assess menstrual hygiene practices, product preferences and vaginal health; and (2) evaluate longitudinal changes in vaginal microbiota associated with the use of pads, tampons and menstrual cups.

METHODS AND ANALYSIS: The IMVAHA project will take place in urban Cameroon, urban Peru, and in Switzerland. The baseline survey will explore vaginal and menstrual health behaviours and preferences, including vaginal complaints, menstrual products and menstrual stigma. Descriptive statistics will be calculated for a cross-sectional profile of vaginal and menstrual health within and between contexts, and mixed effects linear regression models will be run to identify associations between contextual factors and key vaginal and menstrual outcomes. From survey participants, 300 eligible, consenting women (100 per country) will be enrolled in a 7-month crossover clinical trial. As a self-controlled trial, a dedicated control group is not necessary. Each participant will use pads, tampons and menstrual cups for two menstrual cycles per product, providing vaginal swabs at baseline and post-menstruation. Swabs will undergo 16S rRNA sequencing, pH testing and screening for toxic shock syndrome-related bacteria. A short survey on health behaviours and symptoms, menstrual hygiene practices and participant experiences with different menstrual products will be administered during each menstrual period. The primary outcome of the clinical trial is the log ratio of Dialister to Lactobacillus crispatus abundance measured after the use of different menstrual products. Mixed-effects linear regression will assess differences in the primary outcome across product types. Secondary analyses will include per-protocol comparisons and ORs with 95% CIs.

ETHICS AND DISSEMINATION: The study complies with the Declaration of Helsinki, Council for the International Organizations of Medical Sciences guidelines and local regulations. Ethical approval has been obtained in all three countries (National Ethics Committee for Human Health Research in Cameroon (CE N° 2024/03/1649/CE/CNERSH/SP); the Institutional Review Board of the Universidad Peruana Cayetano Heredia and Universidad Nacional de la Amazonía Peruana in Peru (217572) and the Ethics Commission of Northwest and Central Switzerland (2024-02135)). Informed consent will be obtained from all participants after detailed explanation of study procedures and risks. Data will be securely stored, with participant anonymity maintained. A political economy analysis will explore regulatory environments for menstrual products, and findings will be disseminated through policy briefs, stakeholder networks, academic publications and conferences.

TRIAL REGISTRATION NUMBER: NCT06646185.},
}

Humans
Female
*Vagina/microbiology
*Menstrual Hygiene Products
Adult
*Microbiota
Young Adult
Adolescent
Cross-Over Studies
Cameroon
*Menstruation
Switzerland
Peru
Randomized Controlled Trials as Topic
Cross-Sectional Studies
Health Surveys

@article {pmid42020220,
year = {2026},
author = {Zhang, W and Xu, JH and Yu, T and Chen, QK},
title = {Retraction notice to "Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice" [Biomedicine & Pharmacotherapy 118 (2019) 109131].},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {},
number = {},
pages = {119408},
doi = {10.1016/j.biopha.2026.119408},
pmid = {42020220},
issn = {1950-6007},
}

@article {pmid42020299,
year = {2026},
author = {Gao, J and Lau, HC and Fuhler, GM and Yu, J},
title = {Gastric microbiota-mediated immune remodelling in gastric cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338505},
pmid = {42020299},
issn = {1468-3288},
abstract = {Increasing evidence indicates that the gastric microbiota plays crucial roles in regulating the tumour microenvironment (TME), influencing gastric tumourigenesis and progression. Several bacteria, including Streptococcus, Lactobacillus and Bacteroides, have shown robust immunomodulatory effects on TME. In this review, we summarise current understanding of the crosstalk between the gastric microbiota and TME in gastric cancer (GC). Functional alterations of the gastric microbiota from healthy mucosa to malignancy are delineated, with emphasis on the impacts of bacteria on different immune cell populations in gastric tumours, such as CD8[+] T cells, macrophages, dendritic cells and regulatory T cells. The immunomodulatory roles of microbial metabolites and pathogen-associated molecular patterns in shaping immune cell infiltration, cytokine profiles and checkpoint molecule expression are also explored. While immune checkpoint blockade (ICB) has emerged as a promising treatment of various cancers, its efficacy in GC remains unsatisfactory due to the immunosuppressive gastric TME. We therefore evaluate the intricate interplays between the gastric microbiota and immunotherapy, and suggest potential microbiota-targeting strategies (eg, microbiota modulation, probiotics supplementation and combination therapies) to enhance antitumour immune response and boost ICB efficacy. We conclude by highlighting current challenges and providing future directions for microbiota research in GC. Overall, a deeper understanding of host-microbe interactions can provide promising avenues for precision medicine and the development of microbiota-targeting interventions against GC.},
}

@article {pmid42020421,
year = {2026},
author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T},
title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72303-0},
pmid = {42020421},
issn = {2041-1723},
support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.},
}

@article {pmid42020446,
year = {2026},
author = {Goswami, S and Ansari, A and Saraf, C and O'Toole, PW and Shanahan, F and Ahuja, V and Ghosh, TS},
title = {Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72289-9},
pmid = {42020446},
issn = {2041-1723},
support = {BT/RLF/Re-entry/55/2021//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; DST/INSPIRE/Fellowship/2023/IF230228//Department of Science and Technology, Ministry of Science and Technology (DST)/ ; },
abstract = {Bifidobacteria are key health-associated members of the human gut microbiome and are widely used as probiotics, but their colonization success varies substantially between individuals, partly due to baseline microbiome composition. We analyzed 51,244 gut microbiomes from 149 cohorts (45 countries) to identify non-Bifidobacterial taxa associated with the Bifidobacterial features. We observed several consistent and age-/life-style-specific association patterns of different non-Bifidobacterial taxa with the different Bifidobacteria. Multiple Bifidobacteria showed positive associations with butyrate-producing Firmicutes and Collinsella; negative associations involved pathobiont-Firmicutes and specific Bacteroidota taxa. B. adolescentis and B. breve showed the strongest positive and negative associations, respectively, with health-associated adult gut microbiome members. We quantified these relationships as Association-Scores, stratified by age/life-style/sequencing-strategy/disease, which were significantly reproducible after adjusting for multiple microbiome-linked, host life-style/clinical covariates, and predictable using species-specific genomic functions. We used these Association-Scores to derive microbiome-level Receptive-Scores that quantify how permissive a baseline microbiome is to increases or persistence of a given Bifidobacterium. In an external dataset of eight Bifidobacterium interventions (n = 1633 gut microbiomes), Receptive-Scores combined with baseline abundance of the administered Bifidobacteria significantly predicted post-treatment persistence/increase in 69.23% of trial-probiotic pairs. Together, this work identifies microbiome features governing Bifidobacterial colonization and provides tools to predict personalized probiotic responses.},
}

@article {pmid42020464,
year = {2026},
author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH},
title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37419-9},
pmid = {42020464},
issn = {2045-2322},
support = {5850.0109317.18.9 and 21167-2//Petróleo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.},
}

@article {pmid42020632,
year = {2026},
author = {Kalra, A and Dominoni, D and Boonekamp, J},
title = {The impact of microplastics on the mice gut microbiome: a meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49190-y},
pmid = {42020632},
issn = {2045-2322},
}

@article {pmid42020638,
year = {2026},
author = {Ahmadi, S and Sedaghat, FR and Asl, YM and Khabbaz, A and Hosseinzadeh, N and Poortahmasbe, V and Hasani, R and Hosseini, S and Yazdchi, M and Mehdizadehfar, E and Salehi-Pourmehr, H and Naseri, A and Hasani, A},
title = {Faecalibacterium prausnitzii and Akkermansia muciniphila: driving the multiple sclerosis-a systematic review.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {42020638},
issn = {1572-9699},
support = {70699//Research Center for Infectious Diseases and Tropical Medicine, Tabriz University of Medical Sciences/ ; },
mesh = {Humans ; *Multiple Sclerosis/microbiology ; *Gastrointestinal Microbiome ; *Faecalibacterium prausnitzii/physiology ; Dysbiosis/microbiology ; Akkermansia ; },
abstract = {The gut microbiota (GM) is a complex microbial ecosystem, and its alteration contributes to the development of several diseases including multiple sclerosis (MS). Progressive research concerning neurodegenerative diseases and GM reveals that GM dysbiosis has been linked to fostering the development and progression of MS. Among existing bacteria, F.prausnitzii and A.muciniphila are key species implicated in this disease. Thus, the present study systematically reviewed and synthesized the research on the involvement of F. prausnitzii and A. muciniphila in MS patients versus healthy individuals. We systematically searched PubMed, MEDLINE, EMBASE, and Web of Science databases for relevant published articles from January 2010 till January 2023. Out of 400 articles, 16 met the required criteria. The included research investigations originated from the US, Germany, Norway, Egypt, Iran, Brazil, China, the UK, and Romania. Most publications reported decreased levels of F. prausnitzii and increased levels of A. muciniphila in MS patients compared to controls. This review underscored the importance of the F. prausnitzii and A. muciniphila in MS, which could explain the chronic inflammation that characterizes this disease and not only help in understanding its etiology and progression but also open new avenues for the treatment strategies focusing on gut health. Moreover, understanding the role of F. prausnitzii and A. muciniphila could lead to novel biomarkers for early detection and progression monitoring MS.},
}

Humans
*Multiple Sclerosis/microbiology
*Gastrointestinal Microbiome
*Faecalibacterium prausnitzii/physiology
Dysbiosis/microbiology
Akkermansia

@article {pmid42020750,
year = {2026},
author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS},
title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42020750},
issn = {1476-4687},
abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.},
}

@article {pmid42020819,
year = {2026},
author = {Eberly, JO and Berríos-Ortiz, L and Hurd, A and Shergill, L and Dyer, AT and Menalled, FD},
title = {Wheat Rhizosphere Bacterial Community Response to Bromus tectorum (L.) and Fusarium pseudograminearum Crown Rot.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02778-3},
pmid = {42020819},
issn = {1432-184X},
support = {2020-70006-32978//National Institute of Food and Agriculture/ ; },
abstract = {Annual crop yield losses due to plant diseases and weeds can be substantial. In the northern Great Plains, Bromus tectorum (L.) (also known as cheatgrass or downy brome) and Fusarium pseudograminearum (causing crown rot) form a multi-trophic pest complex threatening wheat production sustainability. This study assessed the impact of these pests on the wheat rhizosphere bacterial community. Field trials were conducted over four site-years in plots inoculated with F. pseudograminearum using a randomized split-plot design with two seeding and nitrogen fertilizer rates and B. tectorum presence/absence. A seed fungicide treatment was also used to evaluate its effect on F. pseudograminearum abundance. Rhizosphere bacterial communities were analyzed using full-length 16 S rRNA sequencing on the Oxford Nanopore platform, followed by diversity analysis, structural equation modeling (SEM), and co-occurrence network analysis. Alpha and beta diversity were significantly different between location-years. The SEM results showed a negative relationship (β = -0.180, p = 0.002) between F. pseudograminearum presence and rhizosphere bacterial community alpha and beta diversity. Effects of B. tectorum presence, seeding rate, nitrogen fertilizer, and fungicide treatment were not significant. Correlation analysis identified specific bacterial taxa responsive to F. pseudograminearum presence, including putatively beneficial species belonging to the genera Massilia, Bacillus, and Neobacillus, which were positively correlated with pathogen presence, suggesting a stress response mechanism. Network analysis revealed that F. pseudograminearum presence reduced network cohesion, and connectivity measures compared to treatments with lower pathogen load. These findings demonstrate that fungal pathogen presence can impact rhizosphere bacterial networks even when overall diversity metrics show minimal changes, highlighting the importance of network-based approaches in understanding plant-microbe-pathogen interactions in agricultural systems.},
}

@article {pmid42021054,
year = {2026},
author = {Kennedy, MS and Chang, EB},
title = {From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649448},
doi = {10.1080/19490976.2026.2649448},
pmid = {42021054},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Bacteria/classification/genetics/isolation & purification/growth & development ; Animals ; Anti-Bacterial Agents ; },
abstract = {Predicting and promoting gut microbiome recovery following perturbations such as antibiotic treatment, dietary shifts, or inflammation remain major challenges in microbiome science and clinical practice. In this review, we explore recent advances in microbiome restitution by framing recovery as a dynamic ecological process shaped by complex interactions between microbial taxa, host physiology and environmental conditions. We review current evidence addressing four key questions that outline the salient ecology of perturbation and recovery: which microbial taxa are present in the microbiota and which taxonomic or functional qualities might increase susceptibility to perturbation; what is the nature of the perturbation, including the type and probable targets of the perturbation, as well as the indirect ecological and environmental consequences of that perturbation; what is the time course of perturbation and recovery, exploring prehabilitation strategies and successional trajectories as a staged recovery framework; and where does perturbation and recovery unfold in the gut, with attention to both regional and microscale spatial patterns. Highlighting recent advances from multi-omics approaches and longitudinal studies, we demonstrate how each of these factors and their interactions critically shape both robustness to disturbance and the trajectory of recovery. We advocate for multimodal, context-specific interventions that harness ecological principles to drive regrowth and community assembly, including diet, targeted microbial transplantation and modulation of the abiotic gut environment. Ultimately, resolving the challenge of microbiome restitution will require personalized strategies informed by ecological understanding and longitudinal functional monitoring. This paradigm provides a foundation for future translational advances to promote eubiosis and improve patient outcomes in microbiome-related diseases.},
}

Humans
*Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome/physiology
Bacteria/classification/genetics/isolation & purification/growth & development
Animals
Anti-Bacterial Agents

@article {pmid42021149,
year = {2026},
author = {Sun, RZ and Liu, XQ and Yang, ZL and Liu, XG and Wang, HW and Deng, X},
title = {Compartment-specific assembly and genotype-associated differentiation of root microbiomes in saline-alkali-sensitive and -tolerant maize inbred lines.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08813-2},
pmid = {42021149},
issn = {1471-2229},
support = {XDA 26030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 063GJHZ2025027GC//International Partnership Program of the Chinese Academy of Sciences for Grand Challenges/ ; },
}

@article {pmid42021382,
year = {2026},
author = {Mazumder, M and Pavagadhi, S and Bhattacharya, R and Mukherjee, A and Majedi, SM and Hin, ITC and Swarup, S},
title = {Live-exudation assisted phytobiome culturomics system (LEAP-CS): a high-throughput culturomics system for studying plant-microbiome interactions through diffusible metabolites.},
journal = {Plant methods},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13007-026-01539-0},
pmid = {42021382},
issn = {1746-4811},
}

@article {pmid42021415,
year = {2026},
author = {Faticov, M and Tack, AJM and Ortner, D and Berg, G and Abdelfattah, A},
title = {Multiple origins of the apple seed microbiome: disentangling sexual and asexual transmission pathways.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00901-y},
pmid = {42021415},
issn = {2524-6372},
support = {Grant Number: 844114, awarded to AA//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {BACKGROUND: The seed microbiome plays a key role in the assembly of the plant microbiome, which has major impacts on plant health. Nonetheless, little is known about the origin of the seed microbiome. We investigated the relative contributions of two potential transmission routes: sexual inheritance (via reproductive organs) and asexual inheritance (via the plant vascular system). To do that, we sampled flower ovaries and pollen sacs, fruiting spurs both before bloom and at seed maturity stages and mature seeds from five field-grown apple trees (Malus domestica BORKH. cv 'Gala Galaxy Selecta').

RESULTS: We showed that bacterial alpha diversity differed among tissues: spurs sampled before bloom had significantly higher richness and Shannon diversity than all other compartments, whereas ovary, pollen, spurs at seed maturity, and seeds did not differ in either richness or Shannon diversity. In addition, bacterial community composition differed significantly across all tissue types (ovary, pollen, spurs before bloom, spurs at seed maturity, and seeds). Source tracking revealed that both sexual (30.3%) and asexual (23.8%) pathways contributed to seed microbiome assembly, with spurs at seed maturity being the dominant source. Notably, a large proportion (45.9%) of the seed microbiome originated from unknown sources.

