@article {pmid40796214,
year = {2026},
author = {Kopylov, U and Verstockt, B and Marigorta, UM and Noviello, D and Bossuyt, P and Mookhoek, A and Sinonquel, P and El-Hussuna, A and Sahnan, K and Baumgart, DC and Noor, NM and Allocca, M and Carter, D and Ensari, A and Iacucci, M and Pellino, G and Soriano, A and de Laffolie, J and Daperno, M and Raine, T and Cleynen, I and Sebastian, S},
title = {Results of the Ninth Scientific Workshop of the European Crohn's and Colitis Organisation (ECCO): Artificial Intelligence in medical management and precision medicine.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {4},
pages = {},
doi = {10.1093/ecco-jcc/jjaf134},
pmid = {40796214},
issn = {1876-4479},
mesh = {Humans ; *Artificial Intelligence ; *Precision Medicine/methods ; *Inflammatory Bowel Diseases/therapy/diagnosis ; Natural Language Processing ; Wearable Electronic Devices ; *Crohn Disease/therapy ; Telemedicine ; },
abstract = {BACKGROUND AND AIMS: Artificial intelligence (AI) is increasingly being applied in various fields of medicine, including inflammatory bowel diseases (IBD). This systematic review, conducted as part of the ECCO 9th Scientific Workshop on AI in IBD, explores AI applications in multiomics precision medicine, large language models (LLMs) for textual tasks, and utilization of wearable and remote care technologies.

METHODS: A comprehensive systematic analysis of the literature was undertaken, emphasizing three topics: multiomics predictive models in IBD; natural language processing (NLP) and LLMs for clinical practice, research and patient communication; and the role of remote monitoring and wearable devices.

RESULTS: Key areas of promise include the implementation of NLP and LLMs for case identification and differentiation, tracking disease activity, pharmacovigilance, quality assurance, and patient support. Multiomic approaches, integrating genomics, transcriptomics, proteomics, metabolomics, and metagenomics, show potential for developing more accurate diagnostic and risk prediction models and improving treatment response prediction and detection of actionable drug targets for future therapeutics. Wearables and remote monitoring technologies can transform IBD management from episodic assessments to continuous, less biased tracking of patient-reported outcomes and physiological biomarkers.

CONCLUSIONS: While AI and multiomics approaches hold substantial promise for advancing IBD management and research, further refinement is necessary to ensure content validity and address safety concerns, thereby allowing integration of AI into clinical workflows and safeguarding of data privacy. Future research should prioritize the integration of diverse omic data, conduct of longitudinal studies, and validation in large and diverse cohorts.},
}

Humans
*Artificial Intelligence
*Precision Medicine/methods
*Inflammatory Bowel Diseases/therapy/diagnosis
Natural Language Processing
Wearable Electronic Devices
*Crohn Disease/therapy
Telemedicine

@article {pmid41779268,
year = {2026},
author = {Trujillo-López, MA and Muñoz-Olivos, C and Garduño-Vargas, MÁ and Sánchez-López, JM and Martínez-Ortiz, VM and Pérez-Armendáriz, B and El-Kassis, EG and Bautista-Rodriguez, E},
title = {Bacillus mojavensis postbiotics: transcriptomic and anticancer effects in colon cancer cells.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41779268},
issn = {2191-0855},
support = {CBF-2025-I-3072//SECIHTI/ ; },
abstract = {UNLABELLED: Probiotics have been shown to exert antiproliferative effects on colon cancer cells. While these effects are often attributed to microbiome regulation, they may also result from bioactive metabolites produced by probiotic bacteria. In the present study, we investigated the impact of a cell-free extract, hereafter referred to as a postbiotic, derived from Bacillus mojavensis, a strain isolated from aguamiel (a traditional Mexican beverage). The antiproliferative activity was evaluated in SW480 human colon cancer cells using MTT and crystal violet assays, while antimigratory effects were assessed through a wound-healing assay. In addition, the ability of the postbiotic to counteract inflammatory proliferation was evaluated in SW480 cells treated with lipopolysaccharide (LPS). Biosafety was tested using peripheral blood mononuclear cells (PBMCs) from healthy donors. Results demonstrated that treatment with 25–50 µg/mL of B. mojavensis postbiotic reduced SW480 cell viability by 75.15% and 79.3%, respectively, and significantly inhibited cell migration after 24 h. Moreover, the postbiotic decreased LPS-induced proliferation without exerting any cytotoxic effect on PBMCs, underscoring its selectivity toward malignant cells. To elucidate the underlying mechanisms, transcriptomic profiling was performed, revealing extensive modulation of oncogenes and tumor suppressors, with enrichment of PI3K–Akt, MAPK, apoptosis, and cytokine receptor pathways. In conclusion, postbiotics from B. mojavensis isolated from aguamiel exhibit selective anticancer activity by inhibiting proliferation, migration, and inflammation-induced growth in colorectal cancer cells. Transcriptomic findings further support these effects.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13568-026-02018-4.},
}

@article {pmid41957950,
year = {2026},
author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A},
title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.},
journal = {Oncoimmunology},
volume = {15},
number = {1},
pages = {2656514},
doi = {10.1080/2162402X.2026.2656514},
pmid = {41957950},
issn = {2162-402X},
mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; },
abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.},
}

*Oncolytic Virotherapy/methods
Humans
Animals
Mice
*Adenoviridae/genetics
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
*Oncolytic Viruses
Feces/microbiology
Female
*Neoplasms/therapy/microbiology
Male

@article {pmid41958318,
year = {2026},
author = {Lee, CZ and Worsley, SF and Burke, T and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS},
title = {Social Structure and Interactions Differentially Shape Aerotolerant and Anaerobic Gut Microbiomes in a Cooperative Breeding Species.},
journal = {Molecular ecology},
volume = {35},
number = {7},
pages = {e70304},
pmid = {41958318},
issn = {1365-294X},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/S010939/1//Natural Environment Research Council/ ; ECF-2023-433//Leverhulme Trust/ ; erc-stg-948219 EPYC/ERC_/European Research Council/International ; BBX011089/1//Earlham Institute ISP Decoding Biodiversity/ ; BBS/E/ER/230002A//Earlham Institute ISP Decoding Biodiversity/ ; BBS/E/ER/230002B//Earlham Institute ISP Decoding Biodiversity/ ; ALWOP.531//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 854.11.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 823.01.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Rosalind Franklin Institute/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Songbirds/microbiology ; *Cooperative Behavior ; Breeding ; Anaerobiosis ; Female ; Male ; Social Behavior ; Seychelles ; },
abstract = {Social transmission of microbes has profound impacts on disease epidemiology and host health. However, how social factors influence gut microbiome (GM) transmission in wild populations is not well understood. Here, we use a wild population of the Seychelles warbler, a facultative cooperatively breeding passerine, to determine whether cooperative breeding behaviour influences the GM. Specifically, we hypothesise that close social interactions as part of cooperative breeding should encourage the sharing of anaerobic microbes, which may be less likely to transmit indirectly through the environment. We found that GM composition was more similar within versus between social groups, and this effect was driven by sharing both aerotolerant and anaerobic bacterial genera. As predicted, the similarity of anaerobic, but not aerotolerant, GM communities between pairs of individuals within a group was positively correlated with the strength of their social interactions (defined by their cooperative breeding status). Specifically, anaerobic GM composition was more similar between pairs of individuals that cooperate at the nest (dominant breeders and dominant-helper pairs) than for non-cooperative pairs (involving non-helping subordinate individuals). This is likely because breeders and helpers directly interact while caring for offspring at a nest. This work reveals how cooperative social interactions lead to microbial transmission and thus contribute to shaping specific components of a host's gut microbiome.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Songbirds/microbiology
*Cooperative Behavior
Breeding
Anaerobiosis
Female
Male
Social Behavior
Seychelles

@article {pmid41958322,
year = {2026},
author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B},
title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.},
journal = {American journal of primatology},
volume = {88},
number = {4},
pages = {e70148},
doi = {10.1002/ajp.70148},
pmid = {41958322},
issn = {1098-2345},
support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; },
abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.},
}

Animals
*Gastrointestinal Microbiome
*Macaca/virology/microbiology
*Virome
Tibet
Male
Animals, Zoo/virology
Female

@article {pmid41958469,
year = {2026},
author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A},
title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.},
journal = {Alzheimer's & dementia (New York, N. Y.)},
volume = {12},
number = {2},
pages = {e70239},
pmid = {41958469},
issn = {2352-8737},
abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.

METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.

RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).

DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.},
}

@article {pmid41958528,
year = {2026},
author = {Li, L and Lv, F and Du, C and Yang, L and Pa, C and Dai, Y},
title = {Artificial intelligence-driven gastrointestinal functional assessment: multimodal imaging, digital biomarkers, and real-time monitoring.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1778235},
pmid = {41958528},
issn = {1664-042X},
abstract = {Gastrointestinal (GI) functional disorders and chronic inflammatory diseases impose a substantial health burden, yet their assessment remains challenging because symptoms reflect dynamic interactions among motility, visceral sensation, immune-microbiome regulation, and brain-gut signaling. Artificial intelligence (AI) is rapidly reshaping GI functional medicine by enabling scalable, quantitative interpretation of complex data generated from multimodal imaging, physiological sensing, and real-world patient monitoring. This review synthesizes advances across three tightly connected pillars that map onto a physiology-informed "assessment-to-action" loop: (i) AI-assisted multimodal GI imaging for quantitative phenotyping and integrated diagnosis; (ii) AI-enabled discovery and validation of digital biomarkers that capture dynamic GI function in naturalistic settings; and (iii) real-time monitoring platforms that support early warning, longitudinal assessment, and adaptive management. We summarize representative applications in functional GI disorders, inflammatory bowel disease (IBD), and GI oncology, highlighting methodological themes including multimodal fusion, temporal modeling, uncertainty estimation, and explainable AI. We then discuss barriers to translation-standardization and interoperability, external validation under dataset shift, privacy and governance, and workflow integration-and outline practical directions for building clinically trustworthy AI systems for GI functional assessment. Collectively, physiology-centered AI approaches have the potential to transform GI care from episodic testing to longitudinal, mechanism-aware monitoring and personalized intervention.},
}

@article {pmid41958652,
year = {2026},
author = {Nurgaziyev, M and Kozhakhmetov, S and Issilbayeva, A and Jarmukhanov, Z and Nurgaziyeva, A and Sergazy, S and Kuantkhan, M and Chulenbayeva, L and Kushugulova, A},
title = {Gut microbiome differences by serostatus in rheumatoid arthritis: a systematic review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1722255},
pmid = {41958652},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/blood ; *Gastrointestinal Microbiome/immunology ; Anti-Citrullinated Protein Antibodies/blood/immunology ; Rheumatoid Factor/blood/immunology ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease in which serological status, defined by rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA), influences disease course. Alterations of the gut microbiome have been implicated in RA, but differences between seropositive and seronegative patients, and between seropositive RA and healthy controls, have not been systematically reviewed.

METHODS: PubMed, Scopus, Web of Science, and the Cochrane Library were searched to July 2025 for observational studies of adult RA patients reporting RF and/or ACPA status with gut microbiome analysis. Two reviewers independently screened, extracted data, and assessed quality using the Newcastle-Ottawa Scale (NOS).

RESULTS: Eight studies published between 2016 and 2024 met the inclusion criteria. Six investigated both RF and ACPA, while two focused primarily on ACPA. In seropositive RA, higher abundances of Collinsella and Blautia and lower levels of Faecalibacterium were consistently reported. Several studies demonstrated reduced α-diversity in seropositive patients compared with seronegative RA or healthy controls, particularly in preclinical or early disease, while established RA showed no consistent differences. Findings for β-diversity were heterogeneous, with some cohorts reporting significant associations with serostatus, whereas others found no clear separation.

CONCLUSIONS: Seropositive RA, especially ACPA-positive, is frequently associated with reduced microbial diversity and distinct compositional shifts compared with seronegative RA and healthy controls. Larger standardized studies are required to validate these associations and assess their biomarker potential.

https://www.crd.york.ac.uk/prospero/, identifier CRD420251140715.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/blood
*Gastrointestinal Microbiome/immunology
Anti-Citrullinated Protein Antibodies/blood/immunology
Rheumatoid Factor/blood/immunology

@article {pmid41958661,
year = {2026},
author = {Wuyi, W and Tao, P},
title = {Microbe-driven immune suppression in colorectal cancer: the Fusobacterium nucleatum playbook.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1795703},
pmid = {41958661},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/immunology/microbiology/therapy ; *Fusobacterium nucleatum/immunology ; Tumor Microenvironment/immunology ; Animals ; *Fusobacterium Infections/immunology/microbiology ; },
abstract = {Fusobacterium nucleatum, a key oral-pathobiont in colorectal cancer (CRC), has evolved from a presumed "passenger" to an active "co-conspirator" in tumorigenesis. This review systematically delineates its core role as an "architect of the immune microenvironment," whereby it remodels T-cell immune responses through precise mechanisms to establish an immunosuppressive tumor microenvironment. Specifically, F. nucleatum employs virulence factors such as Fap2 and FadA for specific colonization, and achieves immune evasion by inhibiting NK and T-cell function and recruiting myeloid-derived suppressor cells (MDSCs). Post-colonization, it further fine-tunes T-cell subsets: driving Th17 polarization to create a pro-inflammatory milieu while suppressing the infiltration and function of CD8[+] T cells and promoting their exhaustion. Intriguingly, it upregulates programmed death-ligand 1 (PD-L1) expression, which may conversely enhance tumor sensitivity to anti-PD-1/PD-L1 immunotherapy. Moreover, it collaborates with other microbes via quorum sensing and the oral-gut axis to construct a procarcinogenic ecosystem. Based on these mechanisms, F. nucleatum exhibits substantial clinical translational potential. Its load serves as an effective non-invasive diagnostic biomarker and a prognostic predictor, and may help predict responses to immune checkpoint inhibitors. Therapeutically, strategies targeting the eradication or inhibition of F. nucleatum-including antibiotics, specific phages, virulence factor inhibitors, and combination immunotherapy-represent highly promising novel directions. Despite existing challenges, future efforts to deepen mechanistic understanding, develop precision intervention tools, and establish integrated patient stratification systems hold the potential to revolutionize CRC prevention, diagnosis, and combination therapy by targeting F. nucleatum.},
}

Humans
*Colorectal Neoplasms/immunology/microbiology/therapy
*Fusobacterium nucleatum/immunology
Tumor Microenvironment/immunology
Animals
*Fusobacterium Infections/immunology/microbiology

@article {pmid41958678,
year = {2026},
author = {Li, J and Shen, J and Lu, D and Ding, E and Wei, L},
title = {Gut microbe Terrisporobacter promotes papillary thyroid carcinoma progression by upregulating the NTRK1 oncogene and fostering an immunosuppressive tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1740257},
pmid = {41958678},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Thyroid Cancer, Papillary/immunology/pathology/genetics/microbiology ; *Gastrointestinal Microbiome/immunology ; *Thyroid Neoplasms/immunology/pathology/microbiology/genetics ; *Receptor, trkA/genetics/metabolism ; Disease Progression ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Up-Regulation ; },
abstract = {Growing evidence suggests a link between the gut microbiome and papillary thyroid carcinoma (PTC), but the causal relationships and the impact on the tumor immune microenvironment (TME) are poorly understood. This study aimed to elucidate the causal role of specific gut microbes in PTC and uncover the underlying immunological and molecular mechanisms. We employed a multi-stage design, beginning with a two-sample Mendelian randomization (MR) analysis using large-scale GWAS data to infer causality. Findings were then validated in 450 PTC patients from The Cancer Genome Atlas (TCGA) by analyzing correlations between microbial abundance, gene expression, immune cell infiltration, and survival. Finally, the core mechanism was confirmed through extensive in vitro experiments with PTC cell lines. Our MR analysis identified a causal association between a genetically predicted higher abundance of the genus Terrisporobacter and an increased risk of PTC (Odds Ratio [OR] = 2.06, 95% Confidence Interval [CI]: 1.34-3.16). In the TCGA cohort, higher intratumoral signals of Terrisporobacter was significantly correlated with an immunosuppressive TME, characterized by increased infiltration of M2 macrophages (ρ = 0.25, p < 0.001) and decreased CD8+ T cells (ρ = -0.19, p = 0.008). Mechanistically, Terrisporobacter abundance was also strongly associated with the upregulation of the oncogene NTRK1 (ρ = 0.35, p < 0.001), which independently predicted poorer overall survival (Hazard Ratio [HR] = 2.15, p = 0.004). In vitro experiments confirmed that supernatant from Terrisporobacter culture not only upregulated NTRK1 expression and promoted PTC cell proliferation but also enhanced invasion and induced cell de-differentiation. Importantly, pharmacological inhibition of TRK signaling reversed the bacteria-induced aggressive phenotype. Our integrated analysis provides robust, multi-layered evidence for a causal role of Terrisporobacter in promoting PTC progression. We define a novel gut-thyroid axis where Terrisporobacter contributes to PTC development by upregulating the NTRK1 oncogene and shaping a pro-tumorigenic, immunosuppressive microenvironment. These findings reveal a new dimension of host-microbe interaction in thyroid cancer and highlight the TME as a key downstream target of microbial influence.},
}

Humans
*Tumor Microenvironment/immunology
*Thyroid Cancer, Papillary/immunology/pathology/genetics/microbiology
*Gastrointestinal Microbiome/immunology
*Thyroid Neoplasms/immunology/pathology/microbiology/genetics
*Receptor, trkA/genetics/metabolism
Disease Progression
Cell Line, Tumor
Gene Expression Regulation, Neoplastic
Up-Regulation

@article {pmid41958966,
year = {2022},
author = {Silverman, JD and Roche, K and Holmes, ZC and David, LA and Mukherjee, S},
title = {Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes.},
journal = {Journal of machine learning research : JMLR},
volume = {23},
number = {},
pages = {},
pmid = {41958966},
issn = {1532-4435},
support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; T32 GM007171/GM/NIGMS NIH HHS/United States ; },
abstract = {Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing implementations of MLN models are limited to small datasets due to the non-conjugacy of the multinomial and logistic-normal distributions. Motivated by the need to develop efficient inference for Bayesian MLN models, we develop two key ideas. First, we develop the class of Marginally Latent Matrix-T Process (Marginally LTP) models. We demonstrate that many popular MLN models, including those with latent linear, non-linear, and dynamic linear structure are special cases of this class. Second, we develop an efficient inference scheme for Marginally LTP models with specific accelerations for the MLN subclass. Through application to MLN models, we demonstrate that our inference scheme are both highly accurate and often 4-5 orders of magnitude faster than MCMC.},
}

@article {pmid41959050,
year = {2026},
author = {Wilson, J and Amir Hamzah, AS and Jordan, C and Hayward, JA and Kullin, B and Manhanzva, MT and Tyssen, D and Mehou-Loko, C and Abrahams, AG and Radzey, N and Harryparsad, R and Meyer, B and Hearps, AC and Ziemann, M and Humphries, H and Mkhize, P and Bekker, LG and Passmore, JS and Jaspan, HB and Sheppard, AE and Tachedjian, G and Masson, L},
title = {Characterisation of vaginal Lactobacillus isolates from South African women towards the development of a biotherapeutic to optimise the vaginal microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.26.714511},
pmid = {41959050},
issn = {2692-8205},
abstract = {UNLABELLED: HIV remains among the world's most serious healthcare challenges, with adolescent girls and young women in sub-Saharan Africa at particularly high risk of infection. Bacterial vaginosis (BV) is a key risk factor for HIV acquisition, however current treatment strategies are limited. Optimal vaginal Lactobacillus spp. protect against BV and HIV, largely through immunoregulatory and antimicrobial activities mediated in part by lactic acid. Towards the development of a Lactobacillus -containing live biotherapeutic for African women, we sampled 181 vaginal Lactobacillus isolates from 25 BV-negative South African women. Fifty isolates were selected for evaluation of inflammatory responses using vaginal epithelial cells, D- and L-lactate and lactic acid production and culture acidification. Aside from a single Lactobacillus salivarius strain, L. crispatus isolates acidified the culture media the most and produced the most D- and L-lactic acid. Inflammatory cytokine responses to Lactobacillus strains were variable, with L. crispatus eliciting the lowest levels of cytokine production. When all properties were evaluated collectively, L. crispatus strains exhibited the most desirable biotherapeutic characteristics. Whole genome sequence analysis of ten L. crispatus isolates showed that the majority were more closely related to one another than to isolates from other geographical regions. This supports the need for live biotherapeutics to be tailored for the population of intended use. No antimicrobial resistance elements were detected, while putative bacteriocins and intact prophage sequences were identified in all isolates. L. crispatus isolates displayed characteristics essential for optimal live biotherapeutic performance, however additional analysis is required to determine the functionality of identified putative prophages.

