@article {pmid41994262,
year = {2026},
author = {Li, CM and Kenéz, Á},
title = {Effects of dietary black soldier fly larvae meal inclusion on the serum metabolome of Silkie crossbreed chickens.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1803699},
pmid = {41994262},
issn = {2297-1769},
abstract = {INTRODUCTION: Black soldier fly larvae (BSFL; Hermetia illucens) meal, an alternative to conventional dietary protein sources, such as soybean meal, is rich in medium-chain fatty acids, antimicrobial peptides and other bioactive components. These components may modulate the composition and function of the gut microbiota or, after absorption, affect host metabolic pathways. We hypothesised that the functional effects of BSFL meal would be reflected in alterations in the serum metabolite profile of Silkie crossbreed chickens.

METHODS: Serum samples from chickens fed a control soybean-based diet or a diet containing 150 g/kg partially defatted BSFL meal were analysed using untargeted liquid chromatography-mass spectrometry.

RESULTS AND DISCUSSION: A total of 3304 metabolite features were detected, of which 1341 were annotated, with 777 retained for statistical analysis. Principal component analysis and PERMANOVA revealed a clear separation between dietary groups (p = 0.001). Forty metabolites were significantly altered (FDR ≤ 0.05), with 31 more abundant and nine less abundant in the BSFL group. These shifts were characterised mainly by increased lipid-related metabolites, including medium-chain fatty acids (MCFAs) and phospholipids, indicating alterations in lipid metabolism. In addition, changes in amino acid derivatives and energy-related metabolites suggested the modulation of amino acid and energy metabolic pathways. Several metabolites with putative microbial origin were elevated, consistent with indirect host-microbiome metabolic interactions. These metabolic changes showed correlations with significantly higher average daily gain (p = 0.02), numerically greater final live weight, and a reduced feed conversion ratio in BSFL-fed chickens (p = 0.07 and p = 0.08, respectively). Overall, dietary inclusion of 150 g/kg BSFL meal modified systemic metabolism without detectable negative effects on performance or serum biomarkers, suggesting that this level of BSFL inclusion can be beneficial for slow-growing Silkie chickens.},
}

@article {pmid41994270,
year = {2026},
author = {Albarracín, VH and Gámez-Espinosa, E and Bingjie, M and Gomez de Saravia, SG and Jroundi, F},
title = {Editorial: Microbes and cultural heritage: from biodiversity to applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829794},
doi = {10.3389/fmicb.2026.1829794},
pmid = {41994270},
issn = {1664-302X},
}

@article {pmid41994275,
year = {2026},
author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X},
title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753643},
pmid = {41994275},
issn = {1664-302X},
abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.

METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.

RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.

CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.},
}

@article {pmid41994282,
year = {2026},
author = {Wang, X and Wei, M and Yi, Y and An, J and Wang, J and Zhao, R and Su, Z and Ji, G and Zhang, X and Liu, X},
title = {Elephant-derived Bacillus licheniformis modulates immune cells shedding light on cancer resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753410},
pmid = {41994282},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is currently a leading cause of cancer-related morbidity and mortality globally, underscoring the need for innovative therapeutic strategies. Probiotic treatment is increasingly appreciated as an innovative method for ameliorating inflammation and modulating the tumor microenvironment, especially in gastrointestinal diseases. Many bacterial species isolated from human and animal sources are proven effective in potential disease treatments. Elephants, renowned for their exceptional resistance to cancer, have traditionally been linked to their TP53 gene multiplicity. However, the potential contribution of their evolutionarily-refined gut microbiota to their remarkable cancer resistance remained largely unexplored.

METHODS: Here, we investigated this underexplored avenue by analyzing the elephant gut microbiome and isolating a probiotic bacterium. We utilized whole genome sequencing (WGS) to assess its genomic profile. The in vivo efficacy was evaluated in mouse models of gut inflammation and colorectal tumors. Underlying mechanisms were investigated using transcriptomic analysis, flow cytometry, and integrative metabolomics. Finally, in vitro experimental validations were conducted on mouse and human CRC cell lines using the bacterial culture supernatant.

RESULTS: We found that elephants possess a highly specialized gut microbiome finely tuned to metabolize complex polysaccharides. WGS of the isolated Bacillus licheniformis revealed its metabolic and functioning roles and confirmed the absence of virulence factors. We demonstrated that this elephant-derived strain effectively alleviated gut inflammation and suppressed the progression of colorectal tumors in mouse models. Transcriptomic analysis and flow cytometry revealed that B. licheniformis remodeled the immune microenvironment, specifically activating tumor-infiltrating T cell response and cell cytotoxicity. Integrative metabolomics identified several key metabolites as potential soluble mediators correlated with tumor regression. Furthermore, the supernatant of B. licheniformis culture significantly enhanced cytotoxicity and upregulated p53 expression in CRC cell lines in vitro.

DISCUSSION: Collectively, these findings unveil previously unrecognized therapeutic potentials inherent in elephant-derived probiotics, suggesting a mechanism of functional immune regulation for CRC prevention.},
}

@article {pmid41994290,
year = {2026},
author = {Li, J and Xu, L and Ding, X and Qiu, N and Yue, J},
title = {Gut and skin microbial dysbiosis correlate with systemic inflammation and pruritus in immunological non-responders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758111},
pmid = {41994290},
issn = {1664-302X},
abstract = {INTRODUCTION: Among people living with human immunodeficiency virus (PLWH), those who exhibit immunological non-responders (INR) are highly susceptible to developing pruritus. The aim of this study was to examine the relationships among pruritus, alteration of the gut and skin microbiomes, and systemic inflammation in PLWH with INR.

METHODS: Thirty-three PLWH with INR were enrolled and divided into Pruritus (n = 18) and Control (n = 15) groups. All participants met the defining criterion of a low CD4+ T cell count (≤ 350 cells/μl). We performed 16S rRNA gene sequencing of fecal and skin samples, and measured plasma IL-1β and IL-10 levels.

RESULTS: Microbiome analysis revealed specific, bidirectional patterns of microbial dysbiosis. Specifically, the skin microbiome of the Pruritus Group exhibited significantly greater microbial richness (Chao1 and Faith's Phylogenetic Diversity indices, P < 0.01), coupled with significantly lower representation of the potentially protective genus Bacillus (adjusted P<0.05), compared with that of the INR Control Group. Conversely, the gut microbiome of the Pruritus Group exhibited significantly lower alpha diversity (adjusted P<0.05). Furthermore, we identified a significant positive correlation between levels of plasma pro-inflammatory cytokine IL-1β and the relative abundance of the opportunistic gut genus Veillonella (adjusted P<0.05).

CONCLUSIONS: Pruritic PLWH-INRs exhibit skin microbial hyper-richness, Bacillus depletion, and reduced gut diversity, suggesting a systemic inflammatory basis linked to gut-skin dysbiosis. These findings provide new insights into the pathological process, offering a potential foundation for future microbiome-targeted therapeutic strategies as novel management avenues.},
}

@article {pmid41994309,
year = {2026},
author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R},
title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.},
journal = {Gastro hep advances},
volume = {5},
number = {5},
pages = {100907},
pmid = {41994309},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.

METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.

RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.

CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.},
}

@article {pmid41994453,
year = {2026},
author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C},
title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780981},
pmid = {41994453},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n = 28) and myopia patients who underwent intraocular lens (ICL) implantation (n = 31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.

RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p = 0.066; Simpson index, p = 0.065) and distinct community structures (PERMANOVA, p = 0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.

CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.},
}

@article {pmid41994836,
year = {2026},
author = {Radhika, M and Mohan, S and Singh, HJ and Kadwe, P and Prajapati, J and Mansuri, SH and Sonis, JJ},
title = {Clinical Impact of Macronutrients and Micronutrients: A Review of Nutritional Balance, Deficiency Disorders, and Therapeutic Applications.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105305},
pmid = {41994836},
issn = {2168-8184},
abstract = {Nutrition plays a fundamental role in maintaining human health and modulating disease risk across the life course. This narrative review synthesizes contemporary evidence on the clinical significance of macronutrients, including carbohydrates, proteins, and fats, and micronutrients, including vitamins and minerals, establishing nutritional balance as a central determinant of human health, disease susceptibility, and therapeutic efficacy. These nutrient categories function within an integrated metabolic network in which macronutrients provide energy and structural substrates, while micronutrients serve as essential cofactors and regulatory agents in enzymatic, hormonal, and cellular signalling processes. The synthesis demonstrates that nutritional imbalance, arising from either deficiency, such as iron-deficiency anaemia and vitamin D insufficiency, or excess, including high intakes of refined carbohydrates and saturated fats, constitutes a major contributor to global disease burden, particularly the phenomenon described as the double burden of malnutrition. In response to these challenges, the review highlights the role of evidence-based nutritional therapy, encompassing established dietary patterns such as the Mediterranean and Dietary Approaches to Stop Hypertension (DASH) diets, as well as the clinical implementation of medical nutrition therapy in chronic disease management. It further emphasizes a paradigmatic shift from population-level dietary recommendations toward precision nutrition, an emerging framework that integrates nutrigenomics, metabolomics, and gut microbiome profiling to inform personalized dietary interventions. By conceptualizing nutrition as a dynamic and interactive system, this review offers a comprehensive perspective that integrates biochemical mechanisms with individualized clinical care, positioning nutritional balance as a foundational component of contemporary preventive and therapeutic medicine.},
}

@article {pmid41995085,
year = {2026},
author = {Cao, Y and Chen, W and Li, Q and Liao, Y and Wang, J and Pan, L},
title = {Microbiome and Metabolomics Reveal the Effect of Rhizosphere Microorganisms on Quizalofop-p-ethyl Resistance in Polypogon fugax.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01864},
pmid = {41995085},
issn = {1520-5118},
abstract = {Plant-microbiome interactions are essential for plant health and productivity under stress; however, little is known about these interactions in response to herbicide. Here, we integrated 16S rRNA gene sequencing with nontargeted gas chromatography-mass spectrometry (GC-MS) to investigate the interactions between rhizosphere microbiomes and metabolomes in Polypogon fugax. The results indicated that quizalofop-p-ethyl-resistant (QU-resistant) P. fugax promoted microbial colonization within its microbiome, enriched the abundance of Verrucomicrobia, and increased the levels of d-proline and α,α-trehalose in the rhizosphere, potentially attracting Verrucomicrobia. Furthermore, when the rhizosphere microbiome from R3 populations was transplanted to QU-sensitive plants, the recipients exhibited enhanced antioxidant defense systems and demonstrated reduced sensitivity to QU. These results suggest that the rhizosphere microbiome of QU-resistant P. fugax contributes to its resistance against QU. Overall, our findings highlight the complex interactions among herbicide resistance mechanisms, rhizosphere microbiota, and plant responses, suggesting potential strategies for managing herbicide-resistant weed populations.},
}

@article {pmid41995217,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00282j},
pmid = {41995217},
issn = {2042-650X},
abstract = {The impacts of sugar alcohols (SA) utilized as low-calorie sweeteners on the gut microbiome and metabolome remain undefined. Among six SAs tested, isomalt, erythritol, xylitol and sorbitol significantly lowered fasting serum insulin and hepatic lipid levels in healthy rats, while mannitol and maltitol showed no such effect. Moreover, isomalt consumption lowered body weight gain, low-density lipoprotein and tumor necrosis factor-α, while improving high-density lipoprotein concentrations. All SAs effectively regulated gut microbiota composition and functionality. Most of the microbiota enriched by isomalt were short-chain fatty acid producers, including Faecalibaculum, Bacillus, Dubosiella and Anaerostipes, which led to a significant increase in the propionate proportion in faeces. The elevated Blautia and UCG-008 and lowered Akkermansia were the key specific responders to sorbitol, mannitol and maltitol. Notably, almost all SAs showed inhibitive efficacy on opportunistic pathogens such as Streptococcus, Staphylococcus and Ruminococcus. Dietary SAs significantly shifted stool and global metabolome profiles in rats. Isomalt and maltitol activated aldosterone-regulated sodium reabsorption and suppressed steroid hormone biosynthesis. Isomalt and sorbitol induced the thyroid hormone signaling pathway. Erythritol intake expressively triggered histamine metabolism, chemical carcinogenesis-receptor activation and folate biosynthesis. Xylitol, sorbitol and mannitol robustly promoted nucleotide metabolism, lysine biosynthesis and pyrimidine metabolism. Sorbitol and mannitol administration induced arginine biosynthesis, nicotinate and nicotinamide metabolism and terpenoid backbone biosynthesis. Additionally, stool metabolome suggested that mannitol intake attenuated ferroptosis in rats. Interestingly, structurally similar SAs, e.g. sorbitol, mannitol and maltitol, showed more shared microbiota and metabolites. This systematic comparative study identifies specific microbiota and associated metabolic pathways as responders to each SA and provides novel insights for future application in functional foods.},
}

@article {pmid41995305,
year = {2026},
author = {Haag, KL and Stein, LQ and Nunes da Silva, CG and Mazel, F and Prasad, A and Engel, P},
title = {Conserved gut microbiomes with cross-species spillover between sympatric Neotropical stingless bees and honey bees.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248325},
doi = {10.1128/aem.02483-25},
pmid = {41995305},
issn = {1098-5336},
abstract = {Stingless bees (Meliponini) are ecologically vital pollinators with deep cultural and economic importance in the Neotropics; however, the biogeographic structure of their gut microbiota and the extent of microbial exchange with managed honey bees (Apis mellifera) remain insufficiently understood. Using full-length 16S rRNA gene sequencing of individually sampled workers from 167 colonies across Brazil, we compared gut bacterial communities of Melipona quadrifasciata and Melipona mondury with those of co-occurring A. mellifera through an integrated taxonomic, phylogenetic, and community ecological framework. The core microbiota of Melipona species was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, whose relative abundances covaried inversely with a set of low-prevalence taxa. Although the core communities of stingless bees overlapped only partially with those of honey bees, both groups displayed comparable alpha- and beta-diversity dispersion, suggesting broadly similar assembly dynamics. Notably, 6% of all amplicon sequence variants (ASVs) were shared across hosts, encompassing nearly all canonical honey bee symbionts, consistent with frequent cross-species spillover. Among these, several Snodgrassella ASVs-typically rare in these stingless bee species-reached high abundance in M. quadrifasciata and formed a deeply divergent clade (~96% 16S rRNA identity to Snodgrassella alvi). These patterns indicate that human-mediated management practices, such as mixed apiaries and artificial feeding, create ecological opportunities for interspecific microbial exchange. Overall, our results show that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped jointly by long-term host specificity and recent anthropogenic contact.IMPORTANCEStingless bees are key pollinators in tropical ecosystems and hold long-standing cultural significance in the Neotropics; however, their microbiomes remain far less studied than those of managed honey bees. Understanding how gut bacterial communities vary across landscapes, and whether microbes move between native and non-native hosts, is essential for predicting the ecological consequences of increasing meliponiculture and urban beekeeping. Our study reveals that stingless bee gut microbiota are generally stable and host-associated but nonetheless acquire bacterial symbionts typical of honey bees, indicating that human management practices facilitate cross-species microbial transmission. These findings broaden current knowledge of bee-microbe evolution by showing that gut symbiont boundaries are not fixed but can become permeable under anthropogenic influence. This has important implications for pollinator health, conservation, and biosecurity as managed and native bees increasingly co-occur in human-modified environments.},
}

@article {pmid41995339,
year = {2026},
author = {Ayalew, M and Hoffman, AM and Fuller, K and Kerr, J and Lee, A and Lee, J and Martinez, ES and Ulbricht, K and Xie, X},
title = {Microbiome education at under-resourced institutions: current status, barriers, and approaches to successful implementation.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0028825},
doi = {10.1128/jmbe.00288-25},
pmid = {41995339},
issn = {1935-7877},
abstract = {Microbiome research offers significant promise for advancing public health, medicine, environmental science, and industry. The topic also lends itself well to engaging students and teaching a "new biology" that integrates several disciplines, including computational biology. However, access to microbiome education remains limited, particularly at under-resourced institutions. We conducted a poll showing that over 90% of faculty expressed strong interest in microbiomes; however, only 48% reported that their institutions offer related courses or modules. The most commonly cited barrier was a lack of time and/or funding for design or implementation. A secondary barrier was limited access to professional development or a supportive community of practice. Through case vignettes and reflective analysis, we explore successful efforts to incorporate microbiome education at under-resourced institutions, highlighting the role of faculty development, collaboration, curriculum design, and external funding. These cases demonstrate that implementation is possible with varying levels of investment. We conclude by emphasizing the need for innovative and collaborative strategies, along with sustained resources, to support microbiome education and empower the next generation of genomic data scientists from diverse educational backgrounds.},
}

@article {pmid41995478,
year = {2026},
author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS},
title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70677},
pmid = {41995478},
issn = {1365-2036},
abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.

AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.

METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.

RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.

CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.},
}

@article {pmid41995603,
year = {2026},
author = {Pu, P and Wang, Y and Liu, X and Pang, Y and Qiang, L and Wang, W},
title = {The ecological dynamics of skin microbiota in skin health and diseases.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0030525},
doi = {10.1128/cmr.00305-25},
pmid = {41995603},
issn = {1098-6618},
abstract = {SUMMARYThe skin microbiome, consisting of bacteria, fungi, viruses, and archaea, plays a crucial role in maintaining skin health by regulating immune responses, preserving barrier function, and influencing metabolic processes. Dysbiosis in the microbiome is linked to dermatological diseases such as atopic dermatitis (AD), psoriasis, and acne, with specific microbes, such as Staphylococcus aureus and Cutibacterium acnes, either promoting or protecting against disease. This review summarizes recent advances in understanding the composition and functions of the skin microbiome, its interaction with host immunity, and impact on skin health. We also discuss the implications of environmental and biological factors on microbiome stability and explore emerging therapeutic strategies targeting the skin microbiota. These insights highlight the potential of microbiome-based approaches for advancing dermatological treatment.},
}

@article {pmid41995611,
year = {2026},
author = {Elkatmis, B and Türksoy, GM and Rodríguez, E and Rahmoune, B and Koprivova, A and Kopriva, S},
title = {Sulfur as a Central Integrator of Plant-Microbe Interactions: From Nutrient Cycling to Immune Signalling and Microbiome Assembly.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag186},
pmid = {41995611},
issn = {1460-2431},
abstract = {Sulfur (S) is an essential macronutrient that underpins plant growth, stress resilience, and immunity. Beyond its role in primary metabolism, sulfur is incorporated into a diverse array of secondary metabolites that mediate plant-microbe interactions. In this review, we summarize current knowledge on how microbial sulfur metabolism contributes to plant sulfur nutrition and how plant-derived sulfur-containing compounds shape microbial community assembly and disease outcomes. Microorganisms mobilize organic sulfur in soils through sulfatase activity, volatile sulfur production, and sulfoquinovose degradation, thereby enhancing plant sulfur availability, particularly under limiting conditions. Conversely, plants deploy sulfur-rich metabolites, including volatile organic compounds, glucosinolates, and the phytoalexin camalexin, to restrict pathogens, modulate beneficial associations, and structure rhizosphere communities. These compounds act not only as antimicrobial agents but also as ecological filters that balance defense with microbiome homeostasis. Emerging evidence indicates that sulfur availability and metabolic flux influence the composition and function of plant-associated microbiota, linking primary nutrient assimilation to immune regulation. By integrating insights from sulfur biochemistry, microbial ecology, and plant immunity, we highlight sulfur metabolism as a central node in plant-microbe interactions. Understanding the dynamic exchange of sulfur between plants and their microbiota will be essential for improving crop resilience and sustainable nutrient management in sulfur-limited agricultural systems.},
}

@article {pmid41995892,
year = {2026},
author = {Ali, M and Thakali, O and Idris, O and Sherchan, S},
title = {Comparative Evaluation of DNA Extraction Workflows for Efficient Recovery of pBI143 from Wastewater.},
journal = {Food and environmental virology},
volume = {18},
number = {2},
pages = {},
pmid = {41995892},
issn = {1867-0342},
mesh = {*Wastewater/virology ; Feces/virology ; *DNA, Viral/isolation & purification/genetics ; Workflow ; Tobamovirus/isolation & purification/genetics ; Polyethylene Glycols/chemistry ; Maryland ; },
abstract = {This study aimed to compare the performance of polyethylene glycol (PEG) precipitation, and Nanotrap[®] Microbiome magnetic particle capture workflows for recovering novel fecal marker, pBI143 from 12 wastewater samples collected across six treatment plants in Maryland, USA. Quantitative PCR (qPCR) was used to quantify marker abundance. The Nanotrap workflow yielded significantly higher concentration of pBI143 compared to PEG precipitation workflow (p < 0.05). The Nanotrap workflow used in the study utilized both magnetic nanoparticles A and B, rather than magnetic nanoparticle A alone, highlighting the necessity of optimization based on the intended targets for enhanced recovery. The extracted total nucleic acids by the Nanotrap workflow, were further analyzed to quantify other fecal markers, crAssphage, tomato brown rugose fruit virus (ToBRFV), and pepper mild mottle virus (PMMoV). No significant differences in the concentrations of pBI143, crAssphage, and ToBRFV (p > 0.05) were observed, whereas the concentration of PMMoV was significantly lower than that of the three fecal markers (p < 0.05). Based on the concentration alone, pBI143, ToBRFV, and crAssphage were found to be a better alternative to PMMoV as an endogenous fecal marker.},
}

*Wastewater/virology
Feces/virology
*DNA, Viral/isolation & purification/genetics
Workflow
Tobamovirus/isolation & purification/genetics
Polyethylene Glycols/chemistry
Maryland

@article {pmid41995913,
year = {2026},
author = {Azizan, N and Al-Maleki, AR and Karajacob, AS and Loke, MF and Goh, JPE and Kallarakkal, TG and Ho, GF and Khor, HM and Ong, HC and Tay, ST},
title = {Oral microbiome profiling of primary oral candidiasis during infection and post-antifungal therapy.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {41995913},
issn = {1436-3771},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; Male ; *Antifungal Agents/therapeutic use ; Female ; *Microbiota/drug effects ; Middle Aged ; RNA, Ribosomal, 16S ; *Mouth/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Adult ; Aged ; },
abstract = {OBJECTIVES: Microbial dysbiosis that facilitates Candida proliferation in the oral cavity is a significant factor associated with oral candidiasis. This study aimed to gain insights into microbial dynamics of primary oral candidiasis during infection and following antifungal therapy to enhance our understanding of disease pathogenesis and treatment efficacy.

MATERIALS AND METHODS: Oral rinse samples were collected from 16 patients with primary oral candidiasis, seven of whom returned for follow-up after antifungal treatment, and from seven healthy controls. Microbiome profiling was performed using 16S rRNA gene sequencing (V3-V4 region), followed by microbial diversity and taxonomic analyses.

RESULTS: Twelve bacterial phyla and 138 genera were identified across all samples. Alpha and beta diversity analyses showed no significant differences in microbial richness or overall community structure across both infection and treatment conditions, suggesting a resilient oral microbiome. Compared to controls, oral microbiome of the patients showed a significantly higher abundance of Firmicutes and Campylobacterota, along with a lower abundance of Bacteroidota. At the genus level, Campylobacter, Staphylococcus, and lactobacilli (Lacticaseibacillus, Ligilactobacillus, and Limosilactobacillus) were present at higher abundances during oral candidiasis, while Neisseria, Prevotella, and Alloprevotella were less abundant. Following two weeks of antifungal therapy, alterations in microbial community composition and diversity were observed relative to the control group, suggesting incomplete microbiota restoration.

CONCLUSION: Microbiome analysis revealed dysbiosis with significant taxa changes during primary oral candidiasis. Clinical resolution of oral candidiasis did not correspond well with microbiota restoration, suggesting dysbiosis may persist beyond fungal clearance and contribute to delayed ecological recovery and oral homeostasis.

CLINICAL RELEVANCE: This study highlights the microbial shift during primary oral candidiasis and post-antifungal treatment. Despite clinical resolution with antifungal therapy, oral microbiome of patients with primary oral candidiasis continues to exhibit residual shifts in composition, underscoring the needs for microbiota-targeted intervention to prevent recurrence and maintain oral health. While our results provide preliminary insights into microbial dysbiosis associated with primary oral candidiasis and the effects of antifungal therapy, further validation in larger cohorts is warranted.},
}

Humans
*Candidiasis, Oral/microbiology/drug therapy
Male
*Antifungal Agents/therapeutic use
Female
*Microbiota/drug effects
Middle Aged
RNA, Ribosomal, 16S
*Mouth/microbiology
Dysbiosis/microbiology
Case-Control Studies
Adult
Aged

@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41996042},
issn = {1618-1905},
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}

@article {pmid41996045,
year = {2026},
author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P},
title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41996045},
issn = {1573-4978},
support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; },
}

@article {pmid41996166,
year = {2026},
author = {Liu, L and Liu, L and Luo, X and Zhao, JL and Tan, X and Zhao, W and Huang, L and Yuan, Z and Li, F and Zheng, H and Xing, B},
title = {Novel Insights into Foodborne Microplastics-Enhanced Shoaling Behavior in Marine Korean Rockfish (Sebastes schlegelii): Energy Deficiency-Driven Gut-Brain Axis Dysregulation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16888},
pmid = {41996166},
issn = {1520-5851},
abstract = {Microplastics (MPs) pollution threatens ocean health, yet their impacts on fish shoaling behavior remain poorly understood. Herein, the effects of foodborne polyethylene terephthalate debris (D-PET), PET fiber (F-PET), and tire wear particles (TWPs) at environmentally relevant concentrations (0.1 and 1 mg g[-1]) on behavioral strategies and energy metabolism-mediated gut-brain axis regulation in Korean rockfish (Sebastes schlegelii) were investigated through a 50-day exposure-depuration experiment. MPs induced boldness reduction and hyperactivity, consequently intensifying shoaling behavior in an order of TWPs > F-PET > D-PET, with the interindividual distance decreased by up to 12.14 ± 0.31%. Leachable additives from TWPs, including benzothiazolone, benzothiazole, N,N'-ditolyl-p-phenylenediamine, and N-1,3-dimethylbutyl-N'-phenyl-p-phenylenediamine-quinone, were primarily responsible for the shoaling enhancement. MPs induced hepatic mitochondrial dysfunction and apoptosis that disrupted glucose homeostasis and caused systemic energy deficiency, thereby promoting shoaling as an energetically compensatory strategy. The energy imbalance subsequently triggered oxidative neurotoxicity and perturbed serotonergic, cholinergic, dopaminergic, and GABAergic pathways. Moreover, MPs disrupted the intestinal physicochemical barrier, immune function, and reshaped microbiota, exacerbating neurotransmitter disruption via the gut-brain axis. These findings demonstrate that environmentally relevant MPs exposure can enhance fish shoaling through energy deficiency-driven gut-brain axis dysregulation, revealing the mechanisms by which MPs stress can reorganize population-level behavior and thereby expand understanding of the ecological risks posed by contaminants of emerging concerns.},
}

@article {pmid41996244,
year = {2026},
author = {Liu, X and Zeng, J and Xie, P and Shen, Q and Yuan, J},
title = {Microbial damper: Rhizosphere microbiome mitigates stress-induced plant growth-defense conflicts.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117278},
doi = {10.1016/j.celrep.2026.117278},
pmid = {41996244},
issn = {2211-1247},
abstract = {Plants face constant environmental stresses that induce conflicts between growth and defense. The rhizosphere microbiome helps resolve this conflict by enhancing nutrient-uptake efficiency and activating plant immunity simultaneously. In this review, we first outline the mechanisms and limitations of plant-intrinsic growth-defense trade-offs; we then describe the integrated support that rhizosphere microbial communities provide for plant nutrition and defense. Finally, we propose the "microbial-damper" framework and further elucidate the interactions and feedback mechanisms that constitute this system. The microbial damper is a conceptual framework describing the capacity of the rhizosphere microbiome to stabilize a plant's internal growth-defense resource allocation, which is otherwise perturbed by stresses such as nutrient imbalance and other environmental stresses. This framework highlights how the rhizosphere microbiome can reduce stress-induced plant growth-defense resource-allocation conflicts, thereby providing actionable strategies for designing sustainable agricultural systems.},
}

@article {pmid41996342,
year = {2026},
author = {Rajan, FV and Bucking, C},
title = {Effects of salinity and broad-range antibiotics on oxalate production, transport, and degradation in Poecilia latipinna.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347147},
pmid = {41996342},
issn = {1932-6203},
mesh = {Animals ; *Salinity ; *Oxalates/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Poecilia/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; Seawater ; Biological Transport/drug effects ; Kidney/metabolism/drug effects ; },
abstract = {Oxalate is an anion that readily binds calcium and is thought to contribute to osmoregulation. This study investigated how environmental salinity influences oxalate homeostasis in euryhaline sailfin mollies (Poecilia latipinna), with a focus on the interplay between microbial symbiosis and host transport processes. Gut microbiome profiling demonstrated regional specialization, with the posterior intestine enriched in oxalate-degrading bacterial families. Community shifts across salinities suggests functional redundancy and resilience, ensuring maintenance of oxalate-catabolizing capacity. Antibiotic treatment disrupted this system, impairing microbial degradation and causing systemic oxalate stress. Oxalate concentrations were also measured in the liver, intestine, and kidney, organs central to oxalate metabolism, under freshwater and seawater conditions. Salinity induced a redistribution of oxalate among these organs, with the gut assuming an auxiliary excretory role in seawater. This functional shift parallels mammalian colon physiology and highlights the gut's role in balancing ion and oxalate flux. Expression analyses of the oxalate transporters SLC26A3 (solute carrier family 26, member 3) and SLC26A6 (solute carrier family 26, member 6) revealed organ-specific and salinity-dependent regulation. Both transporters displayed distinct responses to seawater exposure, indicating specialized roles in oxalate handling. These patterns suggest coordinated but nonredundant mechanisms that govern absorption and secretion, linking salt transport with oxalate clearance. These findings underscore the microbial contribution to oxalate balance and reveal that osmoregulatory challenges shape gut microbial composition and function. Collectively, this study presents the first comprehensive analysis of oxalate metabolism in a euryhaline teleost and demonstrates a coordinated host-microbe system that mitigates oxalate accumulation across salinities. By integrating metabolic and osmoregulatory demands, P. latipinna reallocates excretory function from kidney to gut and leverages microbial symbiosis to preserve homeostasis. These findings expand our understanding of teleost physiology and highlight oxalate metabolism as a critical axis of environmental adaptation.},
}

Animals
*Salinity
*Oxalates/metabolism
*Anti-Bacterial Agents/pharmacology
*Poecilia/metabolism/microbiology
Gastrointestinal Microbiome/drug effects
Seawater
Biological Transport/drug effects
Kidney/metabolism/drug effects

@article {pmid41996359,
year = {2026},
author = {Li, G and Wang, Y and Zeng, S and Li, S},
title = {Shared Genetics Implicate Gut Microbiota and Immunity in Anterior Uveitis and Inflammatory Bowel Disease.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09273948.2026.2654978},
pmid = {41996359},
issn = {1744-5078},
abstract = {PURPOSE: Anterior uveitis (AU) is a common extraintestinal manifestation of inflammatory bowel disease (IBD). This study investigates the shared genetic architecture and pleiotropic loci between AU and IBD.

METHODS: Using large-scale GWAS data from European-ancestry cohorts, we performed LD score regression to assess genetic correlations, two-sample Mendelian randomization for causal inference, and PLACO analysis to identify pleiotropic loci. Multi-trait colocalization integrating 412 gut microbiome features was conducted using HyPrColoc. Functional annotation employed FUMA and ANNOVAR, gene-based analysis used MAGMA, and drug-gene interactions were explored via DrugBank.

RESULTS: AU showed significant genetic correlations with IBD (rg = 0.44, p = 2.0 × 10[-4]), ulcerative colitis (rg = 0.52, p = 6.0 × 10[-4]), and Crohn's disease (rg = 0.24, p = 0.029). Mendelian randomization supported causal effects of genetically predicted IBD and its subtypes on AU risk. We identified 62 pleiotropic risk loci, including 18 with strong colocalization evidence. Functional and pathway analyses revealed enrichment of these loci in immune and inflammatory pathways, mainly the IL-17/IL-23 axis and NOD2 signaling. Multi-trait colocalization further linked a shared AU-IBD risk locus to the gut microbial MEP pathway. Several pleiotropic genes (e.g. JAK2, STAT3) represent potential drug targets.

CONCLUSIONS: AU and IBD share pleiotropic genetic loci involved in immune regulatory pathways and gut microbiome-associated metabolic processes, revealing a potential molecular basis for their comorbidity and highlighting actionable therapeutic targets.},
}

@article {pmid41996413,
year = {2026},
author = {He, X and Yazdy, GM and Yeoman, C and Ghanem, KG and Erchick, DJ and Taylor, A and Griffin, K and Holm, J and Ravel, J and Brotman, RM and Tuddenham, S},
title = {Comparing Asymptomatic vs Symptomatic Bacterial Vaginosis: Clinical Characteristics, Vaginal Microbiota, and Lactic Acid Profiles.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002330},
pmid = {41996413},
issn = {1537-4521},
abstract = {BACKGROUND: Irrespective of symptoms, bacterial vaginosis (BV) has been linked to increased risk of sexually transmitted infections (STI) and HIV, yet clinical guidelines recommend treatment only for symptomatic BV (sBV). We compared demographic, clinical, and vaginal microbiota factors between asymptomatic BV (aBV) and sBV.

METHODS: Data from a previously conducted vaginitis cohort study were analyzed. Participants with Amsel-BV were classified as sBV if they reported vaginal symptoms and aBV if asymptomatic. Nugent scores were assigned. Cervicovaginal lavage fluid underwent 16S rRNA gene amplicon sequencing, broad-range qPCR, and lactic acid isomer quantitative assays. Wilcoxon rank-sum, Fisher's exact, and Chi-squared tests compared factors between aBV and sBV. Taxonomic differences were evaluated using elastic net modeling and differential abundance testing.

RESULTS: Among 70 participants with sBV and 270 with aBV, clinician-assessed abnormal discharge was more common in sBV (86%) than aBV (71%). In adjusted analyses, recent use of metronidazole or clindamycin, more sex partners, and education beyond high school were associated with increased odds for sBV, and injectable contraception with aBV. No consistent differences were observed between sBV versus aBV for other Amsel's criteria, Nugent scores, or vaginal microbiota composition. D- and L-lactic acid levels were slightly higher in sBV than aBV.

CONCLUSIONS: Although some demographic, clinical, and behavioral factors differed between sBV and aBV, no consistent differences were found in vaginal microbiota composition; lactic acid isomer levels were low in both groups. Further research is needed to understand why some experience symptoms, to identify whether other biological factors differentiate aBV from sBV, and to evaluate their respective associations with adverse reproductive outcomes.},
}

@article {pmid41996830,
year = {2025},
author = {Kreimeyer, H and Fondevila, MF and Harberts, A and Raya Tonetti, F and Schöler, D and Münte, E and Hartmann, P and Llorente, C and Hube, B and LeibundGut-Landmann, S and Stärkel, P and , and Schnabl, B},
title = {Peptide YY reduces cytotoxicity of Candida albicans in alcohol-associated liver disease.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {5},
pages = {101718},
doi = {10.1016/j.jhepr.2025.101718},
pmid = {41996830},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Transitioning from yeast to hyphal morphology enables Candida albicans (C. albicans) to secrete candidalysin, invade the intestinal mucosa and translocate to the blood stream. Patients with alcohol-associated hepatitis show increased intestinal abundance of C. albicans, and the candidalysin-encoding gene is associated with reduced survival. Paneth cell-derived peptide YY (PC-PYY) inhibits hyphal growth of C. albicans. In this study, we evaluated the potential of different C. albicans strains isolated from patients with alcohol-associated hepatitis to cause systemic infections and explored the therapeutic potential of PC-PYY in ethanol-induced liver disease in mice.

METHODS: C. albicans strains isolated from fecal samples of patients with alcohol-associated hepatitis (n = 105) were co-cultured with intestinal epithelial Caco-2 cells to assess in vitro cytotoxicity. Caco-2 cells and primary mouse hepatocytes were incubated with C. albicans in the presence or absence of PC-PYY. Mice were subjected to a chronic plus binge ethanol-feeding model.

RESULTS: C. albicans strains isolated from stool of patients with alcohol-associated hepatitis induced significant cytotoxicity in Caco-2 cells, and high cytotoxicity was associated with worse 30-day survival (log-rank p = 0.032). This cytotoxicity was primarily mediated by the hyphal form and largely driven by candidalysin. PC-PYY significantly reduced C. albicans-induced cytotoxicity in Caco-2 cells (Wilcoxon rank-sum test, p = 0.015) and in primary mouse hepatocytes (p = 0.03) compared with a scrambled peptide control, by inhibiting hyphal morphogenesis. The peptide YY-to-chromogranin A ratio in intestinal crypts was significantly increased in ethanol-fed mice compared with both isocaloric (p = 0.005) and antifungal-treated controls (p = 0.009), indicating that fungal overgrowth stimulates PC-PYY release. In ethanol-fed mice, PC-PYY administration attenuated liver injury (p = 0.032) and steatosis (p = 0.0498) and reduced fecal hyphae formation (p = 0.0159).

