@article {pmid41811972,
year = {2026},
author = {Berardi, S and Beltz, JK and Rudman, SM and Grainger, TN and Levine, JM and Oken, H and Schmidt, P},
title = {Seasonal evolution of Drosophila melanogaster abdominal pigmentation is associated with a multifarious selective landscape.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag038},
pmid = {41811972},
issn = {1558-5646},
abstract = {Pigmentation has been widely studied by evolutionary biologists due to both ease of measure and relationship to fitness. Drosophila melanogaster pigmentation has represented a particularly useful avenue of investigation, as extensive genetic tools have enabled the characterization of the trait's complex architecture. Drosophila pigmentation also varies predictably across space and time in wild populations, suggesting pigmentation is a component of adaptation to local environmental conditions. Despite this, the impact of D. melanogaster pigmentation on fitness, and the environmental factors that drive the evolution of pigmentation, are not well understood. To address this gap, we experimentally evolved replicated D. melanogaster populations in field mesocosms to determine whether and how pigmentation evolves in response to environmental variation. We found that pigmentation rapidly and predictably adapted to a direct manipulation of temperature, supportive of melanization playing a role in thermoregulation. However, we also determined that pigmentation responded adaptively to direct manipulations of numerous additional factors, including intraspecific competition, diet, and the microbiome. These findings suggest that the selective landscape acting on pigmentation is complex and multifaceted, and that patterns of melanization may be driven, at least in part, by indirect selection due to correlations with other fitness-related traits.},
}

@article {pmid41811823,
year = {2026},
author = {Bautista, J and Echeverría, CE and Maldonado-Noboa, I and Adatty-Molina, J and Suárez Urresta, S and Coral-Riofrio, EC and Araujo-Abad, S and Kyriakidis, NC and López-Cortés, A},
title = {Next-Generation Immune Checkpoints and Tumor Microenvironment Modulation in Cancer Immunotherapy.},
journal = {Journal of immunology research},
volume = {2026},
number = {1},
pages = {e7864229},
doi = {10.1155/jimr/7864229},
pmid = {41811823},
issn = {2314-7156},
support = {//Universidad de Las Américas Ecuador/ ; },
mesh = {Humans ; *Tumor Microenvironment/immunology/drug effects ; *Neoplasms/therapy/immunology/metabolism/etiology ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; Immune Checkpoint Proteins/metabolism ; },
abstract = {Immunotherapy has reshaped the oncology landscape by enabling the immune system to recognize and eliminate malignant cells. Although immune checkpoint inhibitors (ICIs) targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), programmed cell death-1 (PD-1), and programmed death-ligand 1 (PD-L1) have achieved durable responses in several cancers, their therapeutic benefit remains limited to a subset of patients, largely due to immune evasion, tumor heterogeneity, and immunosuppressive features of the tumor microenvironment (TME). This review comprehensively examines the expanding landscape of next-generation immune checkpoints, encompassing both co-inhibitory (lymphocyte activation gene-3 [LAG-3], T cell immunoglobulin and mucin-domain containing-3 [TIM-3], TIGIT, VISTA, and IGSF8) and co-stimulatory (ICOS, OX40, GITR, 4-1BB, CD40, and CD27) pathways that collectively regulate the balance between immune activation and tolerance. We discuss their molecular mechanisms, translational rationale, and emerging clinical evidence, highlighting their potential to reinvigorate antitumor immunity, particularly in ICI-refractory settings. Beyond checkpoint modulation, we explore complementary strategies aimed at remodeling the TME and enhancing immune responsiveness, including targeting immunometabolic pathways (IDO1 and CD73), innate immune sensing (toll-like receptors [TLRs]), cytokine signaling (IL-2), micronutrient immunoregulators (vitamin D), and the gut microbiota. The integration of these approaches into rational combination regimens, guided by predictive features such as T cell infiltration, tumor mutational burden (TMB), and microbiome composition, holds promise for extending the clinical impact of immunotherapy across malignancies. We further advocate for a precision immuno-oncology framework that leverages multiomic profiling, systems biology, and artificial intelligence (AI) to optimize therapeutic selection and mitigate immune-related toxicities. Emerging advances in nanomedicine, synthetic biology, and chronotherapy offer additional opportunities to enhance therapeutic specificity and durability, collectively charting a path from mechanistic insight to clinical translation toward realizing the full curative potential of cancer immunotherapy. Trial Registration: ClinicalTrials.gov identifier: LAG-3 (NCT03470922, NCT04082364, NCT05064059, NCT05352672, NCT02614833, NCT03625323, NCT01968109), TIM-3 (NCT03307785, NCT03680508, NCT02608268, NCT02817633), TIGIT (NCT03563716), VISTA (NCT02671955, NCT02812875), IGSF8 (NCT05669430), CD73 (NCT02503774), B7-H3 (NCT02475213, NCT01391143, NCT02628535, NCT03406949, NCT00089245, NCT01099644, NCT01502917), OX40 (NCT01862900, NCT02315066, NCT02410512, NCT02221960, NCT02528357, NCT02923349, NCT02705482), CD27 (NCT02335918, NCT02924038, NCT02302339, NCT02386111, NCT02543645), 4-1BB (NCT01307267, NCT02444793, NCT01471210, NCT02253992, NCT02554812), CD40 (NCT02588443, NCT03329950), ICOS (NCT02904226, NCT02723955, NCT03251924), GITR (NCT02583165, NCT02132754, NCT02697591, NCT03126110, NCT02740270, NCT02598960, NCT01239134, NCT02628574), IDO1 (NCT02752074, NCT02658890, NCT02077881, NCT01560923, NCT02073123, NCT02327078, NCT02178722), TLRs (NCT02556463, NCT02042781), and IL-2-based therapies (NCT02869295, NCT02983045).},
}

Humans
*Tumor Microenvironment/immunology/drug effects
*Neoplasms/therapy/immunology/metabolism/etiology
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Animals
Immune Checkpoint Proteins/metabolism

@article {pmid41811805,
year = {2026},
author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L},
title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344050},
pmid = {41811805},
issn = {1932-6203},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Adenoma/microbiology/metabolism/pathology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Case-Control Studies ; Aged ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.

OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.

MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.

RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.

CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/pathology
*Adenoma/microbiology/metabolism/pathology
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Colonoscopy
Case-Control Studies
Aged
*Vitamin K 2/metabolism
Cross-Sectional Studies
Feces/microbiology
Adult
Dysbiosis/microbiology

@article {pmid41811768,
year = {2026},
author = {McGee, C and Jafari, AJ and Hebert, AA},
title = {Innovation in pediatric atopic dermatitis care: examining emerging topical treatment options.},
journal = {Expert review of clinical pharmacology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/17512433.2026.2641800},
pmid = {41811768},
issn = {1751-2441},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by pruritus, eczematous lesions, and a relapsing course. The pathophysiology of atopic dermatitis involves an interplay of skin barrier dysfunction, immune dysregulation, genetic predisposition, environmental triggers, and alterations in the skin microbiome. Pediatric AD is frequently associated with allergic comorbidities and imposes a substantial psychosocial burden on affected children and their families. This manuscript will describe recent innovations in topical, steroid-sparing therapies for pediatric AD, highlighting emerging agents such as roflumilast, ruxolitinib, and tapinarof, as well as investigational therapies.

AREAS COVERED: PubMed and Clinicaltrials.gov were used to identify the latest advancements in topical therapies available for pediatric AD treatment, as of November 2025. First-line therapies include topical corticosteroids, topical calcineurin inhibitors, and the phosphodiesterase-4 inhibitor crisaborole, all of which have demonstrated efficacy but are limited by safety considerations, tolerability, and acceptability for long-term use. In recent years, novel topical agents with distinct mechanisms of action have expanded the therapeutic landscape, representing important steroid-sparing alternatives for children with AD.

EXPERT OPINION: Emerging topical therapies for pediatric AD demonstrate substantial promise in addressing longstanding unmet needs, but long-term safety and practice-based effectiveness data remain critical for optimizing care.},
}

@article {pmid41811602,
year = {2026},
author = {İşinibilir, M and Doğan, O and Bilgin, R and Çalıcı, SZ},
title = {Correction to: Microbiome dynamics linked to Aurelia aurita during bloom and post-bloom periods in the Golden Horn Estuary: a snapshot via eDNA metabarcoding.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-026-37518-0},
pmid = {41811602},
issn = {1614-7499},
}

@article {pmid41811570,
year = {2026},
author = {Zeng, L and Han, Y and Li, Q and Han, L},
title = {The co-fermentation water-dispersible granules of two PGPR strains enhances growth, yields and quality of pepper by increasing soil nutrients and changing soil bacterial community.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41811570},
issn = {1573-0972},
support = {QianKeHe Foundation - ZK[2022] Key 009//Natural Science Foundation of Guizhou Province/ ; },
}

@article {pmid41811526,
year = {2026},
author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S},
title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.},
journal = {Cancer causes & control : CCC},
volume = {37},
number = {4},
pages = {},
pmid = {41811526},
issn = {1573-7225},
support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Adult ; Metagenomics/methods ; Risk Factors ; Finland/epidemiology ; Metagenome ; Diet ; },
abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.

METHODS: Our data included 1,228 adults aged 25-64 years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.

RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (< 0.0001).

CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology/etiology
Middle Aged
*Life Style
*Gastrointestinal Microbiome/genetics
Female
Male
Adult
Metagenomics/methods
Risk Factors
Finland/epidemiology
Metagenome
Diet

@article {pmid41811452,
year = {2026},
author = {Powell, CE and McSween, AM and Dohnalová, L and Kim, CH and Eisert, RJ and Sun, ZJ and Seo, HS and Marquardt, V and Dhe-Paganon, S and Thaiss, CA and Devlin, AS},
title = {Gut microbiome-produced bile acid metabolite lengthens the circadian period in host intestinal cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {11},
pages = {e2506313123},
doi = {10.1073/pnas.2506313123},
pmid = {41811452},
issn = {1091-6490},
support = {GM128618//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Humans ; *Circadian Rhythm/physiology/drug effects ; Mice ; *Bile Acids and Salts/metabolism ; *Lithocholic Acid/metabolism/pharmacology ; Mice, Inbred C57BL ; Male ; Cryptochromes/metabolism/genetics ; Colon/metabolism ; },
abstract = {Host circadian signaling, feeding, and the gut microbiome are tightly interconnected. Changes in the gut microbial community can affect the expression of core clock genes, but the specific metabolites and molecular mechanisms that mediate this relationship remain largely unknown. Here, we sought to identify gut microbial metabolites that impact circadian signaling. Through a phenotypic screen of a focused library of gut microbial metabolites, we identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator. LCA lengthened the circadian period of core clock gene hPer2 transcription in a dose-responsive manner in human colonic cells. We found evidence that LCA modulates the casein kinase 1 δ/ε (CK1δ/ε)-protein phosphatase 1 (PP1) feedback loop and stabilizes core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse distal ileum and colon. Taken together, our work identifies LCA as a molecular link between host circadian biology and the microbiome. Because bile acids are secreted in response to feeding, our work provides potential mechanistic insight into the molecular nature of the food-entrainable oscillator (FEO) by which peripheral clocks adapt to the timing of food intake. Given the association between circadian rhythm, feeding, and metabolic disease, our insights may offer an avenue for modulating host health.},
}

*Gastrointestinal Microbiome/physiology
Animals
Humans
*Circadian Rhythm/physiology/drug effects
Mice
*Bile Acids and Salts/metabolism
*Lithocholic Acid/metabolism/pharmacology
Mice, Inbred C57BL
Male
Cryptochromes/metabolism/genetics
Colon/metabolism

@article {pmid41811133,
year = {2026},
author = {Thomassen, GGM and Olguin-Diaz, F and Kostopoulos, I and Preece, K and Wopereis, H and Jourdan, M and Knol, J and Abrahamse, E and Renes, IB},
title = {A Combination of Inulin and Long-Chain Fructooligosaccharides Enhances in Vitro Iron Bioavailability and Supports a Favorable Infant Gut Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13296},
pmid = {41811133},
issn = {1520-5118},
abstract = {Iron deficiency is common during early life. Prebiotics may enhance iron bioavailability (IB) in the small intestine and in the colon. To study this, IMF was supplemented with inulin, lcFOS, their combinations (1:1 or 2:1), or scGOS:lcFOS (9:1). IMFs were digested in vitro, or fermented ex vivo yielding short-chain fatty acids (SCFA) and altering microbiota composition. Digested IMF containing either prebiotics or SCFA were incubated on Caco-2 cells to assess IB under simulated small-intestinal or colonic conditions respectively. Fermentation of inulin:lcFOS and scGOS:lcFOS increased Bifidobacteriaceae, reduced Enterobacteriaceae, and enhanced acetic acid (AA) production. Inulin:lcFOS increased small-intestinal IB (1.2-fold). SCFA from Inulin:lcFOS and scGOS:lcFOS increased colonic IB by 3.7- and 5.0-fold, respectively. When combining small-intestinal and colonic IB, overall IB increased ∼1.5-fold versus the control. Prebiotic-induced AA production played a key role in enhancing IB. Combining inulin or scGOS with lcFOS in IMF may improve iron absorption and support beneficial infant gut microbiota.},
}

@article {pmid41810990,
year = {2026},
author = {Zhang, Y and Han, B and Wang, X and Li, Y and Zou, YR and Li, SH and Li, XQ and Li, YB and Huang, Y and Sun, DZ and Li, YH and Qian, ZQ and Song, SH and Shi, L and Li, X and Zhang, Y},
title = {Maternal microbiome-derived propionate regulates offspring myelination via histone lactylation.},
journal = {Brain : a journal of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/brain/awag034},
pmid = {41810990},
issn = {1460-2156},
abstract = {The maternal gut microbiome plays a crucial role in regulating offspring neurodevelopment through microbial metabolite signaling, yet its influence on CNS myelinogenesis, a pivotal process for neural circuit maturation, remains poorly understood. Here, using antibiotic-induced maternal dysbiosis models, we identify propionate (PA), a short-chain fatty acid (SCFA) derived from the maternal microbiome, as a key epigenetic modulator of oligodendrocyte precursor cell (OPC) differentiation. Maternal antibiotic-induced gut dysbiosis led to significant hypomyelination in offspring, an effect that could be rescued by postnatal PA supplementation. PA not only enhanced developmental myelination but also promoted remyelination following lysolecithin-induced demyelination by inducing OPC differentiation. Mechanistically, PA induced histone H4K12 lactylation (H4K12la), thereby activating transcription of cGMP-PKG signaling components (e.g., Gna12) and upregulating Sox family transcription factors essential for oligodendrocyte differentiation. Taken together, our findings delineate a PA-H4K12la-cGMP-PKG pathway that links maternal microbial metabolism to offspring myelination, offering a promising SCFA-mediated epigenetic strategy for the treatment of CNS demyelinating disorders.},
}

@article {pmid41810941,
year = {2026},
author = {Aufiero, MA and Hohl, TM},
title = {Antibiotic-induced microbiota disruption impairs neutrophil-mediated immunity to respiratory Aspergillus fumigatus infection in mice.},
journal = {mBio},
volume = {},
number = {},
pages = {e0398225},
doi = {10.1128/mbio.03982-25},
pmid = {41810941},
issn = {2150-7511},
abstract = {Aspergillus fumigatus is an ubiquitous environmental mold that forms airborne conidia and can cause life-threatening infections in immunocompromised individuals. Invasive aspergillosis occurs in patients with quantitative or qualitative neutrophil defects who often receive systemic antibiotics to prevent or manage bacterial infections. Antibiotic-induced bacterial dysbiosis has been linked to impaired neutrophil bactericidal activity and to intestinal commensal bacteria escape during systemic candidiasis, though it remains unclear whether receipt of antibacterial antibiotics impairs neutrophil-dependent defenses against inhaled mold pathogens in the lung. Herein, we measured the outcome of A. fumigatus challenge in C57BL/6J mice that were treated with different antibiotics in the drinking water for 3 weeks prior to experimental infection. We found that ampicillin, but not neomycin or vancomycin treatment, significantly increased murine mortality and lung fungal burden. The heightened susceptibility was associated with impaired fungal killing by lung-infiltrating neutrophils and monocytes, as well as reduced neutrophil production of NADPH oxidase 2 (NOX2)-dependent reactive oxygen species (ROS). These findings demonstrate that systemic antibiotic treatment can compromise pulmonary immunity against A. fumigatus and suggest that the host microbiota can enhance neutrophil fungicidal activity by promoting NOX2-mediated ROS production.IMPORTANCEAspergillus fumigatus is an environmental mold that causes invasive pulmonary disease in immunocompromised individuals. Owing to limited diagnostic tools, a narrow arsenal of effective treatments, and rising antifungal resistance, the World Health Organization (WHO) has designated A. fumigatus as a critical priority fungal pathogen, highlighting the urgent need for further research. Patients with compromised immunity often receive broad-spectrum antibiotics to prevent or treat opportunistic infections, leading to significant disruption of the resident commensal microbiota. This antibiotic-induced dysbiosis has been linked to Clostridium difficile colitis and to intestinal overgrowth of vancomycin-resistant Enterococcus and Candida parapsilosis, preceding bloodstream infection. However, the impact of antibiotic treatment on susceptibility to invasive pulmonary aspergillosis remains undefined. In this study, we found that oral treatment with ampicillin, but not neomycin or vancomycin, significantly increased mortality in mice following A. fumigatus infection. Neutrophils from the lungs of ampicillin-treated mice also showed markedly impaired fungal killing. These findings raise the possibility that preserving microbiome integrity during antibiotic treatment could enhance immune protection against invasive aspergillosis in at-risk patient groups.},
}

@article {pmid41810937,
year = {2026},
author = {Lee, J and Kim, H-J and Kim, E-H and Kim, S and Park, B and Hong, S and Kang, J and Lee, J-Y and Lee, S},
title = {Prediction model for periodontitis stage based on the salivary microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0110325},
doi = {10.1128/msystems.01103-25},
pmid = {41810937},
issn = {2379-5077},
abstract = {This study aimed to characterize salivary microbiome compositions that can classify periodontal health and various stages of periodontitis. We collected saliva samples from 250 study subjects, including 100 periodontally healthy controls and 150 periodontitis patients in stages I/II/III. We performed 16S ribosomal RNA gene sequencing to characterize their salivary microbiomes. Alpha diversities show significant differences between healthy and periodontitis. Differentially abundant taxa were identified by ANCOM. Random forest machine learning models were used to classify each periodontitis stage based on the centered log-ratio of differentially abundant taxa. We identified 20 differentially abundant taxa among the groups in the salivary microbiomes of all groups. Among these differentially abundant taxa, Porphyromonas gingivalis and Actinomyces spp. are the most important taxa on the random forest model to classify the periodontitis statuses. Our random forest model classified multiple periodontitis statuses with an area-under-curve of 0.829 ± 0.124, sensitivity 0.884 ± 0.022, and specificity 0.652 ± 0.065. Moreover, because it can be difficult to diagnose in dentistry practice, we performed our classifier model to distinguish healthy or stage I, providing an area-under-curve of 0.736 ± 0.168, sensitivity 0.789 ± 0.102, and specificity 0.622 ± 0.196. Furthermore, our random forest model detected periodontitis patients from healthy individuals with an area-under-curve of 0.924 ± 0.088, sensitivity of 0.862 ± 0.175, and specificity of 0.921 ± 0.061. Finally, we evaluated our classification model with external data sets from Spanish and Portuguese subjects. Some evaluations showed a slight decrease, but it might be due to different salivary microbiome compositions from ethnicity. Significant differences were identified in the differentially abundant taxa among healthy controls and the various stages of periodontitis.IMPORTANCEPeriodontitis is a common but complex oral disease that can lead to tooth loss and contribute to systemic health issues. Early and accurate diagnosis is essential for effective intervention, yet traditional diagnostic methods often rely on invasive clinical assessments that may miss early signs. This study demonstrates that salivary microbiome profiles can be used to classify both periodontal health and multiple periodontitis stages using a machine learning approach. By identifying the 20 key microbial taxa, including Actinomyces spp., we developed a non-invasive predictive model with high diagnostic accuracy. Importantly, the model was also able to detect early-stage disease and performed well across external data sets, highlighting its potential for broader clinical application. These findings suggest that a salivary microbiome-based diagnostic tool may support more precise, accessible, and early diagnosis of periodontitis in dental disease management.},
}

