DataSheet_1_Gallbladder microbial species and host bile acids biosynthesis linked to cholesterol gallstone comparing to pigment individuals.docx

Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment, or mixed stones based on their composition. Microbiota and host metabolism variances among the different types of gallstones remain largely unclear. Here, the bile and gallstone microbial species spectra of 29 subjects with gallstone disease (GSD, 24 cholesterol and 5 pigment) were revealed by type IIB restriction site-associated DNA microbiome sequencing (2bRAD-M). Among them (21 subjects: 18 cholesterol and 3 pigment), plasma samples were subjected to liquid chromatography–mass spectrometry (LC-MS) untargeted metabolomics. The microbiome yielded 896 species comprising 882 bacteria, 13 fungi, and 1 archaeon. Microbial profiling revealed significant enrichment of Cutibacterium acnes and Microbacterium sp005774735 in gallstone and Agrobacterium pusense and Enterovirga sp013044135 in the bile of cholesterol GSD subjects. The metabolome revealed 2296 metabolites, in which malvidin 3-(6’’-malonylglucoside), 2-Methylpropyl glucosinolate, and ergothioneine were markedly enriched in cholesterol GSD subjects. Metabolite set enrichment analysis (MSEA) demonstrated enriched bile acids biosynthesis in individuals with cholesterol GSD. Overall, the multi-omics analysis revealed that microbiota and host metabolism interaction perturbations differ depending on the disease type. Perturbed gallstone type-related microbiota may contribute to unbalanced bile acids metabolism in the gallbladder and host, representing a potential early diagnostic marker and therapeutic target for GSD.

胆结石是胆囊内形成的结晶沉积物，传统上根据其组成可划分为胆固醇型、色素型或混合型结石。不同类型胆结石对应的微生物群与宿主代谢差异，目前仍未得到充分阐明。本研究采用IIB型限制性酶切位点关联DNA微生物组测序（type IIB restriction site-associated DNA microbiome sequencing, 2bRAD-M）技术，解析了29例胆结石疾病（gallstone disease, GSD）患者的胆汁与胆结石微生物物种谱，其中胆固醇型结石患者24例、色素型结石患者5例。其中21例患者（胆固醇型18例、色素型3例）的血浆样本被用于液相色谱-质谱联用（liquid chromatography–mass spectrometry, LC-MS）非靶向代谢组学分析。本次微生物组分析共鉴定得到896个物种，涵盖882种细菌、13种真菌与1种古菌。微生物组特征分析显示，胆固醇型GSD患者的胆结石样本中显著富集Cutibacterium acnes与Microbacterium sp005774735，其胆汁样本中则显著富集Agrobacterium pusense与Enterovirga sp013044135。代谢组学分析共鉴定得到2296个代谢物，其中胆固醇型GSD患者样本中显著富集飞燕草素-3-(6''-丙二酰葡萄糖苷)（malvidin 3-(6''-malonylglucoside)）、2-甲基丙基硫代葡萄糖苷（2-Methylpropyl glucosinolate）与麦角硫因（ergothioneine）。代谢物集富集分析（Metabolite set enrichment analysis, MSEA）结果显示，胆固醇型GSD患者的胆汁酸生物合成通路显著富集。综上，本多组学分析揭示，微生物群与宿主代谢的互作紊乱因胆结石疾病类型不同而存在差异。与胆结石类型相关的紊乱微生物群可能导致胆囊与宿主体内胆汁酸代谢失衡，有望成为GSD潜在的早期诊断标志物与治疗靶点。