CONCLUSION: PYY inhibits filamentous growth of C. albicans in vitro and alleviates ethanol-induced liver disease in mice, highlighting its potential as a therapy for patients with alcohol-associated liver disease.

IMPACT AND IMPLICATIONS: Candida albicans (C. albicans) and particularly its toxin candidalysin are associated with poor outcomes in patients with alcohol-associated hepatitis but the extent to which the cytotoxicity of individual C. albicans strains influences patient survival, and the role of Paneth cell-derived PYY (PC-PYY) in this context remains elusive. This study identifies a link between the cytotoxic effect of patient-derived C. albicans strains and survival in patients with alcohol-associated hepatitis and demonstrates that PC-PYY plays a protective role in ethanol-induced liver disease by limiting candidalysin-producing hyphae. Our work provides insight into why some patients with alcohol-associated liver disease have worse outcomes and highlights the potential of PC-PYY as a therapy for patients with alcohol-associated liver disease.},
}

@article {pmid41996860,
year = {2026},
author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A},
title = {Relationship between pesticide exposure, gut microbiota, and hypertension.},
journal = {Environment international},
volume = {211},
number = {},
pages = {110250},
doi = {10.1016/j.envint.2026.110250},
pmid = {41996860},
issn = {1873-6750},
abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.

METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.

RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC = 0.897) for hypertension.

CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.},
}

@article {pmid41997122,
year = {2026},
author = {Davar, D and Zarour, HM and Trinchieri, G},
title = {Improving immunotherapy in solid tumors using FMT.},
journal = {Cell},
volume = {189},
number = {8},
pages = {2214-2217},
doi = {10.1016/j.cell.2026.03.021},
pmid = {41997122},
issn = {1097-4172},
mesh = {Humans ; *Immunotherapy/methods ; *Fecal Microbiota Transplantation/methods ; *Neoplasms/therapy/immunology/microbiology ; Immune Checkpoint Inhibitors/therapeutic use ; Melanoma/therapy ; Animals ; Carcinoma, Non-Small-Cell Lung/therapy ; Clinical Trials as Topic ; },
abstract = {Recent clinical trials demonstrate that fecal microbiota transplantation (FMT) enhances first-line immune checkpoint inhibitor efficacy in renal cell carcinoma, cutaneous melanoma, and non-small cell lung cancer with acceptable safety. Benefit appears mediated by functional microbiome remodeling, depletion of deleterious taxa, and systemic immunometabolic modulation, supporting microbiome-directed therapeutic strategies for cancer immunotherapy.},
}

Humans
*Immunotherapy/methods
*Fecal Microbiota Transplantation/methods
*Neoplasms/therapy/immunology/microbiology
Immune Checkpoint Inhibitors/therapeutic use
Melanoma/therapy
Animals
Carcinoma, Non-Small-Cell Lung/therapy
Clinical Trials as Topic

@article {pmid41997160,
year = {2026},
author = {Yu, L and Peng, S and Chen, X and Wu, T and Dong, L and Luo, J and Xu, S and Zhou, J and Zhao, X and Zheng, L and Shu, G and Wang, X and Huang, L and Chen, Q and Jiang, D and Sun, LD and Hylemon, P and Wang, XY and Sun, L and Ma, L and Zuo, D},
title = {Intestinal dysbiosis exacerbates skin inflammation via microbial metabolite-driven Th2 cell differentiation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.03.019},
pmid = {41997160},
issn = {1097-4180},
abstract = {The interplay between gut microbiota and the mucosal immune system critically regulates systemic immunity and disease susceptibility. Here, we demonstrate that intestinal epithelial Toll-like receptor (TLR)4 deficiency reshaped the gut microbiome and subsequently exacerbated atopic dermatitis (AD) in mice. Mechanistically, TLR4 deficiency reduced Akkermansia muciniphila abundance and enriched choline trimethylamine-lyase (CutC)-expressing bacteria. This enhanced microbial choline-to-trimethylamine conversion and elevated circulating trimethylamine oxide (TMAO) levels. Clinically, AD patients exhibited increased plasma TMAO levels that positively correlated with disease severity and immunoglobulin E (IgE) levels. UK Biobank data also showed that higher dietary choline intake was associated with increased AD risk. TMAO promoted T helper (Th)2 differentiation by directly interacting with protein phosphatase 5 (PPP5) and enhancing PPP5-mediated dephosphorylation of PPARγ. CD4[+] T cell-specific PPARγ deletion abolished TMAO-driven skin pathology in AD mice. Our results reveal intestinal dysbiosis, as a result of innate immune deficiency, as a driver of inflammatory Th2 cells and AD pathology, highlighting a link among the gut immune environment, microbial metabolites, and skin disease.},
}

@article {pmid41997445,
year = {2026},
author = {Yu, J and Guo, C and Liu, Y and Ren, X and Guo, Y and Ran, B and Xiao, L and Kong, L and Gu, X and Jiang, C and Wu, J},
title = {The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.044},
pmid = {41997445},
issn = {2090-1224},
abstract = {BACKGROUND: The human commensal microbiome, commonly recognized as a "second genome", exerts a crucial regulatory role in host metabolism, immune homeostasis maintenance, and the progression of various diseases. Respiratory tract tumors remain a leading cause of global cancer-related deaths due to their high invasiveness and late-stage diagnosis. With the rapid development of high-throughput sequencing technology, the complex associations between microbial communities and respiratory tract tumors have been gradually uncovered. In lung cancer, distinct microbiota-related signatures, including tissue-specific and microbiota-derived ones have been identified, showing variations across cancer subtypes, anatomical sample sources, and patient demographics. These findings collectively lay the foundation for in-depth investigations into the interplay between the microbiome and respiratory tract tumors.

AIM OF REVIEW: This review aims to systematically synthesize the current understanding of the commensal microbiome across respiratory tract tumors, primarily taking lung cancer as the main example, with systematic extensions to other respiratory tract malignancies, including laryngeal carcinoma and nasopharyngeal carcinoma, focusing on clarifying the ecological characteristics of microorganisms, elucidating the mechanistic links between the microbiome and tumorigenesis as well as progression, and summarizing the translational value of the microbiome in clinical practice, including applications in diagnostics, therapeutics, and prognostic evaluation.

Emerging evidence highlights that the microbiome contributes to the initiation of respiratory tract tumors through multiple pathways: dysbiosis-induced chronic inflammation, immune system dysregulation, and metabolite-mediated epigenetic or functional alterations. Beyond tumorigenesis, the microbiome also plays a vital role in modulating the efficacy of cancer treatments, particularly conventional therapies and immunotherapies. Additionally, the microbiome provides novel opportunities for the development of diagnostic biomarkers and microbiome-targeted intervention strategies. Its prognostic potential in predicting recurrence, metastasis, and survival is increasingly recognized. These core scientific concepts collectively constitute the theoretical framework for exploring the microbiome's role in respiratory tract tumor research and clinical translation.},
}

@article {pmid41997470,
year = {2026},
author = {Saravanan, A and Bai, J and Bajaj, P and Khemmani, M and Rodriguez, A and Choudhury, S and Wolfe, AJ and Young, EE},
title = {Evidence for a shift towards a proinflammatory/pronociceptive signature of gut dysbiosis in patients with axial chronic low back pain: A preliminary cross-sectional analysis.},
journal = {The journal of pain},
volume = {44},
number = {},
pages = {106271},
doi = {10.1016/j.jpain.2026.106271},
pmid = {41997470},
issn = {1528-8447},
abstract = {Nonspecific or axial-chronic low back pain is not attributed to specific pathology yet accounts for 80%- 90% of all chronic low back pain cases and is a major cause of disability affecting one in four adults with treatment costs and lost wages totaling $100-200 billion. Despite its prevalence, there is a knowledge gap around the underlying mechanisms driving susceptibility to this type of chronic pain. Gut microbial colonization plays a role in shaping host physiology directly through interactions with host tissues and indirectly through the production of metabolites, but the role of the microbiome in the etiology of axial-low back pain is unclear. Using a cross-sectional design, in this preliminary study, patients with axial-chronic low back pain and healthy controls completed the NIH minimal dataset for chronic low back pain from the PROMIS short form followed by collection of rectal swabs and 16S rRNA sequencing and determination of microbiome composition differences between controls and patients. Our findings suggest a distinct pattern of altered colonization in axial-chronic low back pain, characterized by a specific pattern of increased formate- and succinate- producing bacterial abundance along with reduced abundance of key taxa associated with butyrate, propionate, and acetate production. A review of the literature available on metabolite production from differentially abundant bacteria suggests a proinflammatory/ pronociceptive shift in microbial colonization. These preliminary findings identify a gut dysbiosis pattern that may contribute to chronic low back pain through pro-inflammatory and pronociceptive mechanisms; however, larger, longitudinal, and metabolically profiled studies are needed to confirm causality. PERSPECTIVE: Chronic low back pain is associated with gut dysbiosis characterized by reduced abundance of butyrate and/or propionate producing bacteria combined with increased succinate- and formate-producing bacterial colonization. These data suggest a proinflammatory/pronociceptive microbial signature that may contribute to development and/or maintenance of chronic low back pain.},
}

@article {pmid41997773,
year = {2026},
author = {Han, VC and Bennett, SJ},
title = {When soils learn to suppress nematodes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.002},
pmid = {41997773},
issn = {1878-4380},
abstract = {An evaluation of banana plantations, sown between 1 and 10 years ago, suggested that over time soils can become suppressive to root-knot nematodes. Lu et al. linked this transition to shifts in rhizosphere microbiomes, enrichment of free-living nematodes, and the emergence of a keystone Bacillus taxon, highlighting cross-kingdom interactions.},
}

@article {pmid41997906,
year = {2026},
author = {Tao, R and Liu, S and Crawford, J and Kramer, P and Bender, S and Tao, F},
title = {Single-cell multi-omics sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {41997906},
issn = {2049-3169},
support = {R01DE031255//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE032061//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R03DE031822//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Chromatin/metabolism/genetics ; *Butyrates/metabolism/pharmacology ; *Transcriptome ; Single-Cell Analysis ; Male ; Mice ; Acetylation ; Multiomics ; Triglycerides ; },
abstract = {Pain is the most common symptom of temporomandibular joint (TMJ) disorders, which present significant clinical challenges due to their complexity and limited treatment options. Our previous study demonstrates that gut microbiome-derived butyrate is critical for the modulation of TMJ pain. In this study, we investigated its underlying mechanisms, and we found that oral administration of tributyrin, a prodrug of butyrate, not only significantly alleviated TMJ pain but also reversed the reduction in histone acetylation in the spinal trigeminal nucleus caudalis (Sp5C) under the TMJ pain condition. Using single-cell multi-omics sequencing, we profiled gene expression and chromatin accessibility in the Sp5C cells at the single-cell resolution. Bioinformatics analysis revealed that TMJ pain disrupted both the expression and chromatin accessibility of Nop14, Matk, Idh3b, Ndst2, and Tomm6 across four cell types in the Sp5C, and these alterations were reversed by tributyrin treatment. Specifically, Nop14 exhibited increased chromatin accessibility at its promoter region under TMJ pain condition, and knockdown of Nop14 in the Sp5C restored histone acetylation and alleviated TMJ pain. Together, our findings reveal cell-type-specific gene regulation that underlies butyrate-mediated epigenetic regulation of TMJ pain, which suggesting that targeting gut microbiome metabolites could develop a non-opioid novel therapy for TMJ disorders.},
}

*Gastrointestinal Microbiome
Animals
*Chromatin/metabolism/genetics
*Butyrates/metabolism/pharmacology
*Transcriptome
Single-Cell Analysis
Male
Mice
Acetylation
Multiomics
Triglycerides

@article {pmid41997944,
year = {2026},
author = {Wu, Y and Alomeir, N and Falsetta, M and Yang, R and Sun, E and Israel, AK and Fiscella, J and Wu, T and Liu, Y and Li, T and Wood, R and Kenney, M and Meng, G and Terando, S and Terio, C and Fiscella, K and Xiao, J},
title = {Cariogenic microorganisms induce oral epithelial atypia through host-microbiome-high sugar diet interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00987-9},
pmid = {41997944},
issn = {2055-5008},
abstract = {Oral mucosal development during infancy is crucial because disruptions at this stage can compromise barrier function and increase susceptibility to oral diseases throughout life. The contribution of oral pathogens to oral mucosal development in infancy remains poorly understood. Here, we show that early-life co-infection with Streptococcus mutans and Candida albicans under a sucrose-enriched diet perturbs oral epithelial homeostasis and is associated with atypical hyperplasia and parakeratosis of the tongue. Using an infant rat model, we utilized OMICS data (microbiome, untargeted metabolomics, and multiplex immune profiling) together with high-dimensional mediation statistic modeling to reveal that microbial co-infection synergizes with dietary sugar to shape oral and gut microbial communities. The microbial alterations were accompanied by systemic metabolic alterations, marked by enhanced amino acid and carbohydrate metabolism, and depletion of vitamin B6 and taurine pathways. Oral microbial and metabolic changes were associated with atypical hyperplasia and parakeratosis on both dorsal and ventral surfaces of tongue mucosa. Complementary in vitro modeling revealed that sucrose-conditioned co-infection disrupted epithelial barrier integrity and orchestrated metabolic remodeling in oral epithelial cells. These findings reveal a host-microbe-diet interaction axis underlying early mucosal remodeling and provide mechanistic insight into how cariogenic microbes may influence oral mucosal disease beyond caries.},
}

@article {pmid41997961,
year = {2026},
author = {Zhao, JJ and Hu, M and Li, S and Wang, Q and Mo, Q and Yu, H},
title = {Oral microbiome signatures predict biological age and host health.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72096-2},
pmid = {41997961},
issn = {2041-1723},
abstract = {Identifying robust, non-invasive biomarkers of biological age is key to preventive medicine. While gut aging clocks exist, the oral microbiome remains underexplored as a quantitative biomarker. Using oral microbiome data from two NHANES cohorts (N = 4,675), we identified 64 age-dependent bacterial genera and developed a machine learning model predicting chronological age, with generalizability in an independent external cohort (N = 1,293). We derived an Oral Microbiome Aging Acceleration (OMAA) Score as the residual of predicted age against chronological age. The OMAA Score independently predicted all-cause mortality (HR = 1.05, P = 0.024) and frailty (OR = 1.05, P = 0.008), correlated with impaired kidney function (lower eGFR: β = -0.066, P = 5.22×10[-4]), and enhanced risk prediction for cancer (AUC 0.70 vs. 0.67, P = 0.009) and heart attack (AUC 0.79 vs. 0.76, P = 0.016) beyond conventional risk factors. Diet and medication had minimal association. The OMAA Score offers a scalable, non-invasive tool to identify high-risk individuals for age-related morbidity and mortality.},
}

@article {pmid41997995,
year = {2026},
author = {Zhong, P and Ren, A and Cui, J and Guo, C and Zhang, Y and Diao, Q and Liu, X and Zhang, N and Tu, Y and Bi, Y},
title = {Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00988-8},
pmid = {41997995},
issn = {2055-5008},
support = {32222081//National Natural Science Foundation of China/ ; },
abstract = {Dairy cow health involves host-microbiome interactions. This review characterized microbial landscapes across anatomical sites in dairy cows-including the gastrointestinal tract, respiratory system, reproductive tract, mammary gland, and skin-and examines their associations with diseases. We elucidated how site-specific dysbiosis drives systemic conditions such as mastitis and ketosis through inter-organ axes. Finally, we evaluated emerging microbiome-based modulation strategies and their application prospects in dairy farming.},
}

@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47816-9},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
}

@article {pmid41998161,
year = {2026},
author = {Ji, S and Liu, Y and Xu, Y and Gao, J and Jin, J and Jiang, P and Li, Y and Su, D and Zhao, Y and Yang, S and Zhang, S and Shi, W and Zhou, Q and Zhang, M},
title = {Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41998161},
issn = {2058-5276},
support = {82322010//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbiome-host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal samples correlates with improved CRC survival outcome and immunotherapy response. In vitro assays and experiments in azoxymethane plus dextran sulfate sodium (AOM/DSS) and Apc[min/+] mouse CRC models show that F. prausnitzii extracts have anti-tumour activity. Mass spectrometry identifies F. prausnitzii phosphoribosyl pyrophosphate synthetase (fpPRPS) as a bacterial enzyme that inhibits tumour development and promotes CD8[+] T-cell responses. Mechanistically, fpPRPS depletes ATP levels in CRC cells, which then inhibits GTP-GDP exchange on Rab11a, reprogramming CRC energy metabolism. This leads to Rab11a degradation and the disruption of PD-L1 trafficking to reduce the inhibition of T-cell responses. fpPRPS inhibition of tumour progression is PD-L1-dependent. We also show that fpPRPS and anti-PD-1 treatment synergize to promote CD8[+] T-cell responses and tumour control in mice. These findings suggest fpPRPS as a potential strategy for sensitizing CRC to immunotherapy.},
}

@article {pmid41998285,
year = {2026},
author = {Mannino, P and Park, M and Wang, MC},
title = {Organellar insights in ageing and longevity.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {41998285},
issn = {1476-4679},
abstract = {Metabolic processes shape ageing and longevity at multiple levels. Emerging evidence shows that many of these processes are orchestrated within and between cellular organelles. Organelles function not only as metabolic reactors but also as signalling hubs, and their coordination plays crucial roles in maintaining cellular homeostasis and promoting organismal fitness. Rather than acting in isolation, organelles engage in dynamic crosstalk through membrane contact sites, metabolite exchange and signalling interplay. In recent years, organelles have been increasingly recognized as critical regulators of ageing and longevity. Here we summarize age-related organellar changes, highlight organelle-mediated intra- and intercellular signalling communication in lifespan and healthspan regulation, and discuss the active roles of organelles in microbiome-host interactions and transgenerational inheritance in regulating longevity. We further outline how longevity-promoting interventions influence organelles, and provide perspectives on how future technological advances may further accelerate progress in this emerging research topic.},
}

@article {pmid41998361,
year = {2026},
author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, Ü and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP},
title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02773-8},
pmid = {41998361},
issn = {1432-184X},
}

@article {pmid41998442,
year = {2026},
author = {Paveen, P and Ryota, K and Kumar, V},
title = {Omics-informed insights into biochar-Trichoderma interactions in plant-soil systems: mechanisms of defense and context-dependent responses.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998442},
issn = {1573-0972},
abstract = {The combined application of biochar and Trichoderma spp. represents a promising strategy for enhancing plant resilience and soil health; however, the molecular mechanisms underlying their synergistic interactions remain poorly understood and inadequately integrated. This review critically synthesizes evidence from transcriptomic, proteomic, metabolomic, and microbiome analyses to elucidate how biochar-Trichoderma interactions modulate plant defense signaling pathways and stress adaptation responses. Transcriptomic analyses reveal context-dependent activation of the jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signaling pathways. Correspondingly, proteomic and metabolomic datasets demonstrate variable yet recurrent upregulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS)-scavenging enzymes, and phenylpropanoid-derived metabolites. Notably, accumulating evidence suggests that these molecular responses are highly context-dependent, varying substantially with soil type, biochar physicochemical characteristics, and Trichoderma strain specificity. We critically examine major methodological limitations in existing omics investigations, including inadequate reproducibility under field conditions and insufficient integration of molecular and ecological datasets. Finally, we propose a systems biology framework for designing functionally optimized biochar–microbe formulations and identify research priorities for translating insights into agronomically robust and field-deployable technologies.},
}

@article {pmid41998480,
year = {2026},
author = {Rodriguez-Martinez, AC and Nair, N and Skinner, J and Welch, AA and Malka, S and Moosajee, M},
title = {Metabolomic signatures suggest altered bile acid and energy metabolism in CRB1- retinopathies.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {3},
pages = {},
pmid = {41998480},
issn = {1573-3890},
support = {205174/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Female ; Male ; Metabolomics/methods ; *Energy Metabolism ; *Bile Acids and Salts/metabolism ; *Nerve Tissue Proteins/metabolism/genetics ; *Eye Proteins/metabolism/genetics ; *Retinal Diseases/metabolism ; Middle Aged ; Metabolome ; Adult ; Membrane Proteins ; },
abstract = {INTRODUCTION: The human CRB1 gene encodes the CRB1 protein, primarily expressed in retinal Muller cells and photoreceptors, where it regulates apical-basal polarity and cellular signalling through its role in adherence junctions and maintaining the outer limiting membrane barrier. Dysfunction of CRB1 results in a range of retinal phenotypes with few systemic implications reported. It has been suggested that disrupted Crb1 expression in the gastrointestinal epithelium of rd8 mouse models (Crb1 [-/-]) results in barrier dysfunction permitting translocation of bacteria to the retina.