IMPORTANCE: HIV is a leading cause of morbidity and mortality in sub-Saharan Africa, where adolescent girls and young women are three times more likely to acquire HIV than their male counterparts. A key risk factor for HIV is bacterial vaginosis (BV), a condition characterised by the loss of beneficial Lactobacillus species and increased abundance of non-optimal, inflammatory bacteria. Although BV affects approximately 25% of women in sub-Saharan Africa, effective therapeutics are lacking. Live biotherapeutics containing optimal Lactobacillus spp. represent a promising strategy to improve BV treatment outcomes and reduce HIV infection risk. We isolated 181 vaginal Lactobacillus spp. from 25 BV-negative South African women and characterized 50 selected isolates. This led to the identification of live biotherapeutic candidates for African women with distinct genomes compared to isolates from other geographical regions. This study contributes to current knowledge of the characteristics that should be considered when screening novel isolates for this purpose.},
}

@article {pmid41959053,
year = {2026},
author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA},
title = {Infant gut microbiomes contribute to metabolic states that impact brain function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.09.710596},
pmid = {41959053},
issn = {2692-8205},
abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.},
}

@article {pmid41959059,
year = {2026},
author = {Voorhees, PJ and Ponek, RM and Liu, JD and Lai, SK},
title = {A Droplet Digital PCR Assay for Quantification of Bacteriophage Viral Vector Titer and Purity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.20.624577},
pmid = {41959059},
issn = {2692-8205},
abstract = {PURPOSE: Bacteriophage (phage) based vectors offer considerable promise as tools for tuning the microbiome with molecular and genetic precision. However, standardized methods to rigorously characterize phage vectors remain lacking. Here, we present an optimized digital droplet PCR (ddPCR)-based assay for quantifying both the purity and potency of phage vector preparations.

METHODS: We utilized central composite design to develop a ddPCR assay capable of quantifying the number of phage vector capsids packed with the phage vector genome or packed with the transgenic DNA of interest. This assay targets 2 unique DNA barcodes, designed to be biologically inert and maximally orthogonal to existing DNA sequences.

RESULTS: Through stringent optimization, we were able to achieve assay conditions that enable a dynamic range of nearly 3 orders of magnitude and correct for systemic error in the assay. We then show that biological activity assays consistently underestimate transgene-packed vectors titers, leading to overestimation of true transduction efficiency, particularly when contamination by genome-packed vectors is high. We further demonstrate how this approach facilitates optimization of vector production conditions and substantially improves the precision and reproducibility of phage vector transduction.

CONCLUSION: Compared to assays of biological activity, this optimized ddPCR assay has improved accuracy and, through design of experiments optimization, high precision (CVs = 5.5 ± 1.3% and 4.5 ± 1.0% for the genome and transgene barcodes, respectively). This assay can be broadly adopted to characterize and quality control vector preparations for various applications.},
}

@article {pmid41959063,
year = {2026},
author = {Moscalu, A and Babygirijia, R and Mathew, T and Chaudhari, SN and Zhang, D and Zhou, L and Sheu, EG and Harris, DA},
title = {Sleeve gastrectomy protects lean mice from future obesity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.09.710623},
pmid = {41959063},
issn = {2692-8205},
abstract = {BACKGROUND: Obesity and metabolic disease drive premature aging and reduced lifespan. While metabolic interventions like calorie restriction, protein restriction, and time restricted feeding have been shown to improved lifespan, they are either not effective or sustainable for most humans. Bariatric surgery is the most efficacious metabolic intervention available and is associated with increased lifespan. However, whether its longevity benefits derive solely from weight reduction or reflect surgery-specific metabolic reprogramming remains unknown.

METHODS: We employed a lean mouse model of sleeve gastrectomy (SG) in which young, lean male C57BL/6J mice underwent SG or sham operation while maintained on low-fat chow, then were challenged with high-fat diet (HFD) in midlife. We assessed glucose metabolism, body composition, energy expenditure, hepatic histology, adipose tissue inflammation, and cecal microbiome composition.

RESULTS: Despite identical weight and food intake on low-fat chow, SG mice demonstrated improved glucose tolerance and insulin sensitivity prior to HFD challenge. Upon HFD exposure, SG animals exhibited enhanced metabolic flexibility with greater capacity for fat oxidation, increased energy expenditure, attenuated weight gain, and reduced adiposity compared to sham controls. SG further reduced hepatic lipid accumulation and attenuated visceral adipose tissue inflammation, marked by decreased pro-inflammatory cytokine expression and reduced macrophage infiltration. These metabolic benefits occurred independently of caloric intake. Cecal microbiome profiling revealed surgery-specific remodeling characterized by Lactobacillus enrichment and reductions in Verrucomicrobia and Clostridia - a pattern distinct from caloric restriction and consistent with prior SG studies.

CONCLUSIONS: Early-life SG confers durable, weight-loss-independent protection against midlife metabolic deterioration. Gut microbiome remodeling, particularly enrichment of Lactobacillus species, represents a candidate mediating mechanism and a potential therapeutic target for aging and metabolic disease.},
}

@article {pmid41959121,
year = {2026},
author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A},
title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.03.715941},
pmid = {41959121},
issn = {2692-8205},
abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.

OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.

METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.

MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.

CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.},
}

@article {pmid41959202,
year = {2026},
author = {Yang, Y and Nettifee, J and Azcarate-Peril, MA and Muñana, KR and Callahan, B},
title = {Gut Microbiome Alterations in Canine Idiopathic Epilepsy: A Pairwise Case-Control Study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.716098},
pmid = {41959202},
issn = {2692-8205},
abstract = {BACKGROUND: Idiopathic epilepsy (IE) is the most common chronic nervous system disorder of dogs, and its cause is poorly understood. Emerging evidence suggests that microbiome alterations can occur with IE via the microbiota-gut-brain axis. Therefore, we analyzed the fecal microbiomes of 98 dogs (49 IE, 49 control) in a pairwise case-control observational study using 16S rRNA gene sequencing.

RESULTS: Although the microbial community was mostly similar between groups, IE was associated with a modest but significant shift in Weighted-Unifrac distance (P = 0.042). We used six differential abundance (DA) methods to identify differentially abundant amplicon sequencing variants (ASVs) between IE and control groups. Notably, one Collinsella ASV was found to be significantly more abundant in IE dogs by all six methods. The gut microbial compositions varied drastically across households (accounting for about 69% of the total variation), but did not have significant differences between sex, age, or breed. Phenobarbital administration in IE dogs had a significant effect on seizure control, and was not associated with changes in the microbiome.

CONCLUSION: Our findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.},
}

@article {pmid41959210,
year = {2026},
author = {Muller, E and Baum, S and Borenstein, E},
title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714614},
pmid = {41959210},
issn = {2692-8205},
abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.

RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.

AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL .},
}

@article {pmid41959214,
year = {2026},
author = {Skupa, SA and Hernandez, JB and Smith, AL and Drengler, EM and Seth, AK and Rai, SN and Clayton, JB and D'Angelo, CR and El-Gamal, D},
title = {Impact of high-fat Western diet on chronic lymphocytic leukemia disease progression and gut microbiome profile in Eμ-TCL1 mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.30.715124},
pmid = {41959214},
issn = {2692-8205},
abstract = {BACKGROUND: The composition and function of the gut microbiome have been shown to contribute to both health and disease. One of the most powerful modulators of microbial composition and function is diet.

MATERIALS & METHODS: Using the Eμ-TCL1 murine model of B-cell chronic lymphocytic leukemia (CLL), we assigned male and female mice to a high-fat, high-carbohydrate Western diet (HF) or standard chow (CH) diet.

RESULTS: Mice consuming a HF diet had significantly shorter survival than those consuming a CH diet, irrespective of sex, with female mice exhibiting particularly poor outcomes. We also observed a significant increase in splenic involvement by CLL in the HF diet-fed mice at time of sacrifice. Mice receiving the HF diet demonstrated immediate and profound effects on the gut microbiome, marked by reduced alpha diversity and significantly different community composition as measured by beta diversity. Notably, there was a sustained increase in Akkermansia muciniphila and Bacteroidetes thetaiotaomicron in HF diet-fed mice, coupled with a corresponding increase in microbiome functional pathways related to arginine and histidine biosynthesis, chitin degradation, and nucleotide biosynthesis.

DISCUSSION: Collectively our data provides evidence of the profound and sustained impact of a high-fat Western diet upon the gut microbiome community and CLL pathogenesis in the Eμ-TCL1 murine model of CLL.},
}

@article {pmid41959235,
year = {2026},
author = {Zhang, YJ and Tanofsky-Kraff, M and Reyes, MM and Zeve, D and Ehrmann, KJ and Lee, J and Schaan, AP and Prado, A and Ma, XC and Parker, MN and Brady, SM and Saint-Denis, E and Sharma, K and Frintu, B and Richmond, C and Desai, N and Yeliseyev, V and Bry, L and Avila-Pacheco, J and Clish, CB and Quealy, M and Clardy, J and Breault, DT and Ding, Y and Wang, X and Jost, M and Poyet, M and Groussin, M and Yanovski, JA and Lencer, WI and Alm, EJ},
title = {Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.13.709143},
pmid = {41959235},
issn = {2692-8205},
abstract = {Metabolites produced by the gut microbiome influence host metabolic health, but how this occurs remains incompletely defined. Here, we report that a common human gut commensal, Blautia wexlerae , converts dietary fats into bioactive metabolites that induce gut hormone production to affect glucose metabolism and suppress appetite. We found that colonization with Blautia wexlerae correlated with healthier eating behaviors in humans. Blautia wexlerae encodes a unique acyl transferase and is capable of producing acyl amines from nutrient substrates. These Blautia acyl amines stimulated human enteroendocrine cells to secrete GLP-1 and other gut peptide hormones more potently than endogenously produced acyl amines. When fed to mice, acyl amines improved glycemic control and decreased appetite. In humans, higher stool levels of Blautia DNA encoding acyl amine synthesis genes correlated with leanness and decreased dietary fat intake. These results define a mechanism of action for how Blautia wexlerae affects host metabolic control.},
}

@article {pmid41959264,
year = {2026},
author = {Rigas, YE and Shane, J and Treat, B and Shanks, RMQ and Leger, AJS},
title = {C. mastitidis requires the protein Sortase F to colonize the eye.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.12.711320},
pmid = {41959264},
issn = {2692-8205},
abstract = {The ocular surface is a mucosal tissue that is constantly exposed to environmental antigens and potential pathogens. Human microbiomes play a critical role in the balance of surveillance and inflammation at sites of colonization. Historically, the investigation of the ocular microbiome has been difficult due to its paucibacterial nature and the inhospitable environment of the ocular surface. Despite this, Corynebacterium mastitidis (C. mast) developed a unique ability to colonize the eye and elicit a protective immune response characterized by induction of IL-17 from γδ T cells and protection from corneal infection. Therefore, we sought to understand the unique bacterial machinery that C. mast utilizes to colonize the eye and how it affects the induction of an eye-specific immune signature. Using a C. mast transposon mutant library, we identified a mutant that completely lacked an ability to form biofilm, colonize the eye, and induce in vivo immunity. Whole genome sequencing revealed a disruption in the sortase F gene, which anchors proteins to the cell wall of C. mast , governing biofilm formation and tethering of adhesins to the cell surface. Additionally, we show that mutation in individual C. mast adhesins does not affect ocular colonization or immune induction. By understanding the molecular mechanism of ocular microbial colonization, this work advances our understanding of how bacteria colonize and induce immune responses on the eye, providing a foundation for developing novel therapeutic strategies against ocular infections.},
}

@article {pmid41959277,
year = {2026},
author = {Bodkhe, RL and Blank, RB and Trepka, KR and Orellana, DA and Scher, JU and Turnbaugh, PJ and Nayak, RR},
title = {Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.30.715090},
pmid = {41959277},
issn = {2692-8205},
abstract = {The human gut microbiome influences treatment outcomes, but whether microbiome signatures of drug response generalize across cohorts remains unclear. Here, we perform a multi-cohort analysis (3 cohorts, N=100 patients) to determine whether cross-cohort microbial signatures are associated with methotrexate (MTX) response in new-onset rheumatoid arthritis (RA) patients. Pre-treatment gut microbiome community structure and function differed by future MTX response status, with MTX-nonresponders (MTX-NR) showing Bacteroides caccae depletion and Ruminococcus bromii enrichment. Multiple microbial functions were depleted in MTX-NR, including nucleotide metabolism, one-carbon pool by folate, and histidine metabolism. Notably, candidate MTX-degrading genes were enriched in MTX-NR. Microbiome functional profiles outperformed clinical metrics in predicting future MTX response. These results show that consistent microbiome signatures are associated with MTX response across different RA cohorts and pave the way for microbiome-based precision medicine in newly diagnosed RA patients.},
}

@article {pmid41959294,
year = {2026},
author = {Binion, B and Ahmad, S and Wang, T and Tang, E and Barnick, B and Olukoya, D and Mbuvi, P and Dutta, D and Erdman, JW and Gaskins, HR and Yang, G and Irudayaraj, J and Ridlon, JM},
title = {The Urinary Tract commensal Peptoniphilus spp. Encodes a Novel 17β-Hydroxysteroid Dehydrogenase.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.29.714803},
pmid = {41959294},
issn = {2692-8205},
abstract = {UNLABELLED: Microbial steroid metabolism represents an underappreciated extension of the vertebrate endocrine system, with growing evidence that host-associated microbes contribute to the diversity and bioavailability of sex steroids within human tissues. Emerging studies have linked microbial androgen metabolism to urinary microbiome composition and to resistance to androgen deprivation therapy (ADT) in prostate cancer. While microbial pathways capable of converting steroid precursors such as cortisol to androgens, via the steroid-17,20-desmolase pathway, such as DesG-mediated interconversion of androstenedione to testosterone have been reported, the diversity of enzymes mediating downstream androgen interconversion remains incompletely defined. Here, we investigate the androgen-forming capabilities of anaerobic bacteria from the male genitourinary microbiome, focusing on NADPH-dependent 17β-hydroxysteroid dehydrogenases (17β-HSDHs) that catalyze interconversion of androstenedione and testosterone. We isolated androgen-forming bacterial strains from human male urine and identified a previously uncharacterized 17β-HSDH encoded by Peptoniphilus obesi , demonstrated that this enzyme catalyzes the NADPH-dependent reduction of androstenedione to testosterone and the reverse oxidation reaction. Sequence similarity searches further identified a homologous 17β-HSDH in Anaerococcus , which was synthesized and functionally validated, revealing conserved activity despite low sequence identity to the previously characterized urinary tract enzyme DesG. The enzymes were found to have broad substrate specificity for C19 and C18 17keto- and 17β-hydroxysteroids. Together, these findings expand the known diversity of microbial 17β-HSDHs and identify previously unrecognized androgen-forming activities within the genitourinary microbiome.

IMPORTANCE: Microbial steroid-transforming pathways may provide a mechanism by which commensal anaerobes contribute to androgen availability in the genitourinary tract. By identifying novel 17β-hydroxysteroid dehydrogenases from Peptoniphilus and Anaerococcus , genera repeatedly associated with prostate cancer, this study provides mechanistic insight into how microbial steroid metabolism may influence hormone-driven disease.},
}

@article {pmid41959308,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.711154},
pmid = {41959308},
issn = {2692-8205},
abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.

IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

@article {pmid41959458,
year = {2026},
author = {Kvitne, KE and Zuffa, S and Charron-Lamoureux, V and Patan, A and Agongo, J and Cai, J and Deleray, V and El Abiead, Y and Xing, S and Zemlin, J and Thomas, S and Nelson, MR and Gant, A and Ghadishah, A and Lam, A and Ho, B and Momper, JD and Suhandynata, RT and Bertrand, K and Knight, R and Chambers, C and Dorrestein, PC and Tsunoda, SM},
title = {Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715750},
pmid = {41959458},
issn = {2692-8205},
abstract = {Infant antibiotic treatment is associated with increased risk of developing non-communicable diseases, potentially through disruption of the gut microbiome. However, the impact of indirect antibiotic exposure via human milk remains largely unexplored. Here, we investigate a cohort (n =80) of antibiotic-treated breastfeeding mother-infant dyads and untreated matching controls using integrative multi-omics analyses of fecal, milk, and skin samples (n =1,455). Maternal antibiotic treatment was associated with different infant fecal microbiome and metabolome profiles, including lower abundance of Bacteroides , Lactobacillus , and Bifidobacterium , and higher levels of antimicrobial resistance gene reads. Further, fecal metabolic alterations associated with indirect antibiotic exposure were exacerbated by formula milk supplementation. In a subset of infants (n =61), indirect exposure was associated with higher body mass index (BMI). These findings suggest that maternal antibiotic treatment during lactation may influence the early-life infant gut microbiome with potential long-term implications.},
}

@article {pmid41959463,
year = {2026},
author = {Noecker, C and Guo, L and Daté, C and Rai, N and Daramy, F and Ramirez Hernandez, LA and Kyaw, TS and Trepka, KR and Gupta, CL and Ha, CWY and Babdor, J and Spitzer, MH and Turnbaugh, PJ},
title = {A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715625},
pmid = {41959463},
issn = {2692-8205},
abstract = {UNLABELLED: Genomic variation within gut microbial species can have consequences for host health and disease. However, for low abundance species, these variations can be difficult to capture by both culture-dependent and -independent approaches. Here, we focus on the prevalent but low abundance gut Actinomycetota Eggerthella lenta . We developed a selective media for sensitive and specific isolation of E. lenta from human stool. Genomes from 87 new E. lenta isolates were combined with prior high-quality assemblies, shedding light on within-species functional diversity. Phylogenetic analysis revealed a broadly distributed subclade, which we refer to as E. lenta Group B. This lineage was differentiated by its metabolic potential and bacteriophage defense, though mobile elements were shared broadly across the species. Notably, Group B was positively associated with intestinal inflammation in subjects with inflammatory bowel disease. Overall, these results emphasize the importance of bacterial population structure in host-microbiome interactions and provide a framework to study low-abundance gut taxa.

HIGHLIGHTS: Selective media enables E. lenta isolation and reveals high prevalence in humans Discovery of a distinctive lineage within E. lenta undergoing genome reduction E. lenta Group B has altered metabolism, phage defense, and disease associations A widespread conjugative plasmid could enable improved genetics.},
}

@article {pmid41959466,
year = {2026},
author = {Sapoval, N and Treangen, TJ and Nakhleh, L},
title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.10.710879},
pmid = {41959466},
issn = {2692-8205},
abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.

RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.

https://github.com/nsapoval/bd-gsl.},
}

@article {pmid41959531,
year = {2026},
author = {Orlov, M and Karr, M and Hara, N and Needell, J and Aherne, CM and Matsuda, JL and Palmer, BE and Lozupone, C and Clark, SE and Janssen, WJ and Evans, CM},
title = {Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.05.709937},
pmid = {41959531},
issn = {2692-8205},
abstract = {T-helper (Th)-17 lymphocytes are central mediators of adaptive type 17 immunity. Decreased type-17 signaling increases severity of infections in humans and mice. However, detrimental effects of excessive type 17 responses in autoimmune and other inflammatory diseases highlight a need for type-17 immune calibration to support beneficial host defense requirements. Mechanisms of type 17 calibration are poorly understood. A gut-lung axis has been proposed to coordinate homeostatic protection and acute host defense. Factors that acutely alter the gut microbiome are heterogeneous and include acute intestinal infections, non-infectious colitis, and medical treatments such as antibiotics. How changes in the gut microbiome affect lung immune tone during homeostasis and acute pulmonary infections are also poorly understood. Prior studies have shown that antibiotics reduce expression of IL-17-mediated host defense in the gut. Since gut microbial homeostasis influences Th17 cell numbers in both the intestine and remote tissues, we postulated that antibiotic treatment would result in gut dysbiosis and weakened type-17 host defense in the lungs. We found that amoxicillin induces significant dysbiosis that is long-lasting and that there is a long-term decrease in type-17 tone in the lungs. We also found that in mice lacking the gut mucin, Muc2, Th17 cells increased in the lungs following inflammatory challenge. These findings suggest that antibiotic-induced dysbiosis can decrease lung immune defenses for long periods of time after cessation of antibiotic treatment.},
}

@article {pmid41959535,
year = {2026},
author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG},
title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715631},
pmid = {41959535},
issn = {2692-8205},
abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.},
}

@article {pmid41959551,
year = {2026},
author = {Lv, W and Hu, H and Huang, Y and Yang, J and Li, Y and He, J and Wang, K and Liu, Y and Wang, Q},
title = {Microbial mechanisms and therapeutic interventions in the periodontitis-inflammatory bowel disease axis: a comprehensive review.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2656084},
pmid = {41959551},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis and inflammatory bowel disease (IBD) are chronic inflammatory conditions of the oral and gastrointestinal tracts that exhibit bidirectional microbial and immunological crosstalk.

OBJECTIVE: Aimed at elucidating the bidirectional crosstalk between periodontitis and IBD at both microbiological and immunological levels and evaluate related therapeutic interventions, this review comprehensively summarizes recent evidence on their interaction via the oral-gut-bone axis, focusing on microbial ecology, host responses, and innovative therapies.