CONCLUSIONS: Overall, such insights into seed microbiome origin offer new opportunities to enhance seed health and crop productivity through microbiome-assisted breeding.},
}

@article {pmid42021487,
year = {2026},
author = {Sokol, H and Elkrief, A and Routy, B},
title = {A "healthy gut state" as the key determinant of immune checkpoint inhibitor efficacy.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2026.04.034},
pmid = {42021487},
issn = {1525-0024},
abstract = {The gut ecosystem emerges as a key determinant of immune checkpoint inhibitor (ICI) efficacy. Rather than individual "beneficial" bacteria, a broader framework of gut health better explains inter-individual variability in ICI response: a non-inflamed gastrointestinal tract with preserved epithelial barrier and functionally eubiotic microbiome promotes responsiveness, while gut inflammation and barrier disruption predict poor outcomes. Integrating human and mechanistic mouse data, we propose shifting research focus toward clinically actionable gut-health axes to optimize cancer immunotherapy.},
}

@article {pmid42021627,
year = {2026},
author = {Aiube, YRA and Moreira, APB and Caires, TA and Tenório, MMB and de Moura, RL and Salomon, PS},
title = {Revealing novelty from the southwestern Atlantic, Yemanjia gen. nov. and Olokunococcus gen. nov. from the coral cyanobiome of the Abrolhos Bank.},
journal = {Journal of phycology},
volume = {62},
number = {2},
pages = {533-555},
pmid = {42021627},
issn = {1529-8817},
support = {001/2018//Fundação Espírito Santense de Tecnologia - FEST-RENOVA/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Cyanobacteria/classification/genetics/physiology ; Animals ; *Anthozoa/microbiology ; Phylogeny ; Atlantic Ocean ; RNA, Ribosomal, 16S/analysis/genetics ; Symbiosis ; Coral Reefs ; },
abstract = {Cyanobacteria comprise over 6000 species and inhabit diverse environments, including marine invertebrates such as sponges and corals. High-throughput sequencing has indicated an abundance of Cyanobacteria communities in these hosts, yet taxonomic resolution has remained low below the phylum level. Most cultured Cyanobacteria from corals have been isolated from black band disease lesions. However, many other associated taxa remain unidentified, such as the Cyanobacteria detected with microscopy and isotopic studies near coral symbiosomes. Recently, a polyphasic approach revealed six new genera from sponges. Following a similar strategy-integrating molecular phylogeny, morphology, ecology, and chemotaxonomy-we describe two novel genera and three new species of Cyanobacteria from reef-building corals of the Abrolhos Banks (southwestern Atlantic). Two filamentous strains were assigned to the new genus Yemanjia (Cymatolegaceae), closely related to the genus Rhodoploca. A third coccoid strain was assigned to the new genus Olokunococcus (Aegeococcaceae), phylogenetically related to Aegeococcus. All isolates presented phycoerythrins. The closest formally described relatives of these new taxa are all sponge-associated, suggesting an evolutionary and ecological link between host and Cyanobacterial lineage. By providing formal taxonomic anchors for coral-associated Cyanobacteria, our results expand the current knowledge of the coral cyanobiome and facilitate the interpretation of existing and future coral microbiome datasets.},
}

*Cyanobacteria/classification/genetics/physiology
Animals
*Anthozoa/microbiology
Phylogeny
Atlantic Ocean
RNA, Ribosomal, 16S/analysis/genetics
Symbiosis
Coral Reefs

@article {pmid42021774,
year = {2026},
author = {Nagybanyai-Nagy, B and Tengölics, R and Sajben, C and Olasz, D and Schwarcz, A and Molnar, T and Csecsei, P},
title = {Serum microbiome-related metabolites-including short-chain fatty acids and indole derivatives-predict outcome and delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage: a two-timepoint LC-MS study.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1768108},
pmid = {42021774},
issn = {1664-2295},
abstract = {BACKGROUND: Delayed cerebral ischemia (DCI) remains a major determinant of poor outcome after aneurysmal subarachnoid hemorrhage (aSAH). Growing evidence suggests that gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs) and tryptophan-related indole compounds, modulate neuroinflammation and cerebrovascular vulnerability. However, their temporal dynamics and clinical relevance after aSAH are insufficiently characterized.

METHODS: In this prospective observational study, 80 consecutive patients with aSAH were enrolled at a tertiary neurocritical care center. Serum concentrations of SCFAs (propionic, butyric, isobutyric, valeric, isovaleric, caproic acids) and tryptophan-derived metabolites (tryptophan, indole-3-propionic acid [IPA], indole-3-acetic acid, indole-3-lactic acid) were quantified using LC-MS on Day 1 and Day 9 after hemorrhage. Functional outcome at 3 months was assessed using the modified Rankin Scale (mRS), and DCI was diagnosed according to consensus criteria. Associations were analyzed using non-parametric statistics, ROC analyses, and multivariable logistic regression adjusted for established clinical confounders.

RESULTS: Patients with unfavorable 3-month outcomes (mRS 4-6) showed significantly lower Day 1 levels of propionic, isobutyric, and isovaleric acids, persistently reduced tryptophan at both time points, and markedly lower IPA concentrations on Day 9. DCI was associated with reduced tryptophan and propionic acid levels on both days and a pronounced decrease in IPA on Day 9. Tryptophan and propionic acid demonstrated excellent discriminative performance for outcome and DCI (AUCs up to 0.99). In multivariable models, low Day 1 propionic acid and low Day 9 IPA independently predicted unfavorable outcome, while Day 9 tryptophan, IPA, and propionic acid independently predicted DCI.

CONCLUSION: Distinct temporal alterations in gut microbiota-derived metabolites after aSAH are strongly associated with functional outcome and DCI. SCFAs and tryptophan-related metabolites-particularly propionic acid, tryptophan, and IPA-emerge as promising biomarkers and potential mechanistic mediators in secondary brain injury after aSAH.},
}

@article {pmid42022011,
year = {2026},
author = {Talavera-Marcos, S and Aguirre de Cárcer, D},
title = {Ecological drift simulations reveal key factors influencing minimal microbiome engineering and community assembly.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag067},
pmid = {42022011},
issn = {2730-6151},
abstract = {In this work, we describe an engineering approach that leverages ecological drift to generate minimal microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. We use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes, within a computational framework that also enables the study of microbial community assembly. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.},
}

@article {pmid42022109,
year = {2026},
author = {Xie, W and Han, D and Tan, J and Zhao, D and Dong, J and Wu, J and Yang, X and Xie, S},
title = {Porphyromonas gingivalis drives trimethylamine-N-oxide accumulation via modulation of gut microbial trimethylamine lyase in mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786725},
pmid = {42022109},
issn = {1664-302X},
abstract = {INTRODUCTION: Trimethylamine N-oxide (TMAO), a gut microbiota-derived metabolite, is linked to cardiovascular, neurodegenerative, and metabolic diseases. Emerging evidence indicates a bidirectional interaction between the periodontal pathogen Porphyromonas gingivalis (Pg) and gut microbiota, potentially influencing host TMAO metabolism. However, whether Pg modulates the choline-trimethylamine (TMA) axis remains unclear.

METHODS: Wild-type male C57BL/6J mice received oral Pg under chow or a high-choline diet. Plasma and cecal concentrations of TMA and TMAO were quantified, intestinal barrier function was evaluated via histological analysis, and the determination of ZO-1 and occludin expression was performed. Cecal microbiota composition was profiled by 16S rRNA gene sequencing, and microbial choline-TMA lyase markers (cutC/cutD) were measured.

RESULTS: Pg elevated plasma TMAO under chow, accompanied by reduced α-diversity, altered β-diversity, and decreased expression of intestinal barrier proteins. Under high-choline conditions, the diet itself increased plasma and intestinal levels of TMAO and TMA. Pg co-exposure further amplified these effects, raising plasma TMAO, cecal TMA, and cutC/cutD levels. Microbiome analysis revealed elevated abundances of Lachnoclostridium, Odoribacter, and Colidextribacter, and reduced levels of taxa (Prevotellaceae NK3B31, Anaerostipes, and Ruminococcus) negatively correlated with TMAO-related parameters. Moreover, cutC/cutD levels were positively correlated with Colidextribacter and Lachnoclostridium, but negatively correlated with Anaerostipes and Prevotellaceae NK3B31, consistent with the modulation of TMA/TMAO metabolism by these taxa.

CONCLUSION: This study demonstrates that oral administration of Pg facilitates systemic TMAO elevation by reshaping gut microbial communities and enhancing choline-TMA lyase function, and compromising intestinal barrier integrity. These findings establish an oral-gut metabolic axis connecting periodontitis to host TMAO metabolism, and highlight promising periodontal and microbiota-targeted strategies for alleviating TMAO-associated systemic disorders.},
}

@article {pmid42022112,
year = {2026},
author = {Phulpoto, IA and Qazi, MA and Yang, J and Wang, H},
title = {Editorial: Forest soil microbiome and their interactions with the plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1819757},
pmid = {42022112},
issn = {1664-302X},
}

@article {pmid42022122,
year = {2026},
author = {Horseman, TS and Fong, KSK and Dombach, JL and Kamau, E and Gehrich, AP},
title = {Vaginal microbiome dysbiosis and a rectal reservoir of uropathogens characterize postmenopausal women with recurrent urinary tract infections: a cross-sectional study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1812000},
pmid = {42022122},
issn = {1664-302X},
abstract = {INTRODUCTION: Recurrent urinary tract infections (rUTIs) in postmenopausal (PM) women pose a significant clinical challenge, complicated by rising antibiotic resistance among uropathogens. The vaginal microbiota in this population remains underexplored. We aim to characterize vaginal flora of PM women with and without a history of rUTIs, and to evaluate relationships to demographic variables, clinical characteristics, and rectal pathogen colonization.

METHODS: We conducted a cross-sectional study of 62 PM women (n = 31 rUTI, (n = 31 control). Vaginal swabs were analyzed using 16S rRNA and a next-generation sequencing tool designed to identify UTI pathogens and antibiotic resistance (AMR) markers. Rectal swabs were cultured to identify uropathogens and their phenotypic resistance. These were integrated with subject demographic and historical clinical data.

RESULTS: Compared to controls, rUTI vaginal microbiota exhibited a marked depletion in Lactobacillus crispatus and L. iners, species commonly associated with vaginal health, alongside an enrichment of L. gasseri and L. jensenii. The rUTI cohort also had a greater burden of AMR markers (p = 0.0003). Notably, Gram-negative uropathogens in the rUTI group frequently carried multidrug resistance genes, at rates nearly three times higher than controls. The rUTI cohort was further characterized by enrichment of Gram-negative uropathogens in the vagina. These alterations were more pronounced with increasing years in menopause.

DISCUSSION: The rectum emerged as a key reservoir, with notable concordance of organisms across rectal and urogenital sites. Our findings indicate that rUTIs in postmenopausal women are associated with a dysbiotic vaginal microbiome that is closely linked to a rectal reservoir of multidrug-resistant uropathogens.},
}

@article {pmid42022125,
year = {2026},
author = {Wang, S and Xie, L and Yan, Z and Ma, J and Zhao, R},
title = {Hybrid expert system for robust detection of rare sequence signals: a computational proof-of-concept in host-dominated backgrounds.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821073},
pmid = {42022125},
issn = {1664-302X},
abstract = {Deciphering microbial symbiosis in robust environmental and host-associated systems increasingly depends on the reliable recovery of weak biological signals from sequencing data dominated by non-target background. In practice, low-abundance symbiont-derived signatures are often obscured by background DNA, recurrent technical artifacts, and context-dependent false-positive calls, limiting the accuracy of downstream ecological and functional inference. Here, we present SymbioFilter, a hybrid expert system designed to improve the specificity and stability of rare-signal detection in host-associated microbiome sequencing data with substantial background noise. (i.e., overwhelming host-derived DNA, recurrent alignment errors, and sequencing artifacts). Specifically, this framework is intended for specialized usage cases where standard host-depletion strategies fail, such as capturing minor microbe-induced host somatic mutations or rare microbial homologs, which reflect subtle and intimate interactions between microbes and the host. SymbioFilter integrates three coordinated layers: (i)ensemble-based candidate detection, (ii)machine-learned background/noise discrimination using an XGBoost classifier, and (iii) rule-guided suppression of artifact-prone genomic regions using curated repetitive and blacklist annotations. Rather than relying on a single decision rule, the framework combines probabilistic classification with expert-defined constraints to preserve weak true signals while reducing recurrent false positives. This design specifically targets analytical failure modes common to host-dominated and low-input datasets, where precision is frequently compromised by rare-event noise. As a stringent proof-of-concept benchmark, we evaluated SymbioFilter in synthetic gradient spike-in datasets. Crucially, to ensure rigorous computational evaluation with an absolute ground truth-a standard that is currently unattainable in complex, real-world microbiome samples at ultra-low abundances-we utilized plasma cfDNA-like low-frequency conditions as a highly controlled, demanding proxy. Across gradient abundance levels, the framework consistently reduced false-positive inflation, improved agreement with the known ground truth, and maintained stable classification performance. Compared with a baseline pipeline and a widely used variant-calling workflow, SymbioFilter achieved lower mean squared error, stronger true-positive/true-negative balance, and consistently high precision-recall behavior, particularly under the most challenging low-abundance settings. Although validated here in a proxy benchmark environment, the computational principles of SymbioFilter address a broader class of sequencing problems central to microbial symbiosis research: identifying rare, functionally relevant biological signals in complex, noise-prone backgrounds. By providing a transferable, modular, and open computational strategy for robust signal recovery, SymbioFilter offers a useful methodological foundation for future studies of host-microbe interactions, resilient community assembly, and symbiosis-associated ecosystem stability. The code is freely available for academic use at https://github.com/hello-json/SymbioFilter.},
}

@article {pmid42022328,
year = {2026},
author = {Wu, Y and Chen, Y and Mao, J and Li, K and He, Q and Zhou, Z},
title = {Mechanistic insights into the role of oral microbiome in the malignant transformation of oral lichen planus to oral squamous cell carcinoma.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1694005},
pmid = {42022328},
issn = {2234-943X},
abstract = {Oral Lichen Planus (OLP) is a common oral potentially malignant disorder, and its transformation into Oral Squamous Cell Carcinoma (OSCC) has become a research focus. In recent years, increasing attention has been paid to the role of the oral microbiome in tumor initiation and progression. Studies have shown that dysbiosis of the oral microbiome may contribute to and accelerate the malignant transformation of OLP to OSCC through multiple mechanisms, including the induction of inflammatory responses, disruption of immune regulation, promotion of oxidative stress, and epithelial-mesenchymal transition (EMT). This review summarizes recent advances in research on the characteristic changes in the oral microbiome and associated molecular mechanisms during the malignant transformation of OLP, aiming to provide a theoretical basis and scientific support for early warning and microecological-targeted interventions in OLP malignancy.},
}

@article {pmid42022578,
year = {2026},
author = {Zeng, Y and Pan, S and Zhang, A and Wang, J and Huang, F and Yu, J and Luo, Q and Ren, B and Tahri, W},
title = {Biogas production and microbial profile estimation in bioreactor landfills.},
journal = {Frontiers in chemistry},
volume = {14},
number = {},
pages = {1742729},
pmid = {42022578},
issn = {2296-2646},
abstract = {INTRODUCTION: This study investigated the municipal solid waste (MSW) biodegradation process, simulating landfill conditions using a bioreactor. A core objective was to identify key markers in leachate that could forecast the methane (CH4) generation process during anaerobic digestion (AD). To further understand the causes of CH4 production inhibition and to propose strategies for enhancing AD system performance, we aimed to compare the microbial community structures in leachate from different reaction periods and in solid MSW samples.

METHODS: A bioreactor was utilized to replicate the landfill's MSW biodegradation process. Research workers analyzed the relationship between the methanogenic process and the properties of leachate from anaerobic digestion. To investigate the underlying causes of inhibition, we compared the features and differences in the microbial community structure of leachate samples from different reaction periods and solid samples (end-state MSW and cover layer).

RESULTS: The biogas production potential was found to be 74.36 L kg[-1], and the rate constant for MSW digestion gas production was 0.0359 days[-1]. A correlation was observed between the leachate's pH, TOC/TN ratio, and the CH4 generation process, though the correlation between pH variation and methanogenesis showed a clear lag, indicating pH alone is not a sufficient predictive signal. The system became unstable due to ammonia buildup, with a TOC/TN value below 13 coinciding with minimal gas output. Microbial analysis showed that the genetic similarity between leachate and MSW samples was inversely related to the length of the reaction period. A key observation was the absence of Nitrospirain leachate, which likely interrupts the nitrogen conversion cycle. The nitrification process was found to primarily occur in the cover layer. Decreased CH4 generation was mostly caused by ammonia inhibition, which reduced the activity of acetate-utilizing methanogenic archaea. The intermediate cover layer acted as a biochemical reaction zone with greater microbial diversity.

DISCUSSION: The findings indicate that due to ammonia buildup, the fermentation system became unstable when the TOC/TN value fell below 13. The absence of Nitrospirain leachate is identified as a critical factor disrupting the nitrogen cycle. Therefore, inoculation with Nitrospira-containing agents is proposed as crucial for maintaining system stability and enhancing treatment efficiency. The intermediate cover layer, harboring greater microbial diversity, contributed to enhanced anaerobic digestion and supported increased system stability, functioning as a vital biochemical reaction zone. These insights provide recommendations for enhancing the AD system's CH4 production capacity.},
}

@article {pmid42022800,
year = {2026},
author = {Liu, Z and Li, H and Xiang, Y and Ren, S and Pan, W and Ling, Z and Dong, J and Liang, Z and Quan, J and Fan, L and Lin, L and Wu, L and Yu, X},
title = {Longitudinal multi-omics evidence reveals lung injury and concurrent disruption of intestinal flora and serum metabolism by cigarette smoke and influenza virus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1731390},
pmid = {42022800},
issn = {2235-2988},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Orthomyxoviridae Infections/pathology/complications/virology ; Influenza A virus ; Biomarkers/blood ; Lung/pathology ; Disease Models, Animal ; *Lung Injury/pathology/metabolism/etiology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Pulmonary Disease, Chronic Obstructive/etiology ; *Smoke/adverse effects ; Metabolomics ; Mice, Inbred C57BL ; Female ; Feces/microbiology/chemistry ; Male ; Multiomics ; },
abstract = {BACKGROUND: Cigarette smoke (CS) exposure is the primary risk factor for chronic obstructive pulmonary disease (COPD), and respiratory viral infections, particularly influenza A virus (IAV), are major triggers of acute exacerbations of COPD (AECOPD). However, the dynamic interactions among pulmonary pathology, gut microbiota, and host metabolism during these episodes remains unclear. This study aimed to delineate the longitudinal characteristics of virus-induced AECOPD and identify potential biomarkers.

METHODS: Mice were exposed to cigarette smoke for eight weeks, followed by intranasal inoculation with IAV. A longitudinal assessment was conducted from day 1 to day 15 post-infection, integrating analyses of lung pathology, lung function, gut microbiome, and both serum and fecal metabolomes. Additionally, random forest modeling was employed to identify specific metabolic biomarkers associated with the acute exacerbation stage.

