Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.

Tofogliflozin alters amino acid metabolism in gut microbiota linked to hepatic transcriptomic signatures in MASLD.

Multi-omics and functional validation reveal that Methanobrevibacter-derived L-3-aminoisobutyrate alleviates subclinical mastitis in dairy goats via the HSPA1B-p65 signaling pathway.

BACKGROUND Subclinical mastitis (SCM) is prevalent in dairy livestock and compromises milk quality and lactation performance. Although often attributed to bacterial infection, many cases lack identifiable pathogens, suggesting alternative mechanisms. While evidence supports a gut-mammary gland axis, the microbial drivers and microbiota-derived metabolites linking gut dysbiosis to SCM remain unclear. Here, we aimed to identify SCM-associated gut microbial markers, prioritize candidate therapeutic metabolites and define the underlying mechanism. RESULTS Based on differences in somatic cell count (SCC) and inflammatory phenotypes across a cohort of 167 mid-lactation Saanen dairy goats, we selected 6 healthy and 6 SCM goats for downstream analyses. By integrating metagenomics, metabolomics, cross-species fecal microbiota transplantation (FMT) and functional validation in vitro and in vivo, we found that SCM was accompanied by reduced milk yield and heightened inflammatory signatures. Compared with the Healthy group, SCM goats exhibited marked remodelling of the gut microbiota, with enrichment of opportunistic taxa (Eubacterium and Blautia) and a pronounced depletion of archaeal Methanobrevibacter spp. Notably, FMT from SCM donors recapitulated mammary inflammatory phenotypes in mice, supporting a causal contribution of gut dysbiosis to mammary inflammation. Joint metagenomic functional profiling and metabolomics further identified the branched-chain amino-acid-derived metabolite L-3-aminoisobutyrate (BAIBA) as significantly enriched in the gut of healthy goats. Moreover, Methanobrevibacter spp. harboured key enzyme genes (vorA, vorB and vorD) implicated in BAIBA biosynthesis. In an LPS-challenged MAC-T model, BAIBA attenuated mammary epithelial inflammation by activating endoplasmic reticulum protein quality control programmes and restoring HSPA1B expression, thereby suppressing NF-κB activation and reducing pro-inflammatory cytokine production. Finally, in naturally infected goats, intramammary administration of BAIBA lowered SCC, highlighting translational potential. CONCLUSIONS This study identifies BAIBA as a microbiota-derived metabolite that protects against SCM by restraining mammary inflammation via the HSPA1B-NF-κB axis, establishing a mechanistic gut-mammary link and highlighting a potential non-antibiotic intervention strategy. Video Abstract.

Pectic oligosaccharides reshape the gut microbiota-mediated intestinal vitamin B7 metabolic network to alleviate metabolic dysfunction-associated steatotic liver disease.

Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a prevalent and severe global health burden closely associated with gut dysbiosis and systemic metabolic disorders. Pectic oligosaccharides (POS) are functional prebiotics with metabolic regulatory potential, yet their exact efficacy and microecological mechanisms against MASLD via the gut-liver axis are still unclear. In this study, multi-omics profiling of HFD-induced MASLD mice revealed that POS alleviates hepatic steatosis and improves lipid metabolism by enriching a core microbiota dominated by Phocaeicola dorei and reactivating its de novo vitamin B7 biosynthesis. Importantly, leveraging serum metabolomics from an external human MASLD cohort, we confirmed a severe systemic deficiency of VB7 and its precursors that strongly correlated with fasting glucose, insulin resistance, and hepatic injury. In summary, this study identified POS as an effective intervention to alleviate MASLD by restoring intestinal endogenous VB7 supply, providing a strong rationale for developing POS as a therapeutic prebiotic.

Multi-omics reveals that rumen fluid transfer affects the immune function of Xizang sheep by regulating enterohepatic metabolic homeostasis.

The gut microbiota plays a crucial role in immune regulation and metabolic homeostasis in ruminants; however, the systemic effects of rumen fluid transfer (RFT) on the gut-liver axis remain unclear. In this study, Xizang sheep were used as the animal model to investigate the effects of RFT using multi-omics approaches, including transcriptomics, metabolomics, and 16S rRNA sequencing. The results showed that RFT was associated with changes in immune- and metabolism-related genes (e.g., TLR4, NOD2, PPARA, and ABCG2) and alterations in several key metabolites, including tryptophan-related compounds, amino acids, and bile acid-associated metabolites. RFT was also associated with shifts in gut microbial composition, as reflected by changes in the relative abundance of genera such as Prevotella, Ruminococcus, and Lactobacillus. Integrated multi-omics analysis indicated coordinated associations among gut microbiota, metabolites, and host gene expression along the gut-liver axis. These findings indicate that RFT may be linked to immune and metabolic regulation in Xizang sheep, providing a systems-level framework for understanding microbiota-host interactions.

Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.

Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.

Conjugated Linoleic Acid‐Enriched Fermented Dairy Modulates Microbiota and Metabolites to Alleviate MASLD: Insights From Multi‐Omics and Causal Mediation Analysis

Metabolic dysfunction‐associated steatotic liver disease (MASLD) is a prevalent metabolic disorder linked to gut–liver axis dysregulation. Dietary interventions targeting gut microbiota and host metabolism are promising, yet the effects of specific bioactive components remain unclear. Conjugated linoleic acid (CLA), a functional fatty acid in dairy, may regulate lipid metabolism and inflammation, but its clinical efficacy and mechanisms in MASLD are not well defined. This study evaluated CLA‐enriched fermented dairy using a multi‐omics and causal modeling framework. In a 120‐day randomized controlled trial, 60 MASLD patients consumed CLA‐enriched fermented dairy or standard yogurt. Fecal samples underwent 16S rRNA sequencing, and serum samples were analyzed by untargeted liquid chromatography–mass spectrometry (LC–MS) metabolomics. Liver function and metabolic markers were assessed before and after the intervention. Causal mediation analyses explored mechanistic links among the intervention, microbiota, metabolites, and clinical outcomes. The intervention group showed significant reductions in serum alanine aminotransferase (ALT), total cholesterol (TC), creatinine, and high‐sensitivity C‐reactive protein (hs‐CRP). Gut microbiota shifts included increased Bacteroides , Blautia , and Fusicatenibacter and decreased Enterococcus and Sutterella . Metabolomics revealed upregulated energy pathways and negative associations between liver enzymes, phosphatidylcholines, and acylcarnitines. Causal mediation identified key microbial (e.g., Lachnospiraceae UCG‐008) and metabolic (e.g., 5‐Benzylacyclouridine and vaccenic acid) mediators linking the intervention to clinical improvements. CLA‐enriched fermented dairy beneficially modulates gut microbiota and host metabolism, improving liver and systemic metabolic health in MASLD patients. The study highlights CLA's therapeutic potential and demonstrates the value of multi‐omics and causal inference to elucidate diet–host interactions.