DESIGN: Distinct yet overlapping dysbiotic signatures are observed in both diseases, with periodontal pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum capable of translocating to the gut and perturbing intestinal homeostasis, while gut inflammation reciprocally reshapes the oral microbiome. Mechanistic links include a spectrum of convergent pathways: (i) microbial metabolites-short-chain fatty acids, choline metabolites, indole derivatives, polyamines, and bile acids-that modulate barrier integrity and immune responses; (ii) shared immune cells and inflammatory mediators driving mucosal damage at both sites; (iii) bacterial extracellular vesicles (BEVs) and lysine lactylation (Kla)-mediated signaling; and (iv) oxidative stress, iron metabolism dysregulation, and ferroptosis contributing to tissue destruction.

RESULTS: Therapeutic strategies targeting this axis encompass bidirectional interventions: periodontal and IBD treatments that mutually influence oral and gut health, natural anti-inflammatory and antimicrobial compounds, probiotics and prebiotics, oral and fecal microbiota transplantation, and emerging bacteriophage therapy. Critically, the clinical translation of collaborative dentistry-gastroenterology management is highlighted as a promising avenue for integrated care.

CONCLUSIONS: By integrating findings across microbial ecology, host response, and therapeutic innovation, this review provides a comprehensive framework for understanding and targeting the periodontitis-IBD axis.},
}

@article {pmid41959571,
year = {2026},
author = {Tang, Y and Dang, M and Xie, W and Chen, X and Zhang, E and Wang, Z},
title = {Spatial heterogeneity of the microbiota in Cypripedium franchetii and Its correlation with organ-specific metabolomes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1751651},
pmid = {41959571},
issn = {1664-462X},
abstract = {INTRODUCTION: Cypripedium franchetii, a plant of ornamental and medicinal value, is designated as a Grade II Protected Species in China. The C. franchetii population inhabiting the fragile ecosystem at Galongla Pass exhibits unclear patterns in microbial composition across rhizosphere soil, root, stem, and leaf tissues, as well as metabolite distribution and plant tissue-specific microbe-metabolite relationships.

METHODS: This study focused on C. franchetii, a plant growing in the fragile ecosystem of Galongla Pass in Tibet. We employed an integrated approach combining high-throughput amplicon sequencing (targeting bacterial 16S rRNA genes and fungal ITS regions) and untargeted metabolomics (LC-MS/MS) to systematically analyze the microbial community structure and metabolite distribution in its rhizosphere soil and root, stem, and leaf tissues. We further explored the associations between endophytic microorganisms and metabolites within plant tissues.

RESULTS: The results revealed significant differences in microbial composition across plant compartments: distinct variations were observed between rhizosphere soil and plant tissues, while stem and leaf microbial communities exhibited greater similarity. At the phylum level, Pseudomonadota dominated among bacteria, while Basidiomycota and Ascomycota were the predominant fungal phyla. At the genus level, dominant taxa showed tissue specificity: Cronobacter and Lactobacillus were dominant bacterial genera in roots, whereas Acinetobacter dominated in stems, and Acinetobacter and Agrobacterium were prominent in leaves. For fungi, Tulasnella was the dominant genus in rhizosphere soil and roots, while Dioszegia prevailed in stems and leaves. Metabolite analysis indicated significant differences in metabolic profiles among tissues, with stem and leaf metabolite compositions being relatively similar. Correlation analysis further revealed statistically significant correlations between differential microorganisms and differential metabolites in roots and stems, identifying 31 microbial genera significantly correlated with 48 high-abundance metabolites.

DISCUSSION: This study systematically unveils the tissue-specific microecological and metabolic characteristics of C. franchetii during its post-flowering nutrient accumulation phase. Key findings include: microbial community assembly involves cooperative mechanisms between core conserved taxa (e.g., Tulasnella) and habitat-specific taxa; microbial diversity exhibits a gradient decline from the rhizosphere into plant tissues accompanied by functional group succession; and extensive yet specific potential interaction networks (based on statistical covariation) exist between microorganisms and host metabolites, indicating potential microbial involvement in regulating plant secondary metabolism. These findings not only provide guidance for the conservation of C. franchetii (requiring consideration of both core symbiotic and habitat-specific taxa) and constructing synthetic microbial communities during artificial propagation, but also offer a new theoretical basis for the targeted regulation of medicinal active ingredient synthesis through the microbiome.},
}

@article {pmid41959663,
year = {2026},
author = {Fognani, A and Rotondo, R and Savo Sardaro, ML and de Iure, A and Gaglione, M and Casali, M and Leonardi, L and Radicati, FG and Vacca, L and Guescini, M and Zeppa, SD and Gatta, L and Stocchi, F and Picconi, B and De Pandis, MF},
title = {Effects of combined Mediterranean diet and physical activity intervention on the gut microbiome and disease progression in individuals with Parkinson's disease: study protocol for a multicenter, randomized controlled pilot study (PRIME study).},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1743490},
pmid = {41959663},
issn = {1663-4365},
abstract = {BACKGROUND AND AIMS: Parkinson's disease (PD) is a neurodegenerative disorder for which no disease-modifying therapy currently exists, making it crucial to investigate alternative strategies that may slow its progression. The PRIME study will investigate the effects of combined dietary and physical activity interventions- performed in rehabilitative settings with health professional supervision and evaluation, versus single interventions on the gut microbiome in PD. The aim is to identify microbiome profiles - comparing traditional 16s rRNA gene sequencing with the third-generation method - as potential non-invasive, stage specific biomarkers of PD. In addition, the study will assess whether the combined intervention affects disease progression, symptoms, cognitive abilities, and quality of life.

METHODS: Eighty participants with PD will be randomized into four arms: a Mediterranean-diet intervention group; a structured physical-activity group; a combination group receiving both dietary and exercise interventions; a control group receiving standard care only.

CONCLUSION: By integrating microbiome characterization with the evaluation of these interventions, the study aims to explore whether intervention-induced changes in the microbiota are associated with clinical improvement in PD, thus paving the way for the design of future non-pharmacological protocols to slow disease progression, mitigate symptom severity, and promote diagnosis.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT07097103.},
}

@article {pmid41959668,
year = {2026},
author = {Chung, HA and Fralish, Z and Tu, T and Reker, D},
title = {Profiling biological effects of microbiome metabolites via machine learning.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115282},
pmid = {41959668},
issn = {2589-0042},
abstract = {Human microbiome-derived metabolites are key mediators of host physiology. However, their biological effects remain largely uncharacterized due to limitations of current low-throughput and untargeted experimental approaches that are time intensive and costly. This has hindered the systematic biological characterization of microbiome metabolites. To address this gap and accelerate the identification of biological effects of microbiome metabolites, we developed and experimentally validated a machine learning platform trained on publicly available drug development data to rapidly predict a wide array of chemical and biological properties of microbiome metabolites. Prospective experimental validation confirmed the accuracy of our models and uncovered previously unknown effects of several metabolites. For example, we identified previously unknown interleukin 8 secretion stimulation by the metabolites spermine and spermidine, which have been regarded anti-inflammatory thus far. Our findings demonstrate the potential power of machine learning to accelerate the functional annotations of microbiome-derived metabolites, paving the way for biomarker and therapeutic discovery.},
}

@article {pmid41959672,
year = {2026},
author = {Jia, C and Zhang, B and Gan, B and Zhao, Y and Lin, X and Chen, J and Zhao, J},
title = {Divergent dynamics in whole-body regeneration and larval development of sponge Haliclona simulans: cytobiology, microbiome, and transcriptomics.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115344},
pmid = {41959672},
issn = {2589-0042},
abstract = {Sponges are capable of rebuilding functional individuals from cell aggregates (primmorphs), a process termed whole-body regeneration that morphologically parallels larval development. To systematically compare these processes, we established an in vitro primmorph regeneration model in Haliclona simulans and performed multi-level analyses across planktonic, settled, and metamorphic stages. Although both processes formed similar structures (e.g., the aquiferous system), planktonic primmorphs exhibited a reduced stem cell proportion (archeocyte/choanocyte), along with the increase of seemingly dedifferentiating cells and vacuolar cells. Microbiome diverged: while sharing core symbionts (e.g., AqS1), primmorphs enriched Tenacibaculum and Vibrio species during remodeling process. Transcriptomics revealed distinct signatures: regeneration upregulated genes potentially related to DNA repair and dedifferentiation but downregulated stem cell markers. Our integrative study indicates that regeneration and development constitute distinct processes, achieving similar functional outcomes via divergent cellular, microbial, and molecular profiles that provides a foundational framework for future mechanistic studies of regeneration.},
}

@article {pmid41959673,
year = {2026},
author = {Ko, CY and Zhang, L and Lin, Y and Zeng, Y},
title = {Gut microbial metabolites, barrier dysfunction, and endotoxemia in men obstructive sleep apnea-associated hypertension.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115291},
pmid = {41959673},
issn = {2589-0042},
abstract = {Obstructive sleep apnea (OSA) is frequently accompanied by hypertension, yet gut-related mechanisms remain unclear. We profiled fecal and plasma short-chain fatty acids, markers of intestinal barrier injury and endotoxemia, immune phenotypes, and the fecal microbiome in men classified as non-OSA, OSA, OSA with prehypertension, or OSA with hypertension, and reassessed a subset after three months of continuous positive airway pressure. OSA with hypertension was characterized by reduced fecal acetate and butyrate, elevated intestinal permeability and endotoxin markers, and a higher proportion of Th17 cells. Lipopolysaccharide tracked with blood pressure severity and showed inverse associations with fecal butyrate and positive associations with plasma propionate. Short-term CPAP exposure was accompanied by improved sleep metrics, reduced barrier injury and endotoxemia, increased microbial diversity, and altered systemic SCFA patterns. These findings support a gut barrier-endotoxin framework linking sleep-disordered breathing with hypertensive risk.},
}

@article {pmid41960322,
year = {2026},
author = {Hu, F and Wang, F and Tessier, AJ and Glenn, A and Liu, Y and Guasch-Ferré, M and Tobias, D and Eliassen, AH and Manson, J and Clish, C and Lee, KH and Shai, I and Qi, Q and Burk, R and Liang, L and Sun, Q and Kaplan, R and Willett, W and Wang, D},
title = {Epidemiological and Multi-Omics Investigation of Phytosterol Intake and Type 2 Diabetes Risk.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9222420/v1},
pmid = {41960322},
issn = {2693-5015},
abstract = {Objectives Limited evidence exists on the association between dietary phytosterol intake and the risk of type 2 diabetes (T2D). We aimed to investigate this association and identify the underlying plasma metabolic, metabolomic, and gut microbial features. Methods We followed 204,633 participants (79% women) from three large US prospective cohorts for up to 36 years. Validated food-frequency questionnaires were used to estimate dietary intake of total phytosterol and three subtypes: β-sitosterol, campesterol, and stigmasterol. We applied Cox proportional hazards models to evaluate their associations with T2D risk. In a subset of 39,879 participants with plasma metabolic biomarkers and 9,528 participants with plasma metabolomics data, we examined the association between phytosterol intake and metabolic biomarkers related to insulinemia, glycemia, lipids, and inflammation, as well as T2D-related metabolomic profiles. Additionally, we explored the gut microbial species and enzymes involved in these associations in a subset of 465 participants with gut microbiome data. Results During follow-up, we documented 20,708 incident T2D cases. After adjustment for covariates, higher intake of total phytosterol was associated with a lower T2D risk (HR comparing extreme quintiles = 0.87, 95% CI: 0.82, 0.92; P trend<0.001). Similar associations were observed for β-sitosterol (HR=0.86, 95% CI: 0.81, 0.91; P trend<0.001) and campestrol (HR=0.89, 95% CI: 0.84, 0.94; P trend<0.001), but not for stigmasterol.β-sitosterol and campestrol were also associated with favorable plasma metabolic profiles, such as lower levels of C-reactive protein, leptin, and C-peptide, as well as beneficial T2D-relevant metabolomic profiles. Moreover, we identified several gut microbial species, and their enzymes involved in these associations. For example, Faecalibacterium prausnitzii and its β-sitosterol-degrading enzyme 3-oxosteroid 1-dehydrogenase (EC1.3.99.4) were associated with higher β-sitosterol intake and a metabolomic profile indicative of lower T2D risk. Conclusions A higher intake of phytosterols, particularly β-sitosterol and campesterol, was associated with a lower risk of T2D, with consistent findings across epidemiological and multi-omics analyses. These findings support the role of a healthy plant-based dietary pattern rich in phytosterol-containing foods such as whole grains, nuts, seeds, fruits, vegetables, and vegetable oils in lowering T2D risk.},
}

@article {pmid41960429,
year = {2026},
author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL},
title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1691133},
pmid = {41960429},
issn = {1664-302X},
abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.

METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.

RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.

DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.},
}

@article {pmid41960430,
year = {2026},
author = {Khelfaoui, I and Wang, W and Shehata, AI and Meskher, H and El Basuini, MF and Mohamed, AMA and Abouelenein, MF and Degha, HE and Alhoshy, M and Teiba, II and Mahmoud, O and Mahmoud, SS},
title = {STROBE-causal machine learning for the human microbiome: systematic review on methodological innovations and validation frameworks.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705116},
pmid = {41960430},
issn = {1664-302X},
abstract = {The reproducibility crisis in causal microbiome research necessitates robust validation frameworks. Current studies often face inconsistent validation methods, limited interpretability, and a lack of standardized reporting, creating a gap in reliable causal inference. This systematic review evaluates over 60 peer-reviewed studies published between 2015 and 2024 to: (1) establish benchmarking standards leveraging synthetic data and biological plausibility assessments; (2) compare advanced causal machine learning (ML) methodologies, including Double/Debiased ML, Deep Instrumental Variables (Deep IV), and Directed Acyclic Graphs (DAGs), in their application to microbiome-host systems; and (3) propose the STROBE-CML (Strengthening the Reporting of Observational Studies in Epidemiology-Causal Machine Learning) guidelines to standardize reporting practices. We emphasize critical innovations such as federated validation pipelines and time-series causal discovery frameworks that address these gaps by facilitating scalable, privacy-preserving, and reproducible inference across heterogeneous cohorts. A decision support tool is introduced to guide researchers in selecting appropriate causal ML approaches based on data structure, research question, and computational constraints. By synthesizing methodological advances with rigorous validation paradigms, this review provides a roadmap for generating reliable, biologically interpretable, and clinically translatable causal claims in microbiome science.},
}

@article {pmid41960682,
year = {2026},
author = {Luo, T and Xue, M and Du, Y and Chen, H and Sun, Y and Sun, H},
title = {The Mechanism of Gut Microbiota in Breast Cancer Based on the Bulk Transcriptome, Mendelian Randomization Analysis and Single Cell RNA Sequencing.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70284},
pmid = {41960682},
issn = {2045-8827},
support = {JCYJ20240813160621028//Shenzhen Science and Technology Program/ ; FTWS075//Futian Healthcare Research Project/ ; //Foundation of Key Clinical Specialty Construction Project in Futian District, Shenzhen City/ ; },
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Female ; Mendelian Randomization Analysis ; *Transcriptome ; Single-Cell Analysis ; Genome-Wide Association Study ; Biomarkers, Tumor/genetics ; Sequence Analysis, RNA ; },
abstract = {Breast cancer (BC) is the leading cause of cancer death in women. Bidirectional regulation between BC and gut microbiota (GM) is established, but GM's mechanistic role in BC pathogenesis remains unclear. Public BC/control samples and GM genome-wide association study data underwent Mendelian randomization to identify GM-BC associations and GMRGs. DEGs between BC and controls were analyzed. Candidate genes were derived from intersecting DEGs and GMRGs. Machine learning identified biomarkers, validated by expression analysis. GSEA, immune infiltration, drug screening with molecular docking, and scRNA-seq were performed. Intersecting 3455 DEGs with GMRGs yielded eight candidates; MCM6 and NR3C1 were validated as biomarkers, enriched in DNA replication pathways. Immune infiltration showed 13 differential immune cells, with macrophages notably influencing biomarkers. Etoposide exhibited strong binding to biomarkers via docking. scRNA-seq identified epithelial cells as key, with stage-dependent biomarker expression. This study redefines BC as a microbiome-regulated network, identifying the MCM6/NR3C1 biomarker pair for early diagnosis and microbiome-targeted interventions.},
}

Humans
*Breast Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Female
Mendelian Randomization Analysis
*Transcriptome
Single-Cell Analysis
Genome-Wide Association Study
Biomarkers, Tumor/genetics
Sequence Analysis, RNA

@article {pmid41960738,
year = {2026},
author = {Cheng, J},
title = {The Microbiome-Gut-Liver Axis Drives Post-Kasai Fibrosis in Biliary Atresia: From Mechanism to Precision Intervention.},
journal = {Hepatology research : the official journal of the Japan Society of Hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/hepr.70184},
pmid = {41960738},
issn = {1386-6346},
abstract = {Biliary atresia (BA) remains the most devastating fibro-inflammatory cholangiopathy of infancy. Even after successful Kasai portoenterostomy (KPE), progressive liver fibrosis ultimately dictates long-term outcomes. The "microbiome-gut-liver axis" has fundamentally reshaped our understanding of liver disease pathogenesis, yet critical questions persist regarding how Kasai surgery reconfigures this axis and whether these changes actively contribute to fibrogenesis. This review traces a mechanistic cascade from anatomical remodeling through dysbiosis, metabolic disruption, immune dysregulation, and ultimately liver fibrosis. We examine how Kasai surgery physically reprograms the gut ecosystem through altered biliary-enteric continuity and bile acid circulation; how microbial metabolites-particularly secondary bile acids and short-chain fatty acids-orchestrate hepatic stellate cell behavior and shape the hepatic immune milieu; and how bacterial translocation sustains inflammation through Toll-like receptor signaling. Recent evidence challenging the primacy of TLR4 in long-term progression instead implicates TLR7 as a potential driver, while acknowledging its complex, context-dependent role that may involve both pro-fibrotic and counter-regulatory functions. Building on this foundation, we critically assess emerging intervention strategies-including probiotics, postbiotics, phage therapy, and personalized approaches-weighing translational potential against current evidence gaps and safety considerations. We propose that post-Kasai alterations in the bile acid pool may drive fibrogenesis through synergistic engagement of FXR and TLR pathways (including TLR4 and TLR7), and outline a stratified, dynamic intervention framework for precision microbiome management grounded in multi-omics integration and longitudinal cohort studies. By synthesizing current knowledge while identifying key uncertainties, this review aims to inform both mechanistic investigation and the development of microbiome-targeted adjunctive therapies for BA.},
}

@article {pmid41960919,
year = {2026},
author = {van Leeuwen, PT and Gadaleta, P and Brul, S and Seppen, J and Wortel, MT},
title = {Environmentally mediated interactions predict community assembly and invasion success in a gut microbiota synthetic community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011326},
doi = {10.1128/msystems.00113-26},
pmid = {41960919},
issn = {2379-5077},
abstract = {The gut microbiome plays a crucial role in host homeostasis, with implications for nutrition, immune development, metabolism, and protection against pathogens. Disturbance of the microbiome by microbial invasion can be negative or positive: invasions of opportunistic pathogens can cause disease while dysbiotic states need invasions to recover. However, the complexity of the microbiome challenges our understanding of what factors determine the ability of microbes to invade. In this study, we measure interactions between members of a synthetic community of prominent gut bacteria using supernatant assays, which quantify the growth of one species in the cell-free culture medium of another. We measure relative abundances of co-cultures of up to four species to validate a generalized Lotka-Volterra model parameterized with these supernatant assays. We predict differential invasion outcomes of the opportunistic pathogens Escherichia coli and Bacteroides ovatus based on their monoculture growth profiles and interactions with other species, and we experimentally confirm model predictions of invasion success. The predictive value of our model indicates that environmentally mediated interactions, e.g., through soluble chemicals, primarily determine co-culture abundances and invasion success. Furthermore, model analyses show that negative interactions within the resident community and neutral to positive interactions with the invading species promote invasion success, but the interactions toward the invading species dominate. Our validated approach opens the way for testing of interactions of human gut microbiome species, thereby developing interventions to avoid pathogenic overgrowth and therapies to enhance health-benefitting invasions.IMPORTANCEThe stability of the human gut microbiome is crucial for host health, with opportunistic pathogen invasions causing diseases and healthy strain replacements needed for recovery. The microbiota's complexity complicates the understanding of invasion outcomes. This study uses a 10-species synthetic community of common gut microbiota to predict stable communities and invasion success. We grow cells in the growth medium of other species with the cells removed to parameterize a computational model, accurately predicting community composition up to four species and invasion success of Escherichia coli and Bacteroides ovatus. Our findings show that interactions through soluble compounds in the environment dictate co-culture growth and invasions. Furthermore, model analysis shows that interactions within the resident community and toward the invader are both important, but the latter dominate. These results pave the way for larger-scale studies to characterize gut microbiome interactions and properties that resist invasions, potentially benefiting health through improved probiotics and fecal microbiota transplants.},
}

@article {pmid41954789,
year = {2026},
author = {Schultz, J and García-Martínez, PM and Altalhi, S and Kontis, N and Dos Santos, A and Rosado, AS},
title = {Extreme Arabian environments and their microbiomes: new frontiers for astrobiology and biosignature discovery.},
journal = {Extremophiles : life under extreme conditions},
volume = {30},
number = {1},
pages = {},
pmid = {41954789},
issn = {1433-4909},
abstract = {Astrobiology assesses the habitability of planetary bodies and the potential for extraterrestrial life. Analog environments on Earth serve as sites for studying extreme environments that resemble extraterrestrial conditions, aiding in validating life-detection methods, mission instrumentation, and biosignature preservation. These environments function as a source of model microorganisms and communities that define the habitability and biochemistry of such extraterrestrial environments. Well-known analog environments include the Atacama Desert (Chile) for space mission validation, the McMurdo Dry Valleys (Antarctica) for Mars analog studies, and Rio Tinto (Spain) for extreme acidic environments. Although significant research has been conducted on these sites, various alternative environments may also offer valuable opportunities for astrobiological studies. Saudi Arabia encompasses a variety of pristine (or with minimal anthropic influence) extreme environments with conditions analogous to extraterrestrial settings (e.g., deserts and salt flats as analogs to Mars, and terrestrial and marine volcanic fields as analogs to icy moons), yet their potential remains largely unexplored. Recent studies have identified a volcanic crater with sodium phosphates and chlorates that mimics Enceladus’s ocean chemistry, and researchers have cultured Halalkalibacterium halodurans strains with adaptations to survive these conditions, offering valuable biological models. Additionally, complex metabolic landscapes with implications for icy moon habitability have been observed in Red Sea systems, which could be employed as valuable natural laboratories in astrobiological research. Furthermore, these findings underscore the potential of the Saudi Arabian extremophilic microbiome for space-related research. This review explores the microbial diversity of extreme environments in Saudi Arabia, emphasizing their potential as new terrestrial analogs to Mars and icy moons and the role of their microbiomes as terrestrial proxies for extraterrestrial life.},
}

@article {pmid41957864,
year = {2026},
author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F},
title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00886-8},
pmid = {41957864},
issn = {2524-6372},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.

RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.

CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.},
}

@article {pmid41957947,
year = {2025},
author = {Cashin, PH and Artursson, S and Sköldberg, F and Melhus, Å},
title = {Association of the gut microbiome to colorectal anastomotic leakage: systematic review.},
journal = {BJS open},
volume = {10},
number = {2},
pages = {},
pmid = {41957947},
issn = {2474-9842},
support = {24-0824//Cancerfonden/ ; },
mesh = {*Anastomotic Leak/microbiology/etiology ; Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/surgery/microbiology ; Animals ; },
abstract = {BACKGROUND: Research into the gut microbiome and its possible association with anastomotic leakage after colorectal surgery has increased recently with the growing availability of sequencing techniques. There is a lack of systematic reviews addressing specifically microbiomic differences between patients with anastomotic leakage and patients with a successful anastomotic healing. The objective was to systematically review the current research on the microbiome and its effect on the risk of anastomotic leakage in colorectal cancer.

METHODS: Pubmed/Medline, Cochrane, and Google scholar were searched on 14th February 2025, to identify relevant publications with the following inclusion criteria: colorectal surgery, microbiome sequencing data, anastomotic leakage as endpoint, and comparative groups. Exclusion criteria were studies conducted exclusively on animals, non-peer-reviewed studies, review articles, and unavailable full text. Alpha/beta diversity and microbiomic functional analyses were the focus of the results.

RESULTS: From 112 studies, 11 studies including 551 patients were included: 143 patients with anastomotic leakage and 408 as controls. Alpha diversity differences were found in 7 of 11 studies-1 of 4 with preoperative sampling versus 6 of 7 studies with intra/postoperative sampling (P = 0.044). Beta diversity differences were found in 5 of 11 studies. Three studies reported on functional analyses, with one study demonstrating an association between methanogenesis and anastomotic leakage. Bacterial abundance was inconsistent across the studies. Three studies involving rodent models indicated a causal effect of the clinical microbiome.

CONCLUSION: Evidence implicates the gut microbiome as a factor associated with anastomotic leakage in colorectal cancer surgery, with three studies suggesting a causal relationship. There is a shortage of studies evaluating cross-species functional profiling. Optimal sampling should be performed during surgery.},
}

*Anastomotic Leak/microbiology/etiology
Humans
*Gastrointestinal Microbiome
*Colorectal Neoplasms/surgery/microbiology
Animals

@article {pmid41678296,
year = {2026},
author = {Tamrakar, K and Chavez, ES and Miller, PW and Hale, B and DuVall, J and Williams, N and Brown, E and Mangan, S and Wijeratne, AJ},
title = {Integrated Multi-Omics Analysis Provides Insights into the Rhizosphere Microbial Dynamics in Soybean-Fusarium virguliforme Interaction.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {MPMI09250121FI},
doi = {10.1094/MPMI-09-25-0121-FI},
pmid = {41678296},
issn = {0894-0282},
abstract = {Sudden death syndrome (SDS) is a major disease that affects soybean (Glycine max) production, primarily caused by the soilborne fungus Fusarium virguliforme in North America. Understanding the interactions among soybeans, F. virguliforme, and microorganisms in the soil near the vicinity of roots can provide microbial candidates for SDS management. The objective of this study was to elucidate the role of rhizosphere microbial composition and activity, both in the presence and absence of F. virguliforme, across two commercial soybean cultivars with differing susceptibility to SDS. Bacterial and fungal community dynamics were assessed using full-length 16S rRNA and internal transcribed spacer 1 (ITS1) sequencing, respectively. Microbial activity was further evaluated with an optimized metatranscriptome workflow. Our analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera Bacillus, Pseudomonas, Trichoderma, Mortierella, and Talaromyces, when exposed to F. virguliforme. This distinct microbial recruitment strategy in response to F. virguliforme could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing Bradyrhizobium spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, whereas pathogen pressure compromises symbiotic nitrogen fixation. The results highlight candidate taxa and interactions for developing synthetic microbial communities to support SDS management. The information generated from this study will be useful for assembling a combined synthetic microbial community and testing. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}

@article {pmid41950813,
year = {2026},
author = {Jacobson, R and Soundararajan, R and Maurin, M and Bulard, B and Mishra, S and Kain, V and Halade, G and Yadav, H and Yeatman, T},
title = {Intratumoral microbiome varies by site of metastatic spread in colorectal cancer.},
journal = {Surgery},
volume = {194},
number = {},
pages = {110167},
doi = {10.1016/j.surg.2026.110167},
pmid = {41950813},
issn = {1532-7361},
}

@article {pmid41950983,
year = {2026},
author = {Šigutová, H and Geislerová, P and Šigut, M and Pyszko, P},
title = {Trace amounts of insecticide, herbicide, and their combination disrupt the bacterial and fungal microbiome of a nontarget aquatic invertebrate.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128065},
doi = {10.1016/j.envpol.2026.128065},
pmid = {41950983},
issn = {1873-6424},
abstract = {The ubiquitous contamination of freshwater by pesticides contributes substantially to the ongoing diversity crisis. The animal microbiome affects a range of important functions, including host immunity and resilience to pesticide stress. Therefore, understanding how pesticides impact the microbiome of nontarget organisms is critical; however, this topic remains understudied in freshwater invertebrates. We investigated the effect of sublethal concentrations of pesticides on the host-associated microbiomes of larval Sympetrum vulgatum (Odonata: Libellulidae). Fifth-instar larvae reared in the laboratory and collected in the field were experimentally exposed to the herbicide metazachlor, the insecticide etofenprox, and their combination, and their bacterial and fungal microbiomes were profiled using 16S and ITS2 rRNA gene metabarcoding. Exposure to pesticides, particularly the insecticide, reduced bacterial richness, altered microbial community composition, reduced the complexity of co-occurrence networks, and neutral model deviations were more consistent with increased deterministic structuring. Simultaneously, our results suggested a loss of potentially beneficial taxa and an increase in pathogens, but also xenobiotic-degrading bacteria. The herbicide-insecticide mixture did not cause more profound effects than the insecticide alone, although it modified community assembly patterns. We found a shared set of prevalent genera persisting across treatments, alongside smaller treatment-associated subsets. Using a prevalence-based definition (detected in ≥3 samples per treatment), 91 bacterial and 22 fungal genera were shared across all treatments. The potentially contrasting responses of bacteria and fungi and the lab-reared and field-collected larvae to pesticides highlight the need to integrate the fungal component into microbiome research and suggest the importance of the naturally assembled microbiomes for host resilience.},
}

@article {pmid41950992,
year = {2026},
author = {Liu, K and Chen, Y and Zhao, M and Yang, D and Hu, Q and Cao, Y and Guo, X and Liu, Z},
title = {Integrative microbiome-transcriptome analysis reveals immune activation linked to gut dysbiosis in Vespa magnifica.},
journal = {Journal of invertebrate pathology},
volume = {217},
number = {},
pages = {108618},
doi = {10.1016/j.jip.2026.108618},
pmid = {41950992},
issn = {1096-0805},
abstract = {The gut microbiota plays a central role in the health of social wasps, contributing to nutrition, immunity, and environmental adaptation. However, its role in disease occurrence and host responses in the hornet Vespa magnifica remains poorly understood. Here, we investigated the gut microbial composition and host transcriptomic responses in diseased and healthy V. magnifica from Yunnan, China. High-throughput 16S rRNA gene sequencing revealed that diseased individuals exhibited significantly reduced microbial richness and diversity, characterized by depletion of beneficial taxa such as Lactobacillus (Lb.), Leuconostoc (Leu.), and Bifidobacterium (B.), alongside increased abundance of potential pathobionts including Lactococcus (Lc.) and Yokenella (Y.). Transcriptomic analysis identified 32 differentially expressed genes (DEGs), some of which were enriched for immune signaling pathways. Key immune-related genes, including peptidoglycan recognition proteins (PGRPs) and defensins (DEF), were strongly upregulated, indicating activation of host immune recognition and effector responses. Mantel correlation analysis further revealed significant associations between the top 30 differentially abundant bacterial genera and host immune genes, highlighting microbiota-host interactions in disease development. Collectively, these findings demonstrate that gut dysbiosis is associated with microbial imbalance and immune activation in V. magnifica, providing new insights into its gut health and potential strategies for disease management in hornet farming.},
}

@article {pmid41951111,
year = {2026},
author = {Fässler, D and Wittfeld, K and Frenzel, S and der Auwera, SV and Merhjerd, A and Gholizadeh, M and Simm, S and Kaderali, L and Franck, M and Rühlemann, M and Bang, C and Franke, A and Friedrich, N and Nauck, M and Lerch, MM and Weiss, FU and Völker, U and Bülow, R and Völzke, H and Peuker, K and Zeißig, S and Grabe, HJ and Frost, F and Hertel, J},
title = {Bilophila wadsworthia is linked to basal ganglia atrophy in the general population.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106587},
doi = {10.1016/j.bbi.2026.106587},
pmid = {41951111},
issn = {1090-2139},
abstract = {Bilophila wadsworthia, a sulfite-reducing bacterium stimulated by bile acids and enriched under high-fat diets, has been linked to several neurological disorders involving disturbances of motor function and basal ganglia circuitry. However, its potential association with alterations of brain structure remains unclear. Here, we investigated relationships between Bilophila (wadsworthia) abundance and basal ganglia volumes in two independent population-based cohorts combining gut microbiome profiling and brain MRI. Genus-level Bilophila abundance was assessed using 16S rRNA gene sequencing and complemented by species-level analyses of B. wadsworthia using whole-genome shotgun sequencing. Higher abundance of Bilophila (wadsworthia) was consistently associated with reduced volumes of basal ganglia regions, particularly the globus pallidus and nucleus accumbens. These associations were largely specific to basal ganglia regions when compared across a broad set of cortical thickness and other volumetric brain measures. Additionally, Bilophila (wadsworthia) was linked to elevated liver enzymes, elevated triglycerides, and pro-inflammatory states, confirming prior evidence from animal models while revealing novel associations in the general population. Constraint-based community modeling revealed that B. wadsworthia-enriched microbiomes exhibit increased functional redundancy for bile acid and sulfur metabolism and may modulate trimethylamine (TMA/TMAO) pathways. Together, these findings link variation in B. wadsworthia abundance to structural differences within basal ganglia regions and to unfavorable metabolic and inflammatory profiles in the general population, suggesting a potential role of this microbial species in gut-brain axis alterations relevant to neurodegenerative disease progression.},
}

@article {pmid41951277,
year = {2026},
author = {Bajer, L and Polakovicova, P and Heczkova, M and Holm, K and Hole, MJ and Hlavaty, M and Bohdanecka, A and Drastich, P and Tichanek, F and Meyer-Myklestad, MH and Medhus, AW and Reikvam, DH and Jørgensen, KK and Brezina, J and Macinga, P and Wohl, P and Fabian, O and Hov, JR and Cahova, M},
title = {Geography-independent mucosal microbiota alterations in primary sclerosing cholangitis persist after liver transplantation.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {4},
pages = {101716},
pmid = {41951277},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Primary sclerosing cholangitis (PSC)-associated alterations of fecal gut microbiota have already been described, but data on the mucosal microbiota are still limited. We aimed to further define disease-specific mucosal microbial patterns independent of geography and assess the relationship to liver transplantation (LTx), gut inflammation (inflammatory bowel disease), and PSC recurrence (rPSC).

METHODS: We performed 16S ribosomal RNA gene (V3-V4) sequencing of ileocolonic biopsies from 115 patients with PSC (pre-LTx), 159 liver-transplanted patients (post_LTx, recurrence occurred in 38), and 96 healthy controls (HC) from Norway and the Czech Republic.

RESULTS: Alpha diversity was lower in all PSC groups compared with HC. Elastic net models discriminated pre_LTx (AUC ileum 0.97; colon 0.93; p <0.001) and post_LTx PSC patients (AUC ileum 0.97; colon 0.97; p <0.001) from HC, and distinguished pre_LTx from post_LTx (AUC ileum 0.83; colon 0.83; p <0.001). The shared, cohort-independent PSC microbiota was dominated by Enterococcus, Pseudomonas, Veillonella, Klebsiella, and Streptococcus, while several common commensals were underrepresented. A microbial dysbiosis index calculated from PSC-associated genera correlated negatively with alpha diversity and serum albumin, while a positive correlation was observed with markers of cholestatic disease (ALP, GGT) and liver fibrosis (APRI). There were no associations with the presence of inflammatory bowel disease or fecal calprotectin. Differences between post-LTx patients with and without recurrence were limited, but several genera deregulated in pre-LTx PSC (Klebsiella, Bilophila, Coprococcus, Odoribacter) showed similar trends in rPSC.

CONCLUSIONS: Our findings in two European countries revealed a distinct mucosal microbiota composition associated with PSC that persists after LTx. These microbial patterns correlate with the severity of liver injury in PSC but not with markers of intestinal inflammation.

IMPACT AND IMPLICATIONS: This study provides an extensive evaluation of mucosa-associated microbiota in primary sclerosing cholangitis (PSC) before and after liver transplantation across two European cohorts. The persistence of PSC-related dysbiosis after transplantation highlights the importance of the gut-liver axis in PSC and supports further investigation into microbiota-driven mechanisms. Together with the strong association between microbiota composition and markers of cholestasis and fibrosis, this suggests potential clinical utility as an indicator of disease activity or even as a target for prevention or therapy.},
}

@article {pmid41951350,
year = {2026},
author = {Shokoohi, E and Masoko, P},
title = {Soil Biodiversity of Eucalyptus saligna: Insights Into Bacterial and Nematode Communities.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70341},
pmid = {41951350},
issn = {1758-2229},
support = {RNA-2022//University of Limpopo/ ; },
mesh = {*Eucalyptus/parasitology/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Animals ; *Nematoda/classification/genetics/isolation & purification ; Soil/chemistry/parasitology ; RNA, Ribosomal, 16S/genetics ; South Africa ; Phylogeny ; Rhizosphere ; },
abstract = {Soil microorganisms and nematodes are key regulators of soil function, yet their co-occurrence in Eucalyptus rhizospheres remains poorly understood. In this exploratory study, we characterised bacterial and nematode communities associated with Eucalyptus saligna soils in Limpopo, South Africa, using high-throughput 16S rRNA gene sequencing and nematode surveys. Bacterial assemblages were dominated by Proteobacteria (42%), Acidobacteria (28%), Actinobacteria (12%) and Planctomycetes (9%). Eleven bacterial genera occurred across all sites, with Rhizobiales (prominence value, PV = 315,350) and Xanthobacteraceae (PV = 292,930) emerging as the most prominent taxa. Nematode surveys identified 19 genera, including plant-parasitic such as Meloidogyne (PV = 5759.1) and abundant free-living such as Tylolaimorphus (PV = 4150.0) and Acrobeloides (PV = 2900.0). Principal component analysis showed that bacterial communities were associated with soil pH, salinity and nitrogen forms, whereas nematode assemblages were associated with phosphate and sand content, together explaining 83%-90% of total variance. Network analysis indicated that all sampling sites functioned as central hubs (degree = 19-23; eigenvector centrality = 0.90-1.0), integrating nematode-bacteria associations. Key connector taxa included Acrobeloides, Wilsonema and Aphelenchoides, as well as bacteria such as Rhizobiales and Acidothermus. These findings provide a baseline framework for understanding belowground biodiversity and co-occurrence patterns in Eucalyptus plantation soils.},
}

*Eucalyptus/parasitology/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Biodiversity
Animals
*Nematoda/classification/genetics/isolation & purification
Soil/chemistry/parasitology
RNA, Ribosomal, 16S/genetics
South Africa
Phylogeny
Rhizosphere

@article {pmid41951359,
year = {2026},
author = {Zhang, J and Hu, J and Tang, X and Ruan, Y and Hao, F and Zhang, W and Trakman, G and Hamilton, AL and Lin, W and Sun, Y and Ching, JYL and Teh, JJ and Kang, S and Wilson-O' Brien, A and Stanley, A and Zhang, L and Sung, JJY and Yu, J and Miao, Y and Chan, FKL and Morrison, M and Kamm, M and Ng, SC},
title = {Quantifying artificial sweeteners and emulsifiers in Crohn's disease and its relationship with disease activity: the ENIGMA study - a novel and targeted approach.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333999},
pmid = {41951359},
issn = {1468-3288},
abstract = {BACKGROUND: Food additives have been linked to increased Crohn's disease (CD) risk and activity, but their human quantification has not been explored.

OBJECTIVE: We aimed to measure artificial sweeteners and emulsifier polysorbate-80 (P-80) in patients with CD and assess their associations with disease activity.

DESIGN: 1461 biosamples from 487 subjects (245 CD and 242 controls) across Australia, Hong Kong and Chinese Mainland were analysed for aspartame, sucralose, saccharin and P-80 levels in stool, urine and serum. CD activity was assessed using Crohn's Disease Activity Index and faecal calprotectin. A generalised linear model (GLM) with P-80 and sweeteners distinguished active CD from inactive CD.

RESULTS: Patients with CD had higher sweetener levels compared with controls across cohorts (all p<0.0001). P-80 underwent predominantly hydrolytic and oxidoreductive degradation in CD and controls, respectively, while its native form was undetectable. CD-associated P-80 metabolites positively correlated with urinary sweeteners in patients with CD. In vitro, CD-associated P-80 metabolites increased gut permeability, enabling translocation of sweeteners across the epithelium. Sweeteners and specific CD-associated P-80 metabolites were higher in active CD. The GLM built using sweeteners and P-80 metabolites distinguished active CD from inactive CD, achieving an area under the curve (AUC) of 0.86 in the discovery cohort and average AUC of 0.94 in two independent validation cohorts from Australia and Chinese Mainland.