RESULTS: Mice exposed to cigarette smoke and IAV exhibited significant pulmonary immune cell recruitment, impaired lung function, and emphysematous changes, peaking at day 5 post-infection. By day 15, acute airway inflammation had subsided; however, interstitial immune cell infiltration, collagen deposition, and emphysema persisted. 16S rRNA sequencing revealed dynamic shifts in gut microbiota composition, with the abundance of Intestinimonas positively correlating with pulmonary inflammatory markers. Untargeted metabolomics demonstrated sustained downregulation of serum unsaturated fatty acid biosynthesis pathways from day 3 to day 15, and these metabolites were negatively correlated with lung inflammation. Random forest analysis identified 1-Methylnicotinamide (1-MNA) as a promising biomarker for distinguishing virus-triggered AECOPD, achieving an area under the curve (AUC) of 1.0.

CONCLUSION: This study demonstrates that cigarette smoke combined with influenza infection induces persistent lung injury alongside concurrent disruption of intestinal flora and serum metabolism. The findings show that gut microbiota and metabolites are potential biomarkers and supplementation with unsaturated fatty acids may represent a novel therapeutic strategy for virus-induced AECOPD.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Orthomyxoviridae Infections/pathology/complications/virology
Influenza A virus
Biomarkers/blood
Lung/pathology
Disease Models, Animal
*Lung Injury/pathology/metabolism/etiology
RNA, Ribosomal, 16S/genetics
Metabolome
Pulmonary Disease, Chronic Obstructive/etiology
*Smoke/adverse effects
Metabolomics
Mice, Inbred C57BL
Female
Feces/microbiology/chemistry
Male
Multiomics

@article {pmid42022809,
year = {2026},
author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH},
title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799859},
pmid = {42022809},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Prospective Studies ; *Metabolome ; Longitudinal Studies ; Female ; Male ; Infant, Newborn ; Feces/microbiology ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Infant ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Dysbiosis/microbiology ; Multiomics ; },
abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.},
}

Humans
*Gastrointestinal Microbiome
*Infant, Premature
Prospective Studies
*Metabolome
Longitudinal Studies
Female
Male
Infant, Newborn
Feces/microbiology
*Neurodevelopmental Disorders/microbiology
Metagenomics
Infant
Metabolomics
Bacteria/classification/genetics/isolation & purification
Biomarkers
Dysbiosis/microbiology
Multiomics

@article {pmid42022943,
year = {2026},
author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z},
title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70318},
pmid = {42022943},
issn = {2397-9070},
abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.},
}

@article {pmid42022944,
year = {2026},
author = {Zhao, Z and Ling, J and Chen, J},
title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70390},
pmid = {42022944},
issn = {2397-9070},
abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.

METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176 629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.

RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR = 3.961, 95% CI = 1.085-14.453, p = 0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR = 0.409, 95% CI = 0.167-0.999, p = 0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR = 4.864, 95% CI = 1.293-18.302, p = 0.019), while Aggregatibacter segnis demonstrated a protective effect (OR = 0.400, 95% CI = 0.188-0.854, p = 0.018).

CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.},
}

@article {pmid42023035,
year = {2026},
author = {Shi, Z and Zhang, Y and Chen, Y and Wu, S and Zhou, Z and Chen, Z},
title = {Investigating oral microbiome profiles of children with cleft lip and palate in different states of caries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2660486},
pmid = {42023035},
issn = {2000-2297},
abstract = {OBJECTIVE: To investigate the characteristics of oral salivary microbiota in children with cleft lip and palate (CLP) under different states of caries.

METHODS: Based on the presence or absence of CLP and the total number of decayed, missing and filled surfaces, 105 participants were divided into four groups: children with CLP and high caries (CLP-HC), children with CLP and low caries (CLP-LC), children without CLP but with high caries (NCLP-HC) and children without CLP but with low caries (NCLP-LC). Saliva samples from them were analyzed using 16S rRNA gene sequencing.

RESULTS: Alpha diversity differed significantly among the four groups with Ace and Chao indices, but not with Shannon and Simpson. Principal coordinate analysis based on the Weighted-UniFrac distance matrix showed no significant differences among the four groups, while results from the Unweighted-UniFrac distance matrix revealed significant differences. CLP-HC and CLP-LC had significantly higher Microbial Dysbiosis Index than NCLP-LC. LEfSe analysis was performed for pairwise comparisons, identifying differentially enriched bacterial genera among groups. Network analysis based on Spearman correlation revealed the interaction characteristics of microbial communities in different groups.

CONCLUSIONS: Differences in microbial features were observed among the four groups, which could provide new insights for personalized oral health management for CLP patients.},
}

@article {pmid42023165,
year = {2026},
author = {Xu, Z and Zhang, L and Guo, J and Xia, Q and Ge, Z and Wang, Z and Mu, R and Dong, J and Qin, Z and Chen, J and Wang, Y},
title = {Controlled release of berberine modulates the wound microbiome to accelerate wound healing.},
journal = {Asian journal of pharmaceutical sciences},
volume = {21},
number = {2},
pages = {101148},
pmid = {42023165},
issn = {2221-285X},
abstract = {The wound microbiome has been shown to play a significant role in influencing the wound healing process. Coptis chinensis, a traditional Chinese medicine (TCM) known for its heat-clearing properties, contains berberine (BER) as major active ingredient, which exhibits notable antibacterial activity. In this study, we investigated the effect of BER on wound healing and wound microbiome through three distinct delivery strategies, including solution form, burst-release scaffolds (PCL/BER), and sustained-release scaffolds (PCL/PLGA/BER), compared with an untreated negative control (NC) group. Drug release studies confirmed that PCL/BER caused a pronounced burst release, while the incorporation of PLGA enabled sustained release of BER for up to 120 h. Further in vivo studies showed that the sustained BER release from the PCL/PLGA/BER resulted in the most effective improvement in wound healing. Microbiome analysis using 16S rRNA sequencing identified Staphylococcus xylosus (S. xylosus) as the key species influencing wound healing outcomes in response to BER delivery. S. xylosus overabundance in the NC group and its depletion in the BER solution and burst BER release groups impaired wound healing. In contrast, sustained BER delivery maintained an optimal S. xylosus abundance that promoted a favorable immune microenvironment by modulating CXCL10 and (IFN-α) expression. Our findings emphasize the importance of coordinating drug release kinetics with microbiome dynamics for optimal wound healing outcomes and provide valuable insights for developing future delivery systems for heat-clearing TCMs, with a focus on microbiome-modulation therapeutic strategies.},
}

@article {pmid42023268,
year = {2026},
author = {Wu, Q and Yu, Z and Cao, J and Li, H and Zhang, S},
title = {Oral microbiome dysbiosis mediates the link between emotional disorders and systemic inflammation in heart failure.},
journal = {Brain, behavior, & immunity - health},
volume = {54},
number = {},
pages = {101240},
pmid = {42023268},
issn = {2666-3546},
abstract = {Emotional disorders (EDs) are prevalent in heart failure (HF) and predict poor outcomes, yet their interplay with oral health and systemic inflammation remains unclear. This integrated cross-sectional analysis of NHANES data and a prospective oral microbiome cohort revealed that EDs were significantly associated with poorer cardiovascular health (Life's Essential 8 score), an effect partially mediated by tooth loss and self-rated oral health. Furthermore, HF patients with EDs exhibited distinct oral dysbiosis, marked by depletion of beneficial bacteria (e.g., Cardiobacterium) and enrichment of pro-inflammatory taxa (e.g., Megasphaera), which correlated with systemic inflammation. Our findings posit that EDs may impact cardiovascular health by disrupting the oral microbiome and promoting inflammation, highlighting a potential psychoneuroimmunological pathway in HF progression.},
}

@article {pmid42023434,
year = {2026},
author = {Han, A and Pattaroni, C},
title = {"Scratching the surface" of cutaneous immunity where the microbiome sets the tone and itch turns the volume up.},
journal = {Immunology and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imcb.70118},
pmid = {42023434},
issn = {1440-1711},
abstract = {Commensal-driven humoral immunity and itch-scratch neuroimmune responses cooperate to shape microbial homeostasis and host defense in the skin.},
}

@article {pmid42023455,
year = {2026},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Gut Microbiome in Sleep Disorders: A Review of Recent Evidence.},
journal = {Actas espanolas de psiquiatria},
volume = {54},
number = {2},
pages = {586-601},
doi = {10.62641/aep.v54i2.2123},
pmid = {42023455},
issn = {1578-2735},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sleep Wake Disorders/microbiology/therapy/physiopathology ; Dysbiosis/complications/microbiology ; Fecal Microbiota Transplantation ; },
abstract = {Alterations in the gut microbiome have been shown to influence sleep through gut-brain interactions. However, the interplay between the gut microbiome and sleep disorders remains insufficiently understood. This narrative review provides an overview of recent evidence on the role of the gut microbiome in sleep disorders, examining host-microbial regulation of the sleep cycle, the relationship between gut microbiome dysbiosis and sleep disorders, the influence of the gut microbiome on sleep-related breathing disorders, sleep deprivation, and sleep fragmentation, as well as microbial therapeutic approaches to sleep disorders. Through its effects on bacterial metabolites, immune responses, and neuronal signaling, the gut microbiome might be potentially involved in the regulation of sleep-wake cycles. Disturbances in sleep have been associated with shifts in gut microbiome composition, but this relationship remains incompletely understood and it suggests a bidirectional nature. Evidence indicates that interventions targeting the gut microbiome, such as the use of psychobiotics and fecal microbiota transplantation, may have potential for improving sleep outcomes, but further research is needed to determine their actual effectiveness. Understanding the full range of factors influencing the gut microbiome and their interactions with other variables will be essential for elucidating the mechanisms behind gut-sleep interactions. Thus, future studies should focus on clarifying causality, identifying key biomarkers, and developing microbial-based interventions to establish effective therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sleep Wake Disorders/microbiology/therapy/physiopathology
Dysbiosis/complications/microbiology
Fecal Microbiota Transplantation

@article {pmid41832248,
year = {2026},
author = {El-Tanani, M and Satyam, SM and Rabbani, SA and Rangraze, IR and Matalka, IIA and Muhana, F and El-Tanani, Y and Aljabali, AAA and Khan, MA and Parvez, S and Porntaveetus, T},
title = {Next generation approaches in cancer immunotherapy targeting mechanisms beyond PD1 and PDL1.},
journal = {Discover oncology},
volume = {17},
number = {1},
pages = {},
pmid = {41832248},
issn = {2730-6011},
abstract = {UNLABELLED: Cancer immunotherapy has revolutionized oncology by leveraging the immune system’s ability to recognize and eliminate tumor cells. Among the most impactful advances are immune checkpoint inhibitors that target the programmed death-1 (PD-1) receptor and its ligand PD-L1, which can restore T cell activity and generate durable responses across several cancer types. However, their effectiveness is limited by both primary and acquired resistance, restricting long-term benefit to a subset of patients. This review highlights current progress in cancer immunotherapy and explores emerging strategies beyond PD-1/PD-L1 blockade. Novel inhibitory and co-stimulatory immune checkpoints such as lymphocyte activation gene-3 (LAG-3), T cell immunoglobulin mucin-3 (TIM-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), OX40, CD137 (4-1BB), and CD40 are examined for their potential to enhance anti-tumor immunity. The rationale for combining immunotherapy with chemotherapy, radiotherapy, targeted therapies, oncolytic viruses, and neoantigen vaccines is discussed in the context of overcoming resistance. Additional emphasis is placed on modifying the tumor microenvironment, targeting tumor metabolism, and overcoming stromal barriers. Advanced delivery systems such as chimeric antigen receptor (CAR) T cells, bispecific antibodies, and nanoparticle-based platforms offer improved specificity and reduced toxicity. Biomarker-guided precision immuno-oncology using tumor mutational burden, microsatellite instability, and immune gene signatures is advancing clinical decision-making. Gut microbiota modulation and artificial intelligence-based tools are also emerging as critical components in optimizing therapeutic outcomes. Collectively, this review proposes a multidimensional and personalized immunotherapy paradigm aimed at broadening clinical efficacy and overcoming resistance beyond conventional PD-1/PD-L1 inhibition.

GRAPHICAL ABSTRACT: [Image: see text]},
}

@article {pmid41857116,
year = {2026},
author = {Frater, J and Nicourt, M and Landi, F and Maxwell, B and Thiodet, J and Mestrallet, E and Warr, SJ and Pizarro, M and Fa, JE and Lemoine, S},
title = {Geophagy in Gibraltar Barbary macaques is a primate tradition anthropogenically induced.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41857116},
issn = {2045-2322},
support = {101034349-6//Marie Skłodowska-Curie Action COFUND - R2STAIR/ ; SRG2223\231596//British Academy Leverhulme Small Research Grant/ ; },
abstract = {UNLABELLED: We report, for the first time, geophagy – the deliberate consumption of earth – in the Barbary macaque (Macaca sylvanus) population living at the human-primate interface in Gibraltar. We evaluate potential adaptive functions of this behavior in an anthropogenic context, drawing on predictions from the protection and supplementation hypotheses. Geophagy occurred at exceptionally high rates compared to other macaque species and locations, and it was more common in summer when tourist numbers peak. It was also more likely when macaques consumed greater amounts of tourist-derived food, supporting a protective function. Local ecological factors contributed as well, with the distribution of red soil (terra rossa) influencing geophagy frequency. Although the behavior was not linked to female reproductive status, supplementation cannot be fully dismissed given the very limited insectivory in this population. We propose that tourist-derived foods may disrupt gut microbiome composition, producing discomfort that individuals mitigate through soil ingestion. Geophagy is likely socially learned, as groups showed consistent preferences for specific soil types, and its practice in presence of conspecifics offered opportunities for social learning. Reports from other sites indicate that geophagy is not unique to Gibraltar, but in this population it appears to be anthropogenically induced and socially transmitted, forming a locally maintained tradition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44607-0.},
}

@article {pmid42013859,
year = {2026},
author = {Estrem, CE and Dua, M and Fees, CP and Hoeprich, GJ and Au, M and Goode, BL and Deng, LL and Flavell, SW},
title = {Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.03.070},
pmid = {42013859},
issn = {1879-0445},
abstract = {The bacterial microbiome influences many aspects of animal health and disease. Bacteria can have beneficial functions, for example providing nutrients, whereas others can act as pathogens. Bacteria are sensed by host cells to induce adaptive changes in physiology and behavior. While immune and intestinal cells detect bacterial signals through well-characterized mechanisms, recent studies indicate that neurons can also directly sense bacteria. However, the bacterial sensory mechanisms in neurons are less well understood. In Caenorhabditis elegans, the enteric sensory neuron NSM innervates the pharyngeal lumen and is directly activated by bacterial ingestion; in turn, NSM releases serotonin to induce feeding-related behaviors. However, the molecular identities of the bacterial signals that activate NSM are unknown. To identify them, we probed bacterial macromolecules from nutritive bacteria using biochemical approaches. We find that polysaccharides from bacteria are sufficient to activate NSM. We further identify peptidoglycans from Gram-positive bacteria as specific components capable of activating NSM. NSM responses to polysaccharides require the acid-sensing ion channels DEL-3 and DEL-7, which localize to NSM's sensory dendrite in the pharyngeal lumen. Ingestion of bacterial polysaccharides enhances feeding and reduces locomotion, matching the known effects of NSM on behavior. We also examine signals produced by pathogenic bacteria. This approach identifies prodigiosin, from pathogenic Serratia marcescens, as a metabolite that prevents NSM activation by nutritive bacterial signals. This study identifies molecular signals that underlie neuronal recognition of nutritive bacteria in the alimentary canal and competing signals from a pathogenic bacterial strain that can mask this form of recognition.},
}

@article {pmid42014006,
year = {2026},
author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W},
title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.},
journal = {International journal of biological macromolecules},
volume = {362},
number = {},
pages = {152109},
doi = {10.1016/j.ijbiomac.2026.152109},
pmid = {42014006},
issn = {1879-0003},
abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.},
}

@article {pmid42014077,
year = {2026},
author = {McCracken, AR and Rodger, A and Saratkar, C and Mariani Sularz, S and Brusch, S and Nunez, JCB and Pespeni, MH},
title = {Precursors of sea star wasting: immune and microbial disruption during initial disease outbreak in southeast Alaska.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2069},
pages = {},
doi = {10.1098/rspb.2025.2947},
pmid = {42014077},
issn = {1471-2954},
support = {//National Science Foundation/ ; },
mesh = {*Starfish/microbiology/immunology ; Animals ; Alaska ; *Vibrio/physiology ; Disease Outbreaks/veterinary ; Transcriptome ; },
abstract = {Sea star wasting (SSW) disease has devastated sea star populations along the North American Pacific coast with some recovery since 2013. Though Vibrio pectenicida has recently been implicated as a causative agent, the dynamics of disease progression and host response in natural environments remain understudied. Here, we integrate transcriptomic and microbial data from wild Pycnopodia helianthoides sampled across sites affected and unaffected by SSW in southeast Alaska during the initial outbreak recorded in the region in 2016. Individuals exposed to SSW but lacking visible signs of disease showed elevated expression of complement system components, pathogen recognition and immune regulatory pathways relative to naive individuals. Differential expression of extracellular matrix and tissue remodelling genes suggests disruption of tissue homeostasis preceding visible signs of disease. Furthermore, network analyses revealed certain microbial abundances, including Vibrio spp., correlated with immune response and tissue integrity gene expression. Although V. pectenicida was detected in some samples, its rarity prevented detailed analysis. Nevertheless, higher prevalence in exposed samples is consistent with growing evidence implicating Vibrio infection as an agent of SSW. Together, our findings offer insight into early host-pathogen dynamics in wild populations, underscoring links between immune activation and microbial shifts with the onset of SSW disease.},
}

*Starfish/microbiology/immunology
Animals
Alaska
*Vibrio/physiology
Disease Outbreaks/veterinary
Transcriptome

@article {pmid42014181,
year = {2026},
author = {Seo, JI and Kim, SM and Yoo, HH},
title = {Phytochemicals in MASLD: A Focused Review of Gut Microbiome-Linked Mechanisms.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70352},
pmid = {42014181},
issn = {1099-1573},
support = {RS-2023-00217123//National Research Foundation of Korea/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as a major global health burden, yet effective pharmacological options remain limited. Recent advances highlight the gut microbiome as a key modulator of liver metabolism, inflammation, and fibrosis, making it a promising therapeutic target. Among various non-pharmacologic strategies, phytochemicals have drawn growing attention for their ability to influence the gut-liver axis through natural, multitarget mechanisms. This mini-review summarizes preclinical and clinical evidence on phytochemicals that demonstrate metabolic benefits in MASLD, with a focus on their microbiome-mediated effects. To this end, we classify these mechanistic pathways into three major continuums: restoration of gut microbial composition (causation), modulation of signaling mediators, i.e., gut microbial metabolites (mediation), and the resulting functional outcomes derived from these causal links (outcome). While early pre-clinical data are encouraging, translation is challenged by issues such as mechanistic complexity, microbiome-dependent heterogeneity, and regulatory ambiguity. Future studies incorporating multi-omics analysis, mechanism-linked trial designs, and stratified patient populations will be critical to advancing phytochemicals as safe, effective, and personalized interventions for MASLD.},
}

@article {pmid42014206,
year = {2026},
author = {George, SM and Chatterjee, P and Chaudhry, R and Bamola, VD and Khan, MA and Purohit, A and Suroliya, V and Muley, R and Chakrawarty, A},
title = {Gut Microbiota Signatures of Sarcopenia: A Comparative 16S rRNA Sequencing Study in Older Indian Adults.},
journal = {Geriatrics & gerontology international},
volume = {26},
number = {4},
pages = {e70500},
doi = {10.1111/ggi.70500},
pmid = {42014206},
issn = {1447-0594},
support = {//National Programme for Health Care of the Elderly, Government of India (NPHCE)/ ; },
mesh = {Humans ; *Sarcopenia/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Aged ; Female ; Cross-Sectional Studies ; India ; *RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Middle Aged ; Feces/microbiology ; Aged, 80 and over ; },
abstract = {AIM: Emerging evidence suggests that alterations in gut microbiota composition may contribute to the onset and progression of sarcopenia through mechanisms involving systemic inflammation, metabolic dysregulation, and reduced production of short-chain fatty acids (SCFAs). However, data from Indian older adults-who exhibit diverse diets and microbiota profiles-are lacking.