@article {pmid41810763,
year = {2026},
author = {Pandey, VK and Tripathi, A and Choudhary, P and Thapliyal, S},
title = {Exploring the role of diet in modulating stress and emotional health: a review on mental nutrition and cognitive resilience.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70526},
pmid = {41810763},
issn = {1097-0010},
abstract = {The rise in mental-health-related disorders, including anxiety, depression, and cognitive impairment worldwide, has increased the demand for preventative non-pharmacological interventions and intervention aimed at modifiable lifestyle factors - particularly diet. Growing evidence shows that plant-based nutrition, with its anti-inflammatory and neuroprotective effects, is critically important for cognitive resilience, emotional stability, and mental wellbeing. Essential nutrient and bioactive compounds such as ω-3 fatty acids, polyphenols, B vitamins, magnesium, and probiotics themselves act on the gut-brain axis to alleviate neuroinflammatory stress. Functional and adaptogenic foods - for example, Ashwagandha, Rhodiola, and Holy Basil - are becoming the focus of interest as they play a significant role in cortisol control and stress adaptation. All plant-based dietary patterns, such as the Mediterranean, DASH (Dietary Approaches to Stop Hypertension), and plant-based diets, show comparable associations with lower risk for depression, anxiety, and cognitive deficits through enhancing gut microbiome richness and balancing neurotransmitters. This review outlines the scientific basis of mental nutrition, highlighting the interconnections between dietary patterns, gut microbiota composition, diet-mediated modulation of neurotransmitter levels, and neuroinflammatory pathways that collectively influence mental health. © 2026 Society of Chemical Industry.},
}

@article {pmid41810553,
year = {2026},
author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ},
title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70264},
pmid = {41810553},
issn = {2045-8827},
support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; },
mesh = {Humans ; *Glycoside Hydrolases/metabolism/genetics ; *Polysaccharides/metabolism ; Infant ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; Substrate Specificity ; Infant, Newborn ; },
abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.},
}

Humans
*Glycoside Hydrolases/metabolism/genetics
*Polysaccharides/metabolism
Infant
*Gastrointestinal Microbiome
*Metagenome
Feces/microbiology
Substrate Specificity
Infant, Newborn

@article {pmid41810506,
year = {2026},
author = {Hirano, Y and Tomofuji, Y and Edahiro, R and Kishikawa, T and Miyawaki, S and Okada, Y},
title = {Association between autoimmune diseases and the gut microbiome.},
journal = {International immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/intimm/dxag013},
pmid = {41810506},
issn = {1460-2377},
abstract = {The gut microbiome has emerged as an important environmental factor in the pathogenesis of autoimmune diseases. Advances in high-throughput sequencing technologies have enabled comprehensive characterization of the gut microbiome, providing detailed insights into its composition and functional potential. These approaches have been widely applied in autoimmune disease research, revealing disease-associated alterations in the gut microbiome of patients with conditions such as rheumatoid arthritis and systemic lupus erythematosus. In addition, microbiome sequencing data can be leveraged to investigate the gut virome, including viruses residing in the intestinal ecosystem. This review summarizes current evidence linking autoimmune diseases and the gut microbiome, with a particular focus on studies employing microbiome sequencing-based analyses.},
}

@article {pmid41810379,
year = {2026},
author = {Anzà, S and Rosa, BA and Herzberg, MP and Lee, G and Herzog, ED and Zhao, P and England, SK and Ndao, IM and Martin, J and Smyser, CD and Rogers, CE and Barch, DM and Hoyniak, C and McCarthy, R and Luby, J and Warner, BB and Mitreva, M},
title = {Simplifying Daily Cortisol Cycle Analysis: Validation and Benchmarking of the Cortisol Sine Score Against Cosinor and JTK_CYCLE models.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.23.26346831},
pmid = {41810379},
abstract = {UNLABELLED: The daily cortisol cycle is a critical indicator of hypothalamic-pituitary-adrenal (HPA) axis function. The current analytical approaches produce several outputs difficult to integrate into simple statistical models, clinical workflows, and ML/AI pipelines requiring single-value inputs. We developed the Cortisol Sine Score (CSS), a model-free scalar metric that quantifies daily cortisol exposure by computing a weighted sum of cortisol measurements across the day, using sine-transformed time-of-day weights. The CSS produces positive values for morning-dominant patterns, negative values for evening-shifted profiles, and near-zero values for flattened rhythms characteristic of chronic stress and circadian disruption. We validated the CSS performance in 3,006 samples from 501 pregnant women enrolled in the March of Dimes program, with cortisol values measured at 6 time points per day collected during the second trimester of pregnancy. The CSS showed strong correlations with observed and model-estimated amplitude and acrophase from Cosinor regression and JTK_CYCLE approaches, with excellent classifying performance (AUC=0.89, high versus low). The CSS successfully captured established associations between social disadvantage and cortisol dysregulation, and demonstrated utility in predicting gut microbiome composition in metagenomic analyses. Importantly, the CSS maintains excellent fidelity to the full 6-sample protocol with as few as 3-4 daily measurements. The 4-sample protocol achieves great performance (r = 0.952, MAE = 0.087) while reducing participant burden. The 06:00 time point was identified as essential for accurate CSS quantification. The CSS bridges the gap between circadian analysis and practical implementation by providing a simple, interpretable, and robust assessment of cortisol daily cycle in large-scale epidemiological studies, clinical screening, and biomedical sensors.

HIGHLIGHTS: Current state-of-the-art approaches estimating the daily cortisol exposures produce multi-output information difficult to implement in simple statistical analyses or ML/AI multi-omics approachesCortisol Sine Score is a novel model-free scalar metric expressing cortisol daily exposure and rhythmicity (morning vs evening exposure)Cortisol Sine Score was validated using 3006 salivary samples from clinical data and golden standards in circadian analyses such as Cosinor and JTK_CYCLECortisol Sine Score was the top performer in our benchmarking approach predicting association with social disadvantage and gut microbiome compositionReliable with 3-4 daily samples, reducing participant burdenOpen-source R package CortSineScore democratizes cortisol cycle analysis.},
}

@article {pmid41810375,
year = {2026},
author = {Anderson, SM and Cing, Z and Drewes, JL and White, JR and Southward, T and Beauregard, H and Ferri, JT and Wanyiri, JW and Roslani, A and Vadivelu, J and Tang, SN and Queen, J and Sears, CL},
title = {Clostridioides difficile Detection in a Human CRC Cohort.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.26346702},
pmid = {41810375},
abstract = {BACKGROUND: The role of the gut microbiome and specific enteric bacteria in influencing the development of colorectal cancer (CRC) remains incompletely understood. Recently, it was shown that human CRC-derived strains of Clostridioides difficile were capable of inducing colonic tumorigenesis in a susceptible mouse model. We hypothesized that C. difficile contributes to the pathogenesis of human CRC and would be enriched in CRC tumors compared to paired normal tissues from the same individual.

METHODS: We analyzed matched tumor/normal tissue samples from a cohort of 108 individuals presenting to a tertiary care hospital in Kuala Lumpur, Malaysia for CRC resection between 2013-2014. We assessed the prevalence of C. difficile detection using 16S rRNA amplicon sequencing with high-resolution taxonomic assignment as well as culture and PCR.

RESULTS: We found that detection of C. difficile was prevalent (38% of individuals), but of low abundance (tumor median relative abundance 0.01%, paired normal 0.006% [p=0.4]). Detection of C. difficile was more prevalent in individuals with biofilm-positive tumor tissues than biofilm-negative (i.e., 81% of C. difficile -positive individuals were biofilm-positive vs. 63% of C. difficile -negative individuals [p=0.04]). Additionally, in exploratory analyses, we describe patterns of taxonomic and inferred functional pathway differences between C. difficile- positive and C. difficile -negative groups.

CONCLUSION: These findings suggest that C. difficile is frequently present in low abundance in the tumor microbiome with a potentially significant impact on community composition and function.},
}

@article {pmid41810263,
year = {2026},
author = {Tan, Y and Wu, Y and Chen, Z and Zhang, Z and Huang, S and Li, Z and Huang, Y},
title = {Intestinal Flora Reconfiguration via Electroacupuncture: A Strategy to Counteract Depressive-Like Symptoms in Rats.},
journal = {Neuropsychiatric disease and treatment},
volume = {22},
number = {},
pages = {565614},
pmid = {41810263},
issn = {1176-6328},
abstract = {BACKGROUND: Depression is a global health concern, and acupuncture has emerged as an effective treatment. The role of intestinal microbiota in depression remains unclear. This study, utilizing 16S rRNA high-throughput sequencing, aimed to explore the relationship between electroacupuncture (EA) and depressive behavior by examining changes in the intestinal microbiota.

MATERIALS AND METHODS: Forty-eight male Sprague-Dawley rats were utilized, with 13 assigned to the normal control (NC) group. The remaining rats underwent a 28-day depression modeling process, and those exhibiting depressive symptoms were randomly divided into chronic unpredictable mild stress (CUMS) and EA groups. The EA group received 14 days of treatment. Behavioral analyses were conducted on rats from the NC, CUMS, and EA groups to assess EA's effectiveness. Additionally, 16S rRNA sequencing was performed on randomly selected rats from each group.

RESULTS: By examining the behavior of 39 rats and the intestinal microbiota of 18 rats, we found that EA may alter the composition of the intestinal microbiota community structure in CUMS rats, particularly modulating the abundance of Akkermansia in a manner potentially linked to gut-brain axis regulation, including stress- and inflammation-related pathways that may influence microbial composition.

CONCLUSION: The potential antidepressant impact of electroacupuncture (EA) might be linked to the modulation of Akkermansia abundance within the brain-gut axis.},
}

@article {pmid41810106,
year = {2026},
author = {Yu, Z and Xu, Y and Li, W and Hu, Y and Zhang, C},
title = {Risk Factors and Biomarkers for Immune Checkpoint Inhibitor-mediated Hepatotoxicity: Emerging Insights and Future Perspectives.},
journal = {Journal of clinical and translational hepatology},
volume = {14},
number = {2},
pages = {215-231},
pmid = {41810106},
issn = {2310-8819},
abstract = {In the past decade, immune checkpoint inhibitors (ICIs) have dramatically changed cancer treatment, significantly improving outcomes for patients with various malignancies. Nonetheless, their widespread application has resulted in a rise in immune-related adverse events due to excessive immune activation, including immune-mediated hepatotoxicity (IMH). IMH can cause serious complications and even death, underscoring the need for early prediction and intervention. This review outlines the current understanding of risk factors and predictive biomarkers for IMH in cancer patients undergoing ICI therapy, with risk factors divided into patient-associated, tumor-associated, and agent-associated categories. Higher IMH risk is related to female sex, younger age, extreme BMI, Asian ethnicity, and chronic liver disease. Cancer type, prior ICI treatment, dual ICI combination therapy, and the concurrent use of chemotherapy, targeted agents, or other hepatotoxic drugs (e.g., acetaminophen, statins) also increase the risk of IMH. Potential predictive biomarkers encompass circulating blood cells, serum proteins, autoantibodies, cytokines, gene profiles, and the gut microbiome. Despite promising findings, the predictive value of these biomarkers remains inconsistent, and no definitive biomarker has been established for routine clinical use. Large-scale prospective studies are essential to verify the predictive value of these biomarkers and facilitate their integration into clinical practice, thereby providing deeper insights into the early identification and individualized management of IMH during ICI therapy.},
}

@article {pmid41810018,
year = {2026},
author = {Ding, Q and Teng, Y and Zhu, H and Jia, Z and Xu, S and Hu, B and Chen, B and Dai, J and Sun, J and Nie, P and Liu, Z and Chen, Q and Wang, X and Xu, X and Zhang, X and Duan, S},
title = {Local periodontal injection, systemic heart repair: A dual-functional hydrogel for non-invasive concurrent treatment of periodontitis and myocardial infarction.},
journal = {Bioactive materials},
volume = {62},
number = {},
pages = {17-33},
pmid = {41810018},
issn = {2452-199X},
abstract = {Periodontitis and myocardial infarction (MI), the leading cause of mortality worldwide, represent globally prevalent inflammatory diseases with bidirectional pathophysiological links. Despite the urgent demand for non-invasive strategies capable of alleviating local periodontal destruction while mitigating associated systemic cardiovascular complications, no integrated treatment modality currently exists. To address this challenge, a protein-loaded antibacterial hydrogel, thiolated chitosan/AMP-PEG-maleimide (C1.5P4/BMP-2), with novel sustained protein release properties was developed. This hydrogel features an interconnected microporous architecture that: (1) enables high-efficiency BMP-2 protein encapsulation, (2) preserves protein bioactivity while ensuring sustained release, thereby addressing the recognized challenge of hydrogel-based protein delivery, (3) confers potent antibacterial properties, (4) facilitates remote cardiac function improvement by resolving periodontal inflammation. In murine models, locally, it attenuated alveolar bone loss (2-fold greater bone regeneration vs controls) while systemically improving post-MI cardiac function (75.6% higher ejection fraction). Mechanistically, the hydrogel's protein-protective microenvironment synergized with its antimicrobial action selectively inhibiting Gram-negative (G[-]) anaerobic pathogens (primary periodontal culprits) while enriching Gram-positive (G[+]) commensals, regulating biofilm G[-]/G[+] ratio. Concomitantly, this dual action modulates the oral-cardiac inflammatory axis, specifically downregulating B2 cell/TNF-α signaling to mitigate systemic inflammation associated with MI. Collectively, this study presents a novel non-invasive protein-stabilizing hydrogel that addresses periodontitis-MI comorbidity through sustained osteogenic factor delivery coupled with microbiome-immune modulation.},
}

@article {pmid41809991,
year = {2026},
author = {Ma, L and Wang, W and Ma, S and Wang, Y and Li, H and Gao, Y and Xie, X},
title = {Association analysis of the differences in intestinal flora and clinical tumor indicators among colorectal cancer patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1742672},
pmid = {41809991},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics ; Biodiversity ; Adult ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common malignant tumor globally, and its development is closely related to intestinal flora dysbiosis. However, the heterogeneity of cancerous tissues, paracancerous tissues, and fecal flora, and their clinical significance, has not been fully elucidated.

AIM: This study aimed to systematically analyze the diversity, composition, and functional differences of intestinal flora in patients with CRC compared to healthy individuals, and to reveal potential associations between the characteristics of these microbial communities and tumorigenesis and development.

METHODS: Thirty CRC patients (30 cancerous tissue samples, 30 paracancerous tissue samples, and 30 fecal samples) and 30 healthy volunteers (30 fecal samples) were enrolled in the study. The microbial communities were analyzed using 16S rRNA sequencing, and the status of the bacterial flora was evaluated by combining alpha and beta diversity, species difference analysis, the Gut Microbiome Health Index (GMHI), and the Gut Microbiome Dysbiosis Index (MDI). The correlation of these factors with clinical parameters was then analyzed.

RESULTS: The alpha diversity of the cancerous tissue from patients with CRC was significantly lower than that of the fecal samples (p < 0.05). The intestinal microbiota of patients with CRC was statistically different from that of healthy individuals (p < 0.01). Additionally, there was a statistically significant difference in beta diversity between the cancerous tissue and fecal gut microbiota of patients with CRC (p < 0.01). The microbiota of the paracancerous tissues exhibited significantly higher GMHIs than the cancerous tissues. Healthy individuals demonstrated better gut health than individuals with CRC. The fecal samples from CRC patients had a higher GMHI than the cancerous tissues. The difference was statistically significant (p < 0.001). For MDI, however, the trend was reversed. A statistically significant positive correlation was observed between Escherichia coli and tumor size (p < 0.05). Similarly, Methylobacterium/Methylorubrum exhibited a statistically significant positive correlation with tumor stage (p < 0.05).The research found that Blautia and Faecalibacterium had higher abundances in the feces of healthy individuals and the tissues adjacent to colorectal cancer, while Escherichia-Shigella, Bacteroides, Enterococcus, and Fusobacterium had higher abundances in colorectal cancer tissues.

CONCLUSION: The intestinal flora of CRC patients is characterized by decreased diversity, an enrichment of pathogenic bacteria, and a reduction in protective flora. these microbial alterations are associated with tumor progression, potentially via inflammatory and metabolic pathways, although causal mechanisms remain to be functionally validated. The flora health index and dysbiosis index have potential for use as adjunctive diagnostic tools. However, individualized preventive intervention strategies need to be developed in the future by combining multi-omics data.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
RNA, Ribosomal, 16S/genetics
Middle Aged
Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
DNA, Bacterial/genetics
Biodiversity
Adult

@article {pmid41809915,
year = {2025},
author = {Karras, J and Schwab, F and Maechler, F},
title = {VRE and antibiotic use in German ICUs-an ecological analysis of 15 years of surveillance data.},
journal = {JAC-antimicrobial resistance},
volume = {7},
number = {6},
pages = {dlaf216},
pmid = {41809915},
issn = {2632-1823},
abstract = {BACKGROUND: This 15 years study reveals highlighting key differences in resistance trends and incidence of vancomycin-resistant Enterococcus faecium versus Enterococcus faecalis in German intensive care units (ICUs). By linking these patterns to antibiotic use, it uncovers crucial insights into the evolving battle against vancomycin-resistant enterococci (VRE) in critical care.

METHODS: A retrospective ecological cohort study using data from the German SARI (Surveillance of Antimicrobial Use and Antimicrobial Resistance in German ICUs) system was conducted from January 2006 to December 2020. Data from 79 ICUs were analysed. Incidence densities (ID) and resistance rates (RR) for E. faecium and E. faecalis were calculated, alongside antibiotic use densities in defined daily doses per 100 patient days. Generalized linear models and generalized estimating equations assessed temporal trends and associations with antibiotic consumption.

RESULTS: A total of 42 701 Enterococcus isolates were analysed: 21 672 E. faecium and 21 029 E. faecalis. VRE was found in 17.0% of E. faecium and 0.2% of E. faecalis. VRE. faecium showed a significant increase in ID and RR, while vancomycin-sensitive E. faecium decreased. VRE. faecalis remained rare. Antibiotic use patterns showed a significant increase in carbapenem (184.9%), glycopeptides (131.7%), and vancomycin (93.9%).

CONCLUSIONS: This study highlights a sustained increase in the incidence and resistance of VRE. faecium. While glycopeptides are well-known contributors, carbapenem use may also play a role in VRE colonization, potentially through disruption of the microbiome. Further research is needed to clarify the complex relationship between antibiotic exposure, microbiome-related mechanisms, and resistance development.},
}

@article {pmid41809889,
year = {2025},
author = {Kim, J and Sim, Y and Kim, D and Kwon, J and Lee, S and Rungratanawanich, W and Kim, J and Jung, J and Lee, Y and Hyun, S and Lee, S and Kwon, H and Song, B and Seo, K and Kim, D and Cho, Y},
title = {Ginseng-derived exosome-like nanovesicles protect against liver fibrosis by regulating TIMP2 pathways and gut dysbiosis.},
journal = {Asian journal of pharmaceutical sciences},
volume = {20},
number = {6},
pages = {101105},
pmid = {41809889},
issn = {2221-285X},
abstract = {Metabolic dysfunction-associated fatty liver disease (MASLD) and alcohol-associated liver disease (ALD) are prevalent chronic liver diseases that can progress to steatohepatitis, fibrosis, cirrhosis, and ultimately liver failure. Here, we demonstrated that oral administration of GNVs provided substantial protection against liver injury and fibrosis in MASLD and ALD mouse models. In a Western-style high-fat diet-induced MASLD model and a chronic binge alcohol-induced ALD model, GNVs treatment significantly reduced gut leakiness by restoring intestinal junctional complex proteins and rebalancing the gut microbiome. GNVs attenuated hepatic lipid accumulation, oxidative stress and fibrogenic markers. GNV treatment downregulated the fibrosis-associated tissue inhibitor of metalloproteinase-2 (TIMP2) pathway in hepatic stellate cells, which is linked to enhanced matrix degradation and reduced fibrogenesis. GNVs prevent MASLD- and ALD-associated gut barrier dysfunction and liver fibrosis through modulation of the gut-liver axis and the TIMP2 pathway. Edible GNVs represent a novel, multifaceted therapeutic strategy for managing chronic liver diseases.},
}

@article {pmid41809810,
year = {2026},
author = {Qi, Y and Shi, J and Zhang, Q and Xuan, Y and Zhang, H and Duan, Y},
title = {Environmental and microbiome determinants of sperm quality: a narrative review on male health.},
journal = {Translational andrology and urology},
volume = {15},
number = {2},
pages = {64},
pmid = {41809810},
issn = {2223-4691},
abstract = {BACKGROUND AND OBJECTIVE: With the rapid development of modern production and daily life, human fertility has shown a declining trend, with male factors accounting for approximately half of the cases. Declining sperm quality is the primary issue in male infertility, and environmental factors play a significant role in its development. This paper aims to thoroughly explore the impact of environmental factors on male sperm quality and provide insights for the etiology and prevention of male infertility.