CONCLUSION: This is the first human study to demonstrate distinct P-80 metabolism in patients with CD compared with controls. Dietary sweeteners and P-80 metabolites showed significant correlations with disease activity, suggesting their potential utility as non-invasive biomarkers for CD activity assessment.},
}

@article {pmid41951494,
year = {2026},
author = {Li, C and Braaten, K and Moser, AB and Fallatah, W and Lorentson, M and Huguenin, S and Torrey, A and Terluk, MR and Durose, W and Nolan, E and Staley, C and Subramanian, S and Lund, TC and Kartha, RV},
title = {Nervonic acid supplementation mitigates disease severity biomarkers in adrenoleukodystrophy.},
journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics},
volume = {},
number = {},
pages = {e00890},
doi = {10.1016/j.neurot.2026.e00890},
pmid = {41951494},
issn = {1878-7479},
abstract = {X-linked adrenoleukodystrophy (ALD) is a severe neurometabolic disorder caused by mutations in the ABCD1 gene, leading to impaired peroxisomal β-oxidation of very long-chain fatty acids (VLCFAs). The accumulation of saturated VLCFAs, predominantly C26:0, in plasma and across all tissues, contributes to adrenal dysfunction and progressive neurodegeneration. No approved therapy addresses the diverse spectrum of ALD manifestations, underscoring the urgent need for safe, accessible, and preventive treatments. Nervonic acid (NA), a monounsaturated fatty acid, is potentially beneficial for ALD through its neuroprotective effects. Here, we report the safety and therapeutic efficacy of NA in a 4-week dietary intervention study using a mouse model of ALD. NA treatment significantly decreased plasma C26:0-lysophosphatidylcholine, a diagnostic and disease-severity biomarker of ALD, by about 60% as early as one week after intervention. After 4-week treatment, NA markedly reduced free C26:0 and total saturated VLCFA levels in plasma and tissues. Moreover, we observed approximately 56% reduction in brain C26:0-lysophosphatidylcholine levels in NA-fed mice, an effect not reported with other drug intervention. Through comparative microbiome analysis, we show for the first time distinct baseline differences between ALD and wild-type mice, with dietary fatty acid supplementation preventing further dysbiosis. No adverse effects on body weight or food intake were observed throughout the study. Overall, this is the first report demonstrating that an oral dietary fatty acid can ameliorate the hallmark biochemical abnormalities of ALD in plasma and brain, highlighting its potential as a safe and effective therapy, particularly for presymptomatic individuals carrying this genetic defect.},
}

@article {pmid41951635,
year = {2026},
author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S},
title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07154-x},
pmid = {41951635},
issn = {2052-4463},
abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.},
}

@article {pmid41951653,
year = {2026},
author = {He, L and Yuan, D and Li, Q and Zhang, X and Niu, K and Li, X and Ou, Y and Du, H and Yuan, J and Duan, Y and Niu, H},
title = {Fecal virome transplantation attenuates arthritis in mice by remodeling gut ecology, systemic tryptophan metabolism, and innate immune responses.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00980-2},
pmid = {41951653},
issn = {2055-5008},
support = {2024VPPC-S02//the Open Project of the Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education/ ; 2025A1515012786//the Natural Science Foundation of Guangdong Province/ ; 2022YFF0710702 and 2022YFF0710701//the National Key &D Programs of China/ ; 202201020381//the Guangzhou Joint Fund for Key Laboratory/ ; YXJC2022004//the Medical Joint Fund of Jinan University/ ; },
abstract = {Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic joint inflammation and systemic immune dysregulation. Emerging evidence suggests that the gut microbiome plays an important role in immune modulation in RA, yet the role of the gut virome remains poorly understood. Here, using the K/BxN serum-transfer arthritis model, we systematically evaluated the potential role of fecal virome transplantation (FVT) in modulating gut ecology and innate inflammatory responses. Arthritic mice exhibited marked alterations in gut virome composition compared with healthy controls. Administration of purified virus-like particles (VLPs) from healthy donors correlated with reductions in paw swelling, histopathological inflammation, bone erosion, circulating proinflammatory cytokines, and myeloid cell infiltration in inflamed tissues. In parallel, 16S rRNA sequencing showed that FVT remodeled the gut bacterial community toward a composition more similar to that of healthy controls. Targeted serum metabolomics revealed increased levels of microbiota-derived tryptophan metabolites, including indole-3-lactic acid and related indole derivatives, suggesting a link between gut microbial remodeling and systemic immunometabolic regulation. Collectively, these findings indicate that FVT may attenuate inflammatory arthritis by remodeling gut microbial ecology, potentially involving virome-bacteriome interactions and immunometabolic pathways.},
}

@article {pmid41951862,
year = {2026},
author = {Ocejo, A and Kotecha, RR and Voss, MH},
title = {From diversity to function: microbiome precision in RCC.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
pmid = {41951862},
issn = {1759-4820},
}

@article {pmid41952069,
year = {2026},
author = {Klimesova, B and Ruane, NM and Domingo-Bretón, R and Moroni, F and Naya-Català, F and Pérez-Sánchez, J and O'Dwyer, K and Lyashevska, O and Rodger, H and Talbot, A},
title = {Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70182},
doi = {10.1111/jfd.70182},
pmid = {41952069},
issn = {1365-2761},
support = {CS/21/005//Marine Institute, Marine Reseach Programme Irish Government/ ; 871108//European Union's Horizon 2020 Research and Innovation Programme/ ; CIAPOS/2024/092//Generalitat Valenciana/ ; FSE+//European Union, Eyropean Social Fun Plus/ ; MMT24-IATS-01-01//NextGeneration EU MOMENTUM-CSIC Postdoctoral Research Contract/ ; },
abstract = {Ectoparasites that penetrate host skin can act as biological or mechanical vectors for pathogens and, in some cases, serve as reservoirs. Crustacean ectoparasites of fish are potential vectors of pathogens, which is especially relevant for obligate pathogens (e.g., Aeromonas salmonicida) with limited seawater survival. Sea lice (Lepeophtheirus salmonis), affecting Atlantic salmon, cause dermal damage and can facilitate secondary infections, resulting in economic losses. While the physical impact of sea lice is well known, their role in pathogen transmission is less clear. The gut bacterial microbiome of lice collected over four months from a salmon farm in Ireland was analysed using Illumina MiSeq and Oxford Nanopore Technologies (ONT) PromethION sequencing for comparison. Illumina and Nanopore sequencing identified 15 and 24 genera of known fish pathogens, respectively. Moreover, Nanopore data revealed up to 15 putative pathogenic species, including Tenacibaculum maritimum, T. dicentrarchi and Vibrio anguillarum, causative agents of tenacibaculosis and vibriosis. The results of this study provide a gut bacterial microbiome characterisation of L. salmonis in a commercial aquaculture setting and demonstrate the potential of sea lice to act as pathogen vectors or reservoirs. These findings have important implications for pathogen surveillance, management, and prevention strategies in salmon aquaculture.},
}

@article {pmid41952172,
year = {2026},
author = {Zhang, J and Jiang, C and Zhou, X and Gao, P and Wong, S and Snyder, M and Shen, X},
title = {Cross-body site microbial interactions influence the human plasma metabolome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02405-w},
pmid = {41952172},
issn = {2049-2618},
support = {#025402-00001//Ministry of Education - Singapore/ ; },
abstract = {BACKGROUND: The human microbiome profoundly influences the host plasma metabolome and health, but most studies have focused on the gut microbiome in isolation. A comprehensive assessment of how microbiomes from multiple body sites jointly shape host metabolism has been lacking.

RESULTS: Using data from three independent human cohorts (n = 435), we systematically analyzed the selective and joint influences of microbiomes from multiple body sites on the human plasma metabolome (814 annotated metabolites). Microbiomes from all body sites contributed to plasma metabolome variation, collectively explaining 30.13% of the inter-individual variation. The gut microbiome showed the largest contribution (18.44%), followed by oral (14.70%), skin (11.5%), and nasal (5.88%) microbiomes. Microbial composition did not necessarily predict metabolic function for example, despite distinct compositions, oral and gut microbiomes exhibited similar associations with circulating metabolites. Machine learning and mediation analyses revealed widespread cooperative and synergistic microbial interactions across body sites, particularly along the oral-gut axis. Over half of the metabolites were jointly influenced by multiple body-site microbiomes. This axis showed cross-site microbial crosstalk and sequential metabolic processing, regulating metabolites such as indole derivatives and carboxylic acids. The oral-gut microbiome-metabolome axis was further amplified in insulin resistance (IR), linking enhanced microbial cooperation to metabolic dysregulation.

CONCLUSION: Our findings reveal the systemic and interactive nature of microbiome-metabolome relationships and highlight the need to integrate spatially distributed microbial ecosystems to fully understand host metabolic regulation and disease mechanisms. Video Abstract.},
}

@article {pmid41952630,
year = {2026},
author = {Wim, T and Mehraveh, S and Katalina, L and Cheah, CW and Pisha, P and Ana, C and Andy, T and Naiera, Z and Wannes, VH},
title = {Not a miracle, not a myth: The role of probiotics in periodontal health.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70039},
pmid = {41952630},
issn = {1600-0757},
support = {C3/24/081//KU Leuven/ ; },
abstract = {BACKGROUND: As the understanding of periodontal disease has evolved, therapeutic strategies have increasingly shifted from pathogen eradication toward ecological modulation of the oral microbiome. Within this paradigm, probiotics have emerged as potential adjuncts for maintaining periodontal health by promoting microbial balance and modulating host responses.

OBJECTIVE: To summarize the historical development, definitions, and mechanisms of probiotics and to critically evaluate the current clinical evidence supporting their use in periodontal therapy.

METHODS: This narrative review examines the conceptual framework of probiotics in oral health, distinguishing them from related approaches including prebiotics, postbiotics, and synbiotics. Literature from randomized controlled trials and meta-analyses was reviewed to assess the clinical effectiveness of probiotic interventions in periodontal therapy and to explore their proposed mechanisms of action.

RESULTS: Probiotic effects are highly strain-specific and involve multiple mechanisms, including production of antimicrobial compounds, competition for ecological niches, inhibition of biofilm formation and quorum sensing, strengthening of epithelial barrier integrity, and modulation of host immune and inflammatory responses. Evidence from randomized controlled trials and meta-analyses, particularly those evaluating Limosilactobacillus reuteri strains, suggests that probiotics used as adjuncts to nonsurgical periodontal therapy can significantly improve clinical parameters such as probing pocket depth, clinical attachment level, and bleeding on probing. However, substantial heterogeneity in study design, probiotic strains, delivery systems, and follow-up periods limits the comparability and generalizability of findings.

CONCLUSIONS: Probiotics represent a biologically plausible and ecologically oriented adjunct in periodontal therapy. While current evidence indicates beneficial clinical effects, further standardized and long-term clinical trials incorporating advanced microbiome analyses (e.g., next-generation sequencing) are needed to clarify mechanisms, optimize formulations, and support personalized probiotic strategies in periodontal care.},
}

@article {pmid41952964,
year = {2026},
author = {Peñalba, F and Guisande, A and Lamberti, L and Rusiñol, C and Irastorza, M and Konik, F and Iglesias, C and Mendive, P and Garrido, G and Parada, A and Riera, N},
title = {Gut microbiota and its association with gastrointestinal symptoms and pharmacological treatments in a sibling-matched cohort with autism spectrum disorder.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1777385},
pmid = {41952964},
issn = {2813-4338},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder marked by difficulties in communication, social interaction, and restricted, repetitive behaviors. The gut microbiota has emerged as a key factor in the gut-brain axis relevant to ASD. We conducted a cross-sectional study comparing the gut bacterial composition of children with ASD (n=29) and their neurotypical siblings (NT, n=29). To minimize environmental and lifestyle confounders, all pairs were 4 to 10 years old and cohabiting in the same household in Uruguay. We used full-length 16S rRNA gene (V1-V9) sequencing with the latest R10.4.1 Oxford Nanopore Technologies chemistry, enabling high-resolution microbial characterization. While overall β-diversity did not differ significantly between the ASD and NT groups, we identified specific taxonomic shifts. The ASD group was enriched in taxa like Sellimonas, while the NT group showed enrichment of genera like Faecalibacterium and Coprococcus. Furthermore, we found GI symptoms to be significantly more prevalent in the ASD group and some bacterial genera associated with GI symptomatology. In addition, we explored the association of pharmacological treatments. Antipsychotic use was associated with reduced Akkermansia abundance, whereas melatonin and methylphenidate use were associated with the enrichment of Negativibacillus. This study provides novel insights into the gut microbiome of Uruguayan children with ASD, delineating the influence of GI symptoms and pharmacological load on microbial diversity and composition.},
}

@article {pmid41953022,
year = {2026},
author = {Han, W and Li, Q and Yuan, G},
title = {The gut microbiome as an actionable drug-sensitivity modulator for immune checkpoint blockade: clinical evidence for FMT, live biotherapeutics, and defined consortia.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1802676},
pmid = {41953022},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Fecal Microbiota Transplantation/methods ; Animals ; },
abstract = {Immune checkpoint inhibitors (ICIs) deliver durable benefit to only a subset of patients and can be limited by immune-related adverse events (irAEs). The gut microbiome has emerged as an actionable, host-level modulator of ICI drug sensitivity and toxicity. This mini-review links microbial ecology to antigen presentation, T-cell priming and fitness, metabolite signaling, and barrier inflammation, and summarizes interventional evidence across three modalities. Responder-derived fecal microbiota transplantation (FMT) provides the strongest proof-of-concept for re-sensitization in anti-PD-1-refractory melanoma. Microbiome repair can also improve refractory ICI-associated colitis. Early trials of live biotherapeutics and defined consortia support scalability but highlight context dependence and design pitfalls, including antibiotic preconditioning. We discuss practical determinants of reproducibility, including co-medications, diet, engraftment and functional readouts, and conclude with safety, regulatory, and reporting priorities for clinically deployable microbiome engineering.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Fecal Microbiota Transplantation/methods
Animals

@article {pmid41953110,
year = {2026},
author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J},
title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101380},
pmid = {41953110},
issn = {2352-7714},
abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.},
}

@article {pmid41953220,
year = {2025},
author = {El-Saadony, MT and Saad, AM and Sitohy, M and Alkafaas, SS and Dladla, M and Ghosh, S and Mohammed, DM and Ibrahim, EH and Fahmy, MA and Elkelish, A and AbuQamar, SF and El-Tarabily, KA},
title = {Probiotics and human health: biological activities, nutritional aspects, immunomodulatory properties, applications, and future perspectives - a comprehensive review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1713426},
pmid = {41953220},
issn = {1664-3224},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; },
abstract = {Probiotics, defined as living microorganisms, are widely recognized for their ability to positively influence the gut microbiota, an effect increasingly linked to a wide array of health benefits. They are claimed to treat or prevent conditions ranging from infant colic to cardiovascular disease, respiratory infections, and certain cancers. Since the beginning of the 21st century, consumer demand for probiotic-enriched foods has risen significantly, propelled by these health assertions. The consumption of such products has been associated with the alleviation of disorders, including irritable bowel syndrome, lactose intolerance, gastroenteritis, obesity, chronic diarrhea, allergies, atopic dermatitis, and infectious diseases. Recent advancements in microbiome and microbiota research are fundamentally transforming probiotic science. Cutting-edge studies on novel strains, their mechanisms, and potential applications are expected to revolutionize our understanding of their roles in human nutrition and medicine. Nevertheless, despite extensive research efforts, critical gaps remain regarding strain-specific mechanisms, optimal dosages, long-term safety, and interactions among probiotics, host genetics, and dietary factors. Addressing these gaps necessitates a comprehensive synthesis of current knowledge and emerging trends. This review aims to critically integrate historical foundations, dosage strategies, mechanisms of action, therapeutic applications, and potential risks associated with probiotics. Unlike previous reviews, this review emphasizes next-generation probiotics, live biotherapeutics, and genetically engineered microbes, and their synergistic interactions with dietary bioactives such as polyphenols and fibers. By providing a forward-looking perspective, this work contributes to the rational design of functional foods, targeted therapies, and microbiome-based interventions, thereby informing future advancements in human nutrition and medicine. It critically examines current and emerging trends in probiotic research, while acknowledging potential adverse effects and risks.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Gastrointestinal Microbiome/immunology
Animals
Immunomodulation

@article {pmid41953221,
year = {2025},
author = {Zhao, Z and Wang, X and Bao, Y and Meng, J and Gong, J and Zhang, L and Li, Z and Yao, W and Chuo, Y and Shi, W and Li, J},
title = {Dietary Bazhen San solid-state fermentation product improves laying performance, immunity and intestinal health in laying hens during the late laying period.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1673604},
pmid = {41953221},
issn = {1664-3224},
mesh = {Animals ; *Chickens/immunology ; Female ; *Animal Feed/analysis ; Fermentation ; *Intestines/immunology/microbiology ; Diet ; Dietary Supplements ; Gastrointestinal Microbiome ; *Oviposition ; Eggs ; Cytokines ; Immunoglobulin A/blood ; },
abstract = {The aim of this study was to investigate the effects of solid-state fermentation products of Bazhen San (FB) on the production performance, immunity, and intestinal health of laying hens during the late laying stage. A total of 150 70-week-old laying hens were randomly assigned to five treatment groups, with five replicates per group and six hens per replicate. The control group (CON) was fed a corn-soybean meal-based diet, whereas the other four treatment groups were supplemented with 0.3% FB (LFB), 0.6% FB (MFB), 0.9% FB (HFB), and 0.6% unfermented Bazhen San (BZ), respectively. The results showed that, compared with the CON group, all treatments significantly increased the egg production rate and reduced the feed-to-egg ratio (P < 0.05). Moreover, the effect in the MFB group was significantly greater than that in the BZ group (P < 0.05). In terms of egg quality, the MFB and HFB groups significantly improved yolk color and Haugh units (P < 0.05). Regarding immune function, serum immunoglobulin A (IgA) levels were significantly increased in all treatment groups (P < 0.05), whereas interleukin-1β (IL-1β) and interleukin-6 (IL-6) concentrations were significantly decreased (P < 0.05). The MFB and HFB groups also significantly increased serum immunoglobulin G (IgG) levels (P < 0.05), as well as jejunal and ileal secretory immunoglobulin A (sIgA) levels (P < 0.05). In addition, serum IgG levels in the MFB group were significantly higher than those in the BZ group (P < 0.05). In terms of intestinal health, FB treatment significantly enhanced antioxidant enzyme activity in the jejunum and ileum, reduced malondialdehyde (MDA) content, improved intestinal morphology. The microbiome analysis of the cecum showed that FB improved the abundance of beneficial bacteria in the intestine. Spearman correlation analysis revealed that the relative abundance of Odoribacter and Enterococcus was positively correlated with serum IgA levels and negatively correlated with IL-6 concentration. Therefore, dietary supplementation with FB can improve intestinal health, and systematically improve the immune status of the body, thereby promoting the health of laying hens during the late laying stage and improving production performance, dietary 0.6% to 0.9% FB inclusion is suggested.},
}

Animals
*Chickens/immunology
Female
*Animal Feed/analysis
Fermentation
*Intestines/immunology/microbiology
Diet
Dietary Supplements
Gastrointestinal Microbiome
*Oviposition
Eggs
Cytokines
Immunoglobulin A/blood

@article {pmid41953438,
year = {2026},
author = {Li, H and Yu, Z and Wu, Z and Lin, Y and Liu, T and Liu, Y and Li, Z and Zhang, S and Su, Z and Wang, H},
title = {Quantifying human-environment interactions through Bayesian modeling of species-resolved microbial transfer signatures: an exploratory proof-of-concept study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781392},
pmid = {41953438},
issn = {1664-302X},
abstract = {BACKGROUND: Microbial trace evidence offers potential for forensic reconstruction of human-environment interactions, but current methods lack standardized quantitative frameworks. While 2bRAD-M (type IIB restriction site-associated DNA markers for microbiomes) sequencing provides species-level resolution from low-biomass samples, its integration with robust statistical models for forensic applications remains unexplored.

METHODS: We developed an integrated framework combining 2bRAD-M sequencing with a Bayesian hierarchical model to quantify microbial transfer patterns. The model incorporates geospatial parameters, substrate-specific persistence kinetics, and temporal decay functions. We generated 2bRAD-M data from host-associated (skin, saliva; n = 12) and environmental samples (personal devices, high-touch surfaces; n = 14), integrated with public 16S rRNA data (Qiita studies; n = 2,263 samples) for model training.

KEY FINDINGS: The Bayesian model demonstrated preliminary accuracy in attributing microbial traces to their likely source environment categories (within ~100 meters in preliminary tests) and provided initial estimates for deposition time. Personal devices were found to retain taxa associated with host such as Staphylococcus hominis for extended periods (exceeding 72 h in our observations), suggesting persistent microbial transfer.

CONCLUSION: This proof-of-concept study suggests that integrating 2bRAD-M sequencing with Bayesian modeling could provide a framework for quantitative reconstruction of microbial transfer histories. The approach indicates potential for forensic applications but is not yet validated for casework. Extensive validation with larger, independent datasets is imperative to assess its reliability and admissibility standards.},
}

@article {pmid41953447,
year = {2026},
author = {Wang, X and Hu, W and Li, R and Sun, R and Liong, MT and Yu, Q and Chen, D},
title = {Gi-MAPS: a quantitative engineering framework for AI-guided pediatric gut microbiome ecological interpretation and digital-twin simulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1739103},
pmid = {41953447},
issn = {1664-302X},
abstract = {BACKGROUND: Quantitative and reproducible microbiome analysis is limited by fragmented workflows lacking standardized anaerobic sampling, absolute quantification methods, and transparent AI inference. Patent-documented engineering integration is required for reliable microbiome analytics at population scale.

METHODS: Gi-MAPS was designed as an end-to-end analytical system integrating several core patented innovations, including (i) a press-activated anaerobic sample-preservation device that maintains ultra-low residual oxygen to protect obligate anaerobes during transport, (ii) a multiplex qPCR assay enabling simultaneous absolute quantification of key HMO-utilizing Bifidobacterium species in a single reaction, and (iii) a CIT-Net-based digital-twin engine that supports forward simulation of gut microbiota ecological trajectories. These modules are coupled with explainable ensemble artificial intelligence models to form a fully quantitative and simulation-enabled microbiome analysis framework. Each subsystem was validated under granted patents to define engineering performance boundaries and reproducibility specifications.

RESULTS: System validation demonstrated <0.1% residual oxygen stability for anaerobic preservation, detection sensitivity down to five genomic copies per microliter, AUC > 0.97 for ecological maturity estimation, 89% accuracy for disease-risk classification, and 95% concordance for digital-twin forecasting. Execution-layer software copyright modules and filed patents extend automation, visualization, and future application domains.