METHODS: This hospital-based cross-sectional pilot study enrolled 30 older adults aged ≥ 60 years, including 15 with sarcopenic and 15 age- and sex-matched nonsarcopenic. Sarcopenia was classified according to the Asian Working Group for Sarcopenia (AWGS-2019) criteria. Stool samples were analyzed using 16S ribosomal RNA (rRNA) sequencing (V3-V4 region, Illumina MiSeq). Taxonomic classification and diversity indices (Chao1, Shannon, UniFrac) were compared between groups.

RESULTS: The mean age (S.D.) of study participants was 73.27 ± 5.96 years. A total of 251 315 high-quality sequences were generated from 30 fresh human fecal samples. The dominant phylum in the nonsarcopenic group was Firmicutes (41.2%), followed by Bacteroidetes (36.0%), whereas in the sarcopenic group, Bacteroidetes (39.2%) was most common, followed by Firmicutes (37.8%). A decrease in Operational Taxonomic Units (OTUs) of genus Bifidobacterium (2.21% vs. 3.71%), Bacteroides (8.50% vs. 11.11%) was observed in the sarcopenic group. An increase in OTUs of genus Faecalibacterium (10.64% vs. 8.23%) in the sarcopenic group was observed. The alpha-diversity index Chao1, Shannon was reduced in sarcopenic population.

CONCLUSIONS: Exploratory differences in microbial diversity and relative abundance were observed between sarcopenic and nonsarcopenic older adults. These findings are descriptive and hypothesis-generating and warrant confirmation in larger, adequately powered studies.},
}

Humans
*Sarcopenia/microbiology
*Gastrointestinal Microbiome/genetics
Male
Aged
Female
Cross-Sectional Studies
India
*RNA, Ribosomal, 16S/genetics
Pilot Projects
Middle Aged
Feces/microbiology
Aged, 80 and over

@article {pmid42014368,
year = {2026},
author = {Li, Y and Niu, S and Wang, H and Li, J},
title = {Microbiome Modulation with Lactobacillus rhamnosus GG Potentiates Curcumin's Efficacy in Reversing Gemcitabine Resistance of Gallbladder Cancer through Gut Microbiota-PI3K/AKT Axis.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601007},
pmid = {42014368},
issn = {1738-8872},
mesh = {*Lacticaseibacillus rhamnosus/physiology ; *Curcumin/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; Gemcitabine ; Phosphatidylinositol 3-Kinases/metabolism ; *Gallbladder Neoplasms/drug therapy/microbiology/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Deoxycytidine/analogs & derivatives/pharmacology ; *Drug Resistance, Neoplasm/drug effects ; Animals ; Cell Proliferation/drug effects ; Probiotics/pharmacology ; Cell Line, Tumor ; Signal Transduction/drug effects ; Mice ; Apoptosis/drug effects ; Xenograft Model Antitumor Assays ; },
abstract = {Gemcitabine (GEM) resistance remains a major challenge in the treatment of gallbladder cancer (GBC). This study investigated the synergistic effect of curcumin (CUR) combined with the probiotic Lactobacillus rhamnosus GG (LGG) in reversing chemoresistance through modulation of the gut microbiota. In GEM-resistant GBC-SD cells, the CUR-LGG combination significantly inhibited cell proliferation, suppressed migration and invasion, and induced apoptosis, as demonstrated by CCK-8, wound healing, Transwell, and flow cytometry assays. Western blot analysis revealed corresponding regulation of proliferation markers (Ki67, PCNA), apoptosis-related proteins (Bcl-2, Bax, cleaved Caspase-3), and epithelial-mesenchymal transition markers. In xenograft models, the combined treatment markedly suppressed tumor growth and altered gut microbial composition, increasing beneficial bacteria (Lactobacillus, Bifidobacterium) while reducing pathogenic taxa. LC-MS analysis further demonstrated restoration of bile acid homeostasis, characterized by elevated primary bile acids (GCA, CDCA) and decreased secondary bile acids (DCA, LCA). Mechanistically, the intervention significantly inhibited PI3K/AKT signaling, as confirmed by Western blot and immunohistochemistry. Bioinformatic analysis further identified PI3K/AKT as a central regulatory pathway. These findings indicate that probiotic-assisted CUR therapy reverses GEM resistance by remodeling the gut microbiota and its metabolic outputs, thereby suppressing oncogenic signaling pathways. This strategy provides a promising microbiota-based approach for improving therapeutic outcomes in GBC.},
}

*Lacticaseibacillus rhamnosus/physiology
*Curcumin/pharmacology
Humans
*Gastrointestinal Microbiome/drug effects
Gemcitabine
Phosphatidylinositol 3-Kinases/metabolism
*Gallbladder Neoplasms/drug therapy/microbiology/metabolism
Proto-Oncogene Proteins c-akt/metabolism
*Deoxycytidine/analogs & derivatives/pharmacology
*Drug Resistance, Neoplasm/drug effects
Animals
Cell Proliferation/drug effects
Probiotics/pharmacology
Cell Line, Tumor
Signal Transduction/drug effects
Mice
Apoptosis/drug effects
Xenograft Model Antitumor Assays

@article {pmid42014402,
year = {2026},
author = {Boscaini, S and Bastiaanssen, TFS and Moloney, GM and Bergamo, F and Zeraik, L and O'Leary, C and Ferri, A and Irfan, M and van der Rhee, M and Lindemann, TIF and Schneider, E and Meyyappan, AC and Harold, KB and Long-Smith, CM and Carbia, C and O'Riordan, KJ and de Alvarenga, JFR and Tosi, N and Del Rio, D and Rosi, A and Bresciani, L and Mena, P and Clarke, G and Cryan, JF},
title = {Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42014402},
issn = {2041-1723},
support = {950050//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Coffee/metabolism ; *Cognition/drug effects/physiology ; Male ; Adult ; Feces/microbiology ; Female ; Caffeine/pharmacology/metabolism ; Young Adult ; Brain/physiology ; Metabolome ; },
abstract = {Coffee influences multiple physiological processes, including gut function, stress, cognition, and the microbiome. However, the mechanisms underlying these effects remain poorly understood. In this study, we examined coffee's impact on the microbiota-gut-brain axis-a bidirectional communication pathway between the gut microbiome and the brain-and assessed whether these effects occur independently of caffeine in healthy participants. Our primary outcome was microbiota composition and function, whereas the secondary outcome was gut microbial metabolites and coffee-related metabolites (NCT05927038 and NCT05927103). Significant group differences emerged in faecal microbiome composition, with coffee drinkers showing increased relative abundance of Cryptobacterium and Eggerthella species, alongside reduced levels of the metabolite's indole-3-propionic acid, indole-3-carboxyaldehyde, and the neurotransmitter γ-aminobutyric acid. Behaviourally, coffee drinkers exhibited greater impulsivity and emotional reactivity, whereas non-coffee drinkers demonstrated better memory performance. Some alterations in the faecal metabolome were reversible following coffee abstinence, and reintroduction triggered acute microbiome changes independent of caffeine. An integrated model identified nine key metabolites-including theophylline, caffeine, and selected phenolic acids-strongly linked to microbial species and cognitive measures. These findings reveal previously unrecognised effects of coffee on the microbiota-gut-brain axis, suggesting that microbiome profiles could potentially predict coffee consumption patterns and highlighting a close association between coffee intake and gut microbial composition.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Coffee/metabolism
*Cognition/drug effects/physiology
Male
Adult
Feces/microbiology
Female
Caffeine/pharmacology/metabolism
Young Adult
Brain/physiology
Metabolome

@article {pmid42014413,
year = {2026},
author = {Zhang, L and Soleimani Samarkhazan, H and Almajidi, Y and Gafarov, R},
title = {The microbial metabolome: remodeling the therapeutic landscape in hematologic malignancies.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00972-2},
pmid = {42014413},
issn = {2055-5008},
abstract = {The gut microbiome's metabolome critically shapes drug efficacy and toxicity in hematologic malignancies. This review explores how microbial metabolites influence chemotherapy, immunotherapy, and transplant outcomes, and how they can be harnessed as biomarkers and therapeutic targets. Moving from association to intervention, we outline a pathway toward metabolome-informed precision oncology, transforming the "second genome" into a actionable ally for improved cancer therapy.},
}

@article {pmid42014454,
year = {2026},
author = {Muller, E and Bamberger, T and Borenstein, E},
title = {Navigating multi-omic integration methods for human microbiome research.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42014454},
issn = {2058-5276},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2266/25//Israel Science Foundation (ISF)/ ; },
abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.},
}

@article {pmid42014606,
year = {2026},
author = {Singh, S and Shahadab, M and Sachin, K and Pandey, RK and Trivedi, P and Mishra, AK and Jha, HC},
title = {Genomic-microbial coevolution in human development: chromosome 2 fusion, and human accelerated regions.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {37},
number = {1},
pages = {},
pmid = {42014606},
issn = {1432-1777},
}

@article {pmid42014676,
year = {2026},
author = {Al, KF and Wammes, M and Warren, M and Lee, JE and Walton, DM and O'Connor, C and Cameron, L and Burton, JP and Osuch, EA},
title = {A case-series of oral acetate supplementation for gut microbiota alteration and metabolic improvement in patients with affective disorders on psychotropics.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04046-x},
pmid = {42014676},
issn = {2158-3188},
support = {NA//London Community Foundation (LCF)/ ; },
abstract = {Mental illnesses affect one in five Canadians and often require psychotropic medications. While effective, many psychotropic medications can cause weight gain and metabolic side effects. The gut microbiota, influenced by short-chain fatty acids like acetate, plays a role in mental health via the gut-brain axis and may be disrupted as a result of medication use. This case-series explored the feasibility of acetate supplementation contained in delayed-release capsules as an intervention to alter the gut microbiota and reduce metabolic side effects in people taking psychotropic medication for mood and anxiety disorders. Eleven participants aged 22-32 with medication-related weight gain were evaluated at baseline, across three months of delayed-release acetate supplementation, and at one-month follow-up. Adherence was high, with no serious adverse events. Six participants showed signs of metabolic improvements, including clinically-meaningful changes in cholesterol and weight. Mood and anxiety symptoms meaningfully improved in two participants. 16S rRNA gene sequencing revealed alterations in the gut microbiota at both the individual and group levels following the intervention, including increased relative abundance of butyrate-producing bacteria and functional changes potentially influencing cholesterol metabolism. Microbiota differences were also noted between participants with and without metabolic improvements, both pre- and post-intervention, suggesting a potential "responder" phenotype. These findings support further exploration of the effectiveness of delayed-release acetate as a safe adjunctive therapy to offset metabolic concerns and gut microbiome changes in people on psychotropic medication. Larger studies with longer follow-up are needed to confirm these effects and validate responder subgroups.},
}

@article {pmid42014741,
year = {2026},
author = {Toner-Bartelds, C and Mimpen, IL and Parra-Martinez, M and Burgering, BMT and Voest, EE},
title = {Microbiota-derived metabolites as modulators of cancer immunotherapy response.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72178-1},
pmid = {42014741},
issn = {2041-1723},
abstract = {The microbiome is a key regulator of host homeostasis and immune activity, in part through the production of metabolites. These microbiota-derived metabolites can modulate both the innate and adaptive immune system, as well as directly target tumour cells, thereby regulating anti-tumour immunity and response to immunotherapy. Here, we describe the current mechanistic knowledge on how these metabolites exert their effects and outline the methodologies used to detect and assess these metabolites. Finally, we summarize microbiota-targeted therapies capable of improving microbial functionality to ultimately enhance immunotherapy responses and improve patient survival.},
}

@article {pmid42014792,
year = {2026},
author = {Głowska-Patyniak, E and Ostrowska, K and Olechnowicz, J and Hubert, J and Konecka, E and Sharma, AK and Som, A and Dabert, M and Trzebny, A},
title = {A Wolbachia lineage likely representing a new supergroup (Y) dominates the microbiome of the quill mite Syringophilus bipectinatus Heller, 1880 (Acariformes: Syringophilidae).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48644-7},
pmid = {42014792},
issn = {2045-2322},
support = {UMO-2021/03/Y/NZ8/00060//The National Science Centre of Poland/ ; },
abstract = {The microbiome plays a key role in animal biology, including host reproduction. Quill mites (Acariformes: Syringophilidae) are understudied ectoparasites of birds, with many species exhibiting strongly female-biased sex ratios. Previous studies have identified unique strains of Wolbachia and Spiroplasma in quill mites, both known to manipulate host reproduction in other arthropods. To further investigate this association, we analyzed the microbiome of Syringophilus bipectinatus Heller, 1880, a relatively early-diverging quill mite species parasitizing the Red Junglefowl (domestic type) (Galliformes: Phasianidae), using 16S rRNA gene profiling. We categorized mite specimens by sex and developmental stage to test for potential associations between microbiome composition and sex ratios. We report the first detection of Wolbachia in S. bipectinatus with a single amplicon sequence variant (ASV) consistently detected across all analyzed samples, accounting for 56-99% of total bacterial sequence reads. Phylogenetic analysis based on 16S rRNA gene and four protein-coding genes (fbpA, ftsZ, gatB, hcpA) recovered this strain as a deeply divergent Wolbachia lineage that does not cluster with any previously described supergroup. This lineage is therefore interpreted as likely representing a novel Wolbachia supergroup (Y), although its formal status requires further validation using genome-scale data. Its consistent presence across both sexes and all developmental stages suggests a stable and potentially obligate association, although its functional role remains to be determined. In addition, we identified bacterial taxa also reported from avian hosts, including potentially pathogenic genera such as Arcobacter, highlighting the complex microbial ecology of quill mites.},
}

@article {pmid42014833,
year = {2026},
author = {Bokszczanin, KŁ and Chojnacka, A and Suchocka, M and Kalaji, HM and Malinowski, R and Kubus, M},
title = {Soil management strategies shape bacterial and eukaryotic community structure in organic and inorganic systems of Malus × domestica production.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49450-x},
pmid = {42014833},
issn = {2045-2322},
abstract = {Understanding the temporal dynamics of soil microbial communities is crucial for assessing the stability of orchard soils. We analyzed bacterial and eukaryotic communities in the rhizosphere of apple trees under seven mulching treatments across two growing seasons (2020 and 2023). To account for potential batch effects between separate sequencing runs, results from each year were juxtaposed to identify recurring microbial patterns. High-throughput 16S and ITS sequencing revealed that management-specific signatures persisted over time despite inter-run variability. Bacterial alpha diversity varied significantly among individual treatments, while beta diversity consistently distinguished management regimes across both years. Fungal alpha diversity remained largely unaffected, but beta diversity revealed significant compositional shifts between organic and inorganic groups. Organic mulching (shredded Miscanthus straw and spent mushroom compost) consistently enriched bacterial families linked to organic matter turnover (Sphingomonadaceae, Flavobacteriaceae, Moraxellaceae), whereas inorganic systems favored Comamonadaceae and Nitrosomonadaceae. Organic soils were also enriched in saprotrophic fungi (Lasiosphaeriaceae) and broader eukaryotes (Ciliophora), while inorganic - Mortierellaceae. Network analyses identified a cohesive bacterial core, whereas fungal/eukaryotic communities were more modular and responsive to mulching type. These findings demonstrate that sustained organic mulching promotes stable microbial configurations associated with soil functioning, highlighting the consistency of management-associated microbial signatures under long-term agricultural practices.},
}