OBJECTIVE: Whole metabolomic analysis in patients can provide further insights into disease pathophysiology and aid the identification of potential systemic biomarkers.

METHODS: Blood plasma from 25 molecularly confirmed CRB1-retinopathy patients from Moorfields Eye Hospital with 25 age- and gender-matched healthy controls underwent ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). MetaboLync pathway analysis identified affected metabolic pathways.

RESULTS: Of 872 compounds, 244 were significantly altered in CRB1 patients. Key findings included disrupted bile acid metabolism, with elevated primary and secondary bile acids alongside increased gut microbial phenylalanine pathway metabolites, indicative of altered gut microbiome-related metabolic activity and altered enterohepatic circulation. However, sucrose and butyrate levels remained unchanged amongst groups, suggesting absence of metabolomic evidence for severe intestinal barrier dysfunction. Reductions in antioxidants and neuroprotective agents were found alongside energy metabolism dysregulation.

CONCLUSION: These findings reveal metabolic dysregulation in CRB1-retinopathy, including altered gut microbiome-related metabolic activity, and no strong metabolomic evidence of severe intestinal barrier disruption. The reductions in antioxidants, energy pathways and neuroprotective agents highlight potential therapeutic targets to delay disease progression. Further investigation into gut microbiome composition and intestinal permeability in humans with CRB1 retinopathies is warranted.},
}

Humans
Female
Male
Metabolomics/methods
*Energy Metabolism
*Bile Acids and Salts/metabolism
*Nerve Tissue Proteins/metabolism/genetics
*Eye Proteins/metabolism/genetics
*Retinal Diseases/metabolism
Middle Aged
Metabolome
Adult
Membrane Proteins

@article {pmid41998513,
year = {2026},
author = {Luo, C and Liu, D and Zhan, Z and Li, J and Lou, F and Zhong, R and Chen, L and Zhang, H},
title = {Identification of Campylobactercoli as a key pathogen in Jinhua piglet diarrhea and its the probiotic control by Enterococcus faecium.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05005-8},
pmid = {41998513},
issn = {1471-2180},
support = {32573254//National Natural Science Foundation of China,China/ ; 2021-WR-01//National High-Level Talents Special Support Program of China/ ; ASTIPIAS07//Agricultural Science and Technology Innovation Program/ ; },
}

@article {pmid41998733,
year = {2026},
author = {Xie, C and Li, N and Liu, H and Liang, S and Gao, L and Liu, Z and Mu, S and Liu, S and Wu, X},
title = {The functional evaluation of Pichia pastoris hydrolysate as a protein source partial replacement of soybean meal in diets of growing-finishing pigs.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00511-7},
pmid = {41998733},
issn = {2055-5660},
support = {XD C0110304//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
}

@article {pmid41998767,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD},
title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {41998767},
issn = {1348-8945},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.},
}

@article {pmid41998770,
year = {2026},
author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH},
title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01655-5},
pmid = {41998770},
issn = {1756-994X},
support = {MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; },
}

@article {pmid41998806,
year = {2026},
author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z},
title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.},
journal = {Journal of medical primatology},
volume = {55},
number = {3},
pages = {e70074},
doi = {10.1111/jmp.70074},
pmid = {41998806},
issn = {1600-0684},
support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; },
abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.},
}

Animals
*Macaca mulatta/immunology
*Gastrointestinal Microbiome
*Diarrhea/veterinary/microbiology/immunology
*Monkey Diseases/immunology/microbiology
Longitudinal Studies
Transcriptome
Male
Anti-Bacterial Agents/therapeutic use
Female
Chronic Disease
Multiomics

@article {pmid41998859,
year = {2026},
author = {Gao, A and Luo, J and Ye, X and Hu, Y},
title = {Comments on "Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort".},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70395},
pmid = {41998859},
issn = {1440-1746},
}

@article {pmid41999025,
year = {2026},
author = {McMullen, E and Hafeez, DA and Pai, N and Mainville, L and Dumont, S and Julanon, N and Shenderey, R and Xiong, G and Towheed, S and Donovan, J},
title = {The Gut Microbiome as a Therapeutic Target in Alopecia Areata: Not Yet Part of the Patient Treatment Plan.},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70437},
pmid = {41999025},
issn = {1365-4632},
abstract = {Interest in the gut microbiome as a therapeutic target for treating alopecia areata (AA) has grown considerably. However, existing evidence remains limited and inconsistent. Currently, there is insufficient evidence to recommend microbiome-directed testing and therapies to patients with AA. Rigorous longitudinal studies are needed before such interventions can be recommended.},
}

@article {pmid41999204,
year = {2026},
author = {Economos, Z and Bloom, EH and Menalled, UD and Pethybridge, SJ and Ryan, MR and Casteel, CL},
title = {Cereal rye (Secale cereale) and canola (Brassica napus) cover crops reduce dry bean (Phaseolus vulgaris) herbivore damage.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70821},
pmid = {41999204},
issn = {1526-4998},
support = {//U.S. Department of Agriculture/ ; //National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Cover crops can support soil health and increase habitats for beneficial insects in diverse cropping systems. The aim of this study was to evaluate the impact of cover crop-conditioned soil on plant defense responses and insect pest damage using dry bean (Phaseolus vulgaris L.) as a model.

RESULTS: In a 2-year, multi-location field experiment comparing four cover crop treatments and a tilled control, we found that dry beans no-till planted into mechanically terminated cereal rye (Secale cereale L.) and canola (Brassica napus L.) experienced less insect damage than controls. In the laboratory, microbiome extracts from canola-enriched field soil increased dry bean jasmonic acid levels and reduced cowpea aphid (Aphis craccivora Koch) survival compared with other soil microbiome extracts. No differences in defense hormones were detected for dry bean grown in cereal rye soil microbiome extracts, however aphid survival was reduced on these plants compared to the controls.

CONCLUSIONS: Cereal rye and canola cover crops reduced insect damage in dry bean fields. Soil microbiomes associated with canola enhanced defense-related compounds in dry bean, suggesting a potential mechanism for pest suppression in the field. However, the impacts of canola varied across microbiome sources, highlighting the need for additional studies. © 2026 Society of Chemical Industry.},
}

@article {pmid41999240,
year = {2026},
author = {Wyss, J and Baehler, S and Ferracini, J and Kroell, D and Rossier, AM and Krupka, N and Misselwitz, B and Yilmaz, B and Wiest, R},
title = {The duodenal microbiota is compartmentalized and clinically stable yet rapidly responsive to nutrient exposure.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2657053},
doi = {10.1080/19490976.2026.2657053},
pmid = {41999240},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Duodenum/microbiology ; Female ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Nutrients/metabolism ; RNA, Ribosomal, 16S/genetics ; Obesity/microbiology ; Intestinal Mucosa/microbiology ; Phylogeny ; Bariatric Surgery ; },
abstract = {The duodenum is one of the most nutrient-exposed and immunologically active regions of the human gastrointestinal tract, yet its microbial ecology and short-term responses to dietary stimuli remain poorly defined. Most studies rely on fasting luminal aspirates, which fail to capture mucosa-associated communities and miss rapid ecological shifts during nutrient exposure, limiting insight into the spatial organization and dynamic behavior of the upper small intestinal microbiota (SIM). To address these limitations, we performed a compartment-resolved analysis of the duodenal microbiota in 94 individuals, including healthy controls, patients with obesity before and after bariatric surgery, individuals with IBS, and subjects with other SIBO-associated risk states. Paired luminal aspirates and mucosal biopsies were obtained during upper endoscopy; bacterial load was quantified by culture, and the community structure was assessed using 16S rRNA gene sequencing and PICRUSt-based pathway inference. In addition, healthy volunteers underwent a controlled intraluminal fat challenge with dense serial duodenal sampling over 180 min to resolve short-term nutrient-driven dynamics. Across all participants, the anatomical niche emerged as the dominant ecological determinant. Mucosal communities displayed higher species richness, broader phylogenetic representation, and distinct beta-diversity signatures compared with luminal aspirates, which were narrowly dominated by Streptococcaceae. Under fasting conditions, SIM remained remarkably stable across obesity, IBS, and culture-defined SIBO, with only minor taxonomic differences in SIBO-positive individuals. In contrast, acute nutrient exposure triggered rapid microbial blooming, increased culture positivity, and a transient rise in species richness within 30-60 min, revealing a highly responsive ecosystem not captured by fasting samples. Together, these findings show that the defining feature of the human duodenal microbiota is not disease-associated dysbiosis under fasting conditions, but rather a conserved spatial architecture coupled with rapid, nutrient-driven ecological plasticity, highlighting the dynamic and compartmentalized nature of the upper small intestinal microbiome.},
}

Humans
*Gastrointestinal Microbiome
Male
*Duodenum/microbiology
Female
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
*Nutrients/metabolism
RNA, Ribosomal, 16S/genetics
Obesity/microbiology
Intestinal Mucosa/microbiology
Phylogeny
Bariatric Surgery

@article {pmid41999333,
year = {2026},
author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG},
title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02641},
pmid = {41999333},
issn = {1520-5851},
abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.},
}

@article {pmid41999406,
year = {2026},
author = {Lisco, A and Borgognone, A and Vanpouille, C and Bricker-Holt, K and Callier, V and Nason, M and Vujkovic-Cvijin, I and Macmath, D and Manion, M and Redd, AD and Galindo, F and Kalibbala, S and Ssempijja, V and Anok, A and Tomusange, S and Reynolds, SJ and Giuliano, AR and Sereti, I},
title = {Bacterial dysbiosis, cervicovaginal human papillomaviruses and inflammation persist in women living with HIV-1 after a year of antiretroviral treatment.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag211},
pmid = {41999406},
issn = {1537-6613},
abstract = {BACKGROUND: The cervicovaginal microbiome may affect HIV-1 susceptibility and can in turn influence the prevalence and clinical course of HIV-1 and other sexually transmitted diseases. As the determinants, immunological correlates and clinical effects of the dysbiosis observed in women living with HIV-1 (WWH) remain elusive, we evaluated the vaginal immunologic milieu, cervicovaginal microbiome and prevalence of human papillomaviruses (HPV) in antiretroviral-naïve WWH over their first year of antiretroviral therapy (ART).

METHODS: 83 ART-naïve Ugandan WWH were enrolled in a longitudinal observational trial. Clinical evaluation and sampling of cervicovaginal secretions and plasma were performed at 0, 8, 24 and 52 weeks post-ART initiation. Amplification of the 16S-rRNA gene V3-V4 region was used to determine the cervicovaginal microbiome. A multiplex bead-array assay was used to quantify the concentration of biomarkers while a PCR-based hybridization assay was utilized for HPV detection and genotyping.

RESULTS: Gardnerella was the most abundant genus with a median relative abundance of 35% before ART maintaining a high prevalence throughout the study. Vaginal bacterial diversity did not change after ART, although the relative abundance of some genera, including the bacterial-vaginosis-associated bacteria Peptostreptococcus and Prevotella, decreased compared to baseline. Inflammatory biomarkers remained elevated in the cervicovaginal compartment despite prompt decreases in plasma.The prevalence of high and low-risk HPV types remained stable despite ART.

CONCLUSIONS: Suppression of HIV-1 replication is not sufficient to revert dysbiotic changes, proinflammatory immunological milieu and persistent HPV infections. Exploration of targeted strategies to restore cervicovaginal mucosal immunological functions in WWH is warranted.},
}

@article {pmid41999447,
year = {2026},
author = {Ganguly, NK and Kalra, S and Kapoor, N and Rao, P and Bakshi, M},
title = {Reconsidering Obesity in India Through a Gut-Metabolic Lens: Mechanistic Insights and the Emerging Role of Synbiotics in Individuals with the Thin-Fat Phenotype.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {41999447},
issn = {1865-8652},
abstract = {India's escalating burden of obesity and metabolic disease is characterized by a distinctive "thin-fat" phenotype, in which individuals with normal or near-normal body mass index exhibit disproportionate visceral adiposity, reduced skeletal muscle mass, and heightened susceptibility to insulin resistance. Conventional obesity models centered primarily on caloric imbalance fail to adequately explain this pattern, underscoring the need for a more integrative pathophysiological framework. Emerging evidence implicates gut microbiome dysbiosis, impaired fermentation of dietary fibers, reduced short-chain fatty acid (SCFA) signaling, altered bile acid metabolism, metabolic endotoxemia, and dysregulated adipose tissue crosstalk as key contributors to metabolic vulnerability in South Asian populations. This commentary synthesizes mechanistic insights into the gut-metabolic axis and examines their relevance to India's phenotype-specific challenges. Key pathways, including SCFA-mediated incretin secretion, Toll-like receptor 4 (TLR4)-driven inflammatory signaling, angiopoietin-like protein 4 (ANGPTL4)-mediated lipid partitioning, and microbiota-dependent bile acid biotransformation, are discussed as interconnected drivers of metabolic dysfunction. Emerging clinical evidence from randomized controlled trials evaluating synbiotic and prebiotic-botanical formulations is also discussed, highlighting their potential benefits as adjuncts to lifestyle modification. Given India's dietary patterns and widespread deficiency of fermentable fiber intake, synbiotics may represent a scalable and biologically coherent strategy to support metabolic health. However, heterogeneity of formulations, interindividual microbiome variability, and limited long-term outcome data necessitate cautious interpretation. Advancing precision microbiome-targeted interventions will require population-specific research, multi-omics integration, and rigorous clinical evaluation.},
}

@article {pmid41999489,
year = {2026},
author = {Nelson, K and Peterson, N and Olson, R and Castillo, H and Antwi, C and Cromwell, S and Benbow, ME and Ayayee, P},
title = {Gut Microbial Nitrate Reduction to Ammonia: A Possible Pathway of Biological Nitrogen Provisioning in Freshwater Insects.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02771-w},
pmid = {41999489},
issn = {1432-184X},
}

@article {pmid41999613,
year = {2026},
author = {Cook, KL and Giles, ED and Sekela, JJ and Simpson, JB and Redinbo, MR and Wilson, AS and Umar, S and Befort, CA and Kimler, BF and Hursting, SD and Fabian, CJ},
title = {Weight loss and omega-3 supplementation modulate the microbiome in women with increased breast cancer risk.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-26-0021},
pmid = {41999613},
issn = {1940-6215},
abstract = {Obesity is associated with gut dysbiosis, chronic inflammation, and insulin resistance. We assessed proportional change in fecal microbial populations in a pilot study (n=34) of peri/postmenopausal women with BMI ≥28 kg/m2 who were randomized to receive either 3.25 g/day of omega-3 fatty acids or a placebo during a weight loss intervention. Body composition was assessed using DXA, and fecal and blood samples were collected. Median weight change was -10%. Among participants who lost ≥10% of their weight, those assigned to omega-3 fatty acids showed the greatest decrease in the Firmicutes/Bacteroidetes phyla ratio and displayed favorable changes in systemic biomarkers. Notable increases in the proportional abundance of short-chain fatty acid (SCFA)-producing microbes including Phocaeicola vulgatus and Alistipes putredinis were observed in women receiving omega-3, which correlated with improvements in breast cancer biomarkers such as bioavailable estradiol, adiponectin-to-leptin ratio, and C-reactive protein levels. Women administered omega-3 fatty acids displayed increased % change in plasma SCFA propionate and decreased butyrate, suggesting intervention differentially modulated circulating bacterial-derived SCFA metabolites. High dose omega-3 fatty acids, when added to a behavioral weight loss intervention, promoted beneficial shifts to the gut microbiome and associated with improved breast cancer risk factors biomarkers.},
}

@article {pmid41999742,
year = {2026},
author = {Moyne, O and Norton, GJ and Al-Bassam, M and Lieng, C and Thiruppathy, D and Kumar, M and Haddad, E and Weng, Y and Raffatellu, M and Zaramela, LS and Zengler, K},
title = {Predicting competition and substrate preferences for targeted microbiome alteration.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.036},
pmid = {41999742},
issn = {1097-4172},
abstract = {Microbiome science has greatly expanded our understanding of microbial life and its roles in the environment and human health. Yet microbiome science often relies on descriptive, correlation-based approaches that limit causal insight and intentional intervention designs. Moving toward predictive and mechanistic understanding requires functional characterization of microbial interactions and metabolic preferences. Here, we present microbial interaction and niche determination (MIND), which quantifies mRNA translation prioritization to infer substrate preferences and competitive interactions in complex communities. Applied to synthetic communities, soil, human fecal samples, and a mouse model, MIND predicted microbial competition and substrate preferences, guiding precision prebiotic and probiotic interventions to selectively modulate community composition. Currently focused on competition and substrate utilization, MIND could be further extended to capture additional interactions and ecological niches. By linking functional measurements to ecological outcomes, MIND offers a broadly applicable framework for targeted microbiome manipulation and rational intervention design rooted in functional insight.},
}

@article {pmid41999744,
year = {2026},
author = {Usyk, M and Hayes, RB and Knight, R and Gonzalez, A and Li, H and Osman, I and Weber, JS and Ahn, J},
title = {Gut microbiome is associated with recurrence-free survival in patients with resected high-risk melanoma receiving adjuvant immune checkpoint blockade.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.03.041},
pmid = {41999744},
issn = {1097-4172},
abstract = {Patients with resected, high-risk melanoma receive adjuvant immune checkpoint blockade (ICB), yet clinical benefit remains unpredictable, with 25%-40% of patients experiencing recurrence. To evaluate whether pre-treatment gut microbiome (GMB) features predict recurrence, we analyzed stool samples from 674 patients enrolled in a phase 3 clinical trial, CheckMate 915, which investigated the combination of nivolumab plus ipilimumab versus nivolumab as a single agent across five geographic regions. Region-specific and cross-region meta-analyses identified pre-treatment taxa associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes, and Clostridium. Recurrence prediction was strongest when the validation cohort exhibited GMB profiles similar to those in the discovery cohort. Among closely matched individuals (Jensen-Shannon divergence [JSD] ≤ 0.11), the area under the curve (AUC) for recurrence prediction ranged from 0.78 to 0.94 across regions. GMB composition remained largely stable following treatment. These findings suggest that gut bacterial markers can predict recurrence after adjuvant ICB treatment in melanoma, supporting their potential as clinically actionable biomarkers to guide personalized therapy.},
}

@article {pmid41999953,
year = {2026},
author = {Ovaska, M and Tamminen, M and Lahdenperä, M and Rautava, S and Jeevannavar, A and Isokääntä, H and Bode, L and Lagström, H},
title = {The role of human milk oligosaccharides in shaping and restoring infant gut microbiota: Population-based cohort study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101318},
doi = {10.1016/j.ajcnut.2026.101318},
pmid = {41999953},
issn = {1938-3207},
abstract = {BACKGROUND: Infant gut microbiota colonization is important for supporting normal development and long-term health of children. Human milk oligosaccharides (HMOs) influence the composition of the gut microbiota, but their specific effects, particularly after breastfeeding, remain poorly understood.