CONCLUSION: Gi-MAPS provides a patent-anchored, standardized engineering framework whose key novelties lie in oxygen-controlled anaerobic sampling, absolute microbial quantification via multiplex qPCR, and digital-twin ecological simulation, enabling quantitative, function-aware, and prospective microbiome analysis. It establishes a reproducible foundation enabling large-scale cohort deployment, longitudinal ecological monitoring, digital-twin simulation, and future multi-omics integration.},
}

@article {pmid41953448,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {Biohacking the human gut microbiome for precision health and therapeutic innovation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1776983},
pmid = {41953448},
issn = {1664-302X},
abstract = {Biohacking, the self-directed application of biotechnology, digital tools, and lifestyle interventions, has rapidly converged with gut microbiome science to create adaptive, individualized, and minimally invasive precision-health paradigms. This narrative review integrates current evidence on diet-based modulation, microbial therapeutics (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation), and synthetic-biology approaches (engineered strains and phage or synthetic consortia) within a multi-omics and continuous-phenotyping framework. Mechanistically, short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan catabolites operate as endocrine-like mediators linking gut microbial ecology with host immunity, metabolism, and neuroendocrine signaling. Pathways mediated by microbial metabolites underpin translational applications that span metabolic optimization, through improved insulin sensitivity, reduced adiposity, and attenuation of inflammation, and neurocognitive enhancement via the microbiome-gut-brain axis. Evidence from oncology further indicates that microbial metabolites and engineered taxa remodel stromal and immune niches, shaping therapeutic response and disease progression. Concurrently, emerging digital infrastructures, wearables, biosensors, metabolic avatars, and AI-driven "health twins," enable real-time, closed-loop modulation of host-microbe dynamics. Persistent challenges include methodological heterogeneity, safety concerns regarding live biotherapeutics and unsupervised fecal microbiota transplantation (FMT), fragmented regulation, and vulnerabilities in cyberbiosecurity and data equity. We propose a translational roadmap emphasizing standardized metadata (STORMS), validated reference frameworks, longitudinal multi-omics for causal inference, strain-level safety genomics, and governance integrating ethical and cybersecurity oversight. Under these conditions, microbiome-focused biohacking may evolve from anecdotal experimentation into a more reproducible and scientifically grounded component of preventive and personalized medicine. This manuscript is presented as a narrative and conceptual review, integrating validated microbiome research with emerging biohacking frameworks while explicitly distinguishing evidence-based findings from exploratory or speculative concepts.},
}

@article {pmid41953516,
year = {2026},
author = {Qu, HQ and Kao, C and Hakonarson, H},
title = {Redefining the role of the thiol-based agent N-acetylcysteine in human health and disease and elucidating potential advantages of its amide derivative.},
journal = {RSC medicinal chemistry},
volume = {},
number = {},
pages = {},
pmid = {41953516},
issn = {2632-8682},
abstract = {N-Acetylcysteine (NAC) is the established antidote for acetaminophen toxicity and an approved mucolytic agent. Beyond these traditional uses, increasing evidence highlights its broader role as a modulator of thiol-redox biology. Rather than functioning as a nonspecific antioxidant, NAC modulates glutathione metabolism, redox-sensitive signaling, immune checkpoints, thiol-based post-translational modifications, ferroptosis susceptibility, and glutamatergic neurotransmission. This review synthesizes mechanistic, preclinical, and clinical evidence across pulmonary, hepatic, neuropsychiatric, metabolic, cardiovascular, and oncologic disorders, emphasizing how variability in baseline redox state, pharmacogenetics, and delivery contributes to heterogeneous outcomes. Strategies to improve pharmacokinetics and tissue targeting include structural derivatives such as N-acetylcysteine amide (NACA), and combination regimens such as NAC with probenecid or GlyNAC. Emerging applications span long COVID, neurodegeneration, psychiatric disorders, microbiome-redox interactions, environmental toxicology, and cancer immunotherapy. NAC and NACA exemplify the evolution of redox-targeted therapeutics. NAC is well established for safety and clinical utility, but its pharmacokinetic and tissue distribution properties constrain broader efficacy. NACA, a lipophilic amide derivative, enhances membrane permeability and cellular uptake, suggesting it may achieve higher tissue exposure at lower doses. Future progress will rely on biomarker-guided, precision approaches that optimize dosing, formulation, and delivery while exploring rational combinations across disease contexts defined by redox biology.},
}

@article {pmid41953552,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Herbal and Natural Product Interventions in Animal Models of Antibiotic-Associated Diarrhea and Their Effects on Gut Microbiota: a protocol for systematic review.},
journal = {Journal of pharmacopuncture},
volume = {29},
number = {1},
pages = {42-47},
pmid = {41953552},
issn = {2093-6966},
abstract = {OBJECTIVES: Antibiotic-associated diarrhea (AAD) is a frequent complication of antibiotic use and is commonly used to investigate gut microbiota dysbiosis and potential therapeutic interventions in animals. Herbal medicines and natural product-derived compounds have shown promising effects in restoring microbial balance; however, no systematic review has yet synthesized the preclinical evidence. Therefore, this review aimed to systematically identify, evaluate, and synthesize animal studies examining herbal and natural product interventions for AAD, with a particular focus on gut microbiota restoration and related functional outcomes.

METHODS: This protocol has been registered in PROSPERO (CRD420251136553). A systematic search was performed in PubMed, Embase, Web of Science, Scopus, CNKI, and other major Korean medical databases from inception to the search date. Controlled preclinical studies that evaluated herbal or natural product interventions for AAD in animal models and reported gut microbiota outcomes were also included. Two reviewers independently screened the studies, extracted the data, and assessed the risk of bias.

RESULTS: This systematic review was conducted in accordance with the PRISMA guidelines. The findings were synthesized narratively and, where appropriate, organized by intervention type, animal model, and microbiome analytic method.

CONCLUSION: This review systematically evaluates the effects of herbal and natural products on the gut microbiota in animal models of antibiotic-associated diarrhea. These findings provide foundational preclinical evidence to support microbiome-directed development of herbal, polysaccharide-based, and synbiotic interventions for antibiotic-associated dysbiosis.},
}

@article {pmid41953674,
year = {2026},
author = {Zhou, H and Saha, S and Morrill, S and Kelly, T and Lewis, WG and Lewis, AL},
title = {Gardnerella biofilm formation in vitro is facilitated by braided sutures: implications for cervical cerclage.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1763531},
pmid = {41953674},
issn = {2235-2988},
mesh = {*Biofilms/growth & development ; *Sutures/microbiology/adverse effects ; Female ; Humans ; *Cerclage, Cervical/adverse effects ; Pregnancy ; *Gardnerella/physiology/growth & development ; *Gardnerella vaginalis/physiology/growth & development ; },
abstract = {INTRODUCTION: In pregnant individuals with certain indications, sutures may be placed circumferentially around the uterine cervix to prevent dilation. Compared to monofilament sutures, the use of braided suture materials has been linked with the development of a dysbiotic vaginal microbiome, as well as higher rates of infection-associated pregnancy outcomes such as chorioamnionitis and preterm birth. In bacterial vaginosis (BV) anaerobic bacteria, including pathogens, overgrow, forming biofilms in direct proximity to the host epithelium. Gardnerella is highly represented among bacterial vaginosis-like microbiotas.

METHODS: To test our working hypothesis that braided sutures may better support the establishment of high biomass bacterial biofilms compared to monofilament sutures, we measured the extent of Gardnerella bacteria biofilm formation on braided and monofilament sutures in the laboratory. Multiple Gardnerella strains were grown in the presence of braided or monofilament suture materials (polyester or polybutylate-coated polyester versus polypropylene or nylon), and the (biofilm) biomass was measured using crystal violet staining.

RESULTS: Sutures incubated without Gardnerella were included as controls. To compare staining of biofilm biomass between groups, one-way ANOVA was performed and Šidák was used for pairwise comparisons to control for multiple comparisons between groups. Gardnerella formed significantly more biofilm biomass (>10-fold) on braided polyethylene terephthalate (polyester) sutures compared to monofilament (polypropylene or nylon) sutures (p < 0.0001). This feature was applicable to multiple strains across different taxonomic subsets of Gardnerella.

DISCUSSION: Together with existing literature, these findings suggest that braided sutures might promote the development of dysbiotic BV-like microbiomes after cerclage placement by facilitating Gardnerella biofilm formation.},
}

*Biofilms/growth & development
*Sutures/microbiology/adverse effects
Female
Humans
*Cerclage, Cervical/adverse effects
Pregnancy
*Gardnerella/physiology/growth & development
*Gardnerella vaginalis/physiology/growth & development

@article {pmid41953764,
year = {2026},
author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF},
title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41953764},
issn = {2312-0541},
abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.

METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.

RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in α- and β-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.

CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.},
}

@article {pmid41953919,
year = {2026},
author = {Murmu, M and Singh, R and Barage, S and Kumar, AWS},
title = {Exploratory Study of Virulence Factors and Protein-Protein Interaction Networks in Major Oral Pathogens.},
journal = {Contemporary clinical dentistry},
volume = {17},
number = {1},
pages = {16-30},
pmid = {41953919},
issn = {0976-237X},
abstract = {INTRODUCTION: Periodontitis is a prevalent inflammatory disease driven by dysbiotic microbial consortia. Red-complex pathogens (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and emerging taxa (Filifactor alocis and Aggregatibacter actinomycetemcomitans) are central contributors, yet their virulence mechanisms remain incompletely defined.

OBJECTIVE: To construct protein-protein interaction (PPI) networks of key periodontopathogens and identify conserved as well as pathogen-specific virulence hubs.

METHODOLOGY: High-confidence PPI networks were generated for 1136 proteins across the five pathogens. Network topology was analyzed to identify hubs, and enrichment analyses were performed to map functional clusters.

RESULTS: Hub proteins such as guaA, metG, pheT, lysS, thrA, rplA, purD, and rpsH demonstrated significant interactions with accessory proteins. Conserved hubs, including guaA and ileS, were shared across pathogens and were essential in purine biosynthesis and aminoacyl-tRNA ligation. Pathogen-specific hubs comprised gingipains (P. gingivalis), leukotoxin (A. actinomycetemcomitans), and dentilisin (T. denticola). Functional clustering revealed adhesion, peptidoglycan biosynthesis, and immune modulation pathways.

CONCLUSION: PPI networks provide system-level mechanistic insights into pathogen virulence, revealing conserved vulnerabilities and species-specific mechanisms.},
}

@article {pmid41954023,
year = {2026},
author = {Anagnostopoulou, L and Ktenopoulos, N and Apostolos, A and Fragoulis, C and Vlachakis, P and Karakasis, P and Sagris, M and Milaras, N and Drakopoulou, M and Synetos, A and Kyriazis, I and Ioannidis, I and Tsioufis, C and Toutouzas, K},
title = {Intersecting Molecular Pathways in Cardiovascular Disease and Diabetes Mellitus: Emerging Roles of Inflammation and Therapeutics.},
journal = {Diabetes/metabolism research and reviews},
volume = {42},
number = {4},
pages = {e70167},
pmid = {41954023},
issn = {1520-7560},
mesh = {Humans ; *Cardiovascular Diseases/metabolism/pathology/etiology ; *Inflammation/metabolism/pathology ; *Hypoglycemic Agents/therapeutic use ; Gastrointestinal Microbiome ; Animals ; *Diabetes Mellitus/metabolism/drug therapy ; },
abstract = {Diabetes mellitus (DM) and cardiovascular diseases (CVD) remain leading contributors to global morbidity and mortality, imposing a substantial burden on healthcare systems worldwide. The pathophysiological mechanisms underlying these conditions are complex and closely interconnected, with chronic low-grade inflammation, oxidative stress, endothelial dysfunction, insulin resistance and dysregulated lipid metabolism serving as pivotal shared pathways. Persistent hyperglycaemia and metabolic imbalance in DM accelerate vascular injury and atherosclerotic progression, thereby significantly increasing cardiovascular risk. Consequently, therapeutic strategies that concurrently target both metabolic and cardiovascular dysfunction may offer meaningful clinical advantages and improved long-term outcomes. In recent years, novel antidiabetic agents such as sodium-glucose co-transporter 2 (SGLT-2) inhibitors and glucagon-like peptide-1 (GLP-1) receptor agonists have demonstrated not only glycaemic control but also substantial cardiovascular protection, including reductions in major adverse cardiovascular events, heart failure hospitalisations and renal disease progression. These pleiotropic effects extend beyond glucose lowering and involve modulation of inflammatory pathways, improvement of endothelial function, attenuation of oxidative stress and favourable haemodynamic changes. Additionally, emerging evidence highlights the role of the gut microbiota as a critical mediator in the bidirectional relationship between DM and CVD. Alterations in microbial composition and diversity, collectively termed dysbiosis, have been associated with systemic inflammation, impaired metabolic homoeostasis, increased intestinal permeability and the production of pro-atherogenic metabolites such as trimethylamine N-oxide. Understanding these microbiome-related mechanisms may open new avenues for preventive and therapeutic interventions targeting the gut-metabolic-cardiovascular axis. This narrative review provides an updated and comprehensive overview of the molecular and cellular mechanisms linking DM and CVD, with particular emphasis on inflammatory signalling, metabolic dysregulation and the emerging influence of the gut microbiome in their shared pathogenesis and therapeutic modulation.},
}

Humans
*Cardiovascular Diseases/metabolism/pathology/etiology
*Inflammation/metabolism/pathology
*Hypoglycemic Agents/therapeutic use
Gastrointestinal Microbiome
Animals
*Diabetes Mellitus/metabolism/drug therapy

@article {pmid41954158,
year = {2026},
author = {Glass, BH and Aichelman, HE and Grupstra, CGB and Valadez-Ingersoll, M and Swank, A and Guerra, V and Gondola, P and Nagree, A and Schipfer, J and Gilmore, TD and Davies, SW},
title = {Legacy Effects of an Extreme Marine Heatwave on a Stress-Tolerant Coral.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70853},
doi = {10.1111/gcb.70853},
pmid = {41954158},
issn = {1365-2486},
support = {//Boston University/ ; 1937650//National Science Foundation/ ; 2506815//National Science Foundation/ ; },
mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; Panama ; *Extreme Heat/adverse effects ; *Coral Bleaching ; Symbiosis ; *Hot Temperature ; Stress, Physiological ; },
abstract = {During the 4th Global Coral Bleaching Event (GCBE4; January 2023-September 2025), an extreme marine heatwave occurred on the Bocas del Toro Reef Complex (BTRC) in Panama. We characterized how this heatwave impacted the health and holobiont communities of the stress-tolerant coral Siderastrea siderea at four sites across the BTRC. Tagged colonies at each site (N = 30-53 colonies per site) were visited before, during, and after the heatwave (early May 2022, mid-August 2023, and late April 2024, respectively), and images and DNA samples were collected at each time point. In situ temperature logger data showed that sites reached maxima of 32.1°C-33.9°C in October 2023, resulting in the accumulation of ~12-20 maximum degree-heating weeks (DHWs). Consequently, S. siderea colonies displayed widespread bleaching (i.e., the loss of algal endosymbionts), with an increase from 8.6% to 33% of colonies bleached per site in May 2022 to 33%-70% in August 2023, followed by a decline to 15%-63% by April 2024. Colony-level partial mortality increased significantly between 2022 and 2024 at three of the four sites, and was observed even in colonies that were not bleached in August 2023. Further, many corals hosting Cladocopium spp. algal symbionts in 2022 shifted towards less diverse communities dominated by heat-tolerant Breviolum and Durusdinium spp., and most of these corals continued to host modified symbiont communities for months. The heatwave also reshaped corals' bacterial microbiomes, including increases in α-diversity and abundances of potentially pathogenic taxa (e.g., Vibrionaceae), and these shifts were persistent following the heatwave. Together, these findings demonstrate that GCBE4 had lasting impacts on S. siderea holobiont health across the BTRC, underscoring that extreme heat events can compromise even stress-tolerant coral species and induce legacy effects that will likely affect their future resilience. Rapid action to minimize further ocean warming is thus necessary to safeguard reef ecosystems.},
}

Animals
*Anthozoa/physiology/microbiology
Coral Reefs
Panama
*Extreme Heat/adverse effects
*Coral Bleaching
Symbiosis
*Hot Temperature
Stress, Physiological

@article {pmid41954174,
year = {2026},
author = {Torregrosa-Chinillach, A and Tsiara, I and Haberek, W and Lin, W and Globisch, D},
title = {Chemical Metabolomics: Chemical Biology Tools for Advanced Metabolism Investigations.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e26122},
doi = {10.1002/anie.202526122},
pmid = {41954174},
issn = {1521-3773},
support = {2020-04707//Swedish Research Council/ ; FO2024-0407//Swedish Brain Foundation/ ; 254898Pj//Swedish Cancer Society/ ; },
abstract = {Human metabolism has been investigated to understand disease onset for the discovery of new selective pharmaceuticals and the development of diagnostics for early disease detection. Metabolomics, as an interdisciplinary research field, has been implemented to investigate the entirety of the complex metabolite profiles predominantly using mass spectrometry. In the past two decades, the development of chemical biology tools for the detailed metabolism investigation has received a boost to advance metabolomics analyses. Especially, the identification of the microbiome and its importance for human physiology were the main motivation for these strategies. These new tools at the intersection of Chemistry and Biology have especially aided to uncover previously unknown metabolites in humans and have slowly elucidated metabolites produced by microbial communities. These Chemical Biology tools, integrated with metabolomics tools and technologies, build the foundation for Chemical Metabolomics investigations, which have led to the discovery of important metabolites that are modulators or readouts for disease development and human homeostasis. This overview article focuses on the recent developments and the diversity of Chemical Biology tools and technologies, particularly methods involving chemoselective probes, in vivo analysis, host-microbiome co-metabolism, and activity metabolomics, in the context of understanding human metabolism at the molecular level.},
}

@article {pmid41954380,
year = {2026},
author = {Hu, J and Chung, R and Odeneal, R and Zhang, SJ},
title = {AANA Journal Course-The Gut-Brain Axis and Chronic Pain: The Emerging Role of Microbiota.},
journal = {AANA journal},
volume = {94},
number = {2},
pages = {141-151},
doi = {10.70278/AANAJ/.0000001078},
pmid = {41954380},
issn = {2162-5239},
mesh = {Humans ; *Chronic Pain/microbiology/physiopathology/nursing ; *Gastrointestinal Microbiome/physiology ; *Nurse Anesthetists/education ; Dysbiosis ; *Brain ; },
abstract = {Chronic pain is a complex and disabling condition that significantly impairs quality of life. It often arises from central sensitization, an amplified response to pain stimuli driven by neuroinflammatory changes in both the peripheral and central nervous systems. Emerging evidence highlights the gut microbiome's crucial role in the process because it modulates inflammation, immune function, and neurotransmitter production via the gut-brain axis. An imbalance in gut flora, known as dysbiosis, can exacerbate neuroinflammation by altering intestinal barrier integrity, facilitating the release of pro-inflammatory mediators, and activating microglia within the central nervous system. These changes contribute to increased pain sensitivity and the progression of chronic pain states. Consequently, strategies promoting a healthy gut microbiome, such as targeted dietary measures and microbiota-focused therapies, represent promising adjuncts to conventional chronic pain management. This journal course evaluates current research on the connection between the gut microbiome and chronic pain, offering a novel perspective on holistic, microbiome-centered interventions for alleviating pain disorders. As certified registered nurse anesthetists increasingly participate in pain management, understanding this emerging approach is vital for improving patient outcomes in chronic pain conditions.},
}

Humans
*Chronic Pain/microbiology/physiopathology/nursing
*Gastrointestinal Microbiome/physiology
*Nurse Anesthetists/education
Dysbiosis
*Brain

@article {pmid41954396,
year = {2026},
author = {Drankhan, HR and Taylor, KR and Shah, DH and Park, CH and Grieser, AM and Wild, MA},
title = {An experimental infection model for rapid reproduction of treponeme-associated hoof disease in captive elk (Cervus canadensis).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0382225},
doi = {10.1128/spectrum.03822-25},
pmid = {41954396},
issn = {2165-0497},
abstract = {Treponeme-associated hoof disease (TAHD) is an emerging, polybacterial infection that causes painful foot lesions and lameness in free-ranging elk (Cervus canadensis) across the northwestern USA. Although TAHD is associated with multiple Treponema species and other anaerobic bacteria, current understanding of disease etiology is limited and based primarily on cross-sectional analyses of naturally infected elk, in which lesions were examined at single time points using histopathology and 16S rRNA gene sequencing. Our objective was to develop a rapid and reliable experimental infection model to study TAHD pathogenesis in captive elk under controlled conditions. Inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria derived from TAHD lesions was applied onto abraded interdigital skin on the hind feet of five treatment elk. Inoculated feet were wrapped to expedite lesion development. Over the 7 week study period, all inoculated feet (10/10) developed interdigital erosions consistent with mild to moderate TAHD lesions observed in free-ranging elk. Lesions were observed on the majority of inoculated feet (9/10) after 28 days, coinciding with concurrent 16S rRNA gene amplicon sequencing detection of three putative pathogens of TAHD: Treponema, Fusobacterium, and Mycoplasma. In contrast, mock-inoculated control elk feet did not exhibit pathological or microbiological changes indicative of TAHD. This experimental infection model provides a valuable platform to investigate the complex interactions between the host, pathogens, and environmental factors that influence TAHD susceptibility, lesion progression, and disease transmission.IMPORTANCEOur study details a new approach for consistent and rapid induction of treponeme-associated hoof disease (TAHD) lesions in captive elk. TAHD is an emerging polybacterial disease of conservation concern that causes chronic lameness and debilitation in free-ranging elk across the northwestern USA. We rapidly and reliably reproduced TAHD lesions following challenge with inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria. This experimental infection model provides a valuable platform for investigation of the complex interactions between the host, pathogens, and environmental factors influencing TAHD susceptibility, lesion progression, and disease transmission in elk.},
}