@article {pmid42014845,
year = {2026},
author = {Yu, P and Zhou, W and Li, C and Sun, Q and Yang, Y},
title = {Construction of an engineered Escherichia coli strain with enhanced intestinal colonization and anti-inflammatory efficacy in colitis.},
journal = {Cellular & molecular immunology},
volume = {},
number = {},
pages = {},
pmid = {42014845},
issn = {2042-0226},
abstract = {Engineered probiotics are considered effective and safe therapeutic strategies for the treatment of various diseases. Escherichia coli Nissle 1917 (EcN) has been widely used as a chassis strain because of its safety and well-established genetic manipulation system. However, the limited intestinal colonization ability of EcN limits its potential as a chassis for the construction of synthetic probiotics. Here, an engineered EcN strain (EcN-CPM) with enhanced gastric acid and bile salt tolerance and improved intestinal adhesion was constructed. Oral administration of EcN-CPM to mice with colitis alleviated disease severity and reshaped the disordered gut microbiome by decreasing the abundance of Escherichia-Shigella while increasing the abundance of norank_f_Muribaculaceae. Mechanistically, the EcN-CPM supernatant directly promoted the proliferation of norank_f_Muribaculaceae, a short-chain fatty acid (SCFA)-producing genus. Targeted metabolomics revealed that EcN-CPM restored the DSS-induced depletion of SCFAs, which were negatively correlated with the abundance of Escherichia-Shigella and positively correlated with the abundance of norank_f_Muribaculaceae. Consistent with these findings, EcN-CPM treatment upregulated the expression of Treg-associated markers (Foxp3, Ctla4, and Cd25) and downregulated the expression of Th17-related genes (IL-17A and Roryt) in colonic tissues, restoring the IL-17A/Foxp3 ratio to homeostasis. Untargeted metabolomics further demonstrated that EcN-CPM uniquely restored the levels of seven anti-inflammatory metabolites depleted by DSS treatment. Collectively, these findings demonstrate that EcN-CPM alleviates intestinal inflammation by remodeling the gut microbiota to increase the production of SCFAs and anti-inflammatory metabolites, thereby driving a shift in Th17- and Treg-associated transcriptional signatures. This study establishes a platform for precision-designed synthetic probiotics with enhanced probiotic properties.},
}

@article {pmid42014976,
year = {2026},
author = {Lardinois, LL and Hinojosa, NA and Quintero-Arrieta, H and Sellers, AJ and Leray, M and Barrett, RDH},
title = {Host matters: coral reef fish species show distinct skin microbiome responses to upwelling-driven environmental changes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05036-1},
pmid = {42014976},
issn = {1471-2180},
support = {doi: 10.69777/330691//Fonds de recherche du Québec/ ; 2019-04549//Natural Sciences and Engineering Research Council of Canada/ ; },
}

@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05043-2},
pmid = {42014993},
issn = {1471-2180},
}

@article {pmid42015254,
year = {2026},
author = {Dillen, J and Eilers, T and Dricot, CEMK and Van Hee, M and Vandenheuvel, D and Masschelein, J and Lebeer, S},
title = {Modular biosynthesis of microbiome-derived polyketides and nonribosomal peptides: insights and opportunities for Lactobacillaceae.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-026-03008-8},
pmid = {42015254},
issn = {1475-2859},
support = {1S28622N//Fonds Wetenschappelijk Onderzoek/ ; 1158725N//Fonds Wetenschappelijk Onderzoek/ ; G049022N//Fonds Wetenschappelijk Onderzoek/ ; 852600//HORIZON EUROPE European Research Council/ ; },
}

@article {pmid42015325,
year = {2026},
author = {Fauszt, P and Szilagyi, E and Mikolas, M and Szilagyi-Tolnai, E and David, P and Kovacs-Forgacs, IN and Csernus, B and Gal, F and Stundl, L and Biro, S and Szabo, C and Remenyik, J and Babinszky, L and Paholcsek, M},
title = {Alleviation of heat stress-induced microbial dysbiosis in pigs through dietary supplementation with vitamins and trace elements.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00575-4},
pmid = {42015325},
issn = {2524-4671},
abstract = {BACKGROUND: Chronic heat stress (HS) is known to impair animal health and productivity, in part by altering gut microbiota. This study investigated how HS affects the pig gut microbiome and whether dietary supplementation with antioxidants and trace elements (vitamins E, C, selenium, and zinc) at moderate (D1) or high (D2) doses can mitigate these effects.

RESULTS: During the adaptation phase, feed efficiency was similar across groups, but as the experiment progressed, the thermoneutral control improved while the heat-stressed control deteriorated. Supplemented diets (D1/D2) partially alleviated this efficiency loss. Microbiome analysis revealed that HS progressively reduced diversity, reaching the lowest Shannon index during exposure. High-dose supplementation markedly increased richness, exceeding control levels. Total microbial abundance declined under HS, with opportunistic pathogens enriched particularly during early exposure. Guild-level indices further indicated a shift under HS. Aerotolerance indices decreased (ATi: TC > D1 > D2 > HSC), reflecting hypoxia-prone conditions favoring obligate anaerobes and SCFA producers. Among supplemented groups, D1 most closely stabilized aerotolerance toward control levels, while D2 maintained an SCFA-dominant community and enhanced butyrate capacity. Genus-level correlations with qPCR-based host gene-expression markers were assessed across all groups. HSP70 was the dominant correlate, and the most extreme associations were confined to a few taxa, indicating marked group specificity.

CONCLUSION: Chronic HS in pigs induced microbial dysbiosis characterized by reduced diversity, loss of beneficial SCFA producers, and expansion of opportunistic pathogens. Dietary supplementation counteracted these adverse changes in a dose-dependent manner. While moderate supplementation provided partial stabilization, high-dose supplementation more effectively restored microbial diversity and enriched beneficial taxa, making it the more effective strategy for mitigating HS-induced microbiome disruption.},
}

@article {pmid42015346,
year = {2026},
author = {Li, Z and Samui, S and Liu, J and Yang, Y and Liu, X and Chen, Q and Li, J and Gopinath, D and Luo, P and Shan, D},
title = {Gut microbiome and metabolic health: mechanisms and precision interventions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644677},
doi = {10.1080/19490976.2026.2644677},
pmid = {42015346},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Precision Medicine ; *Metabolic Diseases/microbiology/metabolism/therapy ; Prebiotics/administration & dosage ; Obesity/microbiology/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Metabolic Syndrome/microbiology/metabolism ; },
abstract = {The gut microbiome is increasingly recognized as a fundamental regulator of metabolic health, shaping energy balance, insulin sensitivity, inflammatory tone, and inter-organ communication through a broad spectrum of microbial metabolites that engage host signaling pathways. In this review, we synthesize current mechanistic insights into how gut microbial communities shape metabolic function, with particular emphasis on short-chain fatty acids, secondary bile acid signaling, gut barrier integrity, immune modulation, and the microbiota-gut-brain-pancreas axis. We further summarize disease-associated alterations in microbial composition and function across obesity, type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, and metabolic syndrome, highlighting key microbial and metabolic features that contribute to metabolic dysfunction. Evidence from germ-free models, fecal microbiota transplantation studies, and strain-level interventions suggests that shifts in microbial ecology may causally shape metabolic outcomes. We also critically evaluate emerging microbiome-centered therapeutic strategies, including targeted probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation, while addressing factors that underlie inter-individual variability in treatment responses. In addition, we discuss the growing influence of multi-omics technologies, microbial metabolic modeling, and machine learning approaches in advancing precision microbiome medicine. To integrate these advances within a coherent framework, we outline a precision microbiome intervention pipeline linking multidimensional profiling to functional stratification and targeted therapeutic design. We also introduce a conceptual Precision Microbiome Intervention Triangle to mechanistically explain heterogeneity in responses to microbiome-targeted therapies. Collectively, these insights establish and position the gut microbiome as both a mechanistic driver and a modifiable therapeutic target in metabolic disease, and highlight key challenges and future directions for the development of personalized microbiome-based metabolic interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
Fecal Microbiota Transplantation
Probiotics
Precision Medicine
*Metabolic Diseases/microbiology/metabolism/therapy
Prebiotics/administration & dosage
Obesity/microbiology/metabolism
Diabetes Mellitus, Type 2/microbiology/metabolism
Metabolic Syndrome/microbiology/metabolism

@article {pmid42015619,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S},
title = {Statin-induced gut dysbiosis and sleep disturbances: Mechanistic insights into microbiota-brain-circadian interactions and chronotherapeutic implications.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/07420528.2026.2660826},
pmid = {42015619},
issn = {1525-6073},
abstract = {Statins are widely prescribed lipid-lowering agents with well-established efficacy in reducing cardiovascular morbidity and mortality. However, accumulating clinical and experimental evidence suggests that statin therapy may be associated with sleep disturbances, including insomnia, altered sleep architecture, vivid dreams, and reduced sleep quality. Emerging insights implicate the gut microbiota as a key regulator of host circadian rhythms and sleep homeostasis through interconnected pathways involving the tryptophan-serotonin-melatonin axis, short-chain fatty acid (SCFA) production, bile acid signaling, and immune-mediated neuroinflammation. Statins have been shown to modulate gut microbial composition, often reducing SCFA producing taxa and altering bile acid pools, which in turn may disrupt neurochemical signaling and circadian regulation. These microbiota-driven perturbations may contribute to central nervous system effects that underlie sleep-related adverse outcomes. This review integrates current mechanistic and clinical evidence linking statin-induced gut dysbiosis with sleep disturbances, highlighting the role of microbiome-host interactions in mediating off-target drug effects. It further examines implications for vulnerable populations, including shift workers, and discusses the potential of chronotherapy in optimizing statin administration. Finally, microbiota targeted interventions, such as probiotics, prebiotics, and dietary modulation, are proposed as promising strategies to mitigate these adverse effects. A deeper understanding of these interactions may enable personalized therapeutic approaches to enhance both cardiovascular outcomes and sleep health.},
}

@article {pmid42015788,
year = {2026},
author = {Kexin, LI and Jinzu, Y and Kunlin, X and Shaojie, D and Kunmin, X},
title = {Tongue-coating microbiome as a predictor of solid tumors: an updated scoping review of clinical studies.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {2},
pages = {501-508},
pmid = {42015788},
issn = {2589-451X},
mesh = {Humans ; *Microbiota ; *Neoplasms/microbiology/diagnosis ; *Tongue/microbiology ; Medicine, Chinese Traditional ; },
abstract = {This study explores the potential of tongue coating microbiota as a non-invasive biomarker for cancer and precancerous lesions by integrating insights from multi-omics technologies and Traditional Chinese Medicine (TCM) tongue diagnosis. By bridging modern molecular research with TCM diagnostic principles, this study systematically reviewed the relationship between tongue microbiota and oncological conditions, identifying 18 eligible studies through searches in PubMed, Embase, and Web of Science. The analysis reveals significant differences in microbial diversity, abundance, metabolic pathways, and functional characteristics, which enable the partial differentiation of cancer patients from healthy individuals. However, existing research remains constrained by limited sample sizes, inconsistent analytical approaches, and a lack of integrated multi-dimensional datasets. This review highlights the promising diagnostic potential of the tongue coating microbiota in cancer detection, while suggesting that future studies should focus on standardizing methodologies and employing integrated multi-omics approaches to elucidate underlying mechanisms and advance clinical applications.},
}

Humans
*Microbiota
*Neoplasms/microbiology/diagnosis
*Tongue/microbiology
Medicine, Chinese Traditional

@article {pmid42015892,
year = {2026},
author = {Satgunaseelan, L and Strbenac, D and Palme, C and Low, TH and Wykes, J and Manzie, T and Clark, JR and Yang, JYH and Gupta, R},
title = {The microbiome landscape of oral cancer in young patients.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkag022},
pmid = {42015892},
issn = {2515-5091},
abstract = {BACKGROUND: The incidence of oral squamous cell carcinoma (OSCC) is rising in patients under the age of 50, without smoking or alcohol abuse. Viruses are not a causative factor of OSCC in younger patients. The oral microbiome has not been evaluated in this unique patient cohort for a potential bacterial aetiology.

METHODS: We report the bacterial diversity and composition of the largest cohort of OSCC patients with whole genome sequencing (WGS) (n = 72) and compare it with oral mucosa from healthy controls (n = 10) using the Strengthening the Organization and Reporting of Microbiome Studies guidelines.

RESULTS: The microbial diversity between tumour, normal mucosa from cancer patients and healthy control mucosa is significantly different, with specific species (Streptococcus mitis, Haemophilus haemolyticus and Cutibacterium acnes) reduced in normal mucosa of cancer patients as compared to healthy controls (adjusted p < 0.05). The microbial diversity is significantly higher in younger patients as compared to older patients (p < 0.001), with a reduced abundance of anaerobes in older patients (Aggregatibacter segnis, Gemella morbillorum, Peptostreptococcus stomatis, Filifactor alocis and Porphyromonas endodontalis; adjusted p < 0.05).

CONCLUSION: The OSCC tissue of younger patients is significantly more polymicrobial, and their OSCC microbiomes harbour more anaerobic bacteria as compared to older patients. This compositional difference builds the hypothesis that the oral microbiome of younger OSCC patients may have a more hypoxic, immunosuppressive tumour microenvironment with its associated implications for treatment resistance and a potential link to baseline poor dentition.},
}

@article {pmid42015905,
year = {2026},
author = {Gibson, GR},
title = {Faecal Attraction: 40 Years of Research in Gut Microbiology.},
journal = {Nutrition bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1111/nbu.70052},
pmid = {42015905},
issn = {1467-3010},
abstract = {This article summarises the 2025 British Nutrition Foundation Annual Lecture given on 25/11/25. It overviews aspects of research in anaerobic microbiology, principally involving the human gut. Until October 2025, Gibson was Professor of Food Microbiology at the University of Reading. His research investigated gut microbiome interactions and dietary intervention. The latter included human studies in healthy persons, patients with gut-related disorders, at-risk populations and specialist groups like sportspersons and those in the military. Initial principles such as the type of intervention, dose, duration and outcomes were tested using in vitro models of the human gut.},
}

@article {pmid42016247,
year = {2026},
author = {Xu, D and Qiu, B and Dong, X and Tan, J and Xie, Y and Wan, Y and Chu, C and Miao, C and Ali, A and Chen, M and He, J and Wu, L and Xie, J},
title = {Multi-Target Mechanisms of Whey Protein Against NAFLD: Integrating Bile Acid Metabolism, Gut Microbiota and Hepatic Inflammation.},
journal = {Food science & nutrition},
volume = {14},
number = {3},
pages = {e71655},
pmid = {42016247},
issn = {2048-7177},
abstract = {This study elucidates the protective mechanisms of whey protein (WP) in treating high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in mice, emphasizing its role in bile acid regulation, intestinal flora homeostasis, and inflammatory suppression. ICR mice were subjected to a 12-week HFD to establish NAFLD, followed by WP intervention (200 g/kg). Comprehensive analyses included histopathological assessment (HE staining), serum biomarkers, hepatic gene expression (qPCR), gut microbial profiling (16S rRNA sequencing), quantitative bile acid and short-chain fatty acid (SCFA) analysis, and serum metabolomics. Core targets were predicted via network pharmacology and validated through molecular docking. WP administration markedly alleviated NAFLD progression by targeting multiple pathways: (1) It suppressed hepatic lipid deposition and inflammatory injury, downregulating NLRP3, NF-κB, and TNF-α (p < 0.05) while enhancing Nrf2/HO-1-mediated antioxidant defenses; (2) Network pharmacology prioritized IL-1β, STAT3, and MMP9 as pivotal targets, with β-lactoglobulin exhibiting high binding potentials (STAT3: -1.42 kcal/mol); (3) WP restored gut microbial balance, enriching beneficial taxa (e.g., Lactobacillus) and fecal SCFAs; (4) It reprogrammed bile acid metabolism, elevating cholesterol-cleaving enzymes (CYP7A1/CYP27A1) but inhibiting FXR/SHP (p < 0.05), alongside increased hepatoprotective bile acids (TDCA/TUDCA). Metabolomics identified WP-induced anti-inflammatory mediators (e.g., eicosapentaenoic acid) and perturbations in arginine and unsaturated fatty acid pathways, synergistically attenuating steatosis and fibrosis. WP counters NAFLD via a tripartite mechanism: gut microbiome-directed SCFA synthesis, bile acid-driven cholesterol disposal, and dual modulation of inflammation (NLRP3/NF-κB) and oxidative stress (Nrf2/HO-1). These insights position WP as a promising dietary strategy targeting the gut-liver axis.},
}

@article {pmid42016370,
year = {2026},
author = {Fan, Y and Ren, Y and An, J and Wang, X},
title = {Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {588781},
pmid = {42016370},
issn = {1178-6973},
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) is associated with high mortality. However, data on the bronchoalveolar lavage fluid (BALF) microbiota in Chinese SCAP patients remain limited. This study aimed to characterize the clinical features and BALF microbiome composition in patients with SCAP compared to non-severe CAP using targeted next-generation sequencing (tNGS).

METHODS: We conducted a retrospective study involving 224 CAP and 97 SCAP patients from two hospitals in Shanxi, China (January 2023-January 2025). Clinical characteristics and inflammatory cytokines were compared between groups. BALF samples were analyzed via tNGS to evaluate microbial alpha and beta diversity. Differentially abundant taxa were identified using Linear Discriminant Analysis Effect Size (LEfSe).