OBJECTIVES: We aimed to deepen the understanding of how HMOs associate with the gut microbiota composition at 3 months and at 13 months of age. Additionally, we assessed the role of HMOs as microbiome-rebalancing agents in cesarean delivered infants.

METHODS: We analyzed fecal samples from infants at 3 months (n=517) and 13 months (n=522), along with human milk samples at 3 months, from a population-based cohort. Gut microbiota was profiled by 16S rRNA sequencing, and 19 HMOs quantified by high-performance liquid chromatography with fluorescent detection. Dirichlet Multinomial Mixtures clustering was used to identify bacterial fecal community types (FCTs) and multinomial logistic regression models to study the association between HMOs and FCTs. PERMANOVA and linear regression models were used to associate HMOs with gut microbiota diversity measures and Spearman correlation to bacterial genera.

RESULTS: HMOs associated with gut microbiota FCTs, diversity measures, and bacterial genera at 3 and 13 months of age. At 3 months, disialyllacto-N-tetraose (DSLNT) and the structurally related lacto-N-sialyllactose b (LSTb) showed notable associations with the gut microbiota while at 13 months, fucodisialyllacto-N-hexaose (FDSLNH) associated with multiple gut microbiota metrics. Maternal secretor status was associated with the gut microbiota beta diversity (R2=0.003, p<0.05) and decreased Shannon diversity (b=-0.24, p<0.05) at 3 months, with diminishing associations at 13 months (Observed richness, b=-11, p<0.05). While no individual HMOs showed microbiome-rebalancing effects in cesarean-born infants, infants fed by non-secretor mothers exhibited stronger cesarean-related microbiota patterns compared to those fed by secretors.

CONCLUSIONS: HMOs exhibit age-dependent and structure-specific associations with infant gut microbiota, extending beyond breastfeeding.},
}

@article {pmid42000112,
year = {2026},
author = {Cao, X and Lou, B and Sun, Z and Wei, Y and Qu, M and Xu, Y and Kang, Q and Xie, S and Wang, Q and Chen, J},
title = {Mechanism of neuroinflammation and cardiovascular toxicity induced by tributyltin: Evidence from zebrafish (Danio rerio) models and network toxicology studies.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128127},
doi = {10.1016/j.envpol.2026.128127},
pmid = {42000112},
issn = {1873-6424},
abstract = {As an antifouling agent, tributyltin (TBT) is widely used in marine anti-fouling coatings. Recent studies have demonstrated that TBT exerts toxic effects on aquatic life and can be transferred to humans via the food chain. In this study, we investigated the impact of varying TBT concentrations on the brain and heart of zebrafish, as well as the underlying mechanisms involved. These findings suggest that TBT exposure caused varying degrees of oxidative stress in the brain and heart of zebrafish, increased lipid peroxidation levels, and induced inflammatory responses, apoptosis, and histopathological damage. Additionally, TBT exposure altered zebrafish behavior, significantly reduced the expression of tight junction protein genes (zo-1, occludin, and claudin-2) in the gut and brain, and suppressed acetylcholinesterase (AChE) activity in the brain. Untargeted metabolomics and gut microbiome analysis revealed that TBT exposure significantly altered the abundance and diversity of microbial communities, leading to metabolic disturbances, with the primary differential metabolites associated with nucleotide, glycerophospholipid, and purine metabolism. Gut microbiota dysbiosis was also strongly correlated with neuro-cardiovascular toxicological responses in zebrafish. Dysbiosis increased lipopolysaccharide (LPS) secretion. In the context of blood-brain barrier disruption, circulating LPS may reach the brain, potentially contributing to neuroinflammation and subsequent neural damage. Concurrently, elevated inflammatory cytokines were associated with activation of the hypothalamic-pituitary-interrenal (HPI) axis, increasing cortisol (Cor) levels, and correlating with cardiovascular system damage. Network toxicology and molecular docking analysis revealed that strong binding affinities between TBT and core targets, including BCL2, GAPDH, IL1B, IL6, TNF, and MMP9.},
}

@article {pmid42000265,
year = {2026},
author = {Chelladurai, G and Jenivi, A and Esther Elsie, T},
title = {Comment on "Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer".},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.04.063},
pmid = {42000265},
issn = {0929-6646},
}

@article {pmid42000466,
year = {2026},
author = {Collins, K and Donnellan, L and Asif, Z and Chan, NSL and Subramaniam, S and Kamath, S and Ariaee, A and Abdelhafez, A and Wignall, A and Hoffman, P and Joyce, P},
title = {The gut microbiome modulates the lipase-mediated digestion of dietary lipid emulsions.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {265},
number = {},
pages = {115715},
doi = {10.1016/j.colsurfb.2026.115715},
pmid = {42000466},
issn = {1873-4367},
abstract = {The gut microbiome plays a critical role in host lipid metabolism, yet its influence on the intraluminal processes governing dietary lipid digestion, particularly lipase-mediated hydrolysis at oil-water interfaces, remains poorly understood. In this study, we combined in vivo microbiome modulation in rats with an ex vivo lipolysis model to examine how microbial perturbations affect intestinal lipid digestion. Rats were pretreated for 14 days with either broad-spectrum antibiotics or a prebiotic to induce distinct microbial profiles. Small intestinal luminal contents were collected from the jejunum and used to monitor the ex vivo digestion of coconut oil and olive oil, representing dietary lipids with varying triglyceride chain lengths. Microbial diversity was positively associated with both the rate and extent of lipid digestion. Notably, the prebiotic group showed a 3-4-fold increase in fatty acid release compared to the antibiotic group after 60 min of digestion (p < 0.0001). Physicochemical analyses indicated that prebiotic treatment enhanced emulsification efficiency, increasing the interfacial surface area available for lipase adsorption by up to 250%. Biomolecular profiling revealed marked changes in the intestinal lipidome and proteome, together with changes in endogenous bile acid and carbohydrate concentrations suggesting that microbial modulation of the luminal milieu plays a critical role in lipid emulsification and bioaccessibility. Together, these findings demonstrate that microbiome composition directly impacts the physicochemical environment of the small intestine and shapes lipid digestion outcomes, highlighting the potential of microbiome-targeted strategies to enhance digestive efficiency and metabolic health.},
}

@article {pmid41994130,
year = {2026},
author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL},
title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8724320/v1},
pmid = {41994130},
issn = {2693-5015},
abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae , 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.},
}

@article {pmid41806005,
year = {2026},
author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y},
title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41806005},
issn = {2191-0855},
abstract = {Atopic dermatitis (AD), an inflammatory skin disease, exhibits increased incidence with autism spectrum disorders (ASD) in children. However, the mechanism underlying the ASD-AD comorbidity remains unclear. Here, we integrated the metagenomic and metabolomics analysis to characterize the compositions and functional profiles of gut microbiome in ASD children with AD. We found significant alteration in the composition of the intestinal microbial species between ASD-AD group and ASD group based on beta diversity analysis. LEfSe analysis showed tyzzerella_nexilis, eubacterium_sp_OM08_24 and clostridium_nexile_CAG348 were significantly increased in ASD children with AD. In addition, metabolite profiles showed that differentially expressed metabolites were mainly lipids and organic acids. Meanwhile, functional profiles showed that the pathway of cholesterol metabolism and biosynthesis of unsaturated fatty acids was abundant in ASD children with AD. Furthermore, the correlation analysis revealed that bacteroides_sp_CAG443, limosilactobacillus_mucosae had a positive correlation with traumatic acid and ricinoleic acid that were decreased in ASD-AD group, respectively. Eubacterium_ramulus and lachnospiraceae_bacterium were positively correlated with 11,14-eicosadienoic acid (EDA). Taken together, our results propose that altered gut microbiota regulates metabolites to affect the development of atopic dermatitis in ASD children.},
}

@article {pmid41968359,
year = {2026},
author = {Senousy, MA and Abo-Elmaaty, RM and Nabil Omar, N and Abdelgawad, HM},
title = {Dapagliflozin-intermittent fasting combination maximizes weight and metabolic regulation through AMPK/sirtuins/clock genes and gut microbiota signaling in high-fat diet-induced obesity: a novel anti-obesity approach.},
journal = {Cell & bioscience},
volume = {16},
number = {1},
pages = {},
pmid = {41968359},
issn = {2045-3701},
abstract = {UNLABELLED: Innovative and affordable treatment options are required to combat obesity and its detrimental impact on health economics. Dapagliflozin (Dapa), an antidiabetic medication, promotes weight loss; however, the extent of weight reduction may be limited. Intermittent fasting (IF) is a dietary approach regarded as a cost-effective and readily accessible regimen. This study investigated the beneficial effects of Dapa, IF, and their combination on weight loss and metabolic derangements in high-fat diet (HFD)-induced obesity in rats. Male Sprague-Dawley rats were allocated into 6 groups: groups 1 (normal control) and 2 (drug control) were administered a normal chow diet, while the obesity groups 3, 4, 5, and 6 were subjected to HFD for 8 weeks. Rats in groups 4, 5, and 6 underwent a further 8-week treatment with Dapa (5 mg/kg, p.o) daily, IF (16/8), or a combination of both, respectively. The HFD group exhibited elevated anthropometric measurements and adiposity index. Upon histopathological examination, the HFD group showed adipocyte hypertrophy, hypercellularity, and possible necrosis, along with hepatic fat accumulation and elevated serum liver enzymes. The HFD group showed a downregulation of p-AMPK/SIRT1 and an upregulation of SIRT7, GPR43, and clock genes BMAL1, CLOCK, and CRY1 expression in adipose tissue, along with a drop in the gut microbiome diversity, serum short-chain fatty acids (SCFAs), POMC, and PYY levels. Dapa and IF combination demonstrated favorable outcomes over monotherapy, as evidenced by normalized anthropometric measurements, improved histopathological and biochemical derangements, regulated p-AMPK/SIRT1, SIRT7, and clock genes expression, and restored gut microbiome and SCFA levels. Conclusively, this study suggests the concurrent administration of Dapa and IF as a new, beneficial, cost-effective anti-obesity strategy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13578-026-01557-4.},
}

@article {pmid41981675,
year = {2026},
author = {Zhang, W and Zhao, W and Ye, L and Wang, H and Chen, Z and Liu, X and Li, Y and Zhang, Q and Zhang, H and Liu, Y and Chen, X and Chen, S and Zeng, J and Huang, R and Li, Y and He, Y},
title = {Profiling the tumor-resident microbiota in small cell lung cancer and its influence on clinical outcomes.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41981675},
issn = {1479-5876},
support = {2022YFF0705300//National Key Research and Development Program of China/ ; Fkcy2515//"Young Eagle Soaring" Youth Talent Funding Program of Shanghai Pulmonary Hospital/ ; },
abstract = {BACKGROUND: Increasing evidence has confirmed the existence of resident microbial communities within solid tumors and indicates that the tumor microbiota may represent a novel component of the tumor microenvironment, actively regulating cancer initiation, progression, metastasis, and therapeutic responsiveness. However, the role of tumor microbiota in small cell lung cancer (SCLC) has not been well explored.

METHODS: Tumor samples were collected from 71 patients with SCLC at Shanghai Pulmonary Hospital between 2019 and 2023. A comprehensive analysis of the tumor-resident microbiota in SCLC was conducted using 16 S rRNA sequencing. The bacterial communities were profiled, and their correlation with clinical outcomes was assessed.

RESULTS: A total of 28 phyla, 79 classes, 135 orders, 251 families, and 428 genera were identified, revealing a diverse tumor microbiota in SCLC. It was shown that tumor microbiota varied markedly among patients. SCLC patients with a smoking history exhibited distinct tumor microbiota, with significantly higher abundances of Brevundimonas and Gemmatimonadetes. When patients were stratified by progression-free survival (PFS) into long-PFS (L-PFS) and short-PFS (S-PFS) cohorts, their tumor microbiota segregated distinctly. LEfSe analysis showed that Lactobacillus, Clostridium, Rothia, and Staphylococcus were selectively enriched in the L-PFS group, whereas Stenotrophomonas, Cetobacterium, and Aerococcus dominated the S-PFS group. Kaplan–Meier analysis confirmed that carriage of Lactobacillus, Clostridium, or Staphylococcus was associated with prolonged survival relative to negative status, while positivity for Stenotrophomonas, Cetobacterium, or Aerococcus conferred a reduction in survival. Subsequent response-stratified analysis revealed that Clostridium- and Lactobacillus-positive SCLC was associated with a significantly higher response rate. Conversely, positivity for Methylobacterium, Pelomonas, Ralstonia, Bradyrhizobium, Variovorax, Microbacterium, Comamonas, or Sphingomonas markedly reduced response. The intersection of survival and response results identify Clostridium and Lactobacillus as promising prognostic tumor microbiota markers in SCLC. In vitro assays demonstrated that the Clostridium and Lactobacillus metabolites, butyrate and lactic acid, lacked direct cytotoxicity against SCLC cells. However, in the syngeneic mouse model, systemic supplementation of butyrate or lactic acid significantly potentiated the anti-tumor efficacy of standard chemotherapy. Notably, flow cytometric analysis revealed that this in vivo synergistic effect was closely associated with a profound increase in CD8 + T cell infiltration within the tumor microenvironment. Furthermore, integrating these two tumor microbiota with key clinical variables (sex, age, smoking, stage, radiotherapy), we constructed three models—therapeutic-response, 1-year PFS, and 1-year overall survival—that maintained robust performance in both training and validation cohorts.

CONCLUSIONS: In conclusion, the tumor-resident microbiota constitutes a critical component of the SCLC tumor microenvironment, exerting profound influence on the therapeutic response and patient prognosis. In detail, Clostridium and Lactobacillus—two pivotal tumor-resident taxa significantly linked to enhanced therapeutic responses and favorable prognosis—indicate their potential as predictive biomarkers for treatment outcomes and patient prognosis, and highlight them as candidate targets for microbiome-directed therapeutic strategies against SCLC, which warrants further functional validation.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-08109-x.},
}

@article {pmid41993062,
year = {2026},
author = {Nuraini, P and Nelwan, SC and Pradopo, S and Pronorahardjo, AS and Andarini, PQ and Antonius, Y and Aljunaid, MA},
title = {Fractionated ethanolic red ginger extract as antibacterial agent against Aggregatibacter actinomycetemcommitans and Porphyromonas gingivalis: In silico and in vitro studies.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {3},
pages = {101446},
pmid = {41993062},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease associated with oral microbiome dysbiosis, where Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis contribute through adhesion, biofilm formation, and tissue-destructive virulence factors. Although chlorhexidine is widely used as an adjunctive antimicrobial agent, its long-term use is limited by adverse effects, highlighting the need for safer natural alternatives. Red ginger (Zingiber officinale var. rubrum) exhibits antibacterial potential; however, data on fractionated extracts and their interaction with specific virulence proteins remain limited.

OBJECTIVE: To evaluate the antibacterial activity of fractionated ethanolic red ginger extract against A. actinomycetemcomitans and P. gingivalis using integrated in silico and in vitro approaches.

METHODS: Twenty-two bioactive compounds identified from the fractionated extract were analyzed via molecular docking against cytolethal distending toxin (Cdt) of A. actinomycetemcomitans and fimbrial protein Mfa5 of P. gingivalis, with chlorhexidine as reference. In vitro assays determined minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), bacterial adherence, biofilm formation, and viability.

RESULTS: Docking analysis showed that cyclooctacosane and gamma-sitosterol demonstrated binding affinities comparable to chlorhexidine toward both target proteins. The extract exhibited MIC/MBC values of 0.062/0.125 mg/mL for A. actinomycetemcomitans and 0.031/0.062 mg/mL for P. gingivalis. Significant reductions in bacterial adherence, biofilm formation, and viability were observed at concentrations of 0.031-0.125 mg/mL.