METHODS: A comprehensive literature search was conducted in PubMed from its inception to June 25, 2025, for articles on the effects of traditional environmental factors on male sperm quality. 84.9% of the references were published between 2020 and 2025, with most studies being recent and related to human male fertility. The search included all articles containing the following keywords: "sperm quality", "environmental factors", "temperature", "heavy metals", "pesticide", "phthalate", "viruses", "bacteria", "Radiofrequency Electromagnetic Radiation (RF-EMR)", "per- and polyfluoroalkyl substances (PFAS)", "air pollution", "Benzo[a]pyrene (BaP)", and "microbiome". The retrieved articles were reviewed to summarize the effects of environmental factors on male sperm quality.

KEY CONTENT AND FINDINGS: A total of 250 articles were identified with these keywords and later screened for inclusion. We finally included 82 publications that were relevant to our topic. Based on recent studies within China and international research, this paper not only examines the effects of traditional pollutants at the molecular mechanism level but also focuses on emerging environmental factors such as the synergistic toxicity of new environmental pollutants-PFAS, and heavy metals-as well as 5G radiofrequency radiation. These environmental factors significantly reduce sperm concentration, motility, morphological integrity, and DNA stability through multiple mechanisms and systemic effects-including reactive oxygen species (ROS), endocrine disruption, DNA damage, and inflammatory responses-thereby impairing male fertility.

CONCLUSIONS: Traditional and emerging environmental factors synergistically impair male sperm quality through multiple mechanisms, including oxidative stress, endocrine disruption, epigenetic alterations, and systemic inflammation. Future experimental research should shift from single-pollutant studies to real-world mixture exposure investigations, utilizing multi-omics technologies to deeply analyze epigenetic mechanisms and transgenerational effects. Clinically, environmental risk factors should be incorporated into routine screening and counseling for male infertility, with enhanced antioxidant intervention measures. At the policy level, there is an urgent need to improve chemical regulation to prevent potentially stronger reproductive toxicity from novel substitutes and to enhance air pollution control. Curbing the global decline in fertility at its source holds significant importance for advancing population reproductive health.},
}

@article {pmid41809656,
year = {2026},
author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M},
title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10894},
pmid = {41809656},
issn = {1535-3699},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration & dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Obesity/microbiology
*Probiotics/administration & dosage/therapeutic use
*Bifidobacterium bifidum/physiology
Male
Female
Adult
Middle Aged
Dysbiosis/microbiology
Feces/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid41809655,
year = {2026},
author = {Zhou, B and Parekh, Z and Phung, C and Rodriguez, SH and Skondra, D},
title = {The gut-retina axis in age-related macular degeneration: immune crosstalk and metabolite production.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10847},
pmid = {41809655},
issn = {1535-3699},
mesh = {Humans ; *Macular Degeneration/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology/physiology ; Animals ; Dysbiosis/immunology ; *Retina/immunology/metabolism/pathology ; },
abstract = {Current therapies slow down advanced features but do not halt or reverse degeneration and neovascularization in dry and wet age-related macular degeneration (AMD). Recent research implicates the gastrointestinal microbiome as a potential critical modulator in AMD pathogenesis through the gut-retina axis. Dysbiosis, characterized by imbalanced microbial diversity, composition and function, can exacerbate systemic and retinal inflammation through microglial priming, inflammasome activation, and secretion of pro-angiogenic cytokines (IL-6, IL-1β, TNF-α, VEGF). Additionally, microbiome-derived metabolites such as short-chain fatty acids and bile acids may exert modulatory roles in host immunity and homeostasis. Their depletion in conjunction with enrichment of specific microbial taxa have been linked to progression of advanced AMD. Together, these complex systems of immune crosstalk in relation to dysbiosis highlight the gut-retina axis as a promising therapeutic target. Dietary modifications, particularly Mediterranean and high-fiber diets, enhance production of protective metabolites and are associated with decreased AMD progression risk compared to Western dietary patterns. Experimental strategies such as fecal microbiota transplantation in animal models and drug repurposing strategies show promise in modulating disease severity. This review synthesizes current mechanistic insights into microbial-immune crosstalk in AMD, emphasizing the interplay of dysbiosis, immune activation, and metabolite signaling.},
}

Humans
*Macular Degeneration/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology/physiology
Animals
Dysbiosis/immunology
*Retina/immunology/metabolism/pathology

@article {pmid41809649,
year = {2026},
author = {Kawano, A and Yamashiro, K and Takahashi, Y and Yoshida, Y},
title = {Effects of Initial Periodontal Therapy on Intraoral Bacterial Flora in Patients With Oral Contraceptive-Related Severe Gingivitis.},
journal = {Case reports in dentistry},
volume = {2026},
number = {},
pages = {5078642},
pmid = {41809649},
issn = {2090-6447},
abstract = {Gingivitis is a common inflammatory condition of the gingival tissues, influenced by microbial plaque and various systemic factors, including hormonal changes. Oral contraceptives containing estrogen and progestin are known to exacerbate gingival inflammation. We report the case of a 20-year-old Japanese woman who presented with gingival swelling and bleeding despite self-care, with a history of orthodontic treatment and oral contraceptive use. Clinical examination revealed probing pocket depths of ≥ 4 mm and bleeding on probing in more than half of the sites, a periodontal inflamed surface area (PISA) of 995.8 mm[2], and a plaque control record of 78%. Bacterial analysis identified elevated levels of Prevotella intermedia, Prevotella melaninogenica, and Fusobacterium nucleatum. Initial periodontal therapy-consisting of scaling and root planing, supported with systemic and topical antibiotics-was provided, followed by gingivectomy at sites lacking adequate gingival attachment. Posttreatment evaluation demonstrated marked reductions in probing depth, bleeding on probing, and PISA (44.9 mm[2]), with plaque control improving to 31.3%. Microbiome analysis revealed a decrease in pathogenic anaerobes and an increase in beneficial aerobic bacteria. The patient's oral hygiene practices improved substantially through targeted education and self-care instruction, supporting the maintenance of periodontal health. This case highlights that initial periodontal therapy, combined with patient education and regular monitoring, can effectively reduce gingival inflammation and favorably modify the oral microbiome in oral contraceptive-related gingivitis. Awareness of the potential impact of oral contraceptives on periodontal health and implementation of individualized oral hygiene measures are essential for preventing disease progression in similar patients.},
}

@article {pmid41809604,
year = {2026},
author = {Srivastava, S and Mir, RA and Hussain, SJ and Mitra, S and Srivastava, S and Kumar, P and Kaur, H},
title = {Microbial engineering for pesticide degradation: current insights and future directions for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1751932},
pmid = {41809604},
issn = {1664-302X},
abstract = {Pesticides are synthetic agrochemicals widely used to protect crops from pests and diseases; however, their limited biodegradability and indiscriminate application pose serious risks to non-target organisms, soil fertility, human health, and overall environmental sustainability. Conventional physical and chemical remediation strategies often fall short in restoring contaminated ecosystems, highlighting the urgent need for effective and sustainable pesticide mitigation approaches. In recent years, in situ bioremediation has emerged as a promising, eco-friendly, and cost-effective strategy for pesticide degradation in agricultural soils. Under favourable conditions, microorganisms utilise pesticides as sources of carbon, sulphur, and electrons, facilitating their breakdown through diverse metabolic pathways, with enzymatic degradation playing a central role in chemical transformation. Microbial consortia exhibit enhanced degradation efficiency by leveraging functional diversity and synergistic interactions among their microbial members. For instance, a consortium comprising Azospirillum, Cloacibacterium, and Ochrobacterium achieved 100% degradation of 50 mg L[-1] glyphosate within 36 h. Advances in microbiome engineering have further expanded the scope of bioremediation by enabling the targeted manipulation of microbial communities to improve degradation specificity and performance. Notably, the recombined genomes of Psathyrella candolleana and Pseudomonas putida, generated through protoplast fusion, degraded 78.98% of pentachlorophenol in contaminated water. Additionally, engineering the rhizosphere with plant growth-promoting microorganisms, combined with microbial genetic modification, has demonstrated significant potential in enhancing pesticide degradation while simultaneously improving crop growth and productivity. Such integrative approaches represent a sustainable pathway towards resilient agroecosystems. This review synthesises current knowledge on the impacts of pesticides on crop physiology and metabolism, explores conventional and advanced microbe-mediated degradation strategies, and highlights the role of microbial engineering and consortia-based systems. Furthermore, it discusses emerging technologies, environmental and economic benefits, and recent patentable innovations, underscoring their relevance for sustainable agriculture and ecological restoration.},
}

@article {pmid41809465,
year = {2026},
author = {Suarez, M and Martínez, R and González-Martínez, F and Torres, AM and Mateo, J},
title = {Artificial intelligence and digital transformation of gastroenterology and hepatology: A critical review of clinical applications and future challenges.},
journal = {World journal of hepatology},
volume = {18},
number = {2},
pages = {114834},
pmid = {41809465},
issn = {1948-5182},
abstract = {Artificial intelligence (AI) is reshaping modern medicine, and gastroenterology and hepatology are among the specialties where its impact is becoming increasingly evident. AI has demonstrated the ability to process and analyze large amounts of clinical, radiological, endoscopic, and multi-omics data, offering unprecedented opportunities to enhance diagnostic accuracy, optimize therapeutic decision-making, and reduce variability in clinical practice. In endoscopy, computer-aided detection and diagnosis systems have shown consistent improvements in adenoma detection rates and real-time polyp characterization, while in hepatology, machine learning models outperform traditional scores for non-invasive assessment of liver fibrosis. Furthermore, multimodal approaches integrating genomics, microbiome, and imaging data are paving the way for precision medicine in inflammatory bowel disease and other complex digestive conditions. Despite these promising advances, significant barriers remain. The quality and heterogeneity of training data, the lack of rigorous external validation, and the opaque "black box" nature of many algorithms limit their clinical reliability. Ethical challenges, including accountability in case of diagnostic errors, protection of patient privacy, cost, and equitable access, also need to be addressed. This narrative review summarizes the current applications of AI in gastroenterology and hepatology, critically examines methodological and ethical challenges, and outlines future perspectives. Responsible, transparent, and equitable implementation will be essential for AI to transition from an emerging promise to a consolidated tool that improves outcomes and advances personalized digestive care.},
}

@article {pmid41809456,
year = {2026},
author = {Salamon, D and Krawczyk, A and Zapała, B and Duplaga, M and Kowalska-Duplaga, K and Gosiewski, T},
title = {Gut bacterial and fungal signatures in relation to human leukocyte antigen-DQ2/DQ8 in children with celiac disease and siblings.},
journal = {World journal of gastroenterology},
volume = {32},
number = {10},
pages = {116128},
pmid = {41809456},
issn = {2219-2840},
mesh = {Humans ; Child ; *Gastrointestinal Microbiome/immunology/genetics ; *Celiac Disease/microbiology/immunology/genetics ; Male ; Female ; Adolescent ; *HLA-DQ Antigens/genetics/immunology ; Siblings ; Child, Preschool ; Feces/microbiology ; Genetic Predisposition to Disease ; Case-Control Studies ; *Fungi/isolation & purification/genetics ; *Bacteria/isolation & purification/genetics/classification ; Infant ; Mycobiome/immunology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The presence of human leukocyte antigen (HLA)-DQ2 and/or HLA-DQ8 alleles is necessary but not sufficient for the development of celiac disease (CeD). This suggests that additional environmental and biological factors, including bacteria and, above all, the still rarely studied fungal gut microbiota, play key roles in disease onset and progression.

AIM: To characterize and compare the intestinal bacteriobiota and mycobiota profiles of children with newly diagnosed CeD and their unaffected siblings, in comparison with a healthy control group.

METHODS: The study included children and adolescents aged 1 to 18 years. Participants were divided into three groups: (1) 14 patients with newly diagnosed CeD; (2) 16 asymptomatic siblings of CeD patients; and (3) 19 healthy children (control group). Stool samples were collected from all eligible participants. Next-generation sequencing was performed, followed by analysis of the relationship between the gut microbiota and genetic predisposition to CeD, with attention to the HLA DQ2/8 alleles.

RESULTS: Regarding alpha diversity, the CeD and sibling groups differed significantly from the control group (bacteria), and the CeD group differed from siblings (fungi). Significant dissimilarities in beta diversity were observed between siblings and both CeD and control groups. In comparisons between CeD group and their siblings, 13 indicator bacterial species were identified, whereas in comparisons between the CeD group and their siblings and controls, 8 indicator fungal species were detected. No significant correlation was found between bacterial species and the presence of the HLA DQ2.5 allele, or between fungal species and HLA DQ2.2. A strong (r = 0.8-0.9) positive relationship was found between Subdoligranulum variabile and several bacterial species. A moderate (r = 0.4-0.7) positive correlation was observed between the fungal species Microidium phyllanthi and Bifidobacterium longum, Clostridium leptum and Romboutsia timonensis.

CONCLUSION: While DQ2.5 plays a central role in disease pathogenesis, it appears to have less direct influence on microbial composition. The distinct fungal signatures observed in siblings may serve as early indicators of risk and warrant further investigation.},
}

Humans
Child
*Gastrointestinal Microbiome/immunology/genetics
*Celiac Disease/microbiology/immunology/genetics
Male
Female
Adolescent
*HLA-DQ Antigens/genetics/immunology
Siblings
Child, Preschool
Feces/microbiology
Genetic Predisposition to Disease
Case-Control Studies
*Fungi/isolation & purification/genetics
*Bacteria/isolation & purification/genetics/classification
Infant
Mycobiome/immunology
High-Throughput Nucleotide Sequencing

@article {pmid41809269,
year = {2026},
author = {Pei, J and Chen, L and Pushparaj, R and Huang, P and Pan, G and Sun, C and Gao, X and Zhang, L and Manirujjaman, M and Huang, CK and Ting, PS and Deng, Z and Chen, S and Zhang, X and Vatsalya, V and McClain, CJ and Feng, W},
title = {High-dose taurine supplementation exacerbates alcohol-associated liver disease by inducing gut microbiota dysbiosis and bile acid dysregulation in mice.},
journal = {eGastroenterology},
volume = {4},
number = {1},
pages = {e100321},
pmid = {41809269},
issn = {2976-7296},
abstract = {BACKGROUND: β-aminoethanesulfonic acid (taurine) is a conditionally essential amino acid that plays critical roles in bile acid (BA) conjugation, antioxidative defence and metabolic regulation. Previous studies showed that faecal taurine level was reduced in patients with alcohol-associated liver disease (ALD), suggesting that taurine supplementation may have beneficial effects. This study aimed to determine whether oral taurine supplementation prevents the development of ALD in mice and to elucidate the underlying mechanisms.

METHODS: A total of 8-week-old male mice were subjected to a chronic-plus-binge ALD model. Taurine was administered orally via the diet for ten days before and during ethanol exposure. Faecal 16S ribosomal RNA metagenomic analysis, liver RNA sequencing and BA profiling were performed.

RESULTS: High-dose taurine supplementation (3 g/kg body weight/day) was associated with worsened ethanol-induced liver injury, as indicated by increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, hepatic steatosis, apoptosis and inflammation. At the molecular level, high-dose taurine treatment was associated with reduced Cpt1a expression, altered expression of genes involved in fatty acid β-oxidation and lipogenic gene Fasn, and decreased expression of Baat, accompanied by changes in taurine-conjugated BA profiles. These alterations were accompanied by changes in BA composition and intestinal FXR-associated gene expression. Taurine supplementation was also associated with shifts in gut microbial composition, including enrichment of hydrogen sulfide-producing bacteria, increased microbial H2S production, impaired intestinal barrier-related parameters and increased bacterial translocation to the liver, paralleling enhanced hepatic inflammatory responses. In contrast, low-dose taurine supplementation (0.2 g/kg body weight/day) was associated with improved liver phenotypes, including reduced steatosis, lower serum ALT and AST levels, decreased Fasn expression and enhanced BA conjugation. Collectively, these results indicate a dose-dependent association between taurine supplementation and ALD-related outcomes.

CONCLUSIONS: Our findings suggest that high-dose taurine supplementation is associated with unfavourable alterations in gut microbiota composition, intestinal barrier integrity, BA metabolism and hepatic taurine-related pathways in ALD, coinciding with exacerbated liver injury. In contrast, low-dose taurine supplementation was associated with improved hepatic outcomes. These results highlight the importance of dose considerations in taurine supplementation and support the concept that taurine may exert divergent effects on ALD depending on the administered dose.},
}

@article {pmid41809178,
year = {2026},
author = {Mundhra, SK and Kochhar, R},
title = {Methodological insights into fecal microbiota transplantation: Dissecting key approaches for success.},
journal = {World journal of methodology},
volume = {16},
number = {1},
pages = {108875},
pmid = {41809178},
issn = {2222-0682},
abstract = {Fecal microbiota transplantation (FMT) has emerged as a revolutionary treatment strategy for restoring gut microbiota in recurrent Clostridioides difficile infection and has also been explored across a broader range of dysbiosis-related diseases such as inflammatory bowel disease where it has demonstrated promising results and potential therapeutic benefits. The success of FMT largely depends on the careful implementation of best practices, which include selecting appropriate donors, preparing the stool properly, and choosing the right delivery methods. This mini-review explores the evolution of FMT methodologies, including donor screening protocols, advances in stool preparation, and innovations in administration routes. We also discuss emerging approaches, such as synthetic microbiota and microbiome engineering, alongside the challenges and future directions for standardizing FMT. These methodological advancements aim to enhance safety, efficacy, and accessibility of FMT, establishing it as a key player in microbiome-based therapies.},
}

@article {pmid41809042,
year = {2026},
author = {Ratsika, A and Bergmann, CA and Valderrama, B and Bastiaanssen, TFS and Sharvin, BL and Renes, IB and Knol, J and Gunnigle, E and Clarke, G and Cryan, JF},
title = {Early-life microbiota disruption-induced deficits in the social brain are sensitive to diet.},
journal = {iScience},
volume = {29},
number = {3},
pages = {114968},
pmid = {41809042},
issn = {2589-0042},
abstract = {Diet is one of the major modulators of the microbiota-gut-brain axis across the lifespan. Milk bioactive components, including human milk oligosaccharides such as fucosyllactose and sialyllactose, and prebiotics, including GOS and FOS, promote the viability of commensal bacteria, fortify the intestinal barrier, and improve cognitive development. Here, we investigate the ability of these dietary components alone or in combination to counter the behavioral and physiological effects of early-life microbiota depletion via broad-spectrum antibiotics in mice. Microbiota depletion impaired social recognition in juvenile mice, which was reversed by supplementation with human milk oligosaccharides, GOS/FOS, and their combination. Transcriptomic analysis in brain areas linked to social memory (amygdala and prefrontal cortex), revealed that pathways for central nervous system development, learning, learning and memory are sensitive only to the combined supplementation. Together, our data show that prebiotics and milk bioactive components exert beneficial effects on the host by reversing microbiota depletion-related deficits on the brain and behavior.},
}

@article {pmid41809000,
year = {2026},
author = {Pishchany, G and Fryling, KE and Vasukuttan, V and Shin, YH and Mortimer, TD and Grad, YH and Clardy, J},
title = {Aerocavin is an antibiotic with potent and specific anti-Neisserial activity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.23.707490},
pmid = {41809000},
issn = {2692-8205},
abstract = {Gonorrhea, caused by N. gonorrhoeae , is a widespread sexually transmitted disease that is becoming resistant to all currently used antibiotics. Therefore, new therapeutics against gonorrhea are desperately needed. Here, we show that a natural product - aerocavin, is highly potent and specific against Neisseria . Aerocavin accumulates in N. gonorrhoeae at high levels and inhibits bacterial RNA polymerase (RNAP) by binding the switch region. Aerocavin resistance mutations evolve in N. gonorrhoeae at a low rate and are absent in clinical isolates. Previously overlooked narrow-spectrum antimicrobials like aerocavin may enable microbiome-sparing treatments of gonorrhea.},
}