RESULTS: Compared to the CAP group, SCAP patients were significantly older, had a higher prevalence of comorbidities (hypertension, coronary heart disease, diabetes), and exhibited elevated inflammatory indices (CRP, IL-6, PCT, ESR). SCAP patients also demonstrated a higher likelihood of mixed infections, and the number of detected pathogens showed a positive correlation with the length of hospital stay. tNGS analysis revealed significant differences in alpha diversity and distinct beta diversity clustering between the two groups. LEfSe analysis identified Pseudomonas as a potential biomarker enriched in SCAP, whereas Streptococcus was predominant in CAP.

CONCLUSION: In patients with SCAP, the BALF microbiota showed a significant increase in alpha diversity, which appears to be closely associated with inflammatory cytokine production and correlates with disease severity. There were pronounced differences between SCAP and CAP in both clinical characteristics and microbiome profiles, highlighting the necessity of integrated diagnostic approaches in pneumonia care. Future research should prioritize delineating the dynamic shifts of microbial communities and their influence on pneumonia severity, with the goal of refining and optimizing treatment strategies.},
}

@article {pmid42016555,
year = {2024},
author = {Gwon, Y and Yu, F and Payne, JB and Mikuls, TR},
title = {Bayesian Modeling on Microbiome Data Analysis: Application to Subgingival Microbiome Study.},
journal = {Statistics in biosciences},
volume = {16},
number = {3},
pages = {556-577},
pmid = {42016555},
issn = {1867-1764},
support = {I01 CX000896/CX/CSRD VA/United States ; U54 GM115458/GM/NIGMS NIH HHS/United States ; },
abstract = {The study of microbiome data has been widely used to investigate associations between the abundance of microbial taxa and human diseases. Identifying and understanding these relationships precisely gives the microbiome a key role in human health, disease status, and the development of new diagnostics and targeted therapeutics. Due to its unique features such as compositional data, excessive zero counts, overdispersion, and complexed structure between taxa, undertaking effective microbiome data analytics presents numerous obstacles. To quantify covariate-taxa effects on the subgingival microbiome study, we proposed a refined Bayesian zero-inflated negative binomial (ZINB) regression model with random subject effects. This proposed approach not only accommodates inflated zero counts and overdispersion similar to the existing ZINB model developed by Jiang et al. (Biostatistics 22(3):522-540, 2021), but also accounts for subject-level heterogeneity through the inclusion of random subject effects. In addition, an efficient Markov chain Monte Carlo (MCMC) sampling algorithm was developed for Bayesian computation. Overall effects of pre-selected group variables on predicted taxa abundance were estimated and tested under the proposed model. We conduct simulation studies and demonstrate that the proposed model outperforms the competing models in achieving a better power with controlling the type I error. The usefulness of the proposed model is applied to a real subgingival microbiome study.},
}

@article {pmid42016568,
year = {2026},
author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ},
title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101401},
pmid = {42016568},
issn = {2665-9271},
abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.},
}

@article {pmid42016597,
year = {2026},
author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG},
title = {Investigating the role of bacterial raw milk community members in chlorate reduction.},
journal = {Access microbiology},
volume = {8},
number = {4},
pages = {},
pmid = {42016597},
issn = {2516-8290},
abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.},
}

@article {pmid42016708,
year = {2026},
author = {Diao, J and Li, H and Zheng, S and Niu, J and Yuan, C},
title = {Nonsurgical periodontal therapy remodels oral microbiome-metabolome networks and associates with glycemic and inflammatory improvements in type 2 diabetes mellitus with periodontitis: a 6-month longitudinal study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2660482},
pmid = {42016708},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis and type 2 diabetes mellitus (T2DM) have a bidirectional relationship, yet how nonsurgical periodontal therapy (NSPT) affects oral microbiome-metabolome interactions in this comorbidity remains unclear.

OBJECTIVE: To longitudinally characterize oral microbiome and metabolome shifts following NSPT in patients with T2DM and periodontitis, and to relate these shifts to periodontal and systemic outcomes.

DESIGN: A total of 42 participants completed the 6-month follow-up. At baseline, they were randomly assigned to NSPT (supragingival scaling plus scaling and root planning, n = 24) or supragingival scaling alone (n = 18). Periodontal parameters, glycated hemoglobin (HbA1c), C-reactive protein (CRP), and glucose/lipid markers were measured at baseline, at 3 and 6 months. Oral samples were collected at each visit for microbiome profiling and metabolomics. Microbe-metabolite-clinical features and associations were explored using correlation analyses and pathway annotation.

RESULTS: NSPT improved periodontal inflammation and was accompanied by favorable changes in systemic inflammation and glucose/lipid indices; HbA1c reduction was more pronounced in those with poorer baseline glycemic control. Both groups showed temporal variability in microbiome and metabolome profiles, but the taxa/metabolites that changed differed between groups. Changes in bleeding index correlated positively with 13-eicosenoic acid, xylose, Rothia aeria, and Alloprevotella tannerae, whereas changes in CRP correlated positively with sorbitol, galactitol, Prevotella nigrescens, and Treponema denticola. Selected microbe-metabolite pairs mapped to glutathione and purine metabolism.

CONCLUSION: NSPT reshapes oral microbe-metabolite networks in T2DM with periodontitis, implicating redox-related pathways that may link periodontal therapy to systemic inflammation and glycemic control.},
}

@article {pmid42016721,
year = {2026},
author = {Ikuta, K and Kunisawa, A and Dekio, I and Ito, A and Wang, Q and Kawamura, K and Yamada, M and Nakamura, S and Hayakawa, Y and Higurashi, T and Iida, J and Fukusaki, E and Suzuki, T and Matsumoto, M},
title = {Development of a multi-targeted metabolomics platform for semi-quantification of faecal metabolites: a proof-of-concept analysis in human faeces.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {7},
pmid = {42016721},
issn = {2771-5965},
abstract = {Objectives: Targeted metabolomic analysis of faecal samples has been limited by narrow chemical coverage. Here, we established a multiplexed, triple quadrupole mass spectrometry (TQMS)-based targeted metabolomics workflow. This workflow allows accurate detection and semi-quantification of diverse faecal metabolites and provides a methodological platform for studying host-microbiome metabolic interactions. Methods: Faecal metabolomes from germ-free (GF) mice, ex-germ-free (Ex-GF) mice, and human participants were analysed using TQMS-based targeted metabolomics. The analysis comprised multiple methods targeting amino acids and their derivatives, carbohydrates, short-chain fatty acids, bile acids, lipid mediators, and phospholipids. Results: In total, 607 low-molecular-weight metabolites in 44 chemical categories were detected and semi-quantified. Faecal metabolomes of GF and Ex-GF mice were analysed, uncovering 341 intestinal microbiome-dependent metabolites. A proof-of-concept analysis using faecal samples from five patients with colorectal cancer demonstrated the successful application of this platform to human clinical material, highlighting its strong potential for future disease-oriented metabolomic investigations. Conclusion: We developed a multi-targeted faecal metabolomics platform that substantially expands the chemical space accessible to targeted analysis. This workflow provides a methodological foundation for future large-scale and translational studies.},
}

@article {pmid42016722,
year = {2026},
author = {Hansen, SH and Bhattacharjee, N and Hu, C and Maseng, MG and Grannö, O and Bang, C and Olbjørn, C and Perminow, G and Valeur, J and Bengtson, MB and Frigstad, SO and Andersen, S and Aabrekk, TB and Detlie, TE and Franke, A and Kristensen, VA and Halfvarson, J and Høivik, ML and Iyer, RK and Hov, J},
title = {Bacterial clusters are associated with the risk of severe disease progression in inflammatory bowel disease irrespective of conventional disease categories.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {4},
pmid = {42016722},
issn = {2771-5965},
abstract = {Background: Inflammatory bowel diseases (IBDs) are complex conditions marked by chronic inflammation in the gastrointestinal tract. Traditional classification separates IBD into Crohn's disease and ulcerative colitis, but this division may not fully capture disease heterogeneity. Here, we examine whether microbiome-driven subtyping can describe novel clinical IBD phenotypes. To achieve this, we applied unsupervised clustering to fecal microbiota profiles from the population-based Inflammatory Bowel Disease in South-Eastern Norway III (IBSEN III) cohort. Methods: A Gaussian Mixture Model (GMM) was used to cluster participants with IBD based on microbiome composition and examine associations between clusters and clinical outcomes, including inflammatory markers and disease severity during the first year after inclusion. Results: Three microbiome-based clusters were identified: CLO (dominated by Clostridia UCG-014), ALF (Agathobacter, Lachnoclostridium, and Faecalibacterium), and RUM (Ruminococcus gnavus). Participants in the RUM cluster had a higher risk of future severe disease than those in the CLO cluster, even among participants with remission-to-mild disease at inclusion (21% vs. 6%, P < 0.00001). This association could not be explained by antibiotic use or baseline disease severity. Cluster membership alone performed comparably to fecal calprotectin in distinguishing severe disease, and a combined model significantly improved accuracy (P < 0.0001). Conclusion: Our findings demonstrate a connection between microbiome composition and the risk of severe disease development, which is partly independent of inflammation levels at the time of sampling. Microbiome-informed subgrouping could lead to more personalized treatment strategies. Further validation is needed to determine the clinical utility of these clusters.},
}

@article {pmid42016780,
year = {2026},
author = {Jabeen, T and Karimi, F and Zomorrodi, AR and Khalilpour, K},
title = {Multi-modal machine learning and gut microbiome pathway analysis for Alzheimer's risk prediction.},
journal = {Alzheimer's & dementia (Amsterdam, Netherlands)},
volume = {18},
number = {},
pages = {e70340},
pmid = {42016780},
issn = {2352-8729},
abstract = {INTRODUCTION: Early Alzheimer's disease (AD) risk assessment requires accessible alternatives to invasive biomarkers. We developed a multi-modal machine learning framework using questionnaire metadata from participants with concurrent microbiome sequencing data.

METHODS: We analyzed 9832 participants with 120 metadata features across five categories (demographic, dietary, lifestyle, nutritional, medical). Features were selected via Pearson correlation and chi-squared tests. Four algorithms were trained using 10-fold cross-validation with synthetic minority oversampling technique (SMOTE), validated on 1967 samples. The 16S rRNA sequencing data from the same cohort with 2000 samples enabled microbiome composition analysis.

RESULTS: Medical history (area under the curve [AUC] = 0.871) and dietary patterns (AUC = 0.874) achieved best performance, outperforming demographic (0.795), lifestyle (0.660), and nutritional (0.569) domains (p < 0.001). Microbiome analysis revealed dysbiosis markers (Prevotella/Bacteroides ratio: 1.921) linking dietary factors to potential neuroinflammatory pathways.

DISCUSSION: These findings support non-invasive, multi-modal screening combining medical and dietary evaluation for AD risk stratification, with preliminary microbiome evidence suggesting gut-brain axis dysbiosis as a mechanistic pathway warranting validation in larger cohorts.},
}

@article {pmid42016853,
year = {2026},
author = {Acharya, AP and Borrelli, MA and Jurczak, MJ and Krakoff, J and Little, SR},
title = {Lipid stress evolved, microbiome-based probiotics reduce lipid uptake in mice.},
journal = {Bioengineering & translational medicine},
volume = {11},
number = {2},
pages = {e70122},
pmid = {42016853},
issn = {2380-6761},
abstract = {Controlling the molecular transport of nutrients through the gut is an attractive strategy to modulate host metabolism. Herein, a technique of stress-based evolution of an individual's own microbiota to enhance lipid metabolism is presented, which is based on sequential culture of these bacteria in higher concentrations of lipids. Using this technique, a probiotic formulation of bacterial colonies that exhibit increased lipid metabolism was generated from oral microbiota samples from mice, canine, and human sources. Mice fed a high-fat diet (HFD) and administered lipid stress evolved (LSE) probiotics excreted increased lipids in stool and reduced triglyceride transport into the blood by three-fold till 3 h post-oral gavage of soybean oil, as compared to controls. In addition, these enhanced probiotics prevented weight gain in mice fed a HFD five-fold better than controls and induced weight loss in mice with diet change three-fold faster than diet change alone. In these mice, there was a marked change in appearance with a more healthy, less oily coat. Controlled metabolic cage experiments demonstrated that the total movement, food intake, and water intake were not significantly different between mice receiving LSE probiotic versus a control probiotic formulation, suggesting that important health measures are unchanged with LSE probiotic administration. Overall, this facile stress-based culture technique can be utilized to modulate bacterial metabolism and applied to different industrial processes of probiotic generation and to affect different disease outcomes such as obesity.},
}

@article {pmid42016931,
year = {2026},
author = {Sun, M and Tu, L and Zhou, Z and Ma, Y and Zhang, H and Jiang, X and Tu, H and Lu, J and Niu, Y and Yue, Y and Yang, R and Chen, M and Fang, H and Si, Z and Chen, P},
title = {Embryonic sheep placenta alleviates muscle-fat wasting symptoms and improves gut microbiome dysbiosis in cachexia mice.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102590},
pmid = {42016931},
issn = {2405-5808},
abstract = {Cachexia is a multifactorial wasting syndrome characterized by muscle-fat depletion, accompanied by significant gut microbiome disturbances. Embryonic sheep placenta (ESP), a functional food known to modulate immunity and gut microbiome, represents a potential intervention substance. By in vitro and in vivo experiments combined with multi-omics analysis, this study provides experimental evidence for the effect of ESP on cachexia. These studies have found that ESP and its extract alleviate cachexia by increasing 91.80% (P < 0.0001) muscle tube diameter, 19.56% (P < 0.01) muscle cross-sectional area and 37.56% (P < 0.05) fat mass. Western blot shows that ESP downregulates the expression of TRIM63 and inhibits the expression of the HSL protein in the AMPK signaling pathway. Integrated multi-omics analysis suggests that ESP reshapes the gut microbiota structure of cachexia mice, restores their gut homeostasis and improves energy metabolism pathways. In conclusion, ESP plays a protective role in cachexia mice by alleviating the symptoms of muscle-fat atrophy, maintaining gut homeostasis and improving energy metabolism pathway.},
}

@article {pmid42017169,
year = {2025},
author = {Lee, JS and Fleming, D and Vulimiri, SV and Powers, M and Davis, JA and Gift, JS and Druwe, IL and Jones, R and Keshava, C and Toledo, M and Cote, I and Persad, AS},
title = {Inorganic arsenic exposure and modifying factors: a systematic evidence map.},
journal = {Human and ecological risk assessment : HERA},
volume = {31},
number = {9-10},
pages = {1525-1542},
pmid = {42017169},
issn = {1080-7039},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Evidence maps employing systematic review screening tools have been used for identifying and categorizing chemical-specific literature that may be potentially relevant to scientific assessment. Inorganic arsenic (iAs), naturally distributed throughout the Earth's crust, is found in water, food, soil, and air. The epidemiologic evidence shows that iAs is associated with cancer and noncancer human health outcomes. Increased susceptibility to iAs-related disease is associated both with intrinsic and extrinsic factors. Our objective was to explore the use and feasibility of the systematic evidence map (SEM) approach to provide a clearer picture of the available literature on modifying factors that may alter the relationship between iAs exposure and health effects. A literature search (2014-2022) was conducted using PubMed, Web of Science, and Toxnet to identify studies with modifying factors of iAs health effects defined in Populations, Exposures, Comparators, Outcomes (PECO) criteria. Where applicable, health effects were also categorized. The literature search identified 584 studies with modifying factors that met the PECO criteria. Studies on the following modifying factors were identified: alcohol consumption (n= 8), chemical co-exposure (n= 104), genetic polymorphisms (n= 172), lifestages (n=228), microbiome (n=6), nutritional deficiencies (n=150), pre-existing conditions (n= 9), sex (n=65), smoking (n= 45), and other (e.g., arsenic metabolism, epigenetics, UV/sun exposure, DNA damage/repair, coffee consumption) (n=227). The SEM method was effectively utilized to identify studies on modifying factors for inorganic arsenic.},
}

@article {pmid42017455,
year = {2026},
author = {Zocateli, PI and de Olímpio, GV and de Almeida, FA and da Rocha, LO and de Sena Martins, DV and Sangi, S and Olivares, FL and de Matos, EM and Siqueira, J and Viccini, LF and da Paschoa, RP and Silveira, V and Grativol, C},
title = {DNA Methylation Shapes Seed-Borne Microbiome and Proteome Responses During Early Maize-Beneficial Bacteria Interactions.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70552},
pmid = {42017455},
issn = {1365-3040},
support = {//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PAPIC-2024//Universidade Estadual do Norte Fluminense Darcy Ribeiro/ ; },
abstract = {Microorganism and plant interactions are crucial for development and environmental adaptation. Plant growth promoting bacteria enhance agricultural productivity in a sustainable manner, while epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. The objective of this study is to determine how DNA hypomethylation influences early interactions between maize (Zea mays) and the endophytic diazotrophic bacterium Herbaspirillum seropedicae, particularly regarding plant growth, metabolism, and the root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) altered maize root morphology without affecting bacterial growth. Inoculation with H. seropedicae promoted plant growth and bacterial colonisation in root mucilage, with higher accumulation in 5-azaC treated roots. Global methylation analysis showed that bacterial inoculation modulates cytosine methylation in a manner similar to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery confirmed that hypomethylation drives plant-microbe interactions. Root microbiome profiling revealed that 5-azaC disrupted microbial composition, which was partially restored by bacterial inoculation. Proteomic analysis identified 1,818 proteins and highlighted significant changes in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation combined with bacterial interaction profoundly affects cellular and metabolic processes and provide insights for sustainable agricultural practices through epigenetic and microbial modulation.},
}

@article {pmid42017663,
year = {2026},
author = {Ma, C and Su, C and Li, J and Wang, J and Liao, J and Cheng, L and Qu, J and Zhang, G and Jiang, J and Shuai, S},
title = {Systematic evaluation of TCGA tumor microbiota reveals context-dependent reliability.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018026},
doi = {10.1128/msystems.00180-26},
pmid = {42017663},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial profiles from The Cancer Genome Atlas (TCGA) are widely used to study the tumor microbiota, a key component of the cancer ecosystem, yet their reliability remains unclear. Here, we systematically benchmarked two leading TCGA microbial profiles (TMPs) to define their consistency, accuracy, and reliability in host-microbe association studies across 24 cancer types, with a primary focus on the bacterial component. We found that while the TMPs showed substantial agreement in microbial composition, their accuracy in detecting known oncomicrobes was variable, ranging from excellent for human papillomavirus (HPV) to poor for Helicobacter pylori. The concordance of downstream host-microbe associations was moderate for gene expression but nearly absent for methylation and protein data. Our permutation-based framework revealed that while most individual associations were statistically reliable, those involving cell type composition and patient survival were statistically spurious. To empower future research with these insights, we introduced Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2), an interactive web portal that stratifies all associations by confidence level. We demonstrated its utility by using high-confidence associations to confirm HPV-driven methylation-gene expression axes and guide a novel experimental investigation. Co-culture with Streptococcus anginosus not only validated its predicted gene expression changes in oral cancer cells but also revealed a significant promotion of cancer cell proliferation and migration. Our study provides a rigorous framework for interpreting TCGA's tumor microbiome and highlights that these data require careful, multi-layered validation to yield robust biological insights.