CONCLUSION: Fractionated ethanolic red ginger extract demonstrates promising antibacterial activity against key periodontal pathogens by targeting virulence mechanisms related to adhesion and biofilm formation, supporting its potential as a natural adjunct in periodontal therapy.},
}

@article {pmid41993122,
year = {2026},
author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M},
title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {297-309},
pmid = {41993122},
issn = {2405-6383},
abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.},
}

@article {pmid41993168,
year = {2026},
author = {Goto, Y and Dolton, G and Thomas, H and Morin, T and Tajima, Y and Imamura, K and Sakata, S and Oka, K and Hayashi, A and Takahashi, M and Ueno, T and Sakagami, T and Tomita, Y and Sewell, AK and Motozono, C},
title = {A probiotic bacterium modulates antitumour γδ T-cell responses in lung cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1750569},
pmid = {41993168},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/therapy ; *Probiotics/therapeutic use/administration & dosage ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; Cell Line, Tumor ; Immune Checkpoint Inhibitors/therapeutic use ; Female ; Male ; *T-Lymphocytes/immunology ; *Carcinoma, Non-Small-Cell Lung/immunology ; Aged ; Middle Aged ; Gastrointestinal Microbiome/immunology ; Antigens, CD/metabolism ; Lymphocyte Activation ; },
abstract = {The link between the intestinal microflora and cancer outcomes has been recognized for over a decade. Several recent studies have demonstrated that the gut microbiome is associated with the efficiency of T-cell checkpoint blockade therapy for cancer, raising interest in strategies to harness this effect via consumption of live microorganisms (probiotics). The probiotic Clostridium butyricum strain MIYAIRI 588 (CBM588) improves response rates and overall survival in patients receiving immune checkpoint inhibitor (ICI) therapy for non-small cell lung cancer and metastatic renal cell carcinoma but the mechanism underlying this benefit remains unclear. Here, we show that CBM588 spores induce a population of Vγ9Vδ2 T-cells from the peripheral blood of healthy donors and lung cancer patients. A subset of these T-cells responded to, and directly lysed, cancer cell lines via a butyrophilin 3A-dependent mechanism. In patients taking CBM588 alongside checkpoint blockade, using samples from a cohort of 38 patients, peripheral blood Vδ2[+] T-cells expressed the activation marker CD69 more frequently than in those receiving checkpoint blockade alone and the frequency of Vδ2[+]CD69[+] cells increased following initiation of CBM588 treatment (p = 0.0041). Pleural effusions from patients receiving ICI with CBM588, although available from only three individuals, also showed a notable shift in the local γδ T-cell compartment from the expected Vδ1 dominance towards Vδ2 cells, suggesting altered recruitment or retention of Vδ2 cells at the tumour site. Across the patient cohort, higher post-treatment frequencies of CD69[+] Vδ2 T-cells were associated with improved survival and more favourable clinical outcomes. These findings provide a potential mechanism by which manipulation of the intestinal microflora might contribute to cancer prognosis through effects on immune effector cells with intrinsic anticancer properties.},
}

Humans
*Lung Neoplasms/immunology/therapy
*Probiotics/therapeutic use/administration & dosage
*Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism
Cell Line, Tumor
Immune Checkpoint Inhibitors/therapeutic use
Female
Male
*T-Lymphocytes/immunology
*Carcinoma, Non-Small-Cell Lung/immunology
Aged
Middle Aged
Gastrointestinal Microbiome/immunology
Antigens, CD/metabolism
Lymphocyte Activation

@article {pmid41993185,
year = {2026},
author = {Kaźmierczak-Siedlecka, K and Kucharski, R and Kosiński, A and Marano, L and Makarewicz, W and Kalinowski, L},
title = {Red-complex bacteria: immunological background leading to the development of head and neck cancers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804268},
pmid = {41993185},
issn = {1664-3224},
mesh = {Humans ; *Head and Neck Neoplasms/immunology/microbiology/etiology ; *Microbiota/immunology ; Animals ; Porphyromonas gingivalis/immunology ; Periodontitis/microbiology/immunology ; },
abstract = {Oral microbiome imbalance is involved in the development of head and neck cancers (HNCs). There is a group of oral pathogens, such as Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, that creates red-complex. Currently, the oral pathogens' role in the pathogenesis of periodontitis is well-described; nevertheless, data regarding the link between HNCs and periopathogens are still limited, especially considering T. forsythia and T. denticola. These microbes utilise various virulence factors to promote the carcinogenesis process, affecting the immunological background. This paper presents modern insights into the role of red-complex bacteria in the development of HNCs, concentrating on the immunological aspects.},
}

Humans
*Head and Neck Neoplasms/immunology/microbiology/etiology
*Microbiota/immunology
Animals
Porphyromonas gingivalis/immunology
Periodontitis/microbiology/immunology

@article {pmid41993272,
year = {2026},
author = {Wei, Z and Hong, Q and Chen, G and Hartert, TV and Rosas-Salazar, C and Das, SR and Shilts, MH and Levin, AM and Tang, ZZ},
title = {Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.09.717497},
pmid = {41993272},
issn = {2692-8205},
abstract = {Identifying microbial features associated with various covariates is a long-standing goal in microbiome research. Modern association studies incorporate an ever-increasing number of microbial features, covariates, and datasets from diverse cohorts. However, the complexity of microbiome data challenges analysis, often leading to poor replication of findings. We introduce PALM, a quasi-Poisson regression framework that enables fast and reliable association discovery in large-scale studies and meta-analyses. Extensive, realistic simulations demonstrate PALM's advantages in controlling false discovery rates, boosting power, improving computational efficiency, and preserving cross-study homogeneity of association effects. Three real-world applications at different scales illustrate PALM's utility, underscoring its potential to advance microbiome research.},
}

@article {pmid41993317,
year = {2026},
author = {Chaki, T and Maruyama, D and Doan, TN and Xiaoli, T and Prakash, A},
title = {Dietary tryptophan mitigates lung ischemia-reperfusion injury via microbiota-derived indole-3-propionate and aryl hydrocarbon receptor signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.714281},
pmid = {41993317},
issn = {2692-8205},
abstract = {BACKGROUND: Lung ischemia-reperfusion (IR) injury drives early morbidity after lung transplantation and cardiothoracic surgery, yet targeted preventive therapies are lacking. The gut-lung axis and microbiota-derived tryptophan metabolites, including indole-3-propionate (IPA), may regulate pulmonary immunity and inflammation. We investigated whether a tryptophan-rich (Trp-Rich) diet attenuates sterile lung IR injury by increasing microbiota-derived indole metabolites and reprogramming alveolar macrophage (AM) inflammatory responses.

METHODS: C57BL/6 mice received isocaloric tryptophan-standard (Trp-Std; 0.18%) or Trp-Rich (0.60%) diets for 14 days, then underwent unilateral left lung IR (60 min ischemia followed by 60 min reperfusion). Oxygen saturation, lung cytokines, and aryl hydrocarbon receptor (AhR) signaling readouts (Cyp1a1 / Cyp1b1) were evaluated. Gut microbiota was profiled by 16S rRNA sequencing, and targeted metabolomics quantified tryptophan metabolites in feces, portal vein (PV) plasma, and lung tissue. To further assess inflammatory priming in vivo , mice were additionally challenged with intratracheal lipopolysaccharide (LPS). Mechanistic studies compared IPA with related indole metabolites in MH-S cells and primary human AMs, including ex vivo nutritional IR, LPS stimulation, and AhR stimulation and blockade using synthetic agonists and antagonists.

RESULTS: Trp-Rich feeding improved post-IR oxygenation, reduced lung IL-1β, and increased pulmonary Cyp1a1 / Cyp1b1 gene expression. Trp-Rich diet remodeled the gut microbiota, including enrichment of Bifidobacterium and Lactobacillus , and increased IPA levels across feces, PV plasma, and lung tissue, with lower kynurenine/IPA ratios across matrices. In the LPS intratracheal challenge, Trp-Rich feeding reduced IL-6 levels in lung tissue and systemic plasma. Primary murine AMs isolated from Trp-Rich mice also showed reduced IL-1β and IL-6 release in an ex vivo nutritional IR model. Among tested indole metabolites, IPA showed the strongest dose-dependent suppression of LPS-induced cytokines and chemokines in MH-S cells and primary human AMs, remained active in the ex vivo nutritional IR model, and its anti-inflammatory effect was abrogated by AhR blockade and enhanced by co-treatment with other indole metabolites.

CONCLUSIONS: A Trp-Rich diet attenuated sterile lung IR injury, coinciding with gut microbiota remodeling, increased systemic and pulmonary IPA, reduced inflammatory priming, and reprogrammed AM responses. These data support diet- or microbiome-directed strategies targeting IPA-AhR signaling to mitigate perioperative lung IR injury.},
}

@article {pmid41993357,
year = {2026},
author = {Malarney, KP and Scott, SA and Chang, PV},
title = {A class of metallohydrolases expands bile salt hydrolase activity in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716488},
pmid = {41993357},
issn = {2692-8205},
abstract = {Bile acids are steroidal metabolites produced by host and microbial metabolism that shape gut microbiome ecology and influence host physiology [1,2] . Bile acid structural diversification requires gut microbial bile salt hydrolase (BSH) activities, which cleave the amide bond of liver-derived bile acid amidates (BAAs) [3] . Beyond this gatekeeping metabolic function, BSHs expand the bile acid pool via their amine N -acyltransferase activity to produce numerous microbially derived BAAs that signal via host receptors and are further metabolized [4,5] . To date, all BSH activity has been attributed to a family of N-terminal nucleophile (Ntn) cysteine hydrolases. However, numerous gut anaerobic bacteria possess BSH activity but do not encode bsh genes from the Ntn family. Here, we describe a previously unknown class of m etal-dependent BSHs (mBSHs) broadly distributed in the gut microbiome. These metalloenzymes have a distinct active site architecture from the canonical Ntn superfamily of cysteine hydolase BSHs (cBSHs) and are selective for taurine-conjugated BAAs. The discovery of this heretofore unappreciated class of BSHs overturns the paradigm that this important, conserved biochemical activity of the gut microbiota is provided exclusively by canonical cysteine hydrolases, greatly expands the known landscape of bile acid metabolism, and reveals a previously unrecognized link connecting host-microbiota bile acid co-metabolism with microbial taurine utilization pathways.},
}

@article {pmid41993390,
year = {2026},
author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J},
title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.716956},
pmid = {41993390},
issn = {2692-8205},
abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.},
}

@article {pmid41993507,
year = {2026},
author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T},
title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.712906},
pmid = {41993507},
issn = {2692-8205},
abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.},
}

@article {pmid41993513,
year = {2026},
author = {Cui, Z and Meng, CJ and Irwin, SM and Augustijn, HE and Papageorgiou, PP and Nguyen, ATP and Yu, R and Aguilar Ramos, MA and Kulik, HJ and Balskus, EP},
title = {A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716592},
pmid = {41993513},
issn = {2692-8205},
abstract = {Bile salt hydrolases (BSHs) are gut microbial enzymes that catalyze the deconjugation of glycine-or taurine-conjugated bile acids (BAs), a key step in shaping the BA pool in the human gastrointestinal tract and modulating host-gut microbiome interactions. [1-3] All known BSHs are members of the N-terminal nucleophile (Ntn) hydrolase superfamily and share a conserved architecture and mechanism involving a nucleophilic active site cysteine. [4,5] This knowledge has guided predictions and study of BSH activity in the gut microbiome [6,7] as well as the development of BSH inhibitors [8] . Here, we report the discovery and characterization of a previously unknown BSH from the human gut bacterium Bilophila wadsworthia that belongs to the metal-dependent amidohydrolase superfamily and exhibits robust and specific activity toward taurine-conjugated bile salts. We show this secreted enzyme, metalloBSH, utilizes a metallocofactor for BA deconjugation, a mechanism distinct from that of canonical Ntn-type BSHs. MetalloBSHs are conserved in B. wadsworthia and present in many other Desulfovibrionaceae found in vertebrate gut microbiomes. Analysis of multi-omic datasets indicates metalloBSHs are expressed in vivo and correlate with BA metabolism. Overall, our findings reshape our understanding of BSH activity in the gut microbiome and highlight the promise of activity guided discovery in revealing previously overlooked gut microbial enzymes.},
}

@article {pmid41993533,
year = {2026},
author = {Awan, A and Blakeley-Ruiz, JA and Kleiner, M and Hinzke, T},
title = {Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716595},
pmid = {41993533},
issn = {2692-8205},
support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {UNLABELLED: Metaproteomics enables the functional characterization of microbiomes and host-microbe interactions by detecting and quantifying thousands of proteins. In data-dependent acquisition metaproteomics, protein quantification is commonly performed using either MS1-based area under the curve (AUC) or MS2-based peptide spectral counts (SpC). In AUC quantification, match between runs (MBR) is frequently employed to minimize data sparsity, yet its impact on metaproteomic data remains unclear. Understanding MBR's impact on metaproteomics data is especially important due to the high peak density in the MS1 mass spectra and the potential presence of not only proteins, but even entire organisms, in one sample and their absence in the other, which would complicate accurate feature mapping and transfer. While accurate quantification is essential for deriving meaningful biological inferences from metaproteomic analyses, systematic evaluations of AUC and SpC quantification in metaproteomics remain scarce. In this study, we used defined complex metaproteomic samples to perform a ground truth-based evaluation of AUC and SpC quantification and to determine the impact of MBR on AUC quantification. We found that MBR led to a substantial number of falsely identified proteins in complex samples. Protein identifications from an organism not present in the sample were wrongly transferred from other samples when MBR was used. We found that MBR-free AUC data had a wider dynamic range, higher quantitative accuracy, and more sensitive detection of abundance differences.

SIGNIFICANCE OF THE STUDY: Although metaproteomics is increasingly used to advance microbiome research, quantification strategies in metaproteomics are mostly selected based on convention rather than evidence, due to a lack of ground truth-based evaluation of quantification strategies in metaproteomics. Accurate protein quantification is key to deriving meaningful biological inferences from metaproteomic samples, yet it remains challenging due to their high complexity and uneven protein abundances. Here, we used defined metaproteomic samples to evaluate widely used quantification strategies in metaproteomics and to determine the effects of match between runs (MBR) on quantitative accuracy. Based on our findings, MBR adds falsely identified proteins to metaproteomic data. While MBR-free AUC offers a broader dynamic range and higher quantitative accuracy, SpC offers better proteome coverage. With this study, we provide an evidence-based framework for the informed selection of quantification strategies in metaproteomics, and highlight the strengths and limitations of these approaches with respect to proteome coverage, dynamic range, quantitative accuracy, and error propagation. Our findings also have important implications for the biological interpretation of data derived from these strategies and lay the groundwork for future studies validating quantitative approaches in data-independent acquisition workflows.},
}

@article {pmid41993548,
year = {2026},
author = {Fodor, KE and Ritter, AC and Schmieley, RA and Ricart Arbona, RJ and Miranda, IC and Lipman, NS},
title = {Microbiome-Dependent Protection Against Corynebacterium bovis -Associated Hyperkeratosis in Nude Mice (Mus musculus).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.11.716586},
pmid = {41993548},
issn = {2692-8205},
abstract = {Corynebacterium bovis , the cause of Corynebacterium -associated hyperkeratosis (CAH), is an important pathogen in immunocompromised mice that is difficult to eliminate and can confound research outcomes. We recently observed that CAH severity varies among outbred athymic nude mouse stocks, but the relative contributions of host genetics and the microbiome remain unclear. We hypothesized that disease course and severity vary based on host genetic stock and/or microbiome composition. Three nude mouse stocks were rederived into the axenic state and either monoinfected with a pathogenic C. bovis isolate (10 [4] ; CFU) or given sterile media (n=6/group). Axenic mice were also reassociated with their source microbiome or microbiomes from three other stocks with known differences in CAH severity, then inoculated with C. bovis (n=6) or sterile media (n=2). In a separate experiment, one axenic stock was used to assess the role of C. amycolatum via monoinfection, monoinfection followed by C. bovis challenge, or addition to a nonprotective microbiome followed by C. bovis challenge. Mice were monitored daily for 21 days and scored for skin lesions (0-5). C. bovis monoinfected mice developed disease comparable in severity and timing to conventionally raised controls. Notably, reassociation with Vendor A2's microbiome prevented clinical lesions and reduced histopathologic changes across all stocks. While C. amycolatum as a monoinfection did not cause disease nor reduce disease severity following C. bovis challenge, it delayed the onset and lowered peak scores when added to a non-protective microbiome. These findings demonstrate that C. bovis can cause CAH as a monoinfection, that both host genetics and microbiome composition influence disease progression, and, together with prior work, support its role as the etiologic agent consistent with Koch's postulates. Identifying protective microbiome constituents may inform strategies to reduce disease burden in susceptible mice.},
}

@article {pmid41993554,
year = {2026},
author = {Rivas, JA and Scieszka, DP and Peralta-Herrera, E and Enriquez, CM and Merkley, SD and Nava, AL and Gullapalli, RR and Castillo, EF},
title = {Colonic metabolomic and transcriptomic alterations in a mouse model of metabolic syndrome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.716131},
pmid = {41993554},
issn = {2692-8205},
abstract = {UNLABELLED: Metabolic syndrome (MetS), characterized by abdominal obesity, insulin resistance, dyslipidemia, and hypertension, affects a substantial proportion of the global population and increases the risk for cardiovascular disease, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite its prevalence, there are currently no effective pharmacological therapies targeting MetS, highlighting the need to identify novel etiological mechanisms, particularly within the gastrointestinal (GI) tract. Using a mouse model of MetS and healthy lean controls, we assessed the colonic microenvironment through metabolomic, transcriptomic, and microbiome analyses. Colonic organoids were cultured to further explore epithelial alterations. Additionally, human MetS fecal metabolomics data were cross-compared with the mouse model to validate translational relevance. MetS mice exhibited upregulation of colonic anabolic pathways, including glycolysis, the pentose phosphate pathway, and the tryptophan/kynurenine pathway, without evidence of intestinal inflammation. Microbiome analysis revealed an increased abundance of the genus Lactobacillus in MS NASH mice. Colonic organoids from MetS mice showed altered goblet cell differentiation. Comparative analysis with human MetS fecal metabolomics demonstrated similar dysregulated pathways, underscoring the translational relevance of these findings. Our study reveals significant metabolic and microbial alterations in the colon of MS NASH mice, implicating a dysfunctional GI tract as a potential etiological factor in MetS. These findings highlight specific metabolic pathways and microbial signatures that could serve as future therapeutic targets for MetS.

NEW & NOTEWORTHY: This study identifies the colon as a metabolically active tissue affected in metabolic syndrome. Despite the absence of intestinal inflammation, MS NASH mice displayed altered colonic metabolism and microbiota composition, with conserved metabolite changes matching those seen in humans with metabolic syndrome. These findings highlight colonic metabolic dysfunction as a potential driver of gut dysbiosis and disease progression in metabolic syndrome and MASLD.},
}

@article {pmid41993555,
year = {2026},
author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC},
title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716562},
pmid = {41993555},
issn = {2692-8205},
abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.

ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.},
}

@article {pmid41993569,
year = {2026},
author = {Wang, S and Hullar, MA and Curtis, K and Kwee, S and Park, SY and Rettenmeier, C and Monroe, KR and Ernst, T and Shepard, J and Wilkens, LR and Le Marchand, L and Lampe, JW and Lim, U and Randolph, TW},
title = {Gut Microbiota Mediates the Association between Diet Quality and Ectopic Adiposity: The Multiethnic Cohort Adiposity Phenotype Study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.10.717245},
pmid = {41993569},
issn = {2692-8205},
support = {P01 CA168530/CA/NCI NIH HHS/United States ; R01 MD018265/MD/NIMHD NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Higher-quality diets have been associated with lower levels of ectopic fat deposited in the viscera and liver, which is hypothesized to be mediated in part by the gut microbiota.