@article {pmid41808841,
year = {2026},
author = {Huo, T and Huang, X and Liao, J and Zhang, H and Hu, L and Xie, M},
title = {The bidirectional effects and mechanisms of the oral and gut microbiomes: a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1697413},
pmid = {41808841},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Mouth/microbiology/immunology ; Dysbiosis/immunology/microbiology ; Animals ; *Microbiota ; },
abstract = {Among the microbial ecosystems of the human body, the gut and oral microbiota constitute the two largest communities, collectively harboring thousands of bacteria, fungi, and viruses. Under physiological conditions, these microbiotas maintain internal homeostasis and stability, thereby protecting the host against pathogenic colonization. However, when pathogens such as Porphyromonas gingivalis translocate from the oral cavity to the gut, disruption of gut microbial homeostasis may occur, increasing the risk of disease development. Potential mechanisms underlying this association include the establishment of new symbiotic relationships, the disruption of the intestinal barrier, the activation or suppression of inflammatory cells-particularly the balance between T helper 17 (Th17) cells and regulatory T cells (Tregs)-and the induction of systemic inflammation. Conversely, gut microbiota dysbiosis, as observed in patients with inflammatory bowel disease, irritable bowel syndrome (IBS), or colorectal cancer, is also associated with alterations in the composition and diversity of the oral microbiota. Factors such as immune cell migration, malnutrition, and taste disturbances may contribute to oral microbial imbalance. In this review, we summarize the bidirectional influences on the composition and diversity of the oral and gut microbiomes and propose potential mechanisms underlying their interactions. A deeper understanding of these processes will enhance our knowledge of microbiota-host interactions and systemic health, and may shed light on the prevention and treatment of systemic diseases related to oral and gut microbiota dysbiosis.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Mouth/microbiology/immunology
Dysbiosis/immunology/microbiology
Animals
*Microbiota

@article {pmid41808840,
year = {2026},
author = {Wang, X and Xiong, D and Cui, S and Duan, B and Ding, G and Huang, Y and Wang, Q},
title = {Artificial intelligence-enabled multi-omics biomarkers for immune checkpoint blockade: mechanisms, predictive modeling, and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1732079},
pmid = {41808840},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Artificial Intelligence ; *Biomarkers, Tumor/genetics ; *Neoplasms/drug therapy/immunology/metabolism/genetics ; Genomics/methods ; Translational Research, Biomedical ; Machine Learning ; Metabolomics ; Proteomics ; Animals ; Multiomics ; },
abstract = {Immune checkpoint inhibitors (ICIs) have transformed oncology, yet durable benefit remains confined to a minority of patients, revealing the limitations of single biomarkers such as PD-L1 expression, tumor mutational burden, and microsatellite instability. Multi-omics profiling, spanning genomics, transcriptomics, epigenomics, proteomics, metabolomics, microbiomics, and imaging-derived radiomics/pathomics, enables a systems-level interrogation of tumor-immune interactions. It captures lineage plasticity, antigen-presentation defects, metabolic and epigenetic suppression, stromal remodeling, and microbiome-driven immune tone that collectively shape ICI sensitivity and resistance. Artificial intelligence (AI) and machine learning are increasingly indispensable for fusing these heterogeneous, high-dimensional data into deployable composite predictors and mechanistically grounded signatures, while explainability approaches (e.g., SHAP, Grad-CAM) help link model outputs to actionable biology. This review synthesizes emerging AI-enabled multi-omics biomarkers across major tumor types, highlights clinical applications in response stratification, combination-therapy selection, and longitudinal monitoring, and discusses key translational barriers, including cohort and platform heterogeneity, limited prospective validation, privacy constraints, model drift, and equity. We conclude by outlining future directions in single-cell and spatial multi-omics integration, federated learning, and generative modeling to accelerate robust, generalizable precision immunotherapy. Pragmatic implementation will require harmonized pre-analytics, clinically feasible assays or distilled panels, and decision-support interfaces that communicate calibrated uncertainty to oncologists.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Artificial Intelligence
*Biomarkers, Tumor/genetics
*Neoplasms/drug therapy/immunology/metabolism/genetics
Genomics/methods
Translational Research, Biomedical
Machine Learning
Metabolomics
Proteomics
Animals
Multiomics

@article {pmid41808832,
year = {2026},
author = {Zhou, S and Tang, J and Wang, Y},
title = {Trichuris suis ova in inflammatory bowel disease-clinical challenges and translational pathways.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1611690},
pmid = {41808832},
issn = {1664-3224},
mesh = {Animals ; *Trichuris/immunology ; Humans ; *Inflammatory Bowel Diseases/therapy/immunology ; Translational Research, Biomedical ; *Ovum/immunology ; Therapy with Helminths ; Gastrointestinal Microbiome ; },
abstract = {This article reviews the mechanisms and clinical trial findings of Trichuris suis ova (TSO) for inflammatory bowel disease (IBD).The results show TSO may exert potential effects on IBD via multiple pathways, yet no significant efficacy has been confirmed in clinical trials. Given its promising anti-inflammatory properties, further research is warranted. However, many knowledge gaps still exist in this field. Future trials should standardize study designs. Considering IBD complexity, priority should be given to precision medicine, with identifying TSO therapy's target populations as a core step. Additionally, enhanced safety monitoring is essential to fully assess short- and long-term risks of TSO treatment. Given the inherent uncertainties of live biotherapeutics, multi-omics and gene-editing tools should be adopted to clarify TSO's anti-inflammatory mechanisms and achieve its "artificial domestication", enabling stable therapeutic performance across diverse clinical settings. The breakthroughs will deepen insights into IBD pathogenesis and advance microbiome-based interventions from empirical practice to the precision medicine era.},
}

Animals
*Trichuris/immunology
Humans
*Inflammatory Bowel Diseases/therapy/immunology
Translational Research, Biomedical
*Ovum/immunology
Therapy with Helminths
Gastrointestinal Microbiome

@article {pmid41808728,
year = {2026},
author = {Pereira, MH and Tyagi, S and Mohanty, A and Garg, S and Kumar, A},
title = {Metagenomic studies reveal diverse microbial community in the developmental stages of highly adaptable malarial vector Anopheles stephensi liston.},
journal = {3 Biotech},
volume = {16},
number = {4},
pages = {124},
pmid = {41808728},
issn = {2190-572X},
abstract = {UNLABELLED: Anopheles stephensi, a highly adaptable malaria vector species, continues to expand its range from South Asia to Sub-Saharan Africa, posing a serious global public health concern. In India, it serves as the principal urban vector of both Plasmodium falciparum and P. vivax. Conventional control measures reliant on chemical insecticides have raised issues of resistance, highlighting the need for alternative strategies such as microbiota-mediated vector control. This study aimed to test the hypothesis that a subset of bacterial taxa persist across developmental stages of An. stephensi, representing potential candidates for transstadial transmission and future paratransgenic manipulation. Using both culture-based data and next-generation sequencing (NGS) approaches targeting the 16 S rRNA gene (V3-V4 region), we characterized bacterial communities from breeding water, larvae, pupae, and adult mosquitoes (male and female) collected in Goa, India. Across all developmental stages, Proteobacteria and Firmicutes were the dominant phyla, while 15 bacterial genera formed the putative core microbiome shared by ≥ 80% of stages at ≥ 0.1% abundance. Among these, Pseudomonas (adult males: 11.5%, pupae: 3.2%), Exiguobacterium, Acinetobacter, Psychrobacter, and Asticcacaulis were consistently detected, together contributing approximately 30% of total microbial composition. Alpha diversity indices indicated higher richness and evenness in pupae and adults than in larvae, suggesting microbial enrichment during metamorphosis. Beta diversity and PCoA analyses clustered pupal and adult stages distinctly from larvae and breeding water, confirming selective microbial retention through development. These findings reveal that An. stephensi harbors a stable, stage-spanning core microbiome dominated by metabolically versatile genera with potential for transstadial persistence. The dominance of Pseudomonas across life stages supports its candidacy for paratransgenic applications aimed at disrupting malaria transmission. This work provides the first integrated culture-NGS baseline of An. stephensi microbiota from India, offering essential insight for microbiome-based vector control strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04739-6.},
}

@article {pmid41808561,
year = {2026},
author = {Ram, S and Corbin, M and 't Mannetje, A and Douwes, J and Kvalsvig, A and Eng, A},
title = {Antibiotic Exposure in Early Life and Risk of Type 1 Diabetes: A Meta-Analysis.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70636},
pmid = {41808561},
issn = {1463-1326},
support = {HD21/053//Health Research Council of New Zealand/ ; },
abstract = {BACKGROUND: Early-life antibiotic use may increase the risk of childhood type 1 diabetes (T1D), potentially through gut microbiota dysbiosis and associated effects on immune development. This meta-analysis evaluated associations between early-life antibiotic use and T1D.

METHODS: A systematic search of PubMed, MEDLINE, Scopus and Web of Science was conducted up to June 2025, which focused on studies reporting associations between antibiotic use in the pre- and postnatal periods and childhood T1D. Pooled effect sizes were assessed using random effects models separately for prenatal and postnatal antibiotic exposure, with subgroup analyses by antibiotic course, class and spectrum. Study quality was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS).

RESULTS: The analysis included 20 studies (11 cohort, 9 case-control), encompassing > 1.5 million participants for prenatal and over 4 million for postnatal antibiotic exposure. A pooled effect size of 1.05 (95% CI 0.98-1.11) for prenatal exposure was found. Further analysis by antibiotic spectrum yielded no significant associations, likely due to the small number of studies. For postnatal antibiotic exposure, a pooled effect size of 1.07 (95% CI 1.01-1.14) was found, with estimates increasing with increased number of antibiotic courses: ≥ 2 courses, 1.11, 95% CI 1.02-1.20; and ≥ 5 courses, 1.14, 95% CI 1.00-1.30. Associations were stronger for broad-spectrum (1.13, 95% CI 1.03-1.23) than for narrow-spectrum antibiotics (1.08, 95% CI 0.93-1.26) but no significant associations were observed by antibiotic class. The impact of mode of obstetric delivery remained inconclusive across studies. The quality of the evidence was high.

CONCLUSION: This meta-analysis suggests that early-life antibiotic use is associated with an increased risk of T1D, particularly with repeated courses and broad-spectrum agents. However, confidence in these findings is constrained by variability in study design and exposure definitions, as well as the potential for confounding by indication. While the observed associations are modest, they highlight the importance of judicious antibiotic prescribing in early life. Further large, well-designed prospective cohort studies are needed to clarify causality and better disentangle the effects of antibiotics from those of underlying infections.},
}

@article {pmid41808525,
year = {2026},
author = {Jiménez, DJ and Rosado, AS},
title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70272},
pmid = {41808525},
issn = {1462-2920},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; },
abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.},
}

*Microbiota
*Polyethylene Terephthalates/metabolism
*Hydrolases/metabolism/genetics
Metagenomics
Biocatalysis
*Bacteria/enzymology/genetics

@article {pmid41808437,
year = {2026},
author = {de Beer, JC and Alayande, KA and Pirk, CWW and Adeleke, RA and Sole, CL},
title = {Dietary Specialisation Shapes Gut Bacterial Diversity in Dung Beetles: Insights From Coprophagy to Millipede Carnivory.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70317},
pmid = {41808437},
issn = {1758-2229},
support = {98696//National Research Foundation of South Africa/ ; SRUG220326856//National Research Foundation of South Africa/ ; //South Africa Sweden University Forum/ ; },
mesh = {Animals ; *Coleoptera/microbiology/physiology/classification ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Diet ; Phylogeny ; *Arthropods/physiology ; Biodiversity ; Carnivory ; Coprophagia ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dung beetles are ecosystem engineers, providing ecosystem services like nutrient cycling, waste degradation and parasite suppression. Their gut microbiome is essential for exploiting specialised diets, yet the eco-evolutionary factors driving microbial composition across diverse feeding strategies remain ambiguous. Here, we show that diet strongly influences gut bacterial composition across seven dung beetle species specialising in coprophagy, necrophagy, detritophagy, fungivory and carnivory. Most dietary specialisations grouped separately, though fungivores clustered with carrion and millipede feeders. The millipede-feeding species, Sceliages brittoni and S. hippias, hosted the most distinct and least diverse gut microbiomes. Taxonomically, differences were driven by distinct marker taxa, many of which are consistently isolated across taxonomic orders with similar diets. For example, the indicative bacterial species I. indica has been identified in various flesh-feeding insect taxa. Crucially, this pattern of shared bacterial communities suggests that diet is a dominant structuring factor which promotes community convergence regardless of host phylogeny. This study highlights the role of diet in shaping the dung beetle gut microbiome and provides the first characterisation of the gut microbiota in millipede-feeding dung beetles. Our findings underscore the critical role of diet, laying the foundation for functional studies into the eco-evolutionary significance of these host-microbe interactions.},
}

Animals
*Coleoptera/microbiology/physiology/classification
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
*Diet
Phylogeny
*Arthropods/physiology
Biodiversity
Carnivory
Coprophagia
RNA, Ribosomal, 16S/genetics

@article {pmid41808169,
year = {2026},
author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J},
title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-026-02977-0},
pmid = {41808169},
issn = {1475-2859},
support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; },
}

@article {pmid41808145,
year = {2026},
author = {Bu, D and Yan, J and Yang, W and Zhang, X and Li, Q},
title = {Ensemble test for microbiome data.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02367-z},
pmid = {41808145},
issn = {2049-2618},
support = {12401359//National Natural Science Foundation of China/ ; 12325110//National Natural Science Foundation of China/ ; QNTD202303//Youth Academic Innovation Team Construction Project of Capital University of Economics and Business/ ; GZC20241867//Postdoctoral Fellowship Program of CPSF/ ; YSBR-034//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {MOTIVATION: Recent research has revealed strong correlations between the human microbiome and various diseases. However, statistical analysis of microbiome data remains challenging due to its inherent sparsity and high dimensionality. PERMANOVA (Permutational multivariate analysis of variance using distance matrices) has been extensively employed to test the association between microbiome data and biological features. Its non-parametric nature makes it appealing, as it does not impose restrictions on data dimension or distribution. Despite its merits, several limitations have restricted its further application.

RESULTS: This paper introduces E-MANOVA (Ensemble multivariate analysis of variance using distance matrices), a method designed to address these limitations. Traditional PERMANOVA lacks consistent robustness across different distance metrics and association signals, which can lead to power reduction in specific scenarios. Leveraging the idea of ensemble learning, we construct base tests by taking the similarity matrix to the rth power and then combine these tests to build a final ensemble test. Our resulting test statistic exhibits high power and robustness compared to other existing methods. Furthermore, we employ direct moment approximation and the Pearson type III distribution to approximate the permutation null distribution, completely avoiding the computationally intensive permutation procedure. Finally, we utilize the Cauchy combination method to aggregate p-values from multiple distances, eliminating the need to pre-specify a single distance measure before analysis.

CONCLUSIONS: Our extensive simulations demonstrate that the proposed method outperforms existing methods across various situations. Further analysis of real data from cigarette smokers and curated microbiome data shows that our proposed method identifies the highest number of significant associations among all competing methods. Video Abstract.},
}

@article {pmid41808137,
year = {2026},
author = {Dothard, MI and Caboni, M and Norment, D and Sigmund, N and Allard, SM and Gilbert, JA and Gavrish, E and Al-Ghalith, G and Der-Avakian, A and Strandwitz, P},
title = {A human-derived Bacteroides strain attenuates depressive-like behavior in a rat model of social defeat-induced stress.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-026-04787-y},
pmid = {41808137},
issn = {1741-7015},
support = {R44DK120181//National Institute of Health Small Business Innovation Research/ ; DGE-2038238//National Science Foundation Graduate Research Fellowship Program/ ; NNX16AO69A//Translational Research Institute for Space Health - Space Health Ingress Program (NASA)/ ; },
abstract = {BACKGROUND: The gut microbiome has been linked to mood disorders via communication along the gut-brain axis. We previously found levels of fecal Bacteroides were inversely associated with brain signatures of depression in the prefrontal cortex of human subjects. Bacteroides are important human commensals, playing a keystone role in regulating the immune system and producing bioactive metabolites, like the neurotransmitter gamma-aminobutyric acid and B vitamins.

METHODS: To better understand the link between Bacteroides and depression - and test a candidate novel next-generation probiotic - we administered a human-derived Bacteroides salyersiae strain, HB32, orally in rats that were subjected to the repeated social defeat model of stress-induced depression. The fecal microbiome and the prefrontal cortex transcriptome were then profiled for intervention-induced alterations.

RESULTS: Orally delivered B. salyersiae HB32 reduced depressive-like behavior in male rats comparable to the drug ketamine, independently of the strain being administered in its viable or inactivated (iHB32) form. Mechanistically, we observed that stress-induced anhedonia required the vagus nerve for its phenotype to develop, suggesting crosstalk between the gut and the brain. In support of this, we found HB32 and iHB32, but not ketamine, rescued stress-induced differential expression patterns in the prefrontal cortex, including those related to serotonin signaling and oxidative stress. In the gut, prolonged exposure to social defeat led to broad shifts in the composition of the gut microbiome, with a predominant reduction of the endogenous Bacteroides. Administration of HB32, iHB32, and ketamine attenuated the impact of stress on the microbiome, and intake of live HB32 resulted in a significant increase of the B. salyersiae species in the fecal microbiome.