IMPORTANCE: Bacteria living inside tumors can influence how cancer grows and responds to treatment, but the field has been hampered by controversy over the reliability of the data. Our study provides a much-needed road map for researchers. We rigorously tested the massive Cancer Genome Atlas data set and developed a statistical framework to separate true biological signals from random noise. We discovered that many widely reported links are statistically unreliable and likely false leads. Importantly, our framework successfully pinpoints trustworthy signals. We used it to identify a specific bacterium, Streptococcus anginosus, and proved in the lab that it makes oral cancer cells grow faster and spread. Our publicly available Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2) web portal now allows scientists to use these reliability-graded findings to accelerate robust cancer microbiome research.},
}

@article {pmid42017723,
year = {2026},
author = {Fatima, M and Omer, H and Nadeem, N and Imtiaz, S},
title = {Cosmetics and their role in modulating skin microbiome health. A narrative review.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {76},
number = {3},
pages = {417-423},
doi = {10.47391/JPMA.30352},
pmid = {42017723},
issn = {0030-9982},
mesh = {Humans ; *Cosmetics/pharmacology/adverse effects ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Probiotics ; Prebiotics ; Dysbiosis ; Skin Microbiome ; },
abstract = {The skin microbiome plays a vital role in immune regulation, barrier function, and protection against pathogens. Cosmetics, traditionally used for aesthetic purposes, also influence skin microbiomes. Depending on their formulation, they can support microbial balance through probiotics, prebiotics and postbiotics, or disrupt it, leading to dysbiosis and conditions such as eczema and acne. Advances in nanotechnology have further altered cosmetic efficacy and microbial interactions. The current narrative review was planned to highlight the dual role of cosmetics in modulating skin microbiome health, to emphasise the need for regulatory oversight, and to explore strategies for developing safe, microbiome friendly skincare products.},
}

Humans
*Cosmetics/pharmacology/adverse effects
*Microbiota/drug effects
*Skin/microbiology/drug effects
Probiotics
Prebiotics
Dysbiosis
Skin Microbiome

@article {pmid42017751,
year = {2026},
author = {Massironi, S and Fanizzi, F and Invernizzi, F and Furfaro, F and Ciocca, L and Arcari, I and Allocca, M and Peyrin-Biroulet, L and Danese, S},
title = {Inflammatory bowel disease and Primary sclerosing cholangitis: immunological links and clinical outlook.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2026.2664055},
pmid = {42017751},
issn = {1744-8409},
abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) represents a progressive fibroinflammatory cholangiopathy intricately linked to inflammatory bowel disease (IBD), forming a distinctive overlap syndrome driven by immune dysregulation and gut - liver axis disruption and characterized by a markedly increased risk of colorectal and hepatobiliary cancers.

AREAS COVERED: This review summarizes current understanding of the immunopathogenesis and clinical spectrum of PSC - IBD. Key mechanisms include aberrant lymphocyte homing through the α4β7/MAdCAM-1 axis, shared genetic susceptibility loci, alterations in bile acid metabolism, and gut microbial dysbiosis. The clinical course and malignancy risk of PSC - IBD are contrasted with those of isolated PSC and IBD, and surveillance strategies are discussed. Therapeutic approaches under investigation, such as advanced therapies and microbiome-targeted interventions including oral vancomycin, are critically appraised based on recent translational and clinical studies.

EXPERT OPINION: PSC - IBD demands multidisciplinary, risk-stratified management and intensive cancer surveillance. Although no medical therapy currently halts disease progression, novel agents modulating immune and microbial pathways represent promising avenues. In the future, integration of hepatology, gastroenterology, and immunology within a precision-medicine framework is expected to reshape disease stratification and therapeutic decision-making for this complex overlap syndrome.},
}

@article {pmid42017823,
year = {2026},
author = {Wilkie, I and Von Possel, N and Sauma-Sánchez, T and Reintjes, G and Orellana, LH},
title = {Conserved glycan-utilization strategies shape Akkermansiaceae success across aquatic and gut ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag096},
pmid = {42017823},
issn = {1751-7370},
abstract = {Elucidating interaction mechanisms and substrate specialization is central to understanding bacterial adaptation across ecological niches. Specialized mucin-degrading bacteria of the genus Akkermansia are widely recognized for their beneficial roles in the human gut, yet it remains unclear whether this specialization is unique to the gut or reflects a conserved ecological strategy across different hosts and environments. Here, we show that members of the family Akkermansiaceae share a deeply conserved genetic and mechanistic framework enabling colonization across gut and aquatic ecosystems. Comparative genomics of Akkermansiaceae representatives revealed niche-specific gene repertoires tightly adapted to substrate source and availability. Marine representatives encode distinct combinations of CAZymes and comparatively expanded sulfatase repertoires that enable the degradation of sulfated polysaccharides such as fucoidan, a recalcitrant substrate linked to carbon sequestration. Structural predictions and comparisons identified a conserved molecular system centered on a type IV-like pilus that mediates attachment to complex, fucose-rich glycans. The genes underlying this system are syntenic with the recently described mucin utilization locus in Akkermansia muciniphila, revealing an evolutionary continuity between aquatic and gut lineages. Seawater incubations with fluorescently labeled substrates confirmed fucoidan uptake and degradation by marine Akkermansiaceae. Together, these results reveal a unified glycan-utilization strategy spanning the environmental breadth of Akkermansiaceae and provide a mechanistic framework linking ecological success in marine environments to traits associated with probiotic functions in the human gut.},
}

@article {pmid42017830,
year = {2026},
author = {Vergara-Florez, DC and Duda, TF},
title = {Taxonomy, tissue, and habitat influence mollusc microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag092},
pmid = {42017830},
issn = {1751-7370},
abstract = {Microbes play a crucial role in the health, development, and resilience of molluscs, yet the ecological and evolutionary factors shaping their microbial communities remain poorly understood. To uncover the drivers of microbial community composition of molluscs, we conducted a systematic review of 85 studies, including 45 on bivalves from marine and freshwater habitats; 33 on gastropods from marine, freshwater, and terrestrial habitats; and seven on cephalopods. Our synthesis reveals that both intrinsic (e.g., host phylogeny, tissue type) and extrinsic (e.g., environment, geography, and seasonality) factors influence microbial community structure, but the effects are highly taxon- and context-dependent. Although studies of bivalves often emphasize environmental drivers, those of cephalopods more frequently highlight intrinsic host features. Despite growing interest in molluscan microbiomes, we identified significant taxonomic and methodological biases, including a predominant focus on economically important species and gut tissues. We advocate for a broader, integrative approach that includes underrepresented molluscan groups, diverse tissue types, and testing of both intrinsic and extrinsic variables across spatial and temporal gradients. This review highlights the need for standardized, multi-factorial research to better understand and predict microbial community responses to environmental change of one of the most diverse and ecologically important invertebrate phyla.},
}

@article {pmid42018226,
year = {2026},
author = {Yang, Y and Lan, C and Jiang, Z},
title = {Impact of Probiotic-Adjunctive Vonoprazan-Amoxicillin Dual Therapy on Gut Microbiota and Clinical Symptoms in Helicobacter pylori Eradication.},
journal = {Tissue engineering and regenerative medicine},
volume = {},
number = {},
pages = {},
pmid = {42018226},
issn = {2212-5469},
abstract = {BACKGROUND: This study evaluates the impact of Bacillus subtilis dual-strain enteric-coated capsules combined with vonoprazan-amoxicillin (VA) therapy on Helicobacter pylori (Hp) eradication rates, gastrointestinal symptoms, adverse events (AEs), and gut microbiota.

METHODS: 60 Hp-positive adults were enrolled, allocated to probiotic (n = 30) or placebo (n = 30) groups. Both groups received a 14-day VA dual therapy, with the probiotic group additionally receiving a 28-day Bacillus subtilis dual-strain capsule regimen and the placebo group receiving matched placebos. Outcomes included Hp eradication rates (intention-to-treat [ITT]/per-protocol [PP] analyses), Gastrointestinal Symptom Rating Scale (GSRS) scores, AEs, antibiotic susceptibility, and gut microbiota changes (16S rRNA sequencing).

RESULTS: ITT analysis showed identical eradication rates (93.33%) in both groups; PP analysis revealed 96.67% (probiotic) versus 93.33% (placebo). The probiotic group exhibited significantly lower GSRS scores at weeks 4 (T2) and 8 (T3), particularly for diarrhea and acid reflux, with milder AEs (severity score: 5). Probiotic supplementation reduced Hp resistance to metronidazole (26.67% vs. 60.00%) without affecting other antibiotics. Microbiota analysis demonstrated post-eradication reductions in gastric pathogens (e.g., Helicobacter) and increased beneficial bacteria (e.g., Lactobacillus). The probiotic group showed faster restoration of gut α-diversity (higher at T2), enriched butyrate producers (e.g., Blautia, Anaerobutyricum), and decreased opportunistic pathogens (e.g., Klebsiella).

CONCLUSIONS: Although Bacillus subtilis supplementation did not enhance Hp eradication rates, it significantly improved gastrointestinal symptoms, reduced AEs, increased Hp susceptibility to metronidazole, and accelerated microbiota recovery, supporting its role in microbiome modulation during Hp eradication therapy.},
}

@article {pmid42018414,
year = {2026},
author = {Boumasmoud, M and León-Sampedro, R and Beusch, V and Benz, F and Arnoldini, M and Hall, AR},
title = {Interspecies interaction controls Escherichia coli growth in human gut microbiome samples.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {17},
pages = {e2527793123},
doi = {10.1073/pnas.2527793123},
pmid = {42018414},
issn = {1091-6490},
support = {310030_192428//Swiss NSF/ ; },
mesh = {Humans ; *Escherichia coli/growth & development ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; },
abstract = {Gut microbial community composition varies from one person to another. Potentially, this means the ecological interactions experienced by individual strains or species also vary among microbiomes of different people. However, testing this directly in human microbiomes and identifying ecological drivers involved are challenging. Here, we use replicated anaerobic microcosms to quantify variability of population growth for a key commensal species among microbiome samples from different individuals and to identify underlying intra- and interspecific interactions. In a reciprocal transplant experiment, both absolute and relative growth performance of different Escherichia coli strains varied among gut microbiome samples from healthy individuals. This was partly explained by intraspecific competition: growth performance of individual E. coli strains was associated with displacement of resident conspecifics. However, the determinants of E. coli growth varied among samples. In one microbiome sample with a distinctive taxonomic composition, culture acidification by resident microbes impaired growth of all E. coli strains. We identified a strain of Clostridium butyricum contributing to this effect and showed that transferring it into other microbiomes predictably altered pH, fermentation product profiles (butyrate accumulation and acetate/lactate depletion), and population growth of other species including E. coli, thereby reshaping overall taxonomic composition. Our results suggest natural interindividual gut microbiome variation translates to variable ecological interactions with incoming bacteria, but these dynamics can be manipulated by a generalizable interspecies interaction.},
}

Humans
*Escherichia coli/growth & development
*Gastrointestinal Microbiome/physiology
Feces/microbiology

@article {pmid42018438,
year = {2026},
author = {Sun, X and Jiang, X and Zhang, L and Li, M},
title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117284},
doi = {10.1016/j.celrep.2026.117284},
pmid = {42018438},
issn = {2211-1247},
abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.},
}

@article {pmid42018480,
year = {2025},
author = {Dormans, T and Kroon, J and Rampanelli, E and Nieuwdorp, M and van Es, N},
title = {Bacterial tryptophan metabolites in cancer and atherosclerosis: insights for a role in immune checkpoint inhibition.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20253060},
pmid = {42018480},
issn = {1744-1358},
mesh = {Humans ; *Tryptophan/metabolism ; *Atherosclerosis/metabolism/immunology/microbiology ; *Neoplasms/metabolism/drug therapy/immunology/microbiology ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Gastrointestinal Microbiome ; Indoles/metabolism ; Animals ; *Bacteria/metabolism ; },
abstract = {The gut microbiota plays a pivotal role in human health, partly through the production of bioactive metabolites from dietary tryptophan. These indole derivatives have emerged as key modulators of immune function, inflammation, and metabolic health and have been linked to various diseases. In the context of cancer, indole derivatives are increasingly being studied as promising modulators of immune checkpoint inhibitor (ICI) therapy, with accumulating evidence indicating potential for various derivatives to enhance therapeutic efficacy. ICI therapy is associated with various immune-related adverse events, including accelerated progression of atherosclerotic cardiovascular disease. Given their immunomodulatory properties, there is a growing interest in the usage of indole metabolites to mitigate these cardiovascular complications. This mini-review summarizes current knowledge on the roles of microbiota-derived indoles in cancer, ICI therapy, and atherosclerosis. Though direct evidence linking bacterial tryptophan-derived metabolites to ICI-associated atherosclerosis is currently lacking, accumulating evidence indicates that indole derivatives regulate pathways involved in both anti-tumor immunity and atherosclerosis. Advancing our understanding of how the microbiome and its metabolites influence both cancer and cardiovascular disease will be crucial for developing personalized, metabolite-based strategies to improve outcomes in patients undergoing ICI therapy.},
}

Humans
*Tryptophan/metabolism
*Atherosclerosis/metabolism/immunology/microbiology
*Neoplasms/metabolism/drug therapy/immunology/microbiology
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Gastrointestinal Microbiome
Indoles/metabolism
Animals
*Bacteria/metabolism

@article {pmid42018486,
year = {2026},
author = {Jung, A and Bartnick, R and Thomas, DC and Lehndorff, E and Lueders, T},
title = {Conventional and biodegradable microplastics elicit contrasting taxon-level responses in rhizosphere microbiomes of maize and strawberry.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag040},
pmid = {42018486},
issn = {1574-6941},
abstract = {Microplastics (MP) are relevant contaminants in agroecosystems, influencing soil nutrient dynamics and soil-plant-microbial interactions. As agriculture shifts from conventional to biodegradable plastics, their impacts on different crop rhizosphere microbiomes considering both total (DNA-derived) and active (rRNA-derived) communities have not been clearly elaborated. We hypothesized that microbiome impacts would be distinct across different plants and polymer types. Maize and strawberry plants were cultivated with 1% MP by soil weight, including two conventional polymers (LDPE, PET) and one biodegradable polymer (PBAT). Strawberry plants increased biomass across all MP treatments, accompanied by greater soil nitrate depletion. MP-induced impacts on soil prokaryotic communities were mostly additive to plant effects, as determined by 16S rRNA amplicon sequence profiling. PBAT stimulated Cupriavidus spp. and members of Saccharimonadales, suggesting a selection of potential polymer-degraders and microbial interactions, independent of plant species and root proximity. In contrast, conventional MPs induced a less selective response with compositional shifts across a greater number of taxa. MP-induced changes were more apparent in rRNA- than DNA-derived profiles, suggesting a profound response of putative active taxa. Together, we demonstrate that plant species and MP type jointly modulate rhizosphere microbial community response to MP pollution, with direct implications for soil biogeochemistry, rhizosphere functioning, and crop performance.},
}

@article {pmid42018976,
year = {2026},
author = {Feles, EA and Mattner, F},
title = {Perioperative Antibiotic Prophylaxis in Cesarean Section and the Maternal Gut Microbiome: Protocol for a Remote Observational Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e84909},
pmid = {42018976},
issn = {1929-0748},
mesh = {Humans ; Female ; *Antibiotic Prophylaxis/methods ; *Cesarean Section/methods/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Prospective Studies ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Adult ; *Surgical Wound Infection/prevention & control ; Cohort Studies ; Observational Studies as Topic ; Perioperative Care/methods ; },
abstract = {BACKGROUND: Cesarean section (CS) requires perioperative antibiotic prophylaxis (PAP) for the prevention of surgical site infections. However, systemic antibiotics during the peripartum period may induce compositional perturbations of the maternal gut microbiome, a system already characterized by reduced resilience. Data on maternal gut microbiome dynamics after CS with PAP are scarce, largely due to logistical and feasibility barriers that limit the participation of pregnant women and new mothers in conventional clinical studies.

OBJECTIVE: This protocol primarily aims to evaluate the feasibility of a fully decentralized, remote study design for longitudinal gut microbiome research in the peripartum period. Secondary exploratory objectives include the comparative analyses of microbiome composition between CS with PAP and vaginal delivery (VD) without antibiotic exposure to inform future adequately powered studies.