OBJECTIVES: We tested this hypothesis in a multi-ethnic imaging study using global (microbiome-wide) testing as well as a high-dimensional multiple-mediators regression framework to identify bacterial genera in the human gut that mediate the association between diet quality and ectopic adiposity.

METHODS: We analyzed the cross-sectional data of 1,400 older adults (age 60-77) from five racial/ethnic groups in the Multiethnic Cohort Adiposity Phenotype Study (2013-2016). Overall diet quality was defined by adherence to the MIND diet. The relative abundance of 151 bacterial genera was quantified from 16S rRNA gene sequencing of the stool samples. Visceral fat, liver fat, and the presence of MASLD (metabolic dysfunction-associated steatotic liver disease) were determined based on magnetic resonance imaging (MRI). We used high-dimensional mediation analysis (HDMA) to estimate gut microbial mediation in the linear regression of visceral fat or liver fat, or in logistic regression of MASLD, on the MIND adherence score, adjusted for potential confounders.

RESULTS: Higher diet quality was associated with lower ectopic adiposity: 12% less visceral fat area, 23% less liver fat, and a 49% less likelihood of having MASLD, comparing the highest to the lowest quartile of the MIND score. Using a distance-based global test, we confirmed overall significant microbial mediation of the inverse diet-ectopic fat association. From HDMA, four bacterial genera were identified as mediating the protective association with visceral fat, with the largest mediation conferred by Lachnospiraceae UCG.001 (12.2%). Two genera (Lachnoclostridium , Weissella) were shown to mediate the MIND association with both liver fat and MASLD. In particular, Lachnoclostridium mediated 13.6% of the liver fat association and 10.8% of the MASLD association, and Lachnospiraceae UCG.001 additionally mediated 12.1% of the liver fat association.

CONCLUSIONS: Our results support the hypothesis that the gut microbiota contributes to conveying the effect of diet quality on preferred body fat distribution, e.g., involving bacteria that are known to produce short-chain fatty acids (Lachnospiraceae) or secondary bile acids (Lachnoclostridium).},
}

@article {pmid41993570,
year = {2026},
author = {He, F and Bai, S and Xie, J and Zhang, Y and Xu, K and Wang, J and Ren, Y and Ren, Z and Chen, J and Wang, Y and Xie, P},
title = {Akkermansia muciniphila improving depression-like behaviors by regulating glycerophospholipid metabolism in gut-brain axis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1790866},
pmid = {41993570},
issn = {1663-9812},
abstract = {BACKGROUND: Akkermansia muciniphila (AKK) is a potential probiotic. Our previous studies have shown that it could alleviate depressive-like behaviors (DLBs) in mice by inhibiting neuroinflammation in brain. To further explore its antidepressant effect, this study focused on the effects of AKK on the metabolic activities in gut-brain axis.

METHODS: After chronic restraint stress (CRS) depression model was successfully built, AKK was used as intervention method for 3 weeks. The gut microbiome in feces and two intestinal permeability proteins in colon (Claudin-1, Occludin) were measured, and the metabolites in feces, colon, liver, and prefrontal cortex were also measured. In addition, two inflammation-related factors in hippocampus (Free fatty acid receptors 3 (FFAR3), phosphorylated NF-κB p65 (p-p65)) were measured.

RESULTS: AKK was successfully colonized in gut of chronic restraint stress (CRS) mice. The DLBs in CRS mice receiving AKK (CRS + AKK) were significantly improved, along with the improved gut microbiome. Both Claudin-1 and Occludin in colon were significantly increased in CRS + AKK mice compared to CRS mice receiving phosphate buffer saline (PBS) (CRS + p). Metabolomics analysis indicated that AKK could significantly improve the changed lipids and lipid-like molecules in gut-brain axis of CRS mice; and function analysis using differential metabolites showed that AKK could significantly improve the disordered glycerophospholipid metabolism in feces, colon, liver, and prefrontal cortex of CRS mice. Additionally, we found that FFAR3 and phosphorylated NF-κB p65 were increased and decreased, respectively, in hippocampus of CRS + AKK mice compared to CRS + p mice.

CONCLUSION: Our results suggested that AKK might improve the disturbances of gut microbiome, intestinal permeability, host's lipid metabolism and inflammation levels in hippocampus. Glycerophospholipid metabolism in gut-brain axis might be the important mediator in the process of AKK producing antidepressants effects.},
}

@article {pmid41993582,
year = {2026},
author = {Simões, JLB and Braga, GC and Assmann, CE and Bagatini, MD},
title = {Targeting the gut-immune-brain axis: pharmacological insights from depression in inflammatory bowel disease.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1793292},
pmid = {41993582},
issn = {1663-9812},
abstract = {Inflammatory Bowel Disease (IBD), comprising Crohn's Disease and Ulcerative Colitis, is a chronic inflammatory condition of the gastrointestinal tract with a remarkably high prevalence of psychiatric comorbidities, particularly Major Depressive Disorder (MDD). The traditional monoaminergic hypothesis of depression is insufficient to explain the complex etiology of MDD, paving the way for new paradigms, such as the inflammatory hypothesis of depression. This narrative review critically explores IBD as a human clinical model to investigate the connection between chronic inflammation and depression. It is argued that gut dysbiosis, a central feature of IBD, is a fundamental trigger that, through a compromised gut barrier, drives systemic inflammation and, subsequently, neuroinflammation. We detail the molecular and cellular mechanisms that link intestinal inflammation to central nervous system (CNS) dysfunction, including microglial activation, hypothalamic-pituitary-adrenal (HPA) axis dysregulation, and kynurenine pathway activation, which diverts tryptophan metabolism from serotonin synthesis to the production of neurotoxic metabolites. Robust epidemiological evidence demonstrating a bidirectional association between IBD and depression is discussed, suggesting a shared pathophysiology rather than a simple cause-and-effect relationship. Furthermore, we review the implications and emerging therapeutics, highlighting the antidepressant effects of immunobiologicals, such as anti-TNF therapies, and the potential of emerging interventions that target the microbiome, such as probiotics, psychobiotics, fecal microbiota transplantation, and anti-inflammatory diets. Furthermore, we address the limitations of the current literature, such as the lack of a quantitative definition for dysbiosis and the scarcity of clinical trials with integrated neuropsychiatric outcomes, and propose directions for future translational research. We conclude that IBD should be considered a systemic disease with significant psychiatric repercussions, advocating for an integrated therapeutic approach that combines immunomodulatory, neuromodulatory, and microbiological interventions to treat both gut and brain pathology effectively.},
}

@article {pmid41993584,
year = {2026},
author = {Liang, X and He, J and Wu, Q and Fu, L and Liu, Y},
title = {Gut microbiome in alcohol-associated liver disease: interactions and therapeutic strategies.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1770833},
pmid = {41993584},
issn = {1663-9812},
abstract = {Alcohol-associated liver disease (ALD), a significant cause of chronic liver disease worldwide, is strongly linked to gut microbiome dysregulation. Heavy alcohol use disrupts the gut bacterial equilibrium and damages the intestinal barrier, making it more permeable to microbial toxins (e.g., endotoxins) that trigger liver inflammation. Many studies have investigated ALD, but no single microbial marker has yet been identified as diagnostic. Results from microbiome studies on this condition have been inconsistent; consequently, scientists are developing new microbiome-based indices and multi-omics approaches to improve their ability to predict diseases. The review evaluates current findings on how disturbances in the gut microbiome and deterioration of the intestinal barrier contribute to the development of ALD. The assessment includes microbiome-based treatments such as probiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy. Research indicates that probiotics and FMT treatments may enhance liver function and reduce inflammation in patients with ALD. The studies present conflicting results because researchers used different methods and worked with limited numbers of participants. Bacteriophage therapy exists as an experimental treatment method. The development of personalized microbiome treatments, along with biomarker standardization and solutions to technical and ethical challenges, will enable these strategies to enter medical practice. The review integrates existing knowledge of the gut-liver axis in ALD to demonstrate the clinical potential of microbiome-based treatments while highlighting the need for additional research to enhance treatment outcomes.},
}

@article {pmid41993800,
year = {2026},
author = {Pande, PM and Tremblay, J and St-Arnaud, M and Yergeau, E},
title = {The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag065},
pmid = {41993800},
issn = {2730-6151},
abstract = {Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we hypothesize that the effect of drought stress on the wheat rhizosphere microbiome would change between key growth stages. We grew wheat in pots and reduced soil water content for two weeks at stem elongation, booting, or heading. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few differentially abundant transcripts were shared across all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the differentially abundant transcripts, taxa, and functions between growth stages of the control plants were not significant anymore for plants that experienced drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities and that it could explain the heightened sensitivity of younger plants to stresses.},
}

@article {pmid41993915,
year = {2026},
author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ},
title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101218},
pmid = {41993915},
issn = {2666-3546},
abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.

METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n = 18), healthy controls (n = 21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n = 8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.

RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.

CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.},
}

@article {pmid41993944,
year = {2026},
author = {Shalmon, G and Shapira, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Youngster, I and Scheinowitz, M and Shomron, N},
title = {Gut microbiota composition correlates with PBMC microRNA expression following maximal exercise testing in endurance athletes.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1734737},
pmid = {41993944},
issn = {2813-4338},
abstract = {INTRODUCTION: MicroRNAs (miRNAs) are key post-transcriptional regulators that also take part in immune responses and recovery processes following exercise. While both gut microbiota composition and peripheral blood mononuclear cell (PBMC)-derived miRNAs are known to be influenced by endurance training, potential correlations between these two systems in athletes remain largely unexplored.

OBJECTIVE: This study aimed to investigate correlations between gut microbiota composition and PBMC miRNA expression following a maximal exercise stress test in endurance athletes.

METHODS: Fifty-eight participants (22 runners, 18 cyclists, and 18 controls) underwent maximal exercise testing, with blood samples collected pre- and post-maximal exercise stress test for small RNA sequencing of PBMCs. Baseline fecal samples were analyzed via 16S rRNA gene sequencing to characterize gut microbiota. Expression data of PBMC miRNAs and microbial taxonomic profiles were integrated to assess potential correlations.

RESULTS: Thirteen significant correlations (|r| = 0.41-0.51, p < 0.005) were identified between gut bacterial taxa known to produce short-chain fatty acids (SCFAs)-including Veillonella, Blautia, Coprococcus, Butyrivibrio, Propionibacterium, and Parabacteroides-and the expression of PBMC miRNAs following a maximal exercise test. The significantly expressed PBMC microRNAs included hsa-miR-545-3p, hsa-miR-126-3p, hsa-miR-1292-3p, hsa-miR-6805-5p, hsa-miR-3668, hsa-miR-196b-5p, hsa-miR-602, hsa-miR-324-5p, and hsa-miR-365a-3p, some of which are known to modulate inflammatory pathways and immune cell signaling.

CONCLUSION: This is the first study demonstrating an association between resting gut microbiota composition and PBMC miRNA expression following maximal exercise stress test in endurance athletes. These findings raise the possibility of a complex association between gut microbial composition and PBMC miRNA expression in response to exercise. While causality cannot be inferred, the observed correlations suggest a candidate microbiota-miRNA that warrants further investigation in the context of exercise-induced immune regulation and recovery in athletes.},
}

@article {pmid41993958,
year = {2026},
author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y},
title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.},
journal = {Food science & nutrition},
volume = {14},
number = {4},
pages = {e71681},
pmid = {41993958},
issn = {2048-7177},
abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.},
}

@article {pmid41993996,
year = {2026},
author = {Au Yong, SJ and Lestari Lee, AS and Subramaniyan, V and Long, CM and Husain, S and Reginald, K and Ser, HL},
title = {Gut microbiome modulation in allergic rhinitis: from current evidence to emerging therapies.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1761840},
pmid = {41993996},
issn = {2673-6101},
abstract = {Allergic rhinitis (AR) is a common inflammatory disorder of the upper airway that is primarily managed with pharmacotherapy, biologics and allergen immunotherapy. However, a substantial proportion of patients experience incomplete or insufficient symptom control, treatment-related adverse effects, or poor adherence. Increasing evidence has linked AR with alterations in microbial composition across multiple mucosal sites, including the gut, highlighting potential roles for host-microbiome interactions in the regulation of allergic inflammation, although causal relationships remain incompletely defined. This narrative mini-review synthesizes current evidence on gut microbiome-based interventions for allergic rhinitis (AR), including probiotics, prebiotics, synbiotics, postbiotics, and emerging approaches such as fecal microbiota transplantation, engineered microbes, and bacteriophage-based therapies. It examines proposed immunological mechanisms involving type 2 inflammation, regulatory immune pathways, and gut-airway axis signalling, while distinguishing clinically evaluated strategies from experimental or preclinical and assessing their translational readiness. Collectively, available evidence suggests that microbiome-targeted therapies represent a promising conceptual avenue for understanding and potentially modulating AR. However, their clinical application remains constrained by heterogeneous study designs, reliance on extrapolated data from preclinical studies, limited standardized outcome measures, insufficient long-term safety data, and evolving regulatory frameworks. Addressing these challenges through well-designed clinical trials and improved mechanistic characterization will be essential to clarify the role of microbiome-based interventions as adjunctive strategies in AR management.},
}

@article {pmid41994099,
year = {2026},
author = {Hossain, MA and Agyei, D and Reynolds, AN and Kebede, B},
title = {Legume intake on gut microbiome and glycemia in type 2 diabetes management: narrative review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785186},
pmid = {41994099},
issn = {2296-861X},
abstract = {Legumes are rich in dietary fiber, plant proteins, micronutrients, and bioactive compounds, offering a sustainable and affordable addition to the diet. However, the extent to which legume-induced modulation of the gut microbiota contributes to glycemic regulation in type 2 diabetes (T2D), relative to microbiota-independent physiological mechanisms, remains insufficiently defined. This narrative review synthesizes current evidence on legume-based interventions and their effects on gut microbiota composition and function in relation to glycemic control. Relevant studies were identified through structured searches of MEDLINE and the Cochrane Central Register of Controlled Trials via Ovid, complemented by manual screening of reference lists. Seventeen studies (three human and 14 animal trials) were considered in this review. Human studies report that consuming legumes is associated with improved glucose tolerance and blood glucose levels, although effects on microbiota composition are variable and modest. Conversely, animal studies demonstrate improvements in insulin sensitivity, glucose tolerance, and microbial diversity with higher dose legume interventions. Legume consumption has been associated with enrichment of beneficial microbial taxa, such as Bifidobacterium, Akkermansia, Ruminococcus, and Bacteroides, as well as increased concentrations of microbial metabolites such as short-chain fatty acids (SCFAs). These microbial features are implicated in metabolic pathways relevant to insulin signaling and glycemic regulation; however, current human evidence does not establish that microbiota alterations causally mediate glycemic improvements. Well-designed, adequately powered clinical studies incorporating functional microbiome analyses and formal mediation approaches are required to clarify microbiota-dependent and microbiota-independent mechanisms.},
}

@article {pmid41994117,
year = {2026},
author = {Byrareddy, S and Kumar, N and Acharya, A and Das, R and Sardarni, U and Olasunkanmi, O and Murakonda, S and Sutar, D and Venkatesan, A and Ampasala, D and Cohen, S and Samuelson, M and Sajja, B and Dettmer, U and Ramalingam, N and Chand, H},
title = {Sex- and Age-Dependent Neuroimmune Dysregulation and Early Neurodegenerative Signatures Following SARS-CoV-2 Infection in Golden Syrian Hamsters.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9130692/v1},
pmid = {41994117},
issn = {2693-5015},
abstract = {Post-acute sequelae of SARS-CoV-2 infection, or Long-COVID, affects millions globally and is characterized by persistent symptoms affecting multiple organs, yet the underlying mechanisms remain poorly defined. Here, we used Golden Syrian Hamsters (GSH) infected with the SARS-CoV-2 to investigate how sex and age shape viral persistence, organ-specific pathology, immune responses, and neurological outcomes during acute infection and Long-COVID. We show that during Long-COVID, viral RNA persists only in the lungs of male hamsters. Lung pathology revealed sustained inflammation and tissue remodeling, with young females exhibiting greater fibrosis. Transcriptomic profiling across brain, lung, and heart identified pronounced sex- and age-dependent regulation of gene expression spanning immune, neuroinflammatory, and neurotransmitter signaling pathways. These transcriptomic alterations were accompanied by sex-specific behavioral changes and persistent microstructural remodeling in cognition-associated brain regions. Additionally, SARS-CoV-2 altered α-synuclein homeostasis and microglial activation alongside gut microbiome composition in a sex- and age-dependent manner. Together, our findings demonstrate that, in GSH Long-COVID is strongly modulated by sex and age, influencing viral RNA persistence, immune and neurobiological responses, and gut microbiota composition mirroring clinical outcomes reported in human cohorts. This study establishes SARS-CoV-2-infected GSH as a model for dissecting the mechanisms of Long-COVID and informing targeted prevention strategies.},
}

@article {pmid41774319,
year = {2026},
author = {Pereira, EJ and de Souza, V and da Silva Braulio, C and de Jesus Santos, AF},
title = {Epiphytic bacteria from Tacinga inamoena (K. Schum.) N.P. Taylor & Stuppy improve plant growth in cucumber seedlings.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {4},
pages = {415-422},
pmid = {41774319},
issn = {1618-1905},
abstract = {The phyllosphere of host plants harbors microorganisms that represent a novel source of agricultural bioinputs. This unique microbiome opens a promising frontier for developing innovative agricultural alternatives. In this study, we evaluated the potential of Brevibacillus sp. UPT4 and Pantoea sp. SPM1, two epiphytic bacterial strains of Tacinga inamoena isolated from the Caatinga biome. In vitro assays exhibited plant growth-promoting traits, such as auxin production, nitrogen fixation, and tolerance to abiotic stresses. Under greenhouse conditions, cucumber plants inoculated with the strains and their consortium exhibited significant increases (p < 0.05) in shoot and root parameters, ranging from 13.58% to 194.86% when compared to the control treatment. Redundancy analysis (RDA) indicated that most of the variability observed in the biometric parameters is associated with the plant growth-promoting reported in this study. These results highlight the potential of epiphytic bacteria from semi-arid land as a promising candidate for the development of new bioinputs, offering an innovative tool for sustainable agriculture.},
}

@article {pmid41803694,
year = {2026},
author = {Sun, F and Lu, J and Qiu, J and Jiao, Y and Zhuang, J and Meng, B and Kwok, LY and Zhong, Z},
title = {Temporal dynamics and functional maturation of the infant gut microbiota during the first year of life.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41803694},
issn = {1471-2180},
support = {BR250107//the Inner Mongolia Agricultural University Young Faculty Research Capacity Enhancement Program/ ; NJYT24055//the Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {BACKGROUND: The infant gut microbiota undergoes structured, time-dependent succession during the first year of life, yet high-resolution longitudinal characterization remains limited. Here, full-length 16S rRNA gene sequencing was performed using PacBio long-read technology on 68 fecal samples from 12 exclusively breastfed infants in Hohhot, China, across six time points from birth to one year (7, 30, 60, 100, 200, and 360 days).