CONCLUSIONS: Depressive-like behavior in male rats induced by repeated social defeat requires vagal signaling, suggesting gut-brain-axis crosstalk. In animals with an intact vagus nerve, oral administration of viable or inactivated B. salyersiae HB32 reversed behavioral changes induced by chronic stress at levels comparable to ketamine. Additionally, supplementation of HB32 and iHB32 was associated with attenuation of stress-related microbiome and prefrontal cortex transcriptional changes.},
}

@article {pmid41808045,
year = {2026},
author = {Khogali, R and Bastos, A and Khamis, FM and Getange, D and Kabii, J and Yuko, E and Masiga, D and Villinger, J},
title = {Comparative tissue-specific microbiome analyses identify keystone endosymbionts shaping pathogen interactions in dromedary camel ticks.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04864-5},
pmid = {41808045},
issn = {1471-2180},
}

@article {pmid41807945,
year = {2026},
author = {Morawski, BM and Morton, ER and Yunus, M and Muñoz-Zanzi, C and Mejia, R and Blekhman, R and Boulware, DR and Lofgren, SM},
title = {Bacterial fecal microbiome composition associated with HIV stage among rural and peri-urban adults living with HIV in Uganda.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12992-6},
pmid = {41807945},
issn = {1471-2334},
support = {Dissertation Funding//Graduate School, University of Minnesota/ ; },
}

@article {pmid41807808,
year = {2026},
author = {Deng, C and Shang, X and Zhang, W and Liu, J and Zhang, H and Li, Z},
title = {Global research trends and hotspots in targeted therapy for IgA nephropathy: a bibliometric and visualization analysis (1999-2025).},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41807808},
issn = {1432-1912},
abstract = {Targeted therapy has emerged as a promising precision medicine strategy for immunoglobulin A nephropathy (IgAN) through the modulation of specific pathogenic pathways. Although research in this area has accelerated, the literature remains scattered, and no bibliometric study has mapped its global knowledge structure or evolving hotspots. We conducted a bibliometric and visualization analysis of 678 publications indexed in the Web of Science Core Collection (1999-2025). CiteSpace 6.4R1, VOSviewer 1.6.20, and the R‑based bibliometric package were used to assess publication and citation trends; identify prolific countries, institutions, authors, and journals; and generate co‑authorship, co‑citation, and keyword co‑occurrence networks. Research frontiers were explored through thematic evolution mapping and keyword burst detection. Annual publications increased notably after 2015, indicating a shift from supportive care to molecularly targeted interventions. China and the United States produce over 60% of the global output, with expanding collaborations. The core themes clustered into three domains: complement inhibition (e.g., C5 blockade), B‑cell-directed therapy (including BAFF/APRIL modulation), and mucosal immune regulation. The gut-immune axis, particularly microbiome modulation, has emerged as a new frontier. Notably, recent trends highlight a growing interest in non-invasive biomarkers (e.g., urinary targets) to guide patient stratification, although clinical translation remains a challenge. This study delineates a rapidly evolving landscape of IgAN-targeted therapy. Precision approaches focusing on complement blockade, B‑cell pathways, mucosal immunity, and microbiome modulation hold substantial potential. While bibliometric data reflect a vibrant academic interest, future efforts should increasingly focus on translating candidate discoveries into clinical validation. Priority should be given to biomarker‑driven stratification and integrated diagnostic-therapeutic frameworks to accelerate translation and improve outcomes.},
}

@article {pmid41807803,
year = {2026},
author = {Zhu, Y and Gao, W and Cheng, M and Li, X and Cai, K and Chen, L and Chu, H},
title = {Harnessing the power of the gut microbiome: a review of supplementation diagnosis and therapy for liver cirrhosis.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-026-06098-0},
pmid = {41807803},
issn = {1420-9071},
support = {No. 2022YFA1305600//Key Technologies Research and Development Program/ ; No. 82470584//National Natural Science Foundation of China/ ; No. 82000561//National Natural Science Foundation of China/ ; No. 82400652//National Natural Science Foundation of China/ ; No. 82170678//National Natural Science Foundation of China/ ; No. 2021xhyn005//Science Foundation of Union Hospital/ ; },
}

@article {pmid41807675,
year = {2026},
author = {Karlsen, C and Meriac, A and Ytteborg, E and Johansson, GS and Timmerhaus, G and Alvestad, R and Noble, C and Kolarevic, J},
title = {Intestinal morphology and host‑ and system‑associated microbiome dynamics during short‑term fasting and refeeding of Atlantic salmon in recirculating aquaculture systems.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42939-5},
pmid = {41807675},
issn = {2045-2322},
}

@article {pmid41807560,
year = {2026},
author = {Conroy, G},
title = {Forget SkinTok: the real science of skincare and why it matters for your health.},
journal = {Nature},
volume = {651},
number = {8105},
pages = {294-296},
pmid = {41807560},
issn = {1476-4687},
}

@article {pmid41807473,
year = {2026},
author = {Cheng, L and Li, Y and Zhang, Y and Qin, C and Yang, L and Yan, X and Nie, G},
title = {Cetobacterium somerae as a microbial correlate of improved muscle quality after intestinal microbiota transplantation in Yellow River carp (Cyprinus carpio).},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00955-3},
pmid = {41807473},
issn = {2055-5008},
support = {U22A20532//National Natural Science Foundation of China/ ; HARS-22-16-S//Special Fund for Henan Agriculture Research System/ ; },
abstract = {Dietary faba bean enhances fish muscle quality but concurrently reduces growth performance. The gut microbiota critically modulates muscle growth and quality. However, the specific microbial taxa, metabolites, and regulatory mechanisms responsible remain to be elucidated. This study established a differential gut microbiota model in faba-bean-fed Yellow River carp (Cyprinus carpio), used whole-intestinal microbiota transplantation (WIMT) to directly test its effect on muscle quality, and supplemented the key bacterium and its metabolite to confirm their contribution. After a 6-week faba bean diet, growth performance declined, whereas muscle texture improved (P < 0.05). This improvement was concomitant with a higher abundance of the genera Aeromonas and Cetobacterium in the gut. Following 8 weeks of daily WIMT from faba-bean-fed donors, Yellow River carp maintained normal growth performance (P > 0.05) and simultaneously showed improved muscle texture, characterized by more small-diameter fibers, lower fat content, and higher collagen levels (P < 0.05), recapitulating the donor's key muscle phenotype. Meanwhile, WIMT reshaped the gut microbiome composition and its metabolic profile, and the marker species Cetobacterium somerae and its metabolite acetic acid showed associations with improvements in muscle quality. Further in vivo validation indicated that C. somerae reduced fat deposition and improved muscle texture, an effect possibly linked to activation of the AMPK-PGC-1α-FoxO pathway, and its metabolite acetic acid mirrored these changes. This study reveals the direct impact of gut microbiota on muscle quality through WIMT in Yellow River carp, provides novel evidence of the fish gut-muscle axis, and offers a scientific basis for improving muscle quality.},
}

@article {pmid41807415,
year = {2026},
author = {Li, DZ and Li, Y and Wang, X and Feng, Y and Liu, Y and Yang, C and Zhang, W and Wen, X and Liu, Z and Yin, W and Zhang, X},
title = {An antifungal effector from a plant-parasitic nematode modulates host fungal community composition and supports ecological fitness.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00954-4},
pmid = {41807415},
issn = {2055-5008},
support = {2022ZD04016//STI 2030-Major Projects/ ; CAFYBB2020SZ008//Fundamental Research Funds of Research Institute of Forest New Technology, CAF/ ; NSFC 3237141290//National Natural Science Foundation of China/ ; },
abstract = {Host-associated microbiomes are increasingly recognized as key determinants of plant health, disease development, and ecosystem functioning. Plant pathogens, especially fungal pathogens, have been reported to secrete antimicrobial effectors to modulate the host microbiota and promote colonization. Plant-parasitic nematodes (PPNs) could also modulate host microbial communities, but the processes involved remain to be clarified. Here, we identify a secreted antifungal effector, BxylTLP6, from Bursaphelenchus xylophilus, the causal agent of pine wilt disease. BxylTLP6 degrades fungal cell walls and inhibits multiple plant-associated fungi, while the released oligoglucans serve as food-derived cues that guide nematode foraging toward fungal resources. In planta, silencing Bxyltlp6 significantly delayed disease progression. ITS-based mycobiome profiling revealed that BxylTLP6 modulates the pine endophytic fungal community by promoting Ascomycota, suppressing Basidiomycota, inhibiting wood-decaying fungi, and enriching pathogenic or parasitic taxa. These shifts are associated with enhanced nematode survival and pathogenicity. Our findings support the view that a TLP effector can modulate behavior and influence the host fungal microbiome, shedding light on how PPN may manipulate microbial environments to enhance their fitness.},
}

@article {pmid41807411,
year = {2026},
author = {Zhang, W and Song, S and Zhang, Y and Pan, Y and Hu, D and Wang, Y},
title = {Emerging strategies in senotherapeutics: from broad-spectrum senolysis to precision reprogramming.},
journal = {npj aging},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41514-026-00355-z},
pmid = {41807411},
issn = {2731-6068},
support = {82172210//National Natural Science Foundation of China/ ; XJZT24CY38//Xijing Hospital Advancement Program/ ; },
abstract = {Cellular senescence, originally described as a finite proliferative arrest in cultured somatic cells, has since been recognized as a central mechanism underlying aging and the development of age-associated disorders. The progressive accumulation of senescent cells (SnCs) promotes chronic inflammation through the senescence-associated secretory phenotype (SASP) and circumvents immune-mediated clearance by upregulating pro-survival and immune checkpoint pathways. Early "first-generation" senolytics, including navitoclax (ABT-263) and the dasatinib-quercetin (D + Q) combination, provided proof-of-concept that selective removal of SnCs can alleviate certain fibrotic, metabolic, and cardiovascular pathologies in preclinical studies. However, these agents exhibited notable drawbacks, such as dose-dependent thrombocytopenia, variable therapeutic efficacy, and the emergence of resistance mechanisms. Consequently, current research has shifted toward precision senotherapy, though significant translational challenges remain. This review synthesizes three next-generation strategies developed to address limitations of early senolytic agents. (1) Immune-based senolysis: This approach applies immuno-oncology principles to counter immune evasion of SnCs. Strategies include blocking immunosuppressive ligands such as GD3 ganglioside, engineering chimeric antigen receptor (CAR) T cells to target senescence-specific surface markers like urokinase-type plasminogen activator receptor (uPAR), and exploiting metabolic vulnerabilities (e.g., glutaminolysis and ferroptosis) to sensitize SnCs to immune-mediated clearance. (2) Tissue-precision proteolysis-targeting chimeras (PROTACs): These agents recruit organ- or tissue-specific E3 ligases (e.g., von Hippel-Lindau (VHL)) to selectively degrade anti-apoptotic proteins such as BCL-xL. Localized activity may reduce systemic toxicity and mitigate dose-limiting effects observed with traditional inhibitors. (3) Microbiome-epigenetic interplay: This strategy modulates the gut-liver axis to enhance senolytic efficacy. Short-chain fatty acids (SCFAs), such as butyrate, epigenetically regulate drug transporter expression and suppress the SASP, while dietary interventions may create a microenvironment favorable to senolysis. These approaches offer potentially more targeted and personalized therapeutic options but face significant challenges, including immunopathology, manufacturing complexity, off-target effects, and long-term safety concerns. The ongoing shift from broad inhibition to precision reprogramming represents a promising but preliminary step in the treatment of age-related diseases.},
}

@article {pmid41688544,
year = {2026},
author = {Murakami, Y and Hosomi, R and Tanaka, G and Murakami, H and Kanto, A and Kimura, T and Imamura, Y and Yoshida, M and Fukunaga, K},
title = {Fish (Alaska Pollock) protein intake attenuates age-related short-term memory decline through gut microbiota modulation.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41688544},
issn = {2045-2322},
support = {20K21587//Japan Society for the Promotion of Science/ ; },
abstract = {UNLABELLED: Dysbiosis leads to decreased intestinal barrier function, causing systemic inflammation and possibly the development of age-related cognitive decline. In this study, we investigated the effect of an Alaska pollack protein (APP) diet on cognitive function, gut microbiota composition, intestinal barrier function, and neuroinflammation in senescence-accelerated mouse prone8 (SAMP8) and senescence-resistant AKR/J (SAMR1) mice. The APP diet produced significant improvements across multiple parameters. It enhanced glucose tolerance in both strains and prevented short-term memory decline in SAMP8 mice. Microbiome analysis revealed that APP intake promoted beneficial bacteria growth, specifically increasing Lactobacillus in SAMR1 and butyrate-producing Lachnospiraceae in SAMP8. Notably, while APP diet increased butyrate-producing bacteria in SAMP8, short-chain fatty acids (SCFAs) analysis showed increased aetate but unchanged butyrate levels, suggesting complex metabolic interactions beyond simple bacterial abundance. Moreover, the APP diet significantly suppressed neuroinflammation in SAMP8, evidenced by decreased proinflammatory cytokine expression, microglia and astrocyte activation, and attenuated demyelination in the hippocampus. These findings suggest that APP intake prevents age-related short-term memory decline through beneficial gut microbiota modulation, and reduced neuroinflammation, supporting the role of the gut-brain axis in cognitive aging.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38717-y.},
}

@article {pmid41807298,
year = {2026},
author = {Huang, J and Qin, Q and Li, X and Jiang, K and Xu, J and Mao, Y and Kang, W and Gao, R and Cheng, Y and Zhao, W and Ke, J and Mou, X},
title = {Bacteroides-associated NAD[+] depletion correlates with exacerbated radiation-induced colorectal injury and impaired mucosal proliferative capacity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2641260},
doi = {10.1080/19490976.2026.2641260},
pmid = {41807298},
issn = {1949-0984},
mesh = {Animals ; Humans ; *NAD/metabolism/deficiency ; *Bacteroides/metabolism/genetics/isolation & purification ; Mice ; Male ; Female ; *Intestinal Mucosa/pathology/radiation effects ; *Radiation Injuries/microbiology/pathology ; Feces/microbiology/chemistry ; Mice, Inbred C57BL ; Middle Aged ; Gastrointestinal Microbiome ; Cell Proliferation ; Aged ; Nicotinamide Mononucleotide/metabolism/administration & dosage ; Fecal Microbiota Transplantation ; Colon/radiation effects/pathology ; },
abstract = {Radiation proctitis (RP) is a frequent complication of pelvic radiotherapy that compromises treatment delivery and patient quality of life, yet the factors shaping injury severity remain incompletely defined. We prospectively profiled pretreatment fecal microbiomes and metabolomes from 55 patients and stratified them by outcome into mild versus severe RP. Baseline microbial composition showed Bacteroidales enriched in severe RP and Firmicutes enriched in mild cases. Multi-omics integration highlighted nicotinate/nicotinamide pathways; severe RP was characterized by concomitant reductions in both fecal and tissue NAD[+] levels, along with an enrichment of microbial nicotinate/nicotinamide metabolism genes, primarily contributed by Bacteroides ovatus, B. xylanisolvens, and B. fragilis. In mice, fecal microbiota transplantation from severe-RP donors exacerbated radiation-induced colorectal injury and decreased colorectal NAD[+], supporting a causal role for the microbiota. Gavage with Bacteroides similarly worsened pathology and lowered NAD[+], whereas nicotinamide mononucleotide (NMN) supplementation attenuated the injury. Mechanistically, Bacteroides gavage reduced mitochondrial membrane potential, decreased the Lgr5[+] stem-cell proportion and proliferative indices, associated with Wnt pathway modulation. NMN reversed these effects in parallel with NAD[+] restoration. Together, these results identify a microbiota‒metabolite association wherein Bacteroidales enrichment is associated with NAD[+] depletion, reduced mucosal proliferative capacity, and exacerbated radiation-induced colorectal injury. The work deepens insight into RP pathogenesis and suggests a potential basis for microbiome- and metabolite-targeted approaches to attenuate severe RP.},
}

Animals
Humans
*NAD/metabolism/deficiency
*Bacteroides/metabolism/genetics/isolation & purification
Mice
Male
Female
*Intestinal Mucosa/pathology/radiation effects
*Radiation Injuries/microbiology/pathology
Feces/microbiology/chemistry
Mice, Inbred C57BL
Middle Aged
Gastrointestinal Microbiome
Cell Proliferation
Aged
Nicotinamide Mononucleotide/metabolism/administration & dosage
Fecal Microbiota Transplantation
Colon/radiation effects/pathology

@article {pmid41807185,
year = {2026},
author = {Tsuji, H and Asahara, T and Sakai, T and Kado, Y and Moriyama-Ohara, K and Takahashi, A and Date, R and Atobe, S and Ishizuka, T and Takahashi, T and Ozaki, S and Shiono, Y and Fukada, Y and Kawashima, K and Yamashiro, K and Matsumoto, S and Yamashiro, Y},
title = {Early establishment of Bifidobacterium-dominant microbiome in planned cesarean-born infants via Bifidobacterium breve strain Yakult supplementation: A randomized, double-blind, placebo-controlled, parallel-group pilot study.},
journal = {Pediatrics and neonatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pedneo.2026.02.001},
pmid = {41807185},
issn = {2212-1692},
abstract = {OBJECTIVES: To investigate the effects of Bifidobacterium breve strain Yakult (BbrY) administration immediately after birth on the microbiome of cesarean-born full-term infants with an immature microbiota at birth.

METHODS: This single-center, placebo-controlled, randomized, double-blind, parallel-group intervention study included healthy, full-term Japanese infants born via planned cesarean section. Infants were administered either BbrY or placebo for the first month of life. The primary endpoint was the early establishment of a Bifidobacterium-dominant microbiome.

RESULTS: This study included 26 infants (14 in the BbrY group and 12 in the placebo group). Compared with the placebo group, the BbrY group showed significantly increased detection rates and counts of BbrY from day three to six months post-birth, with the level and proportion of Bifidobacterium and Bifidobacteriaceae remaining elevated until one month post-birth. Total bacterial counts and total organic acid concentrations, including acetic and lactic acids, were significantly higher in the BbrY group until the sixth day of life, concomitant with a decrease in fecal pH. At nine months, the BbrY group exhibited a significantly higher body weight than the placebo group, and the Kaup index remained within the normal range at six and nine months.

CONCLUSIONS: BbrY supplementation immediately after birth facilitated the early establishment of a Bifidobacterium-dominant microbiome and contributed to intestinal acidification in cesarean-born infants, indicating BbrY administration may support normal growth patterns during infancy.},
}

@article {pmid41806989,
year = {2026},
author = {Marlicz, W and Krawczyk, M and Milkiewicz, P},
title = {Rifaximin in symptomatic uncomplicated diverticular disease: a stewardship perspective following the Fiesole Consensus.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338607},
pmid = {41806989},
issn = {1468-3288},
}

@article {pmid41806837,
year = {2026},
author = {Mi, K and Cao, M and Zhang, L and Zhang, Q and Zhou, W and Deng, C and Zhang, Y and Zhao, Q and Wei, Y and Liu, X and Li, F},
title = {An integrative multi-omics approach identifies microbiome alterations linked to pathological and behavioral features in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102655},
doi = {10.1016/j.xcrm.2026.102655},
pmid = {41806837},
issn = {2666-3791},
abstract = {This study employs a multi-omics approach to investigate the gut-brain axis in 326 children with autism spectrum disorder (ASD) and 169 typically developing (TD) controls, aged 0-10 years. By analyzing neuroimaging, gut microbiome, and plasma metabolome data, we find that microbial features could accurately distinguish ASD from TD children. A key finding is that gut microbial abundance, particularly an increase in Clostridioides difficile, serves as the strongest predictor of both ASD symptom severity and brain structural variations. Crucially, these gut and brain differences are age dependent, diminishing as children with ASD aged and converging toward TD patterns. A mediation model suggests a potential pathway where specific microbes influence brain structure and behavior via metabolites. The findings establish the gut microbiota as a robust predictor of brain and behavioral phenotypes in pediatric ASD, underscoring the necessity for early, age-stratified therapeutic strategies via modulating the composition of the gut microbiome.},
}

@article {pmid41806833,
year = {2026},
author = {Babdor, J and Patel, RK and Davidson, B and Koser, K and Noecker, C and Rahim, MK and Bisanz, JE and Tenvooren, I and Marquez, D and Calvo, M and Johri, V and McCarthy, EE and Shaheed, A and Ekstrand, C and Weakley, AM and Yu, FB and Krip, K and Shaikh, KA and Amatullah, H and Fiehn, O and Turnbaugh, PJ and Combes, AJ and Fragiadakis, GK and Spitzer, MH},
title = {Immune-microbiome coordination defines interferon setpoints in healthy humans.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.02.003},
pmid = {41806833},
issn = {1097-4172},
abstract = {Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains incompletely understood. Therefore, we performed multi-omic profiling of 110 healthy participants through the ImmunoMicrobiome study. A factor-based integrative approach identified coordinated variation, revealing that the interferon response was amongst the most variable immune features in healthy participants. Microbiome composition, pathways, and stool metabolites varied concomitantly with interferon response pathways. Longitudinal data spanning more than a year indicated the significant stability of these parameters within individuals over time. Our study provides extensive data to examine the relationship between the immune states and microbiomes of healthy individuals at steady state, which paves the way for delineating inter-individual differences relevant for disease susceptibility and responses to therapy.},
}

@article {pmid41806724,
year = {2026},
author = {Barril, PA and Brusa, V and Costa, M and Cap, M and Aguilera, P and Belforte, FS and Penas-Steinhardt, A and Leotta, G and Oteiza, JM},
title = {16S rRNA-based profiling of microbiota along the ground meat and sausage production lines in an Argentine meat processing facility.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111716},
doi = {10.1016/j.ijfoodmicro.2026.111716},
pmid = {41806724},
issn = {1879-3460},
abstract = {Microbial contamination in food processing environments can compromise both product quality and safety. This study aimed to characterize the microbiota present along the ground meat and sausage production lines of an Argentine meat processing facility, with a focus on microbial dynamics in raw materials, environmental surfaces, and final products. Using next-generation sequencing (NGS), we identified a total of 57 unique bacterial genera across both production lines (37 in ground meat samples and 34 in sausage samples) showing ≥5% relative abundance in at least one sample. The core microbiota across both lines included Pseudomonas, Acinetobacter, and Psychrobacter, consistently detected in raw materials, pre- and post-operational environments, and final products. Notably, raw materials introduced variable microbial communities that influenced both environmental and product microbiomes. In the ground meat line, Carnobacterium became dominant in final products, likely masking the detection of other genera. In the sausage line, Brochothrix and Vibrio were prominent in final products. Staphylococcus and Clostridium sensu stricto were detected at low relative abundances and were mainly associated with raw materials; however, because the NGS analysis was conducted at the genus level, these findings do not imply the presence of pathogenic species. The persistence of specific genera in the environment, despite cleaning and disinfection, is consistent with the potential presence of biofilms, which may contribute to increased tolerance to Sanitation Standard Operating Procedures (SSOP). This study highlights the importance of raw material microbiota in shaping the production environment and product composition.},
}

