Although the etiology of obesity is not well-understood, genetic, environmental, and microbiome elements are recognized as contributors to this rising pandemic. It is well documented that Roux-en-Y gastric bypass (RYGB) surgery drastically alters the fecal microbiome, but data are sparse on temporal and spatial microbiome and metabolome changes, especially in human populations. We characterized the structure and function (through metabolites) of the microbial communities in the gut lumen and structure of microbial communities on mucosal surfaces in nine morbidly obese individuals before, 6 months, and 12 months after RYGB surgery. Moreover, using a comprehensive multi-omic approach, we compared this longitudinal cohort to a previously studied cross-sectional cohort (n = 24). In addition to the expected weight reduction and improvement in obesity-related comorbidities after RYGB surgery, we observed that the impact of surgery was much greater on fecal communities in comparison to mucosal ones. The changes in the fecal microbiome were linked to increased concentrations of branched-chain fatty acids and an overall decrease in secondary bile acid concentrations. The microbiome and metabolome data sets for this longitudinal cohort strengthen our understanding of the persistent impact of RYGB on the gut microbiome and its metabolism. Our findings highlight the importance of changes in mucosal and fecal microbiomes after RYGB surgery. The spatial modifications in the microbiome after RYGB surgery corresponded to persistent changes in fecal fermentation and bile acid metabolism, both of which are associated with improved metabolic outcomes.

尽管肥胖的病因尚不清楚，但遗传、环境和微生物组元素被认为是导致这种流行病流行的因素。有充分证据表明，Roux-en-Y 胃旁路术 (RYGB) 手术极大地改变了粪便微生物组，但关于时间和空间微生物组和代谢组变化的数据很少，尤其是在人群中。我们对 RYGB 手术前、6 个月和 12 个月后 9 名病态肥胖个体的肠腔内微生物群落的结构和功能（通过代谢物）和黏膜表面微生物群落的结构进行了表征。此外，使用全面的多组学方法，我们将这个纵向队列与之前研究的横断面队列（n = 24)。除了 RYGB 手术后预期的体重减轻和肥胖相关合并症的改善外，我们观察到与粘膜相比，手术对粪便群落的影响要大得多。粪便微生物组的变化与支链脂肪酸浓度的增加和次级胆汁酸浓度的总体降低有关。这个纵向队列的微生物组和代谢组数据集加强了我们对 RYGB 对肠道微生物组及其代谢的持续影响的理解。我们的研究结果强调了 RYGB 手术后黏膜和粪便微生物群变化的重要性。RYGB 手术后微生物组的空间改变对应于粪便发酵和胆汁酸代谢的持续变化，