Multi-omics dataset supporting “Rhein alleviates acute pancreatitis via the gut microbiota–TMAO–TLR4/NF-κB/NLRP3 axis”: integrated 16S, metagenomics, transcriptomics, metabolomics (animal and clinical), and lipidomics analyses

This study investigates the therapeutic effects and underlying mechanisms of rhein, a bioactive compound from Rheum palmatum L., in the treatment of acute pancreatitis (AP), with a focus on the gut microbiota–TMAO–TLR4/NF-κB/NLRP3 signaling axis.The datasets include multi-omics data from animal experiments integrating microbiome, transcriptome, and metabolomic analyses:16S rRNA amplicon sequencing of fecal samples from donor rats (Normal or donor mice), targeting the V4 region (primers 515F/806R) using the Illumina NovaSeq 6000 platform.Shotgun metagenomic sequencing of fecal samples from recipient (FMT) mice to characterize microbial gene-level functional profiles.Transcriptome (RNA-seq) of p266-6 cells from Control, AP, and TMAO-treated AP groups and Rhein+TMAO treated AP groups, revealing differentially expressed genes associated with inflammatory and immune pathways.Metabolomic analysis of serum samples from donor and recipient mice was conducted using liquid chromatography-mass spectrometry/mass spectrometry technology. Metabolite changes related to rhein intervention were identified, including TMAO.Lipidomic profiling of 266-6 cells using LC–MS/MS, highlighting lipid alterations linked to oxidative stress and mitochondrial dysfunction in AP.Untargeted LC–MS/MS metabolomics of human serum samples from acute pancreatitis patients and healthy controls.Together, these datasets provide a comprehensive multi-omics resource for exploring the gut–pancreas axis in AP and for understanding how rhein modulates microbiota-derived metabolites and inflammatory signaling.