@article {pmid41806709,
year = {2026},
author = {Hu, Z and Liu, Q and Song, H and Liu, J},
title = {Environmental factors outweigh seawater microbiomes in synergistically shaping epiphytic bacterial communities of Saccharina japonica.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119535},
doi = {10.1016/j.marpolbul.2026.119535},
pmid = {41806709},
issn = {1879-3363},
abstract = {Saccharina japonica is a commercially significant macroalgal species in coastal areas, where its growth and health are closely linked to epiphytic bacterial communities (EB). Previous studies have indicated that the structure of these EB communities is influenced by seawater microbiomes (SW) and various environmental factors. However, the mechanisms regulating these influences remain incompletely understood, particularly regarding their relative contributions throughout the life cycle, which are important for S. japonica production. To fill this gap, we investigated the diversity, composition, ecological networks, and functional predictions of EB and SW communities, as well as environmental factors from December 2022 to May 2023 in northern China. Mantel test results indicated that EB was significantly correlated with NO2[-], TN, NO3[-], and DIP, which was confirmed by Spearman's rank correlation coefficients and BIOENV analysis. Ecological network analysis revealed that the EB network was more simplified and clustered, with reduced robustness and increased vulnerability than SW. Only one keystone taxon identified in the EB network showed that the stability of the epiphytic microbiome may be highly dependent on the persistence of this key species. Environmental factors had a more substantial influence on EB communities compared to SW communities. Environmental factors uniquely explained 10.4% of the variation, while SW communities contributed only 2.4%. The combination effect accounted for 66.5% of the variation, indicating that their interplay is the key regulating driver of EB communities. Our findings provide a co-regulation framework between the environment and seawater microbiome for the sustainable development of kelp farming.},
}

@article {pmid41806697,
year = {2026},
author = {Faisal, S and Ullah, I and Kambey, PA and Malik, A and Shakeel, M},
title = {Revolutionizing hepatic fibrosis staging: A machine learning approach combining clinical, biochemical, and microbiome insights.},
journal = {Computers in biology and medicine},
volume = {206},
number = {},
pages = {111584},
doi = {10.1016/j.compbiomed.2026.111584},
pmid = {41806697},
issn = {1879-0534},
abstract = {Non-alcoholic Steatohepatitis (NASH) is a common disease that not only affects adults but has also been seen to affect all ages. This includes young adults, children and even babies. Non-alcoholic fatty liver disease (NAFLD), NASH and the progression of it to fibrosis have been the subject of extensive research, as there still remains a great deal we do not understand. There are multiple factors that will influence how quickly and aggressively the progression of the disease occurs and also the way the disease is diagnosed or assessed, such as medical history, blood results and ultrasound imaging. This study aims to look at the use of machine learning (ML) to integrate clinical, biochemical and microbiome data to create a model to allow for non-invasive staging of hepatic fibrosis for NASH patients. A total of 1834 patients with biopsy-confirmed NASH were included in the retrospective analysis. The cohort was comprised of patients from multiple healthcare systems with known biopsy-confirmed NASH and a stated fibrosis stage (F0, F1, F2, F3, F4). A range of clinical variables, including liver function tests, demographics and microbiome profiles (via 16S rRNA gene sequencing), were included to train the machine learning models (Random Forest & Extreme Gradient Boosting). The performance of these models were assessed using 10-fold cross-validation with the primary training cohort and external validation on an independent hospital database. The models demonstrated excellent classification accuracy, specifically a balanced accuracy of 99.1% for RF and an area under the curve (AUC) value of 1.0 for XGBoost. The addition of microbiome features (specifically, diversity indices and the relative abundance of certain taxa) enhanced the models' predictive capability, indicating that the gut-liver axis plays a significant role in the development of NASH. To interpret the machine learning models, we used SHapley Additive Explanations (SHAP) analysis to identify which of the clinical and microbiome features affected the models' predictions for the fibrosis stages. Advanced stages of fibrosis (F3 & F4) were found to have significant dysbiosis in the microbiome with increased relative abundance of pathogenic bacteria including Escherichia-Shigella and Enterococcus, as well as decreased Akkermansia and Ruminococcus. The study provides evidence for the accuracy of a non-invasive method of determining hepatic fibrosis stage in NASH and demonstrates its superiority compared to traditional scoring systems (i.e. APRI, FIB-4) for the purpose of guiding clinical decision making and risk assessment for patients in clinical practice.},
}

@article {pmid41806586,
year = {2026},
author = {Ji, Z and Hong, S and Zhang, Y and Su, Z and Wang, X and Yu, X and Zhu, Z and Shi, K and Wu, D and Hu, G and Jia, G},
title = {Reshaping the lung microenvironment: MSCs attenuate Cr(VI)-induced pulmonary fibrosis associated with metabolic and microbial modulation.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141708},
doi = {10.1016/j.jhazmat.2026.141708},
pmid = {41806586},
issn = {1873-3336},
abstract = {As a common environmental and occupational pollutant, hexavalent chromium [Cr(VI)] has been proved to induce pulmonary fibrosis. In recent years, mesenchymal stem cells (MSCs) have become a promising therapeutic strategy for pulmonary fibrosis. However, whether they can mitigate Cr(VI)-induced pulmonary fibrosis specifically through regulating the lung microenvironment and microbial homeostasis remains an open and critical question. This study aims to establish a Cr(VI)-induced lung fibrosis model in rats and investigate the protective mechanisms of MSCs through integrated metabolomic and microbiome analyses. MSCs attenuated lung structural destruction, reduced abnormal collagen fiber deposition, decreased the levels of TNF-α, IL6, MDA and 8-OHdG and increased T-AOC and T-SOD. In addition, Cr(VI) caused metabolic disorders in lung tissue, which was evidenced by the up-regulation or down-regulation of multiple phospholipid metabolites, down-regulation of immune-related pathways and up-regulation of arachidonic acid metabolism and glycerophospholipid metabolism pathways. Microbiome analysis revealed that Cr(VI) exposure significantly increased both the diversity and abundance of microbial communities in alveolar lavage fluid, promoting the enrichment of opportunistic pathogens and ultimately leading to microbial dysbiosis. After MSCs intervention, lipid metabolism disorder was alleviated, immune-related pathway was up-regulated, opportunistic bacteria was reduced, and dysbiosis was alleviated. Correlation analysis revealed that lung chromium and lipid-related metabolites were closely associated with microbial communities, suggesting that the pulmonary metabolism may interact with the lung microbiota to jointly maintain the homeostasis of the pulmonary microenvironment. Our study provides a new perspective on elucidating the role of MSCs in treating Cr(VI)-induced pulmonary fibrosis from the perspective of lung metabolism and microbiota.},
}

@article {pmid41806585,
year = {2026},
author = {Li, H and Yang, Q and Liu, T and Liu, W and Ding, Y and Xu, Y and Wei, Z},
title = {Habitat-shaped microbial life-history strategies and host niche specialization govern soil ARG transfer potential.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141706},
doi = {10.1016/j.jhazmat.2026.141706},
pmid = {41806585},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) have been extensively studied in terms of their environmental sources and anthropogenic drivers. However, the ecological mechanisms by which soil microbiomes mediate ARG persistence and transfer remain poorly understood, even though microorganisms are the primary hosts, vectors, and regulators of resistance traits. We compared alpine plateaus and lowland plains, two habitats with contrasting ecological and anthropogenic conditions, to investigate how habitat-driven microbiome processes affect ARG transmission. We found that plateau soils harbored lower ARG abundance (6.2%∼86.3%) and reduced horizontal transfer capacity (94.12%) compared to plain soils. This difference was primarily driven by distinct microbial traits shaped by habitat differences. Plateau microbiomes were dominated by k-strategist taxa characterized by slower growth rates and reduced connectivity in co-occurrence networks, thereby limiting opportunities for ARG exchange. In addition, ARG-carrying hosts in plateau soils exhibited broader ecological niches and a higher proportion of generalist taxa (48.2%), which exerted stronger negative interactions on specialists, thereby constraining the spread of resistance traits. These findings highlight how habitat-shaped microbial traits restrict ARG transmission and offer new insights into the ecological containment of antibiotic resistance in agroecosystems.},
}

@article {pmid41806446,
year = {2026},
author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C},
title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.},
journal = {The Science of the total environment},
volume = {1025},
number = {},
pages = {181655},
doi = {10.1016/j.scitotenv.2026.181655},
pmid = {41806446},
issn = {1879-1026},
abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.},
}

@article {pmid41806308,
year = {2026},
author = {Liu, K and He, Q and Lin, Z and Huang, S and Zhong, Z and Zhu, P and Gao, M and Zhao, L and Jin, H and Wu, G and Geoff, GM and Han, Q and Pang, R},
title = {Genome-Wide Association Study Reveals Insect Genetics and Microbial Symbiont Effects on Susceptibility of Diaphorina citri to the Citrus Greening Pathogen, Candidatus Liberibacter Asiaticus.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17056},
doi = {10.1002/advs.202517056},
pmid = {41806308},
issn = {2198-3844},
support = {32001903//National Natural Science Foundation of China/ ; 2022ZDJS020//Guangdong Province Key Discipline Research Capacity Enhancement Project/ ; 2025A1515012591//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023KTSCX046//Guangdong Provincial Universities Characteristic Innovation Project/ ; 2024A04J4995//Guangzhou Science and Technology Plan Project/ ; },
abstract = {Insect-vectored pathogens pose a significant threat to global agriculture. The colonization efficiency of pathogens in vectors plays a central role in these pathosystems, yet studies of the factors that affect this aspect are limited. This study investigates the genetic and microbial symbiont factors influencing the susceptibility of Diaphorina citri to Candidatus Liberibacter asiaticus (CLas), the pathogen causing citrus greening disease (huanglongbing). Through a microbiome Genome Wide Association Study (mGWAS) based on 16S amplicon sequencing and genomic resequencing of 120 D. citri individuals from six populations, we identified 79 SNPs significantly associated with the relative abundance of CLas within insects. Additionally, some of these SNPs were also associated with the relative abundance of Candidatus Profftella armature, a key endosymbiont of D. citri. SNPs in the regulatory region of gene Dcitr04g11610.1 led to its overexpression in CLas-susceptible D. citri, and CLas infection further elevated its expression. Conversely, RNAi knockdown of Dcitr04g11610.1 reduced CLas infection rates and abundance, accompanied by increased abundance of Profftella. Phylogenetic analysis revealed Dcitr04g11610.1's high homology to Major Facilitator Superfamily-type transporter SLC18B1 proteins, suggesting a role in CLas polyamine utilization. These findings highlight the importance and potential interplay of insect genetics and symbiotic microbiota in insect-vectored plant pathogen systems.},
}

@article {pmid41806199,
year = {2026},
author = {Li, H and Huang, X and Luo, Z and Zhou, F and Deng, Y and Tan, C and Jin, Y and Yan, J and Xiao, G},
title = {Prognostic prediction and immune microenvironment analysis in colorectal cancer using exosome-related lncRNA signatures.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-04755-1},
pmid = {41806199},
issn = {2730-6011},
abstract = {BACKGROUND: Exosomes play a crucial role in tumor microenvironment (TME) by mediating cell-cell communication, but their role in colorectal cancer (CRC) remains unclear. This study aimed to investigate exosome-related lncRNAs (ER-lncRNAs) in CRC.

METHODS: mRNA profiles and clinical data from TCGA and GEO, microbiome data from TCMAand exosome-related genes from ExoCarta were analyzed. Consensus clustering, ER-lncRNA-related risk signature, and nomogram were developed.

RESULTS: A total of 797 differentially expressed lncRNAs (DE-lncRNAs)were identified, with 490 ER-lncRNAs selected based on their correlation with exosome-related mRNAs. Consensus clustering stratified CRC samples into four molecular subtypes, with Cluster 2 exhibiting the most favorable prognosis and Cluster 1 the poorest. These subtypes showed significant differences in survival outcomes, immune cell infiltration, and therapeutic responses. Nine ER-lncRNAs were identified as prognostic biomarkers and used to develop a risk score model. Furthermore, a nomogram incorporating the risk score and clinical parameters was constructed to predict individual prognosis.

CONCLUSION: These findings highlight the clinical relevance of ER-lncRNAs as in CRC and underscores their potential as novel diagnostic and therapeutic targets.},
}

@article {pmid41806138,
year = {2026},
author = {Köse, E and Ekren, BY and Doğulu, N and Yolcu, F and Eylem, CC and Nemutlu, E and Sezerman, U and Eminoğlu, FT},
title = {Dietary Protein Modulation, Gut Microbiota, and Metabolic Control in Methylmalonic Acidemia: A Prospective Longitudinal Study.},
journal = {Journal of inherited metabolic disease},
volume = {49},
number = {2},
pages = {e70172},
doi = {10.1002/jimd.70172},
pmid = {41806138},
issn = {1573-2665},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Amino Acid Metabolism, Inborn Errors/diet therapy/metabolism/microbiology ; Prospective Studies ; Male ; Female ; Longitudinal Studies ; *Dietary Proteins/administration & dosage/metabolism ; Child, Preschool ; Child ; Metronidazole/therapeutic use ; Adolescent ; Infant ; Adult ; Amino Acids/blood ; Young Adult ; },
abstract = {Methylmalonic acidemia (MMA) is a rare inherited metabolic disorder caused by defective conversion of methylmalonyl-CoA to succinyl-CoA. Emerging evidence suggests that both dietary protein composition and intestinal microbiota influence metabolic stability and clinical outcomes. This study aimed to evaluate the effects of stepwise dietary modification and short-term metronidazole therapy on systemic and gut-derived metabolic profiles in MMA. In this prospective, longitudinal, single-center study, eight genetically confirmed MMA patients underwent four sequential phases: baseline mixed-protein diet (50% intact protein/50% medical formula), protein restriction, intact protein enrichment (80% intact protein/20% medical formula), and adjunctive metronidazole therapy (20 mg/kg/day, 10 days/month for 3 months). Plasma amino acids, urinary metabolites, stool microbiota (16S rRNA long-read sequencing), and untargeted/tandem metabolomic profiles were analyzed at each phase. Transition to an intact protein-enriched diet significantly reduced plasma leucine levels (p = 0.008) without affecting isoleucine or valine. Urinary methylmalonic acid, 3-hydroxypropionate, lactate, and pyruvate decreased, indicating improved propionyl-CoA clearance. Microbiota diversity progressively declined, accompanied by reductions in butyrate-producing genera (Novisyntrophococcus, Lacrimispora, Hespellia). Metronidazole further lowered urinary methylmalonic acid and 3-hydroxypropionate (p = 0.017 and p = 0.028), with parallel decreases in fecal 3-indolelactic acid and phytosphingosine, suggesting suppression of gut-derived propionate and tryptophan metabolism. Despite antibiotic-induced dysbiosis with expansion of Trabulsiella (Proteobacteria), systemic propiogenic burden decreased. A phased dietary regimen emphasizing intact protein, combined with intermittent metronidazole therapy, favorably modulated biochemical and microbial parameters in MMA. These findings support microbiome-informed dietary strategies and selective gut-targeted interventions to optimize metabolic control in organic acidemias.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Amino Acid Metabolism, Inborn Errors/diet therapy/metabolism/microbiology
Prospective Studies
Male
Female
Longitudinal Studies
*Dietary Proteins/administration & dosage/metabolism
Child, Preschool
Child
Metronidazole/therapeutic use
Adolescent
Infant
Adult
Amino Acids/blood
Young Adult

@article {pmid41805987,
year = {2026},
author = {Kumar, SM and Ragupathy, TV and Dananjeyan, B and Thiyagarajan, C and Loganathan, A and Natarajan, S},
title = {Microbiome-assisted plant breeding: integrating host-microbiome interactions into crop improvement.},
journal = {Archives of microbiology},
volume = {208},
number = {5},
pages = {},
pmid = {41805987},
issn = {1432-072X},
mesh = {*Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth & development ; *Microbiota ; *Host Microbial Interactions ; Seeds/microbiology/genetics ; Quantitative Trait Loci ; Genome, Plant ; },
abstract = {Conventional breeding and domestication have boosted crop productivity but have also narrowed plant genomic diversity and reduced the diversity of associated microbiota, contributing to domestication syndrome and limiting resilience under increasingly variable environments. Thus, genetic improvement remains essential for developing low-input, high-yielding, enhanced nutrient content and stress-tolerant crops. However, traditional breeding has largely focused on plant genomes, overlooking the microbial partners that influence plant performance. Plants function as holobionts where integrated units composed of the host and its microbiome. These microbial communities colonize all plant tissues and regulate nutrient acquisition, immunity, physiology, and yield, often generating novel phenotypes without altering the plant genome. Some beneficial microbial taxa can even restore plant traits lost during domestication, ascertaining their potential as heritable contributors to crop performance. Seeds play a major role in transmitting plant genes and vertically inherited microbiota, making them a strategic entry point for microbiome integration in breeding. Recent advances include seed microbiome inheritance, root-exudate-mediated microbial recruitment, microbiome-associated QTLs and synthetic microbial communities (SynComs) which can be harnessed to enhance crop traits. These insights provide the foundation for Microbiome-Assisted Plant Breeding (MAPB), a complementary breeding paradigm targeting both plant genomes and microbial partners. Hence, incorporating microbial inheritance, recruitment traits and holobiont performance into breeding pipelines positions MAPB as a promising path toward climate-resilient, resource-efficient, and sustainable crop varieties.},
}

*Plant Breeding/methods
*Crops, Agricultural/microbiology/genetics/growth & development
*Microbiota
*Host Microbial Interactions
Seeds/microbiology/genetics
Quantitative Trait Loci
Genome, Plant

@article {pmid41805839,
year = {2026},
author = {Matarrita-Carranza, B and Weiss, B and Sandoval-Calderón, M and Koehler, S and Engl, T and Kaltenpoth, M},
title = {Defensive symbionts of European beewolves face competition from brood cell microbiota during vertical transmission.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag024},
pmid = {41805839},
issn = {1574-6941},
abstract = {Beewolf wasps rely on an ancient defensive symbiosis with Streptomyces bacteria that protect their larvae from fungal infection. Female beewolves apply the bacteria to the brood-cell ceiling, and larvae later transfer the symbionts onto the cocoon surface, where they produce antifungal metabolites. Here, we investigated the mechanism of symbiont transfer from the beewolf brood cell to the larval cocoon and characterized the microbial community dynamics across different beewolf life stages and during larval hibernation. Fluorescence in situ hybridization revealed that the symbionts are transiently taken up into the proximal midgut lumen and then regurgitated onto the cocoon during the spinning process. High-throughput sequencing showed that the bacterial community of beewolf feeding larvae resembles that of the honeybee prey, whereas that of adults and diapausing larvae is dominated by Wolbachia. Moreover, the cocoon bacterial community is initially dominated by the defensive Streptomyces philanthi symbiont, but when larvae excrete the gut content inside the cocoon, other bacterial taxa including Lactobacillus, Gilliamella and Bartonella shift the community composition toward dominance by Pseudomonadota. Our findings provide new insights into the transmission route of an ancient extracellular symbiont and its potential competition with other bacteria in this long-term defensive symbiosis.},
}

@article {pmid41805689,
year = {2026},
author = {Xie, Y and Zhang, A and Wang, Y and Wang, R},
title = {Community-Acquired Pneumonia in Patients With Diabetes: Narrative Review.},
journal = {JMIR diabetes},
volume = {11},
number = {},
pages = {e82215},
pmid = {41805689},
issn = {2371-4379},
abstract = {BACKGROUND: Patients with diabetes carry a 1.5- to 2-fold higher risk of community-acquired pneumonia (CAP) and experience more severe outcomes, yet the mechanisms that integrate metabolic dysregulation, pathogen shifts, and novel cell death pathways remain fragmented.

OBJECTIVE: This study aimed to synthesize current evidence on epidemiology, pathophysiology, causative pathogens, clinical outcomes, and management of CAP in adults with diabetes and to identify research gaps for future trials.

METHODS: A narrative review (1999 to August 2025) of PubMed, EMBASE, the Cochrane Library, and Web of Science was conducted. GRADE (Grading of Recommendations Assessment, Development, and Evaluation) was used to rate evidence from 81 selected English-language studies (randomized controlled trials, cohorts, and meta-analyses).

RESULTS: Diabetes increases CAP incidence (relative risk 1.73, 95% CI 1.46-2.04), hospitalization (+30%-50%), and 30-day mortality (odds ratio 1.67, 95 % CI 1.45-1.92). Key drivers include hyperglycemia-induced immune paralysis, pulmonary microangiopathy, ferroptosis, glycation and methylation changes, and gut-lung dysbiosis that collectively favor multidrug-resistant Gram-negative bacilli (Klebsiella and Pseudomonas) and severe viral and fungal coinfections. Host-targeted therapy with moderate glycemic control (5-10 mmol/L), continued metformin, and pathogen-directed antibiotics improves survival, whereas single-dose PCV20 and annual influenza vaccination prevents approximately 45% of CAP admissions. Emerging strategies (nanozymes, ferroptosis inhibitors, probiotics, and proteolysis-targeting chimeras) are still preclinical.