METHODS: The MAMA (Microbiome Changes Due to Antibiotic Prophylaxis in Mothers at Birth) study is a prospective, 2-arm observational cohort study conducted entirely off-site. Women in the third trimester of pregnancy were recruited at 2 German level-1 perinatal centers and affiliated outpatient facilities. Participants underwent either CS with PAP (single dose cefuroxime 1.5 g intravenously) or VD without antibiotics. Stool samples were self-collected at home and returned by mail at 3 predefined time points: late pregnancy (T0), 2 to 3 days post partum (T1), and 90±10 days post partum (T2). Primary outcomes are feasibility indicators, including recruitment rate, sample and questionnaire return rates at each time point, adherence to sampling windows, and participant retention across follow-up. Secondary outcomes are exploratory microbiome measures based on 16S rRNA gene sequencing (V3-V4), including alpha diversity indices, beta diversity metrics, and relative taxonomic abundances. Microbiome analyses are explicitly compositional and hypothesis-generating. Group comparisons and longitudinal within-individual changes will be assessed using nonparametric diversity metrics and multivariate distance-based methods. No confirmatory hypothesis testing is planned.

RESULTS: Recruitment occurred between May 2022 and October 2023, with 37 women enrolled (25 CSs and 12 VDs). Follow-up was completed with receipt of the final stool sample in March 2024. DNA extraction and sequencing were completed in a single batch in October 2024. Bioinformatic processing and statistical analyses were initiated in June 2025 and are ongoing as of December 2025. Results from the exploratory microbiome analyses are expected to be published in 2026.

CONCLUSIONS: This protocol demonstrates the feasibility of conducting fully decentralized, longitudinal microbiome research in a peripartum population without requiring on-site visits. By integrating study procedures into maternal realities, the remote design reduces participation barriers and addresses a clinically relevant research gap that has remained largely unexamined despite routine use of PAP. While microbiome-related outcomes are exploratory, the methodological framework established here provides a scalable model for future maternal and postpartum research, supporting ethically grounded, participant-centered study designs and evidence-informed care strategies.},
}

Humans
Female
*Antibiotic Prophylaxis/methods
*Cesarean Section/methods/adverse effects
*Gastrointestinal Microbiome/drug effects
Pregnancy
Prospective Studies
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Adult
*Surgical Wound Infection/prevention & control
Cohort Studies
Observational Studies as Topic
Perioperative Care/methods

@article {pmid42019076,
year = {2026},
author = {Baig, AM and Iqbal, H and Shi, R and Zeb, A and Khan, S and Tariq, H and Li, X and Irshad, F and Miao, X and Hussain, S and Liu, W},
title = {6PPD-Quinone Triggers Oxidative Stress, Metabolic Reprogramming, and Rhizosphere Microbiota Shifts in Wheat.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01118},
pmid = {42019076},
issn = {1520-5118},
abstract = {The highly toxic tire-derived compound N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) poses emerging environmental risks, yet its fate within the soil-plant system remains unclear. This study reveals that 6PPD-Q induces significant oxidative stress in wheat (Triticum aestivum L.), increasing reactive oxygen species (ROS) by 259% in shoots and 217% in roots and malondialdehyde (MDA) by 57 and 59%, respectively, at a concentration of 200 ng/g compared to the control. This oxidative stress disrupted key antioxidant enzymes (SOD and POD) and reduced the uptake of essential nutrients (Fe, Cu, Mg, Mn, and P). Metabolomic analysis showed perturbation in central carbon metabolism, fatty acid turnover, and amino acid biosynthesis. 16S rRNA sequencing indicated reduced rhizosphere bacterial diversity and shifts in key phyla, linked to nutrient cycling. This work provides mechanistic insights into tire-derived contaminant toxicity in soil-plant systems and highlights the need for further ecological risk assessment.},
}

@article {pmid42019202,
year = {2026},
author = {Chai, S and Zhang, Y and Guo, Y and Cao, D and Wang, J and Yan, Y and Shi, Y and Yuan, Z and Wang, X and Tong, T and Zhen, Z and Huo, Y and Zhang, K and Wang, F and Liu, GR and Li, W and Xu, X and Ban, T and Liu, SL and Liu, H},
title = {Enterolactone mitigates atherosclerosis by facilitating resolution of ferroptosis-associated intimal inflammation via the Keap1/Nrf2/GPX4 pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158178},
doi = {10.1016/j.phymed.2026.158178},
pmid = {42019202},
issn = {1618-095X},
abstract = {BACKGROUND: Atherosclerosis is the inflammatory consequence of lipid accumulation with plaque formation in the vascular intima and is a common condition to develop into various cardiovascular diseases. Current therapies do not always lead to satisfactory treatment outcomes. Enterolactone, a mammalian lignan produced by bacterial transformation from plant lignans, has a preventive effect against cardiovascular disease. However, its effect on atherosclerosis and the underlying mechanism of action remain unclear.

PURPOSE: To explore the therapeutic effect of ENL on atherosclerosis and elucidate the underlying mechanism.

METHODS: We established a model of atherosclerosis on ApoE-/- C57BL/6 mice by high fat diet. The aortic root was collected and sectioned to assess arterial plaque area, collagen fibrillar proliferation, and lipid content. RT-qPCR was used to determine the inflammatory response in the artery of mice. The serum from mice was isolated to measure lipid levels, and the fecal microbiota was analyzed by 16S rDNA. H2O2 was used to induce HUVEC injury and ferroptosis to mimic endothelial cell dysfunction in atherosclerosis, and the inhibitory effect of ENL on HUVEC ferroptosis was appraised by monitoring ferroptosis indexes and levels of iron-related proteins.

RESULTS: In the animals, enterolactone significantly improved lipid metabolism, attenuated ferroptosis occurring in the intima, facilitated the antioxidant mechanisms, and promoted healing of the endothelial lesions, by interacting with Nrf2. Of great importance, enterolactone massively altered the gut microbiota toward a curative outcome by elevating the abundance of beneficial bacteria, such as the SCFA-producing taxa. Additionally, ENL suppresses lipid peroxidation and inflammatory activation in HUVECs by regulating the Keap1/Nrf2/GPX4 pathway, and knocking down Nrf2 attenuates the treatment effect of ENL.

CONCLUSION: Enterolactone effectively resolves intimal inflammation and redresses atherosclerosis by ameliorating the gut microbiome and modulating lipid metabolism via the Keap1/Nrf2/GPX4 pathway.},
}

@article {pmid42019335,
year = {2026},
author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A},
title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129718},
doi = {10.1016/j.jenvman.2026.129718},
pmid = {42019335},
issn = {1095-8630},
abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.},
}

@article {pmid42019337,
year = {2026},
author = {Yu, B and Jiang, C and Yang, K and Zhang, Y and Gao, Y and Chen, Z and Qian, X and Ouyang, S},
title = {Correlation analysis of heavy metal, antibiotics accumulation, and antibiotic resistance genes induced by long-term biogas slurry application.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129745},
doi = {10.1016/j.jenvman.2026.129745},
pmid = {42019337},
issn = {1095-8630},
abstract = {Biogas slurry (BS), as product of animal manure fermentation, is often used as a fertilizer in farmland. However, the long-term application impact on the soil remains not fully understood. Studies have shown that although long-term application of BS does not lead to excessive antibiotic residues in the soil, it increases the abundance of antibiotic resistance genes (ARGs) and promotes their transfer among potential hosts. The complex co-occurrence of bacteria and ARGs implies enhanced horizontal gene transfer, and the increased abundance of the intl1 gene supports this change. Moreover, the distribution of antibiotic-resistant bacteria and ARGs is closely related to the duration of application. Meanwhile, tetracyclines and fluoroquinolones antibiotics, as well as ARGs, are significantly enriched in soils irrigated with BS, and various potentially pathogenic bacterial genera are present. In addition, the application of BS can increase the soil organic carbon stock and alter the soil bacterial and fungal communities. Long-term application of BS results in the accumulation of tetracyclines and the enrichment of ARGs in the soil. It also has an impact on the diversity of soil microbial functional genes. These findings provide a basis for the formulation of relevant policies and sustainable soil management.},
}

@article {pmid42019448,
year = {2026},
author = {Miao, Z and Huang, Z and Wang, J and Li, Z and Shi, J},
title = {Unveiling the enhancement mechanisms of bio-carriers in anoxic treatment of composite phenolic wastewater: A multi-dimensional comparison from macro-performance to microbiome.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142163},
doi = {10.1016/j.jhazmat.2026.142163},
pmid = {42019448},
issn = {1873-3336},
abstract = {This study conducted a comparative investigation into the enhancement of anoxic biodegradation of composite phenols in simulated coal chemical wastewater using four distinct bio-carriers: activated carbon, ceramsite, iron-carbon, and polyurethane (PU). Five parallel anoxic reactors (R1: blank, R2: activated carbon, R3: ceramsite, R4: iron-carbon, R5: PU) were operated under progressively increasing phenol loads (10-350 mg/L). Results demonstrated that all carriers improved treatment performance compared to the blank reactor (R1). The iron-carbon carrier (R4) exhibited exceptional resilience, maintaining complete phenol degradation up to 300 mg/L, attributed to micro-electrolysis pre-treatment that enhanced biodegradability. The PU carrier (R5) achieved the highest and most stable removal efficiencies for both phenol and COD at the highest loadings, coupled with the most diverse bacterial community and a uniquely enriched fungal genus, Cutaneotrichosporon (76.3%), identified as a key degrader. Microbial community analysis revealed that carrier type significantly shaped the microbial structure. The PU and ceramsite carriers fostered higher biodiversity, while the iron-carbon environment selected for specific functional genera. The findings provide critical insights into the mechanisms-adsorption-biofilm synergy, micro-electrolysis, and targeted microbial enrichment-by which different carriers enhance anoxic treatment, offering a scientific basis for selecting optimal carriers in treating high-strength phenolic wastewater.},
}

@article {pmid42019450,
year = {2026},
author = {Guo, Z and Wang, Z and Liu, Y and Wang, M and Ma, H and Wang, Z and Zhang, S and Chang, Y and Ge, H and Li, C and Yang, H and Miao, H and Zhang, X and Cui, P},
title = {Early-life and lifelong exposure to environmentally relevant enrofloxacin reorganizes a proteobacteria-centered gut-lipid-resistome steady state in marine medaka.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142146},
doi = {10.1016/j.jhazmat.2026.142146},
pmid = {42019450},
issn = {1873-3336},
abstract = {Environmental fluoroquinolone residues such as enrofloxacin (ENR) are increasingly detected in coastal waters, yet the persistence of low-dose effects on gut ecosystem organization remains unclear. We compared an early-life window exposure (5 μg/L ENR, 20-35 days post-hatch; depurated to 150 dph) with a lifelong exposure (5 μg/L ENR from fertilization to 150 dph) in marine medaka (Oryzias melastigma), using an environmentally realistic upper-bound concentration reflecting aquaculture-impacted conditions. We integrated intestinal histology and ultrastructure, inflammatory and lipid-metabolic transcriptional programs, intestinal fatty-acid profiles, 16S rRNA and 2bRAD-M characterization of the gut microbiota and antibiotic-resistance genes. Both regimens increased intestinal hypertrophy or densification and rewired communities into more positively connected, Proteobacteria-centered networks. Lifelong exposure produced a pronounced shift in intestinal lipid programming, marked by enhanced lipogenesis and reduced fatty-acid catabolism, together with selective changes in fatty-acid composition and desaturation balance. Early-life window exposure left persistent, albeit weaker, adult signatures in intestinal morphology, microbial network topology, and lipid-related transcription after prolonged withdrawal. Across cohorts, Proteobacteria indicator taxa covaried with inflammatory and lipid gene modules and with coordinated resistance-gene modules, consistent with a Proteobacteria-rich gut-lipid-resistome steady state. These findings indicate that ENR at an environmentally realistic upper-bound concentration reflecting aquaculture-impacted and hotspot contamination scenarios can durably reorganize host-microbe-resistome linkages, supporting re-evaluation of "no-effect" thresholds for antibiotic pollution from a One Health perspective.},
}

@article {pmid42019469,
year = {2026},
author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH},
title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106914},
doi = {10.1016/j.psj.2026.106914},
pmid = {42019469},
issn = {1525-3171},
abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.},
}

@article {pmid42019500,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Mao, K and Yu, Z and Li, J and Guo, X and Xu, H and Wang, Y and Wang, Y and Pang, B and Liu, H and Tang, H and Han, JJ},
title = {A generative AI framework unifies human multi-omics to model aging, metabolic health, and intervention response.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.03.014},
pmid = {42019500},
issn = {1932-7420},
abstract = {Understanding aging and complex diseases requires diverse data, ranging from molecular profiles to imaging and routine clinical tests. However, most multi-omic datasets measure only a subset of modalities and are confounded by batch effects. Here, we present AURORA (AI unification and reconstruction of omics reassembly atlas), a generative deep-learning platform that integrates seven modalities (including transcriptomics, metabolomics, microbiome, 3D and thermal facial imaging, and clinical laboratory tests) across 581,763 samples from 425,258 individuals. AURORA harmonizes batch effects and reconstructs missing data across modalities, enabling highly accurate multimodal aging clocks and disease risk predictors. It also supports personalized in silico perturbation analyses to predict intervention and drug responses, validated using longitudinal cohorts. As a proof of concept, we provide a prototype AI agent that converts single-input modalities into a multimodal report for users and researchers. Together, AURORA links non-invasive inputs to comprehensive aging biomarkers and therapeutic discovery.},
}

@article {pmid42019590,
year = {2026},
author = {Martínez-López, N and Figueras, A and Novoa, B and Pereiro, P},
title = {Dissecting the host transcriptome and microbiota responses to Viral Hemorrhagic Septicemia Virus (VHSV) in the turbot (Scophthalmus maximus) intestine: insights from moribund and asymptomatic phenotypes.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111370},
doi = {10.1016/j.fsi.2026.111370},
pmid = {42019590},
issn = {1095-9947},
abstract = {Viral infections profoundly influence host physiology, not only by triggering complex immune responses but also by reshaping the associated microbiota. Conversely, the microbiota can modulate antiviral defenses and disease outcomes through its interactions with the host immune system. This dynamic triad -virus, microbiota, and host immunity- has emerged as a central determinant of infection severity and recovery. Yet, despite growing evidence from mammalian models, its functional implications in fish remain poorly understood. Here, we investigated the effects of viral hemorrhagic septicemia virus (VHSV) infection on the intestinal transcriptomic and microbiota profiles of turbot (Scophthalmus maximus), an aquaculture species highly susceptible to this pathogen. Comparative analyses were conducted among asymptomatic and moribund fish at 10 days post-infection, and uninfected controls. Transcriptomic data revealed that moribund individuals exhibited a dysregulated immune response characterized by a strong induction of complement- and coagulation-related genes and other inflammatory pathways, whereas asymptomatic fish displayed expression patterns more closely resembling those of uninfected controls, indicating a more controlled or resolved immune activation. Microbiota analyses showed that VHSV infection induced widespread, severity-dependent changes in the intestinal microbiota, with progressive shifts in the relative abundance of most bacterial taxa from controls to asymptomatic and moribund fish. Interestingly, a subset of bacterial genera deviated from this general trend, displaying an opposite pattern to that observed in both uninfected and moribund individuals, suggesting their potential involvement in resistance mechanisms. Integrative analyses further revealed significant correlations between specific bacterial genera and host genes differentially expressed between asymptomatic and moribund fish, highlighting functional links between microbial composition and immune regulation. Together, these findings reveal complex interactions between VHSV infection, host immunity, and microbiota composition in turbot, providing novel insights into host-microbe-virus relationships that may inform disease management and selective breeding strategies in aquaculture.},
}

@article {pmid41803210,
year = {2026},
author = {Kim, MG and Seo, E and Eor, JY and Kang, A and Kim, TR and Sohn, M and Kim, Y},
title = {Hypnotic and sleep-promoting effects of Limosilactobacillus reuteri LM1063 on pentobarbital-induced sleep and electroencephalogram analysis in mice.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803210},
issn = {2045-2322},
support = {RS-2025-16068814//National Research Foundation of Korea/ ; },
abstract = {UNLABELLED: Sleep disturbances are an increasing health concern, and limitations associated with long-term use of conventional hypnotics have prompted interest in alternative approaches that support sleep health. Growing evidence suggests that the gut–brain axis contributes to sleep regulation; however, the effects of probiotics on objective sleep parameters and their underlying mechanisms remain incompletely understood and may vary across probiotic strains. The present study investigated the sleep–modulating effects of a selected probiotic strain, Limosilactobacillus reuteri LM1063 (LM1063), using murine models. Sleep latency and duration were assessed using a pentobarbital-induced sleep test, and sleep architecture was evaluated by electroencephalogram (EEG) recordings, including rapid eye movement (REM) and non-rapid eye movement (NREM) sleep. To explore potential mechanisms, neurochemical analyses focusing on key neurotransmitters, including gamma-aminobutyric acid (GABA) and serotonin, were conducted. Administration of LM1063 significantly shortened sleep latency and prolonged sleep duration in mice. EEG analysis revealed shifts in overall sleep architecture toward a sleep-favorable state without disruption of normal sleep organization. These sleep-related changes were accompanied by modulation of GABAergic and serotonergic neurochemical pathways. In conclusion, LM1063 exerts strain-specific sleep-modulating effects through neurochemical mechanisms associated with the gut–brain axis. By integrating behavioral sleep assessment, electrophysiological analysis, and neurochemical profiling, this study provides mechanistic insight supporting the potential translational application of microbiome-targeted approaches for promoting sleep health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42833-0.},
}