@article {pmid41954620,
year = {2026},
author = {Gou, YR and Gu, H and Wang, L},
title = {Beyond tumor biology: nursing interventions for psychological and immune health in cancer patients.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {5},
pages = {},
pmid = {41954620},
issn = {1433-7339},
mesh = {Humans ; *Neoplasms/psychology/immunology/nursing/therapy ; *Stress, Psychological/therapy/etiology/nursing ; *Oncology Nursing/methods/organization & administration ; Depression ; Social Support ; Anxiety ; },
abstract = {Cancer care requires an integrative approach that addresses psychological distress, immune dysfunction, and health disparities across global populations. Psychoneuroimmunology research reveals bidirectional links between psychological well-being, neural signaling, immune activity, and clinical outcomes, underscoring the need for nursing‑led holistic interventions. This review synthesizes evidence on the prevalence and impact of anxiety, depression, fear of recurrence, and stress-mediated neuroendocrine pathways that suppress immune surveillance. It examines tumor-associated immune dysregulation, therapy-induced immune imbalance, and inflammation as a mechanistic bridge between emotional and physical health. Nursing-driven strategies including cognitive-behavioral therapy, mindfulness, narrative care, social support, lifestyle counseling, nutrition, microbiome support, physical rehabilitation, and integrative practices demonstrate measurable benefits for resilience, immune stability, and treatment adherence. Emerging technologies such as AI-enabled telehealth expand the reach and personalization of oncology nursing pathways. Persistent barriers workload, training gaps, cultural differences, and limited resources require policy reform, multidisciplinary integration, and capacity-building. Future directions highlight precision nursing models utilizing biomarkers, digital analytics, and survivorship planning to deliver equitable, patient-centered psychological-immune oncology care.},
}

Humans
*Neoplasms/psychology/immunology/nursing/therapy
*Stress, Psychological/therapy/etiology/nursing
*Oncology Nursing/methods/organization & administration
Depression
Social Support
Anxiety

@article {pmid41954752,
year = {2026},
author = {Saha, S and Shah, AS and Wang, P and Burgess, TI and Bayliss, KL},
title = {Seed Potato Bacteria Transfer Across Generations Within the Tuber Flesh.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02758-7},
pmid = {41954752},
issn = {1432-184X},
abstract = {Potato crops are susceptible to pathogens and environmental extremes. Microbiomes support plant health and stress tolerance, and microbes can transfer across generations in vegetatively propagated potatoes. However, the extent and functional relevance of this transfer are poorly understood. This study investigated bacterial transfer across three tuber generations, from seed to granddaughter in two potato cultivars, Nadine and Royal Blue. Bacterial communities in the peel and flesh compartments were sequenced. The granddaughter generation was cultivated in two separate fields to determine the consistency of vertical transfer, and the tare soil bacterial community was a proxy for environmental acquisition. The overall community composition was influenced by generation, compartment, cultivar and field. Horizontal acquisition significantly increased across generations and was the primary source, accounting for more than 98% of the granddaughter tuber bacteria. Peel had a significantly higher number of horizontally acquired ASVs than flesh. Only a small set of seed tuber bacteria ASVs were vertically transferred to the granddaughter tubers. The overall vertical transfer probability was 1.8% across compartments, cultivars, and fields, and it was higher in flesh than in peel. Cultivar-specific probabilities were 1.8% for Nadine and 1.5% for Royal Blue. Field variance was minimal, indicating consistent vertical transfer regardless of where the tubers were grown. Taxa with stable vertical transfer included Streptomycetaceae, Xanthobacteraceae, Devosiaceae, Sphingomonadaceae, and Micrococcaceae. Vertically transferred ASVs were predicted to have functions associated with core metabolic and stress response pathways. This study confirmed consistent vertical transfer of bacteria across potato tuber generations, mainly in the flesh.},
}

@article {pmid41954871,
year = {2026},
author = {Mac Aogáin, M and Gilmour, A and Chalmers, JD and Chotirmall, SH},
title = {Targeting Inflammation in Bronchiectasis.},
journal = {Drugs},
volume = {},
number = {},
pages = {},
pmid = {41954871},
issn = {1179-1950},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001636//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-001855//National Medical Research Council/ ; },
abstract = {Bronchiectasis is defined by chronic infection, dysregulated inflammation and impaired mucociliary clearance underpinning progressive structural lung injury. While airway infection remains a clinical hallmark, numerous studies demonstrate that excessive neutrophil-dominated inflammation is a key determinant of disease severity, exacerbation risk and quality of life. Recent developments have transformed our understanding of inflammatory drivers uncovering distinct inflammatory endotypes defined by dominant microbial species, pattern-recognition receptor activation, inflammasome signalling, Th17-associated cytokine networks and failures of mucosal immunity. The emerging roles of viral-bacterial interactions, fungi, pathobionts and the broader microbiome challenge the conventional infection-only paradigm and highlight gaps in current therapeutic strategies. Such developments underpin the rationale behind anti-inflammatory strategies in bronchiectasis, ranging from suppression of neutrophil-driven injury through direct neutrophil elastase or upstream dipeptidyl peptidase-1 (DPP-1) inhibition, to immunomodulatory macrolides, toward therapies aimed at recalibrating epithelial and mucosal homeostasis. While several antibacterial and anti-infective trials have produced mixed results, this is likely to reflect unresolved heterogeneity in microbiome composition and host immune signalling. In contrast, emerging anti-inflammatory strategies show strong positive signals, reinforcing the need for better endotyping and biomarker-guided patient selection. Here we synthesize recent mechanistic and clinical insights to propose a more integrated framework for understanding and ultimately targeting airway inflammation in bronchiectasis.},
}

@article {pmid41954918,
year = {2026},
author = {Specchia, ML and Beccia, F and Cacciuttolo, MG and Petrella, L and Mungo, T and Thiella, S and Lucarelli, A and Zace, D and Di Pietro, ML},
title = {Maternal and child nutrition insecurity, microbiome, and early neurodevelopment: an intricate interplay. Results from a systematic review.},
journal = {European journal of public health},
volume = {36},
number = {2},
pages = {},
pmid = {41954918},
issn = {1464-360X},
mesh = {Humans ; Female ; Infant ; *Child Development/physiology ; *Gastrointestinal Microbiome/physiology ; *Food Insecurity ; *Neurodevelopmental Disorders ; Child ; *Nutritional Status ; Pregnancy ; Child, Preschool ; Infant, Newborn ; },
abstract = {Emerging research suggests nutrition insecurity influences microbiome composition, which in turn affects early neurodevelopment through the gut-brain axis. This systematic review aimed to evaluate evidence on these relationships. A comprehensive search of the scientific literature was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies investigating the links between nutrition insecurity in mothers and children, microbiome, and early neurodevelopment were included. Data on maternal characteristics, microbiota composition, neurodevelopmental outcomes, and nutritional status were extracted from eligible studies. The review included 11 studies, primarily cohort studies, conducted in various countries. According to the study findings, gut maternal and infant microbiota composition in early life appear to be closely connected to early neurodevelopment both in terms of cognitive/motor skills and temperament. Nutrition insecurity has a significant influence in shaping these outcomes as it can alter microbiota balance and contribute to gut dysbiosis and delayed neurodevelopmental milestones. Breastfeeding emerges as a crucial factor in modulating the infant microbiome and supporting neurodevelopment. Also, other factors such as pre-pregnancy overweight/obesity and environment seem to influence offspring gut colonization and neurodevelopmental outcomes. This systematic review highlights the intricate interplay between maternal and child nutrition insecurity, microbiota, and early neurodevelopment. These findings underscore the critical need for targeted interventions addressing maternal and child nutrition to mitigate the adverse effects of nutrition insecurity and support optimal early-life neurodevelopment. Future research should focus on longitudinal studies to explore the causal pathways and to develop nutrition-based strategies to prioritize microbiome health in vulnerable and at-risk populations.},
}

Humans
Female
Infant
*Child Development/physiology
*Gastrointestinal Microbiome/physiology
*Food Insecurity
*Neurodevelopmental Disorders
Child
*Nutritional Status
Pregnancy
Child, Preschool
Infant, Newborn

@article {pmid41955160,
year = {2026},
author = {Liu, J and Li, K and Zhang, Y and Huang, K and Guan, X},
title = {Predicting gut metabolites from gut microbiome and their interpretability analysis of IBD prediction based on LIME.},
journal = {Integrative biology : quantitative biosciences from nano to macro},
volume = {18},
number = {},
pages = {},
doi = {10.1093/intbio/zyaf023},
pmid = {41955160},
issn = {1757-9708},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/diagnosis ; Dysbiosis/microbiology ; Oxides ; Calcium Compounds ; },
abstract = {The pathophysiology of inflammatory bowel disease (IBD) is influenced by the gut microbiome and gut metabolite, but understanding how IBD is affected remains challenging. It is crucial to understand which features affect IBD in order to effectively diagnose the disease. Traditional technology for measuring metabolite features is time-consuming and costly. The abundance of metabolite features in IBD patients is altered depending to changes in the abundance of gut microbiome. LSTM-VAE is proposed to predict gut metabolite features using gut microbiome of IBD patients. The pathogenesis of IBD is investigated by LSTM-VAE without gut metabolite data. In order to explore IBD is affected by the features, GBDT-LR is used to predict IBD disease using the gut microbiome and the generated gut metabolites. GBDT-LR achieved high-precision prediction, with an accuracy of 0.97 at the genus level and 0.95 at the species level. It is noteworthy that LIME is used to explain the prediction process of GBDT-LR, solving the prediction of the 'black box model'. The cost of measuring intestinal metabolites were reduced in this study and the researches were assisted in the diagnosis and drug research of IBD diseases. Insight Box Dysbiosis of the gut microbiota and the resulting abnormal metabolites were influenced in the IBD, promoting inflammatory responses and damaging intestinal barrier function. LSTM-VAE was proposed to predict changes in gut metabolite features in IBD patients without the need for direct measurement of costly and time-consuming metabolite data. Furthermore, high-precision prediction of IBD based on gut microbiome data was demonstrated and metabolite features were generated in the GBDT-LR, achieving accuracy rates of 0.97 at the genus level and 0.95 at the species level. Additionally, the LIME is employed to interpret the "black box" prediction process of GBDT-LR. The cost of measuring gut metabolites was reduced, but also strong support for the diagnosis and drug development of IBD was provided.},
}

*Gastrointestinal Microbiome
Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/diagnosis
Dysbiosis/microbiology
Oxides
Calcium Compounds

@article {pmid41955174,
year = {2026},
author = {Kowarsky, M and Dalman, M and Moufarrej, MN and Okamoto, J and Xie, Y and Neff, NF and Abdool Karim, SS and Garrett, N and Moore, PL and Camunas-Soler, J and Quake, SR},
title = {Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV.},
journal = {PLoS pathogens},
volume = {22},
number = {4},
pages = {e1014066},
pmid = {41955174},
issn = {1553-7374},
mesh = {Humans ; *HIV Infections/immunology/virology ; *HIV-1/immunology/genetics ; *HIV Antibodies/immunology ; *Broadly Neutralizing Antibodies/immunology ; Male ; Female ; Adult ; *RNA, Viral/genetics/blood ; Middle Aged ; Longitudinal Studies ; Microbiota/immunology ; },
abstract = {A small number of people living with HIV (PLWH) develop broadly neutralizing antibodies (bNAbs) targeting multiple HIV strains. Although several viral and immune factors contribute to bNAb development, the genetic and environmental factors driving this response remain largely unknown. We performed combined cell-free DNA (cfDNA) and cell-free RNA (cfRNA) sequencing in 42 plasma samples from a longitudinal cohort of 14 PLWH (7 who develop bNAbs and 7 matched controls). This approach enabled us to non-invasively monitor the host transcriptome, viral genetic variation, and microbiome composition during HIV infection, and to identify molecular correlates of bNAb development. We find that development of bNAbs is associated with a transcriptomic signature of early immune activation characterized by elevated levels of MHC class I antigen presentation genes. This signature is independent of viral load or CD4 count and declines over time. In addition to host features, we recovered sufficient viral reads to reconstruct HIV consensus sequences, supporting the utility of cfRNA for viral genotyping. Finally, we also identified an enrichment of several microbial taxa in bNAb producers and increased levels of GB virus C (GBV-C), a non-pathogenic lymphotropic virus. Our findings suggest a distinct early immune activation profile in PLWH who develop bNAbs. More broadly, we show that combined cfDNA/cfRNA sequencing can reveal relationships between a protective immunogenic response to HIV infection, the host immune system, and microbiome, highlighting its potential for biomarker discovery in future vaccine and therapeutic studies.},
}

Humans
*HIV Infections/immunology/virology
*HIV-1/immunology/genetics
*HIV Antibodies/immunology
*Broadly Neutralizing Antibodies/immunology
Male
Female
Adult
*RNA, Viral/genetics/blood
Middle Aged
Longitudinal Studies
Microbiota/immunology

@article {pmid41955218,
year = {2026},
author = {Yaakop, S and Senen, MA and Adila Rosli, NA and Mohammed, MA},
title = {Molecular identification and microbiome profiling of household casebearer, Phereoeca sp. (Lepidoptera: Tineidae) from Malaysia: Potential implications for human skin irritation.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346590},
pmid = {41955218},
issn = {1932-6203},
mesh = {Animals ; Malaysia ; *Microbiota/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Skin/microbiology ; *Lepidoptera/microbiology/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Moths/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Electron Transport Complex IV/genetics ; },
abstract = {In Malaysia, anecdotal accounts have linked the household casebearer (Lepidoptera: Tineidae) to skin lesions and localized inflammation; however, scientific evidence is lacking, and the species' taxonomic identity remains unclear. This study aimed to confirm the species identity and examine the bacteria associated with larvae that may be linked to skin irritation. Larvae were collected from three locations in Peninsular Malaysia and preserved. DNA was extracted from the larvae, and species identification was conducted by analyzing the cytochrome c oxidase subunit I (COI) gene through DNA barcoding. To study the bacteria present, the bacterial 16S rRNA gene was amplified and sequenced using Next-generation sequencing technology. The DNA sequences were analyzed to determine the species and profile the bacterial communities. The results identified the specimens as Phereoeca sp., suggesting they may represent an undescribed lineage. Microbiome analysis revealed that Proteobacteria (40.18%) and Actinobacteriota (32.13%) were the dominant bacterial phyla, with Cutibacterium acnes, Enterobacter, and Pseudomonas among the taxa previously associated with skin irritation or opportunistic infections. Several unclassified but potentially relevant taxa were also identified. These findings provide new insights into the microbial ecology and taxonomy of Phereoeca and underscore its potential role in medically significant interactions within human environments.},
}

Animals
Malaysia
*Microbiota/genetics
Humans
RNA, Ribosomal, 16S/genetics
Larva/microbiology
*Bacteria/genetics/classification/isolation & purification
Phylogeny
Skin/microbiology
*Lepidoptera/microbiology/genetics
DNA Barcoding, Taxonomic
DNA, Bacterial/genetics
*Moths/microbiology/genetics
High-Throughput Nucleotide Sequencing
Electron Transport Complex IV/genetics

@article {pmid41955304,
year = {2026},
author = {Yang, JC and Situ, J and Troutman, R and Zhu, R and Black, M and Buri, H and Gutta, A and Tian, F and Kang, A and Aja, E and Zeng, A and Lai, RW and Tan, J and Liang, F and Brahim, C and Murphy, G and Ahdoot, A and Peng, C and Jacobs, JP},
title = {A microbiome quantitative trait locus in SLC39A8 modulates disease severity in synucleinopathy-induced models of Parkinson's disease.},
journal = {Human molecular genetics},
volume = {35},
number = {6},
pages = {},
doi = {10.1093/hmg/ddag024},
pmid = {41955304},
issn = {1460-2083},
mesh = {Animals ; Mice ; *Parkinson Disease/genetics/microbiology/pathology ; Humans ; alpha-Synuclein/genetics/metabolism ; Disease Models, Animal ; *Cation Transport Proteins/genetics ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci/genetics ; *Gastrointestinal Microbiome/genetics ; *Synucleinopathies/genetics/microbiology/pathology ; Male ; Dopaminergic Neurons/pathology/metabolism ; Female ; Genetic Predisposition to Disease ; Mice, Transgenic ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor deficits, dopaminergic neuron loss, and α-synuclein (α-syn) aggregation. While rare mutations underlie familial PD, around 85% of cases are idiopathic. Emerging evidence implicates common genetic variants and the gut microbiome in PD risk, but their interaction has not been studied. We previously demonstrated that the PD-protective SLC39A8 variant rs13107325 (human A391T, corresponding to A393T in mouse) is associated with microbial compositional shifts in humans and reshapes the microbiome in SLC39A8 A393T knock-in mice. Here, we test whether this SNP modifies PD phenotypes in two α-synucleinopathy mouse models. In the human α-synuclein overexpression model, A393T carrier mice show reduced motor deficits, consistent with a protective role. However, in the α-synuclein preformed fibril (PFF) injection model, A393T carriers exhibit worsened motor deficits, increased dopaminergic terminal loss, and enhanced α-synuclein pathology spread. SNP- and model-specific microbiome changes correlated with motor outcomes. These included enrichment of Lactobacillus and Lactobacillaceae HT002 genera in A393T carriers with α-synuclein overexpression, and enrichment of Erysipelatoclostridium in PFF-injected A393T carriers. These findings suggest that SLC39A8 A393T-induced microbiome alterations are associated with differential disease outcomes depending on context. Our results are consistent with a model in which susceptibility gene SNPs may influence PD progression via the gut microbiome, though direct causal effects remain to be tested.},
}

Animals
Mice
*Parkinson Disease/genetics/microbiology/pathology
Humans
alpha-Synuclein/genetics/metabolism
Disease Models, Animal
*Cation Transport Proteins/genetics
Polymorphism, Single Nucleotide
*Quantitative Trait Loci/genetics
*Gastrointestinal Microbiome/genetics
*Synucleinopathies/genetics/microbiology/pathology
Male
Dopaminergic Neurons/pathology/metabolism
Female
Genetic Predisposition to Disease
Mice, Transgenic

@article {pmid41955364,
year = {2026},
author = {Jain, S},
title = {Pesticides may wreak havoc on the gut microbiome.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6794},
pages = {134-135},
doi = {10.1126/science.aeh8589},
pmid = {41955364},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Pesticides/toxicity/adverse effects ; Animals ; },
abstract = {Disruption of complex intestinal ecosystem could contribute to diabetes and other health issues, scientists say.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Pesticides/toxicity/adverse effects
Animals

@article {pmid41955483,
year = {2026},
author = {Wang, M and Luo, N and Li, Y and Zhai, H and Xi, J and Li, HB and Zhou, D},
title = {Unlocking the Phyllosphere's Role: Selenium Nanoparticles Reprogram Sulfur Metabolism and Enrich Sphingomonas to Reduce Cadmium in Wheat.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12411},
pmid = {41955483},
issn = {1520-5851},
abstract = {Although selenium nanoparticles (SeNPs) can mitigate cadmium (Cd) accumulation in crops, comparative system-level mechanisms among different SeNPs remain unclear, particularly in wheat. Herein, we compare chemically and biologically synthesized SeNPs (CH/BI-SeNPs) to elucidate Cd detoxification via phyllosphere metabolism-microbiome interactions. Results showed that foliar application of both SeNPs significantly reduced Cd accumulation and mitigated cell membrane damage in wheat. CH-SeNPs exhibited the strongest Cd reduction effect, decreasing grain Cd content by 30.9%. Metabolomic profiling revealed a substantial reorganization of sulfur metabolic pathways under CH-SeNPs treatment, characterized by the accumulation of S-adenosylhomocysteine (SAH), decreased homomethionine, and reduced oxidized glutathione (GSSG), indicating a shift in sulfur flux toward enhanced synthesis of reduced thiol compounds. CH-SeNPs activated the glutathione biosynthesis pathway, significantly increasing the activity of γ-glutamylcysteine synthetase and the contents of cysteine and glutathione, thereby promoting Cd chelation, and reducing its translocation to grains. 16S rRNA sequencing further demonstrated that CH-SeNPs significantly enriched Sphingomonas, a genus involved in sulfur cycling, in the phyllosphere, rhizosphere, and rhizosphere soil, suggesting that microbial interactions facilitated sulfur metabolism and contributed to a systemic reduction in Cd bioavailability. Additionally, HPLC-ICP-MS analysis indicated an increased proportion of selenomethionine in grains under CH-SeNPs treatment, enhancing both nutritional value and food safety. This study reveals that SeNPs alleviate Cd stress in wheat via coordinated regulation involving phyllosphere sulfur metabolism and microbial interactions related to sulfur, providing a mechanistic basis for the application of SeNPs in the remediation of heavy metal contamination and nutritional fortification in agriculture.},
}