CONCLUSIONS: CAP in patients with diabetes is a distinct, more severe entity mediated by metabolic-immune crosstalk. Multicenter randomized controlled trials integrating tight glucose monitoring, novel host-directed agents, and microbiome modulation are warranted to translate mechanistic insights into better outcomes.},
}

@article {pmid41805583,
year = {2026},
author = {Unzueta-Martínez, A and Delaney, JA and Morkeski, K and Ross, A and Wang, ZA and Girguis, PR},
title = {Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {11},
pages = {e2521539123},
doi = {10.1073/pnas.2521539123},
pmid = {41805583},
issn = {1091-6490},
support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Calcification, Physiologic/genetics ; Hydrogen-Ion Concentration ; *Ostreidae/genetics/microbiology/metabolism ; Transcriptome ; Seawater/chemistry ; },
abstract = {Marine animals that build shells, such as oysters, carefully regulate the chemistry of their internal calcifying fluids, but the molecular mechanisms behind this control, as well as whether microbes play a role in calcification, are poorly understood. To better understand oysters' molecular mechanisms and the role of their calcifying-fluid microbes, we conducted experiments that simulated a tidal cycle, measured calcifying fluid pH and total dissolved inorganic carbon, and characterized host and microbial gene expression via transcriptomics. These experiments showed that calcifying fluid pH remained relatively stable throughout tidal pH fluctuations, with corresponding increases in oyster transcripts for ion transport and acid-base regulation. These data provide direct evidence that tidal fluctuations drive rapid changes in oyster calcifying fluid chemistry. Most surprisingly, increases in microbial transcripts related to nitrogen and sulfur cycling correlated to higher calcifying fluid DIC, and coexpression network analysis revealed patterns of gene expression that linked oyster immune and neural pathways to microbial redox processes, providing molecular evidence of potential host modulation of microbial metabolism. Together, these results reveal that oysters actively regulate their calcifying fluid pH over short timescales, and the endemic microbiome metabolic responses can yield metabolites that influence calcifying fluid pH, alkalinity, and ultimately calcification. These data offer a perspective on oyster physiological capacity and, most importantly, the potential role of microbes in oyster calcification. In light of ongoing changes in ocean pH and temperature, oysters provide a model for studying animal-microbial responses to environmental acidification and how their interactions may shape biomineralization.},
}

Animals
*Microbiota/genetics
*Calcification, Physiologic/genetics
Hydrogen-Ion Concentration
*Ostreidae/genetics/microbiology/metabolism
Transcriptome
Seawater/chemistry

@article {pmid41805347,
year = {2026},
author = {Song, L and Zhang, H and Wang, M and Li, S and Wang, F and Zhang, M and Qu, Y and Ma, Y and Ma, Q and Wen, C and Zhao, Y and Liu, M and Wang, F},
title = {Metacycloprodigiosin from Rhizosphere Streptomyces aurantiacus as a Natural Antifungal Agent against Fusarium oxysporum.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15856},
pmid = {41805347},
issn = {1520-5118},
abstract = {Microbiome-guided crop protection increasingly emphasizes the chemical basis of disease suppression. Here, we identify Streptomyces aurantiacus YS-4, a rhizosphere-enriched actinobacterium selectively recruited by resistant cultivars of Salvia miltiorrhiza, as a producer of metacycloprodigiosin, a previously reported secondary metabolite that is reported for the first time in this strain and further investigated for its role in suppressing Fusarium oxysporum-induced root rot in S. miltiorrhiza. Metacycloprodigiosin inhibited Fusarium oxysporum growth by 81.66% at 200 μg mL[-1] and induced extensive cellular and transcriptional changes related to membrane function and virulence-associated pathways. Transmission electron microscopy confirmed severe hyphal damage, while transcriptomic profiling revealed broad downregulation of virulence-associated genes. Pot experiments demonstrated that YS-4 application alleviated root rot symptoms and enhanced plant biomass. Collectively, these findings establish a direct link between metabolite chemistry and pathogen suppression, advancing molecular understanding of plant-fungal interactions and highlighting metacycloprodigiosin as a promising biocontrol agent for sustainable management of crops.},
}

@article {pmid41805251,
year = {2026},
author = {Zhou, H and Zhao, X and Li, Y and Wang, Y and Zhang, S and Xu, H and Sui, S and Wang, Q and He, Y and Gu, J},
title = {Nicotinamide mononucleotide supplementation modulates gut microbiota and metabolites to mitigate Alzheimer's disease pathology in APP/PS1 mice.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261422502},
doi = {10.1177/13872877261422502},
pmid = {41805251},
issn = {1875-8908},
abstract = {BackgroundEmerging evidence indicates that gut microbiome dysbiosis may be linked to Nicotinamide adenine dinucleotide (NAD[+]) deficiency during Alzheimer's disease (AD) progression, a condition potentially alleviated by nicotinamide mononucleotide (NMN) supplementation.ObjectiveTo explore the therapeutic potential of NMN supplementation in regulating AD pathology as well as gut microbiome dynamics, APP/PS1 transgenic mouse models were employed in the research.MethodsMetagenomic and metabolomics analysis were conducted to assess modifications in the intestinal microbiota and metabolites of AD mice post-NMN treatment. Moreover, immunohistochemistry, immunofluorescence, western blot, and Morris water maze were applied to evaluate NMN's ameliorative effects on AD.ResultsNMN administration significantly altered gut microbial composition and fecal metabolite profiles, leading to improvements in colon damage and AD-related neuropathology. Key findings include the restoration of gut microbial balance, particularly increasing Bacteroides abundance, and the modulation of metabolites involved in lipid metabolism. Furthermore, NMN was found to regulate ferroptosis, improving gut barrier function in AD mice, which were mediated through gut-brain communication pathways. NMN supplementation also enhanced ATP production, mitochondrial function, and synaptic density in the hippocampus while reducing oxidative stress and Aβ accumulation in the brain. Ultimately, these multi-faceted improvements collectively alleviated cognitive deficits in AD mice.ConclusionsIn summary, NMN supplementation effectively modulated gut microbiota and metabolites, thus mitigating AD pathology in APP/PS1 mice. Our study offers novel perspectives on the mechanisms underlying NMN's therapeutic effects in AD and underlines its potential as a promising intervention strategy.},
}

@article {pmid41805178,
year = {2026},
author = {Skolnick, S and Hall, B},
title = {Draft genome sequence of a family Acutalibacteraceae isolate, a human gut-derived cholesterol metabolizer.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0113725},
doi = {10.1128/mra.01137-25},
pmid = {41805178},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a family Acutalibacteraceae isolate, which is an obligate anaerobe that converts cholesterol to coprostanol. The organism was isolated from a healthy adult's fecal sample, plated on cholesterol brain agar, and incubated anaerobically, yielding distinctive star-shaped colonies. This isolate is from an unclassified genus within the Acutalibacteraceae, highlighting the unexplored diversity within the gut microbiome.},
}

@article {pmid41805144,
year = {2026},
author = {Zhou, B and Mokhashi, N and Skondra, D},
title = {Emerging strategies in drug repurposing for decreasing the risk of age-related macular degeneration.},
journal = {Expert opinion on drug discovery},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/17460441.2026.2635492},
pmid = {41805144},
issn = {1746-045X},
abstract = {INTRODUCTION: Vision loss in older adults is largely driven by age-related macular degeneration (AMD), characterized by progressive damage central visual field damage and functional decline. While current options for wet and dry AMD are limited and expensive, drug repurposing represents a promising strategy to accelerate the discovery of effective, accessible treatment by leveraging medications with established safety profiles. Notably, anti-diabetic agents including metformin, sulfonylureas, glucagon-like peptide-1 receptor agonists (GLP-1RAs), and insulin have emerged as modulators of the retinal pigment epithelium (RPE) function, photoreceptors, and retinal vascular integrity.

AREAS COVERED: This review highlights the roles of oxidative stress, inflammation, and complement-mediated immune dysregulation in AMD pathogenesis, alongside preclinical data demonstrating metformin's protective effects via AMP-activated protein kinase (AMPK) activation. Population-based studies and meta-analyses further suggest a modest reduction in AMD risk associated with metformin use in both diabetic and non-diabetic cohorts. Additional pharmacological agents include statins, glyburide, L-DOPA, fluoxetine, dimethyl fumarate, and nutraceuticals such as curcumin, melatonin, and N-acetylcysteine.

EXPERT OPINION: Early AMD prevention through repurposed therapeutics, guided by AI-driven design and systems biology, may enable personalized care via multimodal risk stratification incorporating genetic, metabolomic, and microbiome data. Rigorous, stratified clinical trials integrating bioinformatics and precision medicine are essential to validate the most effective candidates.},
}

@article {pmid41805117,
year = {2026},
author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE},
title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15254},
pmid = {41805117},
issn = {1520-5118},
abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.},
}

@article {pmid41804973,
year = {2026},
author = {Mehl, A and Blacher, E},
title = {Gut microbiome and aging-A dynamic interplay of microbes, metabolites, and the immune system.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70324},
pmid = {41804973},
issn = {1873-3468},
support = {03-23-24//The National Institute for Psychobiology in Israel/ ; 2023061//The United States-Israel Binational Science Foundation/ ; //Uncle Kory Foundation/ ; //Keren Shemesh: HUJI-STMC collaborative grant/ ; //The Abisch Frenkel Foundation for the Promotion of Life Sciences/ ; //ERA-Net NEURON MOODYGUT/ ; //The Azrieli Foundation Faculty Fellowship/ ; 888494//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
abstract = {Aging is accompanied by profound changes in both the gut microbiome and the immune system, which engage in continuous, bidirectional communication. Alterations in microbial diversity and metabolism, particularly reductions in short-chain fatty acid (SCFA) producers as well as shifts in bile acid and tryptophan-metabolizing species, can incite and worsen inflammation, damage barrier integrity, and accelerate immunosenescence. Concomitantly, immune aging and reduced mucosal IgA promote microbial dysbiosis, forming a self-reinforcing cycle that fuels chronic inflammation ("inflammaging"). Microbial metabolites such as SCFAs, secondary bile acids, and indole derivatives play central roles in this gut-immune dialog, influencing regulatory T-cell balance, epithelial repair, and neurological health through the gut-brain axis. Emerging evidence suggests that diet, probiotics, postbiotics, and microbiome transplantations can restore beneficial microbial and, consequently, immune functions, offering opportunities to promote healthy aging and potentially reverse adverse symptoms. Understanding and targeting the gut microbiome-immune feedback loops may reveal new strategies to modulate inflammaging and extend health span.},
}

@article {pmid41804971,
year = {2026},
author = {Wang, Y and Cao, B and Liu, C and Ling, Q and Qiu, Z and Yan, W},
title = {Integrated Multiomics Analysis Indicates Seasonal and Geographical Drivers of Rhizosphere Microbiome-Metabolome Interactions and Dihydrochalcone Accumulation in Lithocarpus litseifolius (Hance) Chun.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11982},
pmid = {41804971},
issn = {1520-5118},
abstract = {Lithocarpus litseifolius (L. litseifolius) is a valuable economic crop rich in dihydrochalcones (DHCs), with wide applications in medicines, tea, and sweeteners. By integrating multiomics approaches, the relationship between rhizosphere microecology and quality formation in L. litseifolius was systematically elucidated. Key bacterial groups, such as Burkholderia-Caballeronia-Paraburkholderia, Conexibacter, and Bradyrhizobium, were driven by soil physicochemical properties (available copper, exchangeable manganese, alkali-hydrolyzable nitrogen, and organic matter) and rhizosphere metabolome and were strongly associated with the up-regulation of key genes in phenylpropanoid biosynthesis (phenylalanine ammonia lyase, cinnamate 4 hydroxylase, chalcone synthase, phloretin 4'-O-glucosyltransferase), thereby promoting DHC accumulation. A pot experiment confirmed the functional contribution of Burkholderia in promoting the growth of L. litseifolius and the accumulation of its secondary metabolites. The mechanisms by which soil characteristics and microbial communities regulate DHC biosynthesis in L. litseifolius were elucidated, providing insights into the coupling mechanism of "soil-microbiome-metabolome-plant secondary metabolism".},
}

@article {pmid41804865,
year = {2026},
author = {Ma, J},
title = {Inference for microbe-metabolite association networks using a latent graph model.},
journal = {Biometrics},
volume = {82},
number = {1},
pages = {},
doi = {10.1093/biomtc/ujag042},
pmid = {41804865},
issn = {1541-0420},
support = {R01 GM145772/GF/NIH HHS/United States ; },
mesh = {Algorithms ; Computer Simulation ; Humans ; *Models, Statistical ; Female ; *Microbiota ; *Metabolic Networks and Pathways ; Stochastic Processes ; },
abstract = {Correlation networks are commonly used to infer associations between microbes and metabolites. The resulting $p$-values are then corrected for multiple comparisons using existing methods such as the Benjamini & Hochberg (BH) procedure to control the false discovery rate (FDR). However, most existing methods for FDR control assume the $p$-values are weakly dependent. Consequently, they can have low power in recovering microbe-metabolite association networks that exhibit important topological features, such as the presence of densely associated modules. We propose a novel inference procedure that is both powerful for detecting significant associations in the microbe-metabolite network and capable of controlling the FDR. Power enhancement is achieved by modeling latent structures in the form of a bipartite stochastic block model. We develop a variational expectation-maximization (EM) algorithm to estimate the model parameters and incorporate the learned graph in the testing procedure. In addition to FDR control, this procedure provides a clustering of microbes and metabolites into modules, which is useful for interpretation. We demonstrate the merit of the proposed method in simulations and an application to bacterial vaginosis.},
}

Algorithms
Computer Simulation
Humans
*Models, Statistical
Female
*Microbiota
*Metabolic Networks and Pathways
Stochastic Processes

@article {pmid41804664,
year = {2026},
author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B},
title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70278},
doi = {10.1111/1462-2920.70278},
pmid = {41804664},
issn = {1462-2920},
support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; },
mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; },
abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.},
}

Biodegradation, Environmental
*Composting
*Microplastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Polymers/metabolism/chemistry
*Soil Microbiology
Microbiota
Polyesters/metabolism
*Soil Pollutants/metabolism
Soil/chemistry

@article {pmid41804655,
year = {2026},
author = {Zhang, Y and Li, S and Li, Q and Wang, R and Sun, Y and Wang, Y and Yan, X and Wang, X and Wang, Y and Xue, Y and Ding, C and Gong, J and Ding, L and Ju, H},
title = {Synthetic Antibody Mimetics with ROS-Gated Saccharide Release for Targeted Colitis Therapy.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e05869},
doi = {10.1002/adhm.202505869},
pmid = {41804655},
issn = {2192-2659},
support = {22574077//National Natural Science Foundation of China/ ; 22274073//National Natural Science Foundation of China/ ; 5431ZZXM2504//State Key Laboratory of Analytical Chemistry for Life Science/ ; },
abstract = {Conventional targeted therapies for inflammatory bowel disease (IBD) often rely on unstable biological recognition elements. While molecularly imprinted polymers (MIP) offer robust synthetic alternatives, their utility is limited by an "always-on" binding state: even weak non-specific adsorption can significantly compromise their target-binding capacity. We convert static MIP into reactive oxygen species (ROS)-activated therapeutic actuators by conjugating mannose to transferrin-imprinted MIP via a ROS-cleavable linker. The saccharide acts dually as a therapeutic agent and a protective cloak. It sterically blocks non-specific binding during intestinal transit. At inflammatory sites, elevated ROS levels (higher than in healthy tissue) trigger simultaneous mannose release and activation of high-affinity targeting. This enables precise MIP anchoring to the inflamed epithelium for physical barrier formation and localized microbiome modulation. In murine colitis models, this achieved mucosal healing, mitigated inflammation, and microbiota rebalancing using a mannose equivalent dose of 27.2 mg/kg/d, benchmarking against free mannose and non-responsive MIP controls. This work establishes a generalizable paradigm for targeted recognition and drug delivery in complex physiological environments, paving the way for intelligent, disease-responsive nanomedicines.},
}

@article {pmid41804549,
year = {2026},
author = {Tufvesson-Alm, M and Walsh, L and Pierce, S and Keohane, F and Clarke, G and O'Connor, K and Cryan, JF and Schellekens, H},
title = {Unravelling the role of the gut microbiome in antipsychotic-induced weight gain and metabolic dysfunction in humans and rodents: A systematic review.},
journal = {Dialogues in clinical neuroscience},
volume = {28},
number = {1},
pages = {131-144},
doi = {10.1080/19585969.2026.2637716},
pmid = {41804549},
issn = {1958-5969},
mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Humans ; *Antipsychotic Agents/adverse effects ; *Weight Gain/drug effects/physiology ; Animals ; *Metabolic Diseases/chemically induced/microbiology ; },
abstract = {Second-generation antipsychotics are frequently linked to weight gain and metabolic dysfunction, yet the mechanisms driving these effects remain elusive. The gut microbiome has been proposed as a potential mediator of these adverse outcomes. This study aimed to investigate the role of the gut microbiota in antipsychotic-induced weight gain. A systematic search of PubMed and Embase was conducted. In total, 24 publications were included in this review, including clinical and preclinical observational and intervention studies. Collectively, there is strong evidence that atypical antipsychotic-induced weight gain and metabolic dysfunction is accompanied by microbiota alterations. However, there is a lack of consensus with regards to the exact mechanisms and involvement of the microbiome in antipsychotic-induced weight gain. Nevertheless, a few patterns and common observations were found across studies, such as reduced diversity, increased Firmicutes/Bacteroidetes ratio and a reduction in Akkermansia species. While microbiota-targeted interventions had generally weak effects on weight gain and metabolic dysfunction in clinical cohorts, the use of specific probiotic strains and microbiota metabolites showed promise in preclinical studies. Thus, while the relationship between antipsychotic-induced weight gain, metabolic dysfunction, and changes in the gut microbiome are evident, further research is warranted to establish definitive causal relationships and to aid in the development of precision microbiota-targeted interventions to counteract these adverse effects.},
}

*Gastrointestinal Microbiome/drug effects/physiology
Humans
*Antipsychotic Agents/adverse effects
*Weight Gain/drug effects/physiology
Animals
*Metabolic Diseases/chemically induced/microbiology

@article {pmid41804484,
year = {2026},
author = {Rodríguez-Barreras, R and Suárez-Pérez, J and Godoy-Vitorino, F},
title = {Seasonality shapes gut microbiota composition in two sympatric sea urchins.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20918},
pmid = {41804484},
issn = {2167-8359},
mesh = {Animals ; *Seasons ; *Sea Urchins/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Puerto Rico ; Sympatry ; *Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The gut microbiota plays critical roles in digestion, immunity, and environmental adaptation in marine invertebrates. Its composition is shaped by both host traits and abiotic factors such as temperature and seasonality. In Caribbean reefs, sea urchins like Diadema antillarum and Echinometra lucunter are important grazers that regulate algal biomass and influence benthic community dynamics. This study used 16S rRNA gene sequencing to compare, for the first time, the gut microbiota of these two sympatric species across contrasting seasons.

METHODS: Adults of D. antillarum and E. lucunter were collected during summer and winter from three fringing reefs in Puerto Rico. Gut contents were extracted under sterile conditions, and bacterial DNA was extracted amplified for their 16S rRNA genes and sequenced. Microbial diversity and structure were assessed standard microbiota pipelines.

