Gastrointestinal microbiota and immune cells interact closely and display regional specificity; however, little is known about how these communities differ with location. Here, we simultaneously assess microbiota and single immune cells across the healthy, adult human colon, with paired characterization of immune cells in the mesenteric lymph nodes, to delineate colonic immune niches at steady state. We describe distinct helper T cell activation and migration profiles along the colon and characterize the transcriptional adaptation trajectory of regulatory T cells between lymphoid tissue and colon. Finally, we show increasing B cell accumulation, clonal expansion and mutational frequency from the cecum to the sigmoid colon and link this to the increasing number of reactive bacterial species.

胃肠道微生物群与免疫细胞相互作用密切并表现出区域特异性；然而，人们对这些社区因位置而异的情况知之甚少。在这里，我们同时评估健康成人结肠中的微生物群和单个免疫细胞，并对肠系膜淋巴结中的免疫细胞进行配对表征，以描绘稳态下的结肠免疫生态位。我们描述了沿结肠的不同辅助 T 细胞激活和迁移概况，并描述了淋巴组织和结肠之间调节性 T 细胞的转录适应轨迹。最后，我们发现从盲肠到乙状结肠的 B 细胞积累、克隆扩张和突变频率不断增加，并将其与反应性细菌种类数量的增加联系起来。