RESULTS: In this study, 68 fecal samples from 12 infants were analyzed. A total of 16 bacterial phyla, 192 genera and 251 species were annotated, with the dominant phyla being Firmicutes, Actinobacteriota and Proteobacteria; the dominant genera including Bifidobacterium, Streptococcus and Escherichia-Shigella; and the dominant species comprising Streptococcus_salivarius, Bifidobacterium_longum and Bifidobacterium_pseudocatenulatum. Alpha diversity generally increased by days 360, while community composition shifted from early Bifidobacterium dominance toward greater taxonomic and functional complexity. Permutational multivariate analysis of variance (PERMANOVA) revealed that host and environmental factors collectively explained 33.92% of community variation (P = 0.001). Six temporal colonization patterns were observed through MaAsLin2 analyses., including mid-term explosive and sustained increasing trajectories. Functional profiling using Tax4Fun2 revealed time-specific enrichment of metabolic pathways, including fatty acid biosynthesis, xenobiotic degradation, and autophagy regulation at day 360. The findings of this longitudinal study be interpreted considering its modest sample size (n = 68). Future studies with larger cohorts are needed to validate and generalize these observations.

CONCLUSIONS: These findings demonstrate that infant gut microbiota assembly follows a non-random, host-guided trajectory, with dietary transitions and microbial interactions driving structural and functional maturation, providing a high-resolution framework for understanding early-life microbiome development and its implications for infant health. However, due to the limited sample size, the relevant research results have certain limitations. In the future, it is necessary to expand the sample scale and conduct more convincing studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04930-y.},
}

@article {pmid41803805,
year = {2026},
author = {Park, SY and Jung, MY and Nguyen, CD},
title = {Effect of biodegradable microneedle acupuncture for symptom relief moderate or milder atopic dermatitis: a study protocol for a multicenter, randomized, sham-controlled trial.},
journal = {BMC complementary medicine and therapies},
volume = {26},
number = {1},
pages = {},
pmid = {41803805},
issn = {2662-7671},
abstract = {BACKGROUND: Atopic dermatitis (AD) has no definitive cure; therefore, alternative treatments should be developed. We have demonstrated in preliminary clinical trials that Biodegradable Microneedle Acupuncture (BMA) treatment improves symptoms and is safe for mild to moderate AD.

AIMS: The study focused on evaluating the effectiveness and safety of a new medical device called BMA for AD, while also assessing its cost-effectiveness. It also explored the gut microbiome of patients with AD before and after BMA treatment.

METHODS: This multicenter, participant-assessor-blinded, sham-controlled trial will be conducted from January 10, 2025, to January 10, 2026. In total, 184 participants with AD (n = 92 per group) will be recruited. Participants will be assigned randomly to two equal-sized groups: the BMA and sham groups. Treatment will be administered three times per weekduring the 4-week intervention phase. The primary outcome measure will be the objective SCORing Atopic Dermatitis index. Secondary outcome measures will include the Eczema Area and Severity Index, Dermatology Life Quality Index, Patient-Oriented Eczema Measure, and pruritus Visual Analog Scale scores. Other outcome measures will include gut microbiome, economic and safety evaluations.

DISCUSSION: This study protocol will provide an important and thorough assessment of the effectiveness of BMA treatment in improving the symptoms of moderate or milder AD. In addition, we will evaluate the safety and costeffectiveness of BMA. We will also determine the link between AD and the microbiome. This clinical trial has been registered with the Korean Clinical Trial Registry (registration number: KCT0009870; date of registration: 25 October 2024).},
}

@article {pmid41803883,
year = {2026},
author = {Wei, Z and Xu, T and Gu, X and He, Q and Feng, Q and Li, M},
title = {Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41803883},
issn = {1479-5876},
abstract = {BACKGROUND: The pathogenesis of type 2 diabetes is characterized by insulin resistance and a progressive decline in β-cell function. A key driver of this dysfunction is the loss of β-cell identity, which reduces functional β-cell mass and leads to inadequate insulin secretion. Periodontal pathogens have been implicated in promoting insulin resistance; however, their role in the transformation of β-cell identity remains poorly understood. This study aims to investigate the impact of periodontal pathogen Fusobacterium nucleatum (F. nucleatum) on β-cell identity maintenance and the underlying molecular mechanisms.

METHOD: Single-cell RNA sequencing (scRNA-seq) data from human pancreatic islets of nondiabetic (ND), prediabetic (Pre-T2D), and type 2 diabetes (T2D) donors were analyzed to assess changes in β-cell proportion, differentiation trajectory, and associated molecular pathways. The Single-cell Analysis of Host-Microbiome Interactions (SAHMI) method was used to detect F. nucleatum sequences in pancreatic islets. Pearson correlation analysis identified key genes associated with the action of F. nucleatum, followed by in vitro validation using a co-culture model of F. nucleatum and MIN6 cells to elucidate the underlying mechanisms.

RESULTS: scRNA-seq analysis revealed a reduced proportion of β-cells and decreased expression of key β-cell identity-maintenance genes in the T2D group. The expression levels of transdifferentiation markers and β-cell disallowed genes were elevated, alongside a trend toward α-cell transdifferentiation. The NF-κB signaling pathway was significantly activated in the T2D group, accompanied by a significant increase in the SPP1 inflammatory signal, while the WNT pathway was markedly diminished. Integrated Pearson correlation and in vitro analyses identified the cell cycle regulator CDKN1C as a central mediator through which F. nucleatum promotes β-cell identity loss. Mechanistically, F. nucleatum activated the NF-κB pathway, leading to downregulation of CDKN1C expression and thereby promoting loss of β-cell identity, which played an important role in the progression of diabetes associated with periodontitis.

CONCLUSION: This study demonstrates that β-cells in T2D primarily undergo transdifferentiation towards α-cells, and the periodontal pathogen F. nucleatum promotes β-cell identity loss via NF-κB-mediated downregulation of CDKN1C.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07981-x.},
}

@article {pmid41917955,
year = {2026},
author = {Nazir, SM and Saied, SMM and Eskander, ME and Mansour, MM and Abdelrahman, H and Elbackly, RM and Elnawam, HM},
title = {Is apical periodontitis a matter of microbial diversity or time? A scoping review.},
journal = {Head & face medicine},
volume = {22},
number = {1},
pages = {},
pmid = {41917955},
issn = {1746-160X},
abstract = {BACKGROUND: The pathophysiology of apical periodontitis is complicated involving host immunological response, virulence factors, and a diverse microbiome. Understanding how microbial diversity influences lesion size is crucial for improving therapeutic strategies.

OBJECTIVE: This scoping review aimed to have an insight through literature to determine whether primary or secondary apical periodontitis lesions of different sizes are correlated with the quantity and diversity of microorganisms or the duration of the disease.

METHODS: The Joanna Briggs Institute (JBI) methodology for conducting scoping reviews was followed. A comprehensive electronic search was conducted through PubMed, Scopus, Web of Science, and Google Scholar to identify relevant studies published up to February 2025. In addition, handsearching was performed to identify additional studies that were not retrieved in the electronic search. Eligibility criteria of the screened papers included clinical studies performed in healthy patients with symptomatic or asymptomatic apical periodontitis where microbial analysis was performed. The EndNote Web reference manager (EndNote X9; Thomson Reuters) was used to ingest articles from various sources, categorize the references, and automatically eliminate duplicates.

RESULTS: Out of 4010 papers, 132 studies met the inclusion requirements and were added to the current review. Approximately half of the papers examined bacterial diversity in endodontic infections, while just a small percentage discussed lesion size and were identified as randomized clinical trials. Brazil, USA, Germany and China were found to have the highest frequency of published articles. Fusobacteria, Streptococcus, Enterococcus faecalis and Porphyromonas species were the most detected microorganisms responsible for apical pathosis regardless of lesion size, while other microbiomes were associated with large lesions only, such as Olsenella, Lactococcus lactus and HHV-6 with 3% each and HPV with 6.1%. Other microbiomes such as Candida albicans, Filifactor alocis, HSV1, Pyramidobacter piscolens and Phocaeicola abscessus were seen only associated with small sized lesions with 4.3% each.

CONCLUSIONS: Microbial diversity and microbial load seem to be a strong determinant of apical lesion size while lesion duration could not be adequately assessed due to cross-sectional study designs. Lesion size is an important variant to be recorded to give insight into microbial diversity and provide the basis for personalized targeted antimicrobial therapies in the future. This scoping review was registered in the open science framework; DOI: 10.17605/OSF.IO/DC95Z.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13005-026-00610-4.},
}

@article {pmid41981054,
year = {2026},
author = {Mansour, NY and Ismail, MF and Sayed, NH and El-Ansary, AR and Mohanad, M},
title = {Serum metabolomics identifies gut-derived uremic toxins and bile acid dysregulation associated with chronic kidney disease severity.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41981054},
issn = {2045-2322},
abstract = {UNLABELLED: Chronic kidney disease (CKD) affects more than 700 million people worldwide, however conventional biomarkers like creatinine cannot identify early-stage disease or accurately predict progression. In this study, untargeted and targeted metabolomic approaches were combined to identify novel biomarkers relevant for CKD staging and early detection in an underrepresented Egyptian population. Untargeted ultra-high-performance liquid chromatography–mass spectrometry analyses in both ionization modes were performed on serum samples of 50 CKD patients [25 early-stage CKD (eCKD), 25 end-stage kidney disease (ESKD)] and 20 controls. Differential metabolites were determined by univariate and multivariate analyses, coupled with pathway analysis and correlations with estimated glomerular filtration rate (eGFR). Five discriminating metabolites (p-hydroxyphenyllactic acid, indoxyl sulfate, xanthurenic acid, trimethylamine-N-oxide, and glycochenodeoxycholate) were subjected to targeted LC-MS/MS validation in an independent cohort (35 eCKD, 35 ESKD, 15 controls). Gut-derived uremic toxins, bile acid and tryptophan–kynurenine metabolic dysregulation were associated with CKD severity. p-hydroxyphenyllactic acid, xanthurenic acid, glutamyl-valine and indoxyl sulfate showed strong inverse correlations with eGFR (r = -0.75 to -0.85). A five-metabolite panel (indoxyl sulfate, p-hydroxyphenyllactic acid, trimethylamine-N-oxide, glycochenodeoxycholate, xanthurenic acid), demonstrated superior discriminatory performance compared with creatinine alone for distinguishing ESKD, especially indoxyl sulfate and p-hydroxyphenyllactic acid (AUC 0.847 and 0.828, respectively vs. 0.688). This first comprehensive metabolomics study in Egyptian CKD patients identifies alterations in gut microbiome–derived metabolites and bile acid metabolism associated with CKD severity. The multi-metabolite panel demonstrates potential for non-invasive discrimination between CKD stages and supports future longitudinal metabolomic studies aimed at improving CKD risk stratification and patient management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44271-4.},
}

@article {pmid41982989,
year = {2026},
author = {Yoon, KN and Lee, HG and Yeom, SJ and Kim, SS and Park, JH and Song, BS and Yi, SW and Hur, TY and Eun, JB and Park, SH and Lee, JH and Kim, HB and Lee, JH and Kim, JK},
title = {Modulation of microbial community and metabolism through Lactiplantibacillus argentoratensis AGMB00912 supplementation in weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {562-585},
pmid = {41982989},
issn = {2055-0391},
abstract = {Dietary supplementation effects with Lactiplantibacillus argentoratensis strain AGMB00912 (LA) on gut microbiota and metabolic functions of weaned piglets were investigated. Eight 25-day-old weaned piglets were evenly divided into a control group and an LA-supplemented group, with the LA group receiving 1.0 × 10[8] CFU/mL of LA daily for 10 days. Fecal samples taken on the 10[th] day were analyzed using 16S rRNA gene sequencing to assess microbial composition and metabolic function prediction. Supplementation with LA promoted a stable microbial environment by increasing the relative abundance of short-chain fatty acid-producing bacteria, including Faecalitalea, Catenibacterium, and Butyrivibrio, while reducing harmful genera like Treponema and Campylobacter. Administration of LA significantly influenced the metabolic activity of the microbial community, particularly by upregulating carbohydrate metabolism pathways, which enhanced the capacity for short-chain fatty acid production. This shift in microbial metabolism also extended to pathways involved in the biosynthesis of amino acids, lipids, cofactors, and vitamins, indicating an improved capacity for microbial-driven nutrient assimilation and utilization. Furthermore, LA supplementation promoted the biosynthesis of antimicrobial non-ribosomal peptides within the microbiome, crucial for inhibiting the growth of pathogenic microorganisms and maintaining microbial balance. The modulation of microbial metabolism is also predicted to reduce glycan degradation and increase peptidoglycan biosynthesis, contributing to enhanced gut barrier function and a more regulated immune response. These metabolic changes within the microbial community are predicted to stabilize the gut microbiota, providing enhanced disease resistance and supporting the overall health and growth of weaned piglets.},
}

@article {pmid41983000,
year = {2026},
author = {Lee, JY and Lim, C and Seo, YJ and Kyoung, H and Lee, S and Kim, Y and Shin, M and Song, M and Ryu, Y and Kim, JM},
title = {Multi-omics integrated approach reveals host-microbiome interactions in the adaptive mechanisms of weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {603-628},
pmid = {41983000},
issn = {2055-0391},
abstract = {The weaning transition is a critical phase in piglet development, marked by physiological challenges that influence growth and health. Therefore, this study aims to investigate host-microbiome interactions during the weaning transition using a multi-omics integrated approach. Fecal samples were collected from piglets on the weaning day (W0), 7 days post-weaning (W7), and 14 days post-weaning (W14). Ileal microbiota, microbial-derived metabolites, and tissue samples (ileum, thymus, and mesenteric lymph nodes) were collected at W0 and W14. Fecal microbiota analysis revealed a more stable community at W14 than at W7, with increased presence of fiber-degrading bacteria, including Prevotella, Treponema, Muribaculaceae, and Lachnospiraceae. The ileal microbiota exhibited an adaptive pattern with increases in Lactobacillus, Clostridium_sensu stricto_1, and Enterobacteriaceae, optimized for solid feed digestion and gut stabilization. Morphological analysis of the ileum showed changes in villus architecture between W0 and W14, including increased crypt depth and villus area and decreased villus width, while villus height and goblet cell counts were numerically higher at W14. Transcriptomic profiling revealed the ileum as the primary site of molecular adaptation, with 506 differentially expressed genes (DEGs) involved in immune response pathways, including viral protein interactions with cytokine and cytokine receptor pathways and T cell receptor signaling. The thymus (158 DEGs) and mesenteric lymph nodes (30 DEGs) exhibited modulation of structural pathways linked to systemic immune development, indicating tissue-specific molecular adaptation. Integrated analysis of the host transcriptome and microbial-derived metabolites revealed upregulated glycerophospholipid and glutathione metabolic pathways in piglets 14 days post-weaning, consistent with modulation of membrane structure, barrier function, and antioxidant defense during gut adaptation. Overall, the multi-omics findings provide a comprehensive description of molecular changes associated with weaning adaptation and identify candidate targets for piglet health management during the weaning transition.},
}

@article {pmid41983002,
year = {2026},
author = {Jeong, JY and Kim, J and Kim, M and Kim, YB and Park, C and Song, J and Kim, DW and Kim, M and Park, NG},
title = {Effect of probiotics on growth performance, cytokine levels, and gut microbiome composition of broiler chickens for 7 and 35 days.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {586-602},
pmid = {41983002},
issn = {2055-0391},
abstract = {Through microbial fermentation, probiotics are essential for improving growth performance and gut health in broiler chickens. This study aimed to assess the effects of three additives on growth performance, cytokine levels, and cecal microbiota in broiler chickens. One-day-old Arbor Acres chicks (total 300) were randomized into four groups: (1) control: basal diet, (2) Bacillus subtilis (BS) + basal diet, (3) essential oil + basal diet, and (4) Bacillus velezensis + basal diet. All chickens were fed and watered ad libitum throughout the experiment. Feed intake and body weight were measured weekly. On days 7 and 35, cecal contents of one bird per replicate, based on average body weight, were collected and analyzed for microbiota using 16S rRNA gene amplicon sequencing. The BS group exhibited enhanced growth performance, including increased final body weight, average daily gain, and reduced feed conversion ratio compared to that of the other groups. On day 7, the BS group exhibited a higher abundance of Eisenbergiella (8.24%), and on day 35, there was an increased abundance of Firmicutes (99.63%) and Lachnoclostridium (1.4%). These results indicate that B. subtilis may be a promising probiotic for enhancing broiler health by modulating gut microbiota.},
}

@article {pmid41983140,
year = {2026},
author = {Liu, P and Cui, L and Peng, G and Han, X},
title = {Molecular insights into the role of vitamin D in atopic dermatitis: pathogenesis, diagnosis, and emerging therapies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1739412},
pmid = {41983140},
issn = {1664-3224},
mesh = {Humans ; *Vitamin D/metabolism/therapeutic use/analogs & derivatives ; *Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology ; *Vitamin D Deficiency/immunology/epidemiology ; Skin/immunology/metabolism/pathology ; Animals ; Receptors, Calcitriol/metabolism ; Biomarkers ; Microbiota/immunology ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by skin barrier dysfunction, immune dysregulation, and microbial imbalance. Increasing evidence suggests that vitamin D, a secosteroid hormone with pleiotropic effects, plays a key role in modulating the pathogenesis of AD. This review provides a comprehensive overview of the molecular mechanisms through which vitamin D influences skin integrity and immune function, focusing on vitamin D receptor-mediated pathways, genetic and epigenetic modifiers, and the interplay with immune cells and microbiota. We also examine the epidemiological correlations between vitamin D deficiency and AD prevalence, diagnostic considerations including biomarkers and serum 25-hydroxyvitamin D evaluation, and therapeutic strategies involving systemic and topical vitamin D interventions. The review further discusses ongoing controversies regarding optimal dosing and evaluates the limitations of current clinical evidence. Finally, emerging research directions, such as vitamin D-microbiota-skin axis and personalized vitamin D therapy, are proposed as promising avenues for advancing AD management.},
}

Humans
*Vitamin D/metabolism/therapeutic use/analogs & derivatives
*Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology
*Vitamin D Deficiency/immunology/epidemiology
Skin/immunology/metabolism/pathology
Animals
Receptors, Calcitriol/metabolism
Biomarkers
Microbiota/immunology