@article {pmid41955497,
year = {2026},
author = {Zhang, W and Yang, Z and Zhang, Y and Wang, L and Zhang, X and Mao, J and Dai, Y and Yuan, Y and Wang, M and Yang, X and Yu, X and Liu, J and Chen, C},
title = {Multi-Enzyme Mimetic Molybdenum Nitride Nanozymes Reshape Subgingival Microenvironment for Synergistic Periodontitis Therapy via ROS Regulation and Microbiome Remodeling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17770},
doi = {10.1002/advs.202517770},
pmid = {41955497},
issn = {2198-3844},
support = {2024YFA1210004//National Key Research and Development Program of China/ ; T2422006//National Natural Science Foundation of China/ ; T242200557//National Natural Science Foundation of China/ ; 82201017//National Natural Science Foundation of China/ ; 52422213//National Natural Science Foundation of China/ ; 52272212//National Natural Science Foundation of China/ ; F251001//Beijing Natural Science Foundation/ ; 22388101//Basic Science Center Project of the National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientist Sponsorship Program by CAST/ ; //Hundred-Talent Program of Chinese Academy of Sciences/ ; tsqn202211168//Taishan Scholar Project of Shandong Province/ ; ZR2022JQ20//Natural Science Foundation of Shandong Province/ ; },
abstract = {Periodontitis, a chronic inflammatory disease initiated and sustained by plaque microorganisms and host immune response, remains an intractable oral disease and a leading cause of tooth loss worldwide. Traditional mechanical debridement and adjunctive antibiotic or antiseptic therapy often shows limited efficacy due to the complex anatomical structure, concerns regarding antimicrobial resistance, and poor penetration and retention within the subgingival infection niche. To overcome this limitation, we designed a Mo-N coordinated nanozyme exhibiting synergistic mimetic activities of multiple enzymes, including peroxidase (POD)-like, oxidase (OXD)-like, and catalase (CAT)-like activity. Benefiting from Mo-N coordination and multi-enzyme mimetic behavior, Mo5N6 nanozymes dynamically modulate local oxidative reactions within the gingival sulcus, thereby effectively damaging pathogenic bacteria while avoiding excessive oxidative stress. The nanozymes efficiently suppress anaerobic Gram-negative periodontal pathogens sensitive to elevated reactive oxygen species (ROS), facilitating efficient attenuation of pathogenic stimuli. This strategy not only enhances the periodontal microenvironment but also facilitates the restoration of commensal microbiota and regeneration of periodontal tissues, highlighting the therapeutic potential of Mo5N6 nanozymes in periodontitis treatment.},
}

@article {pmid41955508,
year = {2026},
author = {Chatrizeh, M and Tian, J and Rogers, M and Feturi, F and Wu, G and Firek, B and Nikonov, R and Cass, L and Sheppeck, A and Ojha, L and Carroll, A and Henkel, M and Azar, J and Aneja, RK and Campfield, B and Simon, D and Morowitz, MJ},
title = {Plant-based enteral nutrition outperforms ultra-processed formulas in mitigating consequences of antibiotic-induced dysbiosis.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.199827},
pmid = {41955508},
issn = {2379-3708},
abstract = {Malnutrition, gut inflammation, and antibiotic-induced dysbiosis (AID) are well-recognized risk factors for poor clinical outcomes among critically ill patients. We previously showed that commercially available plant-based enteral nutrition (PBEN) preserves a commensal microbiome compared with commonly used artificial enteral nutrition (AEN). In this study, PBEN was superior to AEN in promoting recovery from antibiotic-induced dysbiosis in mice and humans. PBEN effectively mitigated anemia and leukopenia, restored naïve lymphocyte populations, and reduced bone marrow myeloid expansion. Animals randomized to PBEN also exhibited improved responses to infectious challenges following antibiotic exposure. A pilot clinical study validated these findings, demonstrating increased gut commensals, reduced pathogens, and improved leukocyte balance in critically ill children receiving PBEN compared with AEN. Together, these results suggest that PBEN offers a practical dietary approach to mitigate antibiotic-associated complications and potentially improve clinical outcomes among hospitalized patients requiring supplemental nutrition.},
}

@article {pmid41955569,
year = {2026},
author = {Trunfio, M and Gianella, S and Gaitan, N and Porrachia, M and Gomez-Moreno, V and Lapke, B and Navarrete, A and Wells, A and Smith, D and Little, SJ and Chaillon, A},
title = {Minimal Disruption of the Rectal Microbiome in Acute and Early Untreated HIV Infection.},
journal = {Journal of acquired immune deficiency syndromes (1999)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAI.0000000000003883},
pmid = {41955569},
issn = {1944-7884},
abstract = {BACKGROUND: Alterations in the gut microbiome have been linked to chronic HIV infection, yet less is known about microbiome dynamics during the earliest phases of HIV acquisition. It remains unclear whether microbial changes precede or follow HIV infection, and whether specific taxa could serve as early biomarkers or modulators of disease progression.

SETTING: The San Diego Primary Infection Resource Consortium (PIRC), a large HIV resource infrastructure program that enrolled predominantly men who have sex with men in Southern California, USA.

METHODS: We analyzed rectal swabs from 316 participants, 86 without HIV, 100 with acute (≤30 days post-infection) and 130 with early (31-180 days) untreated HIV infection. 16S rRNA sequencing was used to characterize bacterial communities. Alpha and beta diversity metrics, and taxon-level relative abundance were compared across groups using generalized linear models and MaAsLin3, adjusting for confounders and correcting for false discovery rate (FDR).

RESULTS: No significant differences in Shannon and Pielou index or beta diversity were observed by HIV status or stage. However, HIV infection was independently associated with a modest reduction in microbial richness (observed species; p=0.039). Enterocloster clostridioformis was significantly depleted among people with HIV (aβ -1.31, FDR p<0.001). Among participants with HIV, relative abundance of Akkermansia muciniphila was positively correlated with plasma HIV RNA levels (aβ 0.48, FDR p=0.016).

CONCLUSION: The rectal bacteriome remains largely preserved during the first six months of untreated HIV infection. Subtle taxon-specific changes may reflect early viro-immunological perturbations but suggest limited diagnostic and prognostic utility of microbiome profiling.},
}

@article {pmid41955745,
year = {2026},
author = {Etesami, H and Schaller, J},
title = {The soil silicon filter: A conceptual model of how mycorrhizal fungi and their microbiome may govern biosilicification and plant-silicon availability.},
journal = {Plant physiology and biochemistry : PPB},
volume = {233},
number = {},
pages = {111235},
doi = {10.1016/j.plaphy.2026.111235},
pmid = {41955745},
issn = {1873-2690},
abstract = {Silicon (Si) plays an important role in plant health and ecosystem function, yet the biological pathways controlling its cycling are often too simplified and underlying mechanisms are not clear. While the plant-centric model of Si uptake and phytolith formation is mostly used, it underestimates the complex role of the soil microbiome. This review synthesizes growing evidence on the importance of the mycorrhizosphere-the zone of interaction between roots, mycorrhizal fungi, and bacteria-as a central processing unit in the terrestrial Si cycle. We develop and evaluate the concept of a "microbial silicon filter" as a working hypothesis, where symbiotic partnerships, particularly between mycorrhizal fungi and their associated bacteria, may collectively influence the Si flux. We line out the mechanisms of mycorrhizal-mediated Si transport and review evidence for bacterial biosilicification alongside the more speculative evidence and open questions regarding fungal (particularly mycorrhizal) biosilicification. Furthermore, we examine potential synergistic microbial weathering of minerals that mobilizes Si and how biofilm matrices may enhance its retention within the hyphosphere. By integrating these processes, we present a more integrated, microbiome-inclusive model of the Si cycle that emphasizes the potential interdependencies between plants, mycorrhizal fungi, and bacteria. This perspective has profound implications, potentially influencing plant stress resilience modulated by Si supply and suggesting a possible, though not yet quantified, role in enhancing long-term carbon sequestration through phytolith formation. Finally, we outline future research directions to unravel the underlying mechanisms of this partnership of plants, mycorrhizal fungi, and bacteria and to harness it for sustainable agriculture and ecosystem restoration. A central focus of these recommendations is the critical need for advanced methodologies-particularly stable isotope tracing and nanoscale secondary ion mass spectrometry (NanoSIMS)-to move from correlative evidence to quantitative, mechanistic understanding of the microbial Si filter.},
}

@article {pmid41955806,
year = {2026},
author = {Lee, EY and Lee, DG and Noh, G and Kwon, S and Shin, H and Shin, Y},
title = {Hierarchical alginate-bentonite beads enable instrument-free pre-analytic enrichment of liter-scale wastewater.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142013},
doi = {10.1016/j.jhazmat.2026.142013},
pmid = {41955806},
issn = {1873-3336},
abstract = {Wastewater-based surveillance (WBS) offers a test-independent window into public community health, but its fidelity depends critically on pre-analytic enrichment that must convert liter-scale, inhibitor-rich influent into microliter analytical inputs without compromising low-titer targets. Here we introduce hierarchical alginate-sulfuric acid-activated bentonite beads (Alg@SAB) that recast pre-analytic enrichment as an interfacial mass-transfer problem. A diffusion-optimized macro-mesoporous scaffold, amine-functionalized surfaces (-NH3[+]), and Ba[2+] crosslinks collectively enable dual-mode capture-electrostatic adsorption and Ba[2+]↔M[n+] cation-exchange-to retain free pathogens and pathogen-metal complexes under passive, pump-free operation, while batch-friendly fabrication from commodity precursors delivers reproducibility with per-test consumables of ∼US$0.06. Alg@SAB retains the two-fold-one-cycle linearity in input viral titer-Ct value while extending instrument-free concentration to the liter scale: 1 L inputs remain measurable where a vacuum-membrane kit fails at ≥ 500 mL; at 100 mL Alg@SAB achieves higher apparent recovery (56%, +27% versus kit). Validation used real municipal wastewater rather than synthetic surrogates, ensuring field realism in matrix complexity and inhibitor profiles. A single-tube, pH-dependent reversible crosslinking chemistry releases nucleic acids in situ while maintaining agreement and collapsing handoffs, enabling low-hardware deployment. Method-dependent microbiome profiling on these raw influent wastewater reveals mechanistically consistent selectivity without systematic inflation of alpha diversity, preserving ecological interpretability under real wastewater plant conditions. By integrating scalable materials engineering with practical deployment, Alg@SAB provides a simple and tunable route to decentralized, interpretable WBS, lowering technical barriers for real-time pathogen monitoring in diverse settings.},
}

@article {pmid41955863,
year = {2026},
author = {Temiz, A and Tascilar, K},
title = {Why we need to maintain a critical view on big data and artificial intelligence predictions.},
journal = {Current opinion in immunology},
volume = {100},
number = {},
pages = {102776},
doi = {10.1016/j.coi.2026.102776},
pmid = {41955863},
issn = {1879-0372},
abstract = {Artificial intelligence (AI) and machine learning are widely promoted as transformative tools for medical practice, yet their impact in daily rheumatology remains limited. This review examines the gap between expectations and reality using historical parallels, conceptual considerations, and recent methodological evidence. Experiences with antioxidant supplementation, vitamin D, the microbiome, and the Human Genome Project illustrate a recurring pattern: early studies report large effects that diminish or disappear in larger, higher-quality studies. Meta-epidemiological work and the 'cursed auction' analogy explain why early and small studies systematically overestimate effects. Conceptually, individualized clinical risk remains a group-based construct, constrained by the reference class problem and irreducible uncertainty. Methodologically, many AI models in rheumatology suffer from small and heterogeneous datasets, overfitting, inadequate handling of missing data, poor calibration, and limited external or prospective validation. The failure of COVID-19 prediction models and the neutral trial of the Ada diagnostic assistant in rheumatology illustrate how strong retrospective performance often collapses in real-world use. In contrast, AI performs well in high signal-to-noise domains with abundant, structured data. Overall, AI can generate valuable insights and support narrowly defined tasks, but it cannot yet overcome the fundamental limits of noisy clinical data and group-based risk. Progress in rheumatology will require realistic expectations, large representative datasets, transparent methods, rigorous validation, and a focus on robust, interpretable tools that improve decisions for populations and well-defined patient subgroups rather than precise individual prediction.},
}

@article {pmid41955934,
year = {2026},
author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM},
title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.},
journal = {The Science of the total environment},
volume = {1030},
number = {},
pages = {181776},
doi = {10.1016/j.scitotenv.2026.181776},
pmid = {41955934},
issn = {1879-1026},
abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.

METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.

RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.

CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.},
}

@article {pmid41955946,
year = {2026},
author = {Jiang, S and Li, T and Lu, J and Cai, F and Pang, G and Liu, J and Liu, D and Shen, Q},
title = {From degradation to alleviation: Trichoderma facilitates plants resisting the PBAT stress through secreting a cutinase-like enzyme.},
journal = {Environment international},
volume = {210},
number = {},
pages = {110228},
doi = {10.1016/j.envint.2026.110228},
pmid = {41955946},
issn = {1873-6750},
abstract = {The ecological impacts of biodegradable plastics like poly (butylene adipate-co-terephthalate) (PBAT) demand urgent investigation due to their unresolved risks to soil-plant systems, including physical interference with root development, disruption of indigenous microbial ecology. While PBAT depolymerization is a prerequisite for its removal, the slow and inefficient breakdown of these polymers in soil often results in the persistent accumulation of phytotoxic monomers, creating a bottleneck for biological remediation. In this study, through transcriptomic and phylogenetic analyses, we identified a key secreted hydrolase CUT2, belonging to a distinct clade of cutinase-like polyester hydrolases. Overexpression of cut2 (OEThcut2) significantly enhanced PBAT depolymerization, resulting in 27.0% and 22.4% increases in the release of terephthalic acid (TPA) and butanediolic acid (BTA) compared to the wild-type strain, respectively. The direct catalytic activity of purified CUT2 was confirmed through vitro film weight-loss assays with a degradation rate of 4.3% observed. In pot experiments, integrated multi-omics analysis revealed that the OEThcut2 strain reconfigured the rhizosphere microbial community and activated the aromatic degradation pathways, coinciding with the attenuated accumulation of degradation monomers. Furthermore, the enrichment of carbohydrate-active enzymes (CAZys) and the reduction of monomer burdens which revitalized the tricarboxylic acid cycle (TCA) and normalized redox homeostasis thereby clearing the metabolic bottleneck for intermediate turnover. Complementary monomer-exposure assays established that the reduction of PBAT monomers is critical for alleviating plant oxidative stress and growth inhibition. These findings provide a depolymerization to detoxification framework that links fungal enzymatic activity to rhizosphere metabolic recovery, offering a robust strategy for mitigating biodegradable plastic toxicity in agroecosystem.},
}

@article {pmid41956062,
year = {2026},
author = {Flury, JD and Schwartz, DJ},
title = {Don't keep this endopeptidase on the DL.},
journal = {Cell host & microbe},
volume = {34},
number = {4},
pages = {551-553},
doi = {10.1016/j.chom.2026.03.007},
pmid = {41956062},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Premature ; *Sepsis/microbiology/prevention & control ; Infant, Newborn ; *Nod2 Signaling Adaptor Protein/metabolism/genetics ; *Endopeptidases/metabolism ; *Bacteria/enzymology ; },
abstract = {Gut-derived bacterial DL-endopeptidase may confer protection from late onset sepsis (LOS) in preterm infants. In this issue of Cell Host & Microbe, Shen et al. identified delayed gut microbiome development in preterm infants as a risk factor for LOS and proposed a protective regulatory response by NOD2.},
}

Humans
*Gastrointestinal Microbiome
Infant, Premature
*Sepsis/microbiology/prevention & control
Infant, Newborn
*Nod2 Signaling Adaptor Protein/metabolism/genetics
*Endopeptidases/metabolism
*Bacteria/enzymology

@article {pmid41956066,
year = {2026},
author = {Potiron, A and Francken, JC and El Aidy, S},
title = {Rethinking microbiome health through functional dynamics.},
journal = {Cell host & microbe},
volume = {34},
number = {4},
pages = {562-566},
doi = {10.1016/j.chom.2026.03.005},
pmid = {41956066},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/physiology ; *Host Microbial Interactions/physiology ; *Gastrointestinal Microbiome ; Health ; },
abstract = {Translation in microbiome science is limited by static concepts of health that obscure dynamic host-microbe processes. We propose adaptive coherence: the capacity of host-microbiome systems to sustain integrated function through reorganization. This reframes health as emergent and relational, directing measurement toward system adaptability, functional integrity, and network interactions.},
}

Humans
*Microbiota/physiology
*Host Microbial Interactions/physiology
*Gastrointestinal Microbiome
Health

@article {pmid41956067,
year = {2026},
author = {Dillen, J and Dricot, CEMK and Croatti, V and Lebeer, S},
title = {The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms.},
journal = {Cell host & microbe},
volume = {34},
number = {4},
pages = {567-587},
doi = {10.1016/j.chom.2026.03.015},
pmid = {41956067},
issn = {1934-6069},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology ; Probiotics/therapeutic use ; *Urogenital System/microbiology ; Host Microbial Interactions ; },
abstract = {Microbiome-based interventions for female urogenital health have gained attention, particularly in strategies aimed at restoring lactobacilli dominance to reduce infection and improve reproductive outcomes. These approaches include defined probiotic strains, engineered microbial consortia, and vaginal microbiota transfer. Observational studies have provided ecological insights into the composition and dynamics of the vaginal microbiome; its associations with infections, inflammation, and reproductive complications; and its interplay with urinary and mucosal niches. These data establish a correlative framework linking microbial community structure to health and disease. However, the efficacy of current interventions remains constrained by an incomplete mechanistic understanding of host-microbiome and microbe-microbe interactions. Recent discoveries highlight the role of vaginally derived microbial molecules in modulating host immune responses, stabilizing microbial communities, and influencing disease outcomes. These mechanistic insights provide a basis for the rational design of microbiome-based therapies. This review synthesizes clinical, observational, and mechanistic evidence and outlines research priorities for translation into clinical practice.},
}

Humans
Female
*Microbiota/physiology
*Vagina/microbiology
Probiotics/therapeutic use
*Urogenital System/microbiology
Host Microbial Interactions

@article {pmid41956093,
year = {2026},
author = {Cao, Z and Zuo, W and Wang, L and Dai, L},
title = {Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101381},
doi = {10.1016/j.crmeth.2026.101381},
pmid = {41956093},
issn = {2667-2375},
abstract = {Spatial mapping of microbial communities at single-cell resolution is opening up dimensions to understand microbiome organization and function. However, current fluorescence in situ hybridization (FISH) methods for microbiomes are limited by multiplexity and scalability. Here, we present the sequential error-robust FISH spatial mapping platform (SEER-Map) for fully automated imaging of complex microbial communities. We show that an integrated platform of fluidics control and fluorescence microscopy can perform 40 rounds of sequential FISH. We apply SEER-Map to profile complex microbial communities colonized on plant roots and identify distinct spatial patterns and species co-occurrence at the micron-scale. Our work establishes SEER-Map as a high-throughput and scalable platform for high-resolution spatial profiling of microbiomes.},
}

@article {pmid41956108,
year = {2026},
author = {Kadandelu, M and Periya, S and Rekha, PD and Raghu, SV},
title = {Gut-brain axis mediated therapeutic intervention to mitigate the epileptogenesis: insights from Drosophila melanogaster.},
journal = {Reviews in the neurosciences},
volume = {},
number = {},
pages = {},
pmid = {41956108},
issn = {2191-0200},
abstract = {Drug-resistant epilepsy (DRE) is a prominent concern in the management of recurrent seizures. Anti-seizure medications (ASM), surgical intervention, and neurostimulation are a few classical remedial measures of epilepsy. Nevertheless, DRE requires immense investigation, a comprehensive understanding of holistic management, and additional therapeutic effects. Dysbiosis, an imbalance of the gut microbiome, is the foremost concern associated with various neurological disorders. In epilepsy, the gut microbiome plays a pivotal role in its pathophysiology, unveiling new avenues for microbiome-mediated strategies to treat epileptic patients. Furthermore, the differential gut microbial composition in epileptic patients serves as a cornerstone for advanced research to delineate the influence of each bacterial species on epilepsy. Drosophila melanogaster, a simple model organism with an evolutionarily conserved gut microbiome composition, can be efficiently deployed to scrutinize the role of discrete microbes and their influence on the gut-brain axis, impacting neurological disorders. In this review, the role of distinct bacterial species in influencing epileptic conditions and how model organisms like Drosophila can be employed to explore this realm are deliberated as a comprehensive overview.},
}