RESULTS: Microbial communities in both echinoids were dominated by Bacillota, Bacteroidota, Desulfobacterota, and Pseudomonadota. Core microbiota analysis revealed stable taxa across hosts and seasons, most notably Propionigenium, supporting host-driven selection mechanisms that maintain functional stability despite seasonal turnover. Core microbiome analyses revealed Bacillota, Bacteroidota, Desulfobacterota_G_459543, and Pseudomonadota as persistent phyla across seasons, and genera such as Desulfotalea, Photobacterium, and Propionigenium consistently present in both species. Alpha diversity was significantly higher in winter for both D. antillarum and E. lucunter, while species-level differences were not significant. Beta diversity analyses showed significant seasonal clustering, with no consistent segregation between species within seasons. Our findings demonstrate that shared environmental conditions, particularly seasonality, are the primary modulators of gut microbiota in sympatric sea urchins, while host selection preserves a conserved core community. This dual influence of environment and host highlights the ecological plasticity and resilience of sea urchin microbiotas under fluctuating reef conditions.},
}

Animals
*Seasons
*Sea Urchins/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Puerto Rico
Sympatry
*Bacteria/genetics/classification

@article {pmid41804293,
year = {2026},
author = {Oringher, JL and Afruza, R and Chakraborty, M and Akiva, KL and Zhang, GY and Townsend, EC and Quinn, GM and Scheuing, L and Menkart, MG and Rai, A and Kleiner, DE and Levy, EB and Koh, C and Ali, RO and Etzion, O and Heller, T},
title = {Portal Vein Tryptophan Pathway Analysis Reveals Gut-Mediated Inflammatory Pathway Predominance in HCV Infection.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {4},
pages = {e70584},
doi = {10.1111/liv.70584},
pmid = {41804293},
issn = {1478-3231},
support = {DK054514/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Tryptophan/blood/metabolism ; Male ; Female ; Middle Aged ; Kynurenine/blood ; *Gastrointestinal Microbiome ; *Portal Vein/metabolism ; Adult ; Antiviral Agents/therapeutic use ; Cytokines/blood ; Sofosbuvir/therapeutic use ; Sustained Virologic Response ; Liver/pathology ; *Hepatitis C, Chronic/drug therapy/blood ; Xanthurenates/blood ; Inflammation ; *Hepatitis C/drug therapy ; Biomarkers/blood ; Aged ; Heterocyclic Compounds, 4 or More Rings/therapeutic use ; },
abstract = {BACKGROUND AND AIMS: The tryptophan pathway is an integral component of the gut-liver axis; however, the role in hepatitis C virus infection (HCV) and liver disease progression remains poorly understood. This study investigated tryptophan metabolites in portal and peripheral serum during and after HCV, and their relationship to inflammatory and clinical markers.

METHODS: HCV infected patients were evaluated during infection (HCVi, n = 24) and 6 months after sofosbuvir/velpatasvir mediated sustained virologic response (SVR, n = 19) (NCT02400216). Liver biopsies, portal and peripheral blood collection, and stool sampling were performed at both time points. Statistical analyses assessed metabolite abundance during infection and recovery, and their associations with cytokines, clinical parameters, and the microbiome.

RESULTS: During infection, peripheral tryptophan and kynurenine were elevated while indolelactate and xanthurenate were reduced (p < 0.05). In the portal blood, kynurenine/tryptophan ratio and kynurenine were increased, whereas indoleacetate and xanthurenate were decreased (p < 0.05). Tryptophan metabolites positively correlated with hepatic activity index, gamma-glutamyl transferase, total bilirubin, spleen volume/height ratio, and pro-inflammatory cytokines including CXCL9, CXCL10, TNFα, IL6, and IL-12p40. Negatively, correlations were observed with gut microbes Dorea longicatena and Qiania dongpingenesis.

CONCLUSIONS: Elevated kynurenine in portal blood suggests upregulation of gut-mediated pro-inflammatory pathways during HCV infection. Integration of multi-omics data from the gut-liver axis highlights the contribution of the tryptophan pathway to inflammatory responses in HCV. However, small sample size, absence of quantitative values for all pathway metabolites, and reliance on correlative rather than causative associations limit mechanistic interpretation. Future studies with larger cohorts and functional analyses are needed to clarify causal mechanisms and evaluate therapeutic potential of targeting the tryptophan pathway.

TRIAL REGISTRATION: NCT02400216.},
}

Humans
*Tryptophan/blood/metabolism
Male
Female
Middle Aged
Kynurenine/blood
*Gastrointestinal Microbiome
*Portal Vein/metabolism
Adult
Antiviral Agents/therapeutic use
Cytokines/blood
Sofosbuvir/therapeutic use
Sustained Virologic Response
Liver/pathology
*Hepatitis C, Chronic/drug therapy/blood
Xanthurenates/blood
Inflammation
*Hepatitis C/drug therapy
Biomarkers/blood
Aged
Heterocyclic Compounds, 4 or More Rings/therapeutic use

@article {pmid41803943,
year = {2026},
author = {Dai, W and Jiang, X and Liu, Y and Yu, Y and Hou, J and Xia, J and Li, SC and Li, C and Du, H and Wu, R},
title = {Integrated cross-sectional study and functional validation indicate the association of lactobacillus crispatus-derived D-lactic acid with cervical gene expression and precancerous cervical lesions.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07982-w},
pmid = {41803943},
issn = {1479-5876},
}

@article {pmid41803939,
year = {2026},
author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M},
title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00544-x},
pmid = {41803939},
issn = {2524-4671},
}

@article {pmid41803924,
year = {2026},
author = {Enokela, SO and Yergaliyev, T and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A},
title = {Towards standardization in pig microbiome research based on a comprehensive twenty-year review.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00541-0},
pmid = {41803924},
issn = {2524-4671},
support = {28N-2-051-01//German Federal Ministry of Food and Agriculture/ ; 28N-2-051-01//German Federal Ministry of Food and Agriculture/ ; },
}

@article {pmid41803907,
year = {2026},
author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM},
title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02345-5},
pmid = {41803907},
issn = {2049-2618},
support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; },
abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.

RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.

CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.},
}

@article {pmid41803902,
year = {2026},
author = {Liu, Q and Wang, C and Si, G and He, J},
title = {Integrated multiomics profiling predicts anti-tuberculosis drug-induced liver injury.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03608-3},
pmid = {41803902},
issn = {1465-993X},
support = {2023YFS0236//Sichuan Science and Technology Program Key R&D Project/ ; },
}

@article {pmid41803738,
year = {2026},
author = {Liu, G and Zhou, K and An, Q and Yang, C and Yang, S and Xu, L},
title = {Regulatory effects of winter Morchella esculenta cultivation on the summer maize phyllosphere microbiome and plant health-related traits.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08489-8},
pmid = {41803738},
issn = {1471-2229},
support = {202305AC160057//Project for Reserve Talents of Young and Middle-aged Academic and Technical Leaders/ ; 2023//Xingzhao Talent Support Program/ ; 2025//Yunnan Colorful Clouds Postdoctoral Program Innovation Project/ ; },
}

@article {pmid41803419,
year = {2026},
author = {Liu, Y and Liu, R and Zheng, K and Wang, Z and Shao, H and McMinn, A and Wang, M and Liang, Y},
title = {Global genomic diversity of temperate P2-like viruses.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09823-4},
pmid = {41803419},
issn = {2399-3642},
support = {42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42120104006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025M770867//China Postdoctoral Science Foundation/ ; },
abstract = {P2-like viruses (P2Vs), temperate phages of the Peduoviridae family, possess a lysogenic lifestyle that renders traditional isolation unsuitable, hindering our understanding of their diversity and ecological roles. Utilizing profile-hidden Markov models to analyze public databases, this study achieved four major advances: (1) Identified 5945 P2V genomes and built the P2V Genome Dataset (P2VGD), expanding known genomes 48-fold; (2) Phylogenetic classification into 13 superclades and 4671 genus-level clusters, a 106-fold diversity increase; (3) Identification of 757 auxiliary metabolic genes with biome-specific metatranscriptomic activities: human gut P2Vs encode antibiotic efflux and cell-wall remodeling enzymes, while oligotrophic marine P2Vs express glycan-scavenging enzymes; (4) Uncovering their widespread distribution across diverse biomes, dominated by host-associated environments but extending to under-sampled natural ecosystems. These findings greatly expand the genomic and functional understanding of P2Vs, highlighting their biological strategies in host adaptation, virus-host co-evolution, and microbiome dynamics.},
}

@article {pmid41803343,
year = {2026},
author = {Pal, SK and Davar, D},
title = {Microbiome modulation in cancer immunotherapy.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41803343},
issn = {1546-170X},
}

@article {pmid41803338,
year = {2026},
author = {Tamang, KR and Mahdi, S and Koirala, P and Asiamah, JY and Sharma, S and Padyana, S and Carson, CB and Valliyodan, B},
title = {Soil Microbiome for Climate Smart Agriculture in Legumes: A Review.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41803338},
issn = {1432-0991},
support = {U.S. Department of Agriculture//U.S. Department of Agriculture/ ; },
abstract = {Climate-smart agriculture is a multidisciplinary farm model approach that helps reduce the impact of climate change not only on soil but on entire agricultural systems. One of the critical approaches of climate-smart agriculture is using the soil microbiome to help the crop adapt to the changing climate and increase crop production. The microorganisms that are present in the soil play a crucial role in ecosystem services, crop protection and performance, and productivity. Legumes are essential for their nutritional value and interaction with soil microbes, particularly in fixing atmospheric nitrogen and improving soil health through plant-microbe association. Beyond Rhizobium, a wide range of microorganisms and fungi assist legumes in adapting to climate stresses such as drought stress and salinity, which ultimately enhances biomass and legume yield. However, the molecular mechanisms behind the interactions between microbiomes and plant growth, ecosystem services, and carbon sequestration remain unclear in legumes. This review aims to explain the key roles of the soil microbiome, legume rhizobiome, and the microbial genes associated with functional plant traits that help plants adapt to a changing climate. Understanding how microbial populations shift due to climate variations and how these changes affect legume yields is crucial, given the ever-changing nature of ecosystems due to climatic shifts. Therefore, more research is warranted to explore plant microbial interactions, understand the dynamics of climatic shifts, and develop microbiome engineering tools for the improved health of crop and rhizobiome ecosystems. Furthermore, a parallel study is required to examine the harmful microbiome that causes crop destruction and antagonizes important bacteria.},
}

@article {pmid41803336,
year = {2026},
author = {Mandal, S and Aran, KR},
title = {Symbiotic in Alzheimer's disease: modulating the gut-brain axis for neuroimmune homeostasis and cognitive protection.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41803336},
issn = {1568-5608},
abstract = {Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder defined by progressive cognitive impairment, neuroinflammation, oxidative stress, amyloid-β (Aβ) accumulation, synaptic dysfunction, mitochondrial impairment, and tau hyperphosphorylation. The gut-brain axis (GBA) is a crucial regulatory signaling cascade that links intestinal microbiome composition with both neural health and disease through the vagus nerve. Gut dysbiosis has increasingly been implicated in AD pathogenesis by exacerbating systemic and neuroinflammatory signaling, disrupting intestinal and blood-brain barrier (BBB) structural stability, and promoting microglial activation, thereby facilitating Aβ aggregation and neurodegeneration. Preclinical studies indicate that symbiotic interventions restore microbial balance and improve gut-brain communication, contributing to neuroprotective effects. Additionally, it has been demonstrated that symbiotics can restore synaptic plasticity and cognitive resilience by suppressing pro-inflammatory cytokines, as exemplified by interleukin-1β (IL-1β) and tumour necrosis factor-α (TNF-α), and by upregulating neurotrophic factors, particularly brain-derived neurotrophic factor (BDNF). These effects are associated with normalised glial reactivity, attenuation of oxidative stress, and improved mitochondrial bioenergetics, together contributing to enhanced synaptic function, reduced neuroinflammation, and preservation of cognitive performance. This review highlights a critical assessment of the treatment potential of symbiotic interventions in modulating the GBA in AD, emphasising mechanistic insights into neurodegenerative pathways and evaluating their capacity to mitigate symptoms and delay disease progression, as supported by current preclinical evidence.},
}

@article {pmid41803252,
year = {2026},
author = {Jurry, AG and Sahoo, JP and Sharma, SS and Praveena, J and Hossain, SN and Sahu, N and Pradhan, S and Nayak, P and Tripathy, S and Vijayakumar, D and Dash, SS and Jena, B and Pradhan, P and Pradhan, SS},
title = {Morpho-biochemical and molecular identification of Bacillus licheniformis and Bacillus cereus isolates from sorghum (Sorghum bicolor L.) rhizosphere.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42932-y},
pmid = {41803252},
issn = {2045-2322},
abstract = {This study isolated, characterized, and identified rhizosphere-associated soil bacteria from sorghum-cultivated soils in Bhubaneswar, India, using serial dilution and spread plate techniques on Nutrient Agar. Morphological and biochemical analyses (Gram staining, catalase, oxidase, MR, and indole tests) identified 13 bacterial isolates, predominantly Gram-positive rods (Bacillus, Paenibacillus) and cocci (Staphylococcus, Micrococcus), with one Gram-negative isolate. Molecular characterization involved 16S rRNA gene amplification (~ 1500 bp), sanger sequencing, and phylogenetic analysis. BLASTN confirmed AG3 as Bacillus licheniformis (99.37% identity) (GenBank: PV590072), and AG11 as Bacillus cereus (100% identity) (GenBank: PV590099). The phylogenetic tress analysis of bacterial isolates AG3 and AG11 revealed distinct evolutionary rate variations. For AG3, site-specific rates ranged from 0.07 to 3.64 substitutions/site (nucleotide frequencies: A = 24.50%, T/U = 19.99%, C = 24.70%, G = 30.81%), while AG11 exhibited more uniform rates ranged from 0.90 to 1.10 substitutions/site (nucleotide frequencies: A = 25.79%, T/U = 20.86%, C = 22.71%, G = 30.64%). Maximum likelihood trees (log-likelihood: - 4077.853 for AG3, - 1928.562 for AG11) with 1,531 (AG3) and 1,402 (AG11) aligned positions resolved their phylogenetic relationships. This study provides valuable insights into the diversity and evolutionary dynamics of rhizosphere-associated Bacillus spp. in sorghum-cultivated soils, contributing to a better understanding of their ecological significance and potential application in sustainable agriculture and plant growth promotion.},
}

@article {pmid41803235,
year = {2026},
author = {Chowdary, DD and Sridhar, Y and Rao, GR and Madhav, MS and Latha, PC and Malathi, VM and Padmakumari, AP and Sundaram, RM},
title = {Diversity of culturable gut bacteria associated with brown planthopper, Nilaparvata lugens (Stål) and their role in imidacloprid degradation.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41348-y},
pmid = {41803235},
issn = {2045-2322},
abstract = {The brown planthopper, Nilaparvata lugens (Stål), is a major pest of rice across Asia and has developed significant metabolic resistance to multiple insecticides. Microbiome-mediated insecticide resistance is of emerging interest in various insect pests, including N. lugens. In this study, we assessed the diversity of culturable gut bacteria in imidacloprid-susceptible (IMI-S) and imidacloprid-resistant (IMI-R) populations of N. lugens and their potential to degrade imidacloprid. Molecular characterization and phylogenetic analysis identified 13 bacterial isolates, representing ten families from three phyla: Proteobacteria, Actinobacteria and Firmicutes. The IMI-R population has contributed to nine of the 13 isolates. Screening for imidacloprid degradation identified four bacterial strains viz., Paenibacillus amylolyticus, Serratia marcescens, Acinetobacter soli and Brucella sp. associated with the IMI-R population were capable of growing in minimal salt medium supplemented with imidacloprid. Notably, S. marcescens and P. amylolyticus could utilize imidacloprid as a sole source of carbon and nitrogen, respectively. LC-MS/MS analysis revealed that P. amylolyticus and S. marcescens after 14 days of inoculation degraded 73.07 and 66.92% of imidacloprid (100 mg/L), respectively. These findings underscore a strong association between gut-microbial composition and insecticide resistance in N. lugens and highlight the potential of specific bacterial strains for microbiome-based pest and resistance management strategies.},
}

@article {pmid41803202,
year = {2026},
author = {Kaczvinsky, C and Levy, H and Preston, S and Youngflesh, C and Clucas, G and Lynch, HJ and Christodoulou, MD and Hart, T and Smith, AL},
title = {Large-scale distribution of cestode infections in wild gentoo penguins and their impact on the host microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39642-w},
pmid = {41803202},
issn = {2045-2322},
}

@article {pmid41803165,
year = {2026},
author = {Bearson, BL and Whelan, SJ and Encinosa, MPN and Neupane, DP and Bradshaw, DJ and Monson, MS and Anderson, CL and Bearson, SMD},
title = {Chicken vaccination reduces colonization and dissemination of Salmonella serovar Enteritidis with decreased susceptibility to ciprofloxacin.},
journal = {NPJ vaccines},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41541-026-01414-y},
pmid = {41803165},
issn = {2059-0105},
support = {CRIS project 5030-31000-007-000-D//United States Department of Agriculture (USDA), Agricultural Research Service (ARS) appropriated funds/ ; CRIS project 5030-32000-227-000D//United States Department of Agriculture (USDA), Agricultural Research Service (ARS) appropriated funds/ ; },
abstract = {Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of most common Salmonella serovars associated with human illness in the U.S. and worldwide. Surveillance from the U.S. National Antimicrobial Resistance Monitoring System indicates an increase in both chicken and human isolates of S. Enteritidis with decreased susceptibility to ciprofloxacin (DSC), a critical antibiotic prescribed for complicated human salmonellosis infections. S. Enteritidis reduction in chickens is a priority of poultry producers and public health agencies to improve food safety. In the current study, efficacy assessment of a live Salmonella vaccine (BBS 1134) revealed significant reduction of cecal and splenic colonization, and prevention of dissemination to the bone marrow by DSC S. Enteritidis in broiler chickens. Microbiome analysis indicated the cecal microbiota of vaccinated chickens is distinct compared to mock-vaccinated birds. The IDEXX SE Ab X2 Test did not detect antibodies to S. Enteritidis in vaccinated chicken serum, thereby permitting differentiation of infected from vaccinated animals (DIVA). Altogether, the Salmonella vaccine is a DIVA vaccine, afforded cross-protection, and significantly reduced intestinal colonization and dissemination to the spleen and bone marrow by DSC S. Enteritidis in chickens, thereby offering a prospective intervention for animal production to reduce food product contamination and improve food safety.},
}

@article {pmid41803145,
year = {2026},
author = {Cazzaniga, M and Bra, KK and Herzog, MKM and Hardt, WD and Claesson, MJ and Mathur, H and Gahan, CGM},
title = {Impact of the defined Oligo-MM[12] microbiota on intestinal colonisation and dissemination of Listeria monocytogenes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803145},
issn = {2045-2322},
support = {NCCR Microbiomes//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Marie Skłodowska-Curie grant agreement No 956279//H2020 European Institute of Innovation and Technology/ ; centres grant number SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Animals ; *Listeria monocytogenes/pathogenicity/physiology ; *Gastrointestinal Microbiome ; *Listeriosis/microbiology/immunology ; Mice ; Disease Models, Animal ; Feces/microbiology ; Specific Pathogen-Free Organisms ; Mice, Inbred C57BL ; Female ; },
abstract = {Listeria monocytogenes is a foodborne pathogen of global concern, particularly for immunocompromised individuals at risk of severe disease. In mice, infection outcomes are strongly influenced by host immunity and gut microbiome composition. The Oligo-MM[12] defined microbiota mouse model, containing a simplified community of 12 bacterial strains, offers a controlled system to study L. monocytogenes pathogenesis and microbiome interactions. Defined or reduced-complexity microbiota models are increasingly used to investigate colonisation resistance and identify protective taxa. In this study, we compared Oligo-MM[12] mice with conventionally raised Specific Pathogen Free (SPF) mice to assess how microbiome complexity shapes infection. This allowed us to explore how microbiome complexity affects resistance to L. monocytogenes. We performed an in vivo infection study to assess host responses and pathogen-related outcomes, alongside an ex vivo fermentation assay that simulated the murine distal colon, to monitor microbial dynamics. Building on our earlier work, we now demonstrate that in vivo, Oligo-MM[12] mice showed significantly higher L. monocytogenes shedding in faeces during infection, whereas SPF mice progressively reduced L. monocytogenes levels. Despite this, L. monocytogenes dissemination to internal organs after three days of infection was similar in both models. Alterations to gut Prevotella, Akkermansia and Blautia species following L. monocytogenes infection were noteworthy. Ex vivo fermentation mirrored in vivo patterns, validating the Oligo-MM[12] system for mechanistic studies. Together, these results highlight the importance of microbiome complexity in modulating infection outcomes and establish a foundation for identifying protective taxa and mechanisms of colonization resistance.},
}

Animals
*Listeria monocytogenes/pathogenicity/physiology
*Gastrointestinal Microbiome
*Listeriosis/microbiology/immunology
Mice
Disease Models, Animal
Feces/microbiology
Specific Pathogen-Free Organisms
Mice, Inbred C57BL
Female