A central goal of microbiome research is to understand the factors that balance gut-associated microbial communities, thereby creating longitudinal and cross-sectional heterogeneity in their composition and density. Whereas the diet dictates taxa dominance, microbial communities are linked intimately to host physiology through digestive and absorptive functions that generate longitudinal heterogeneity in nutrient availability. Additionally, the host differentially controls the access to electron acceptors along the longitudinal axis of the intestine to drive the development of microbial communities that are dominated by facultatively anaerobic bacteria in the small intestine or obligately anaerobic bacteria in the large intestine. By secreting mucus and antimicrobials, the host further constructs microhabitats that generate cross-sectional heterogeneity in the colonic microbiota composition. Here we will review how understanding the host factors involved in generating longitudinal and cross-sectional microbiota heterogeneity helps define physiological states that are characteristic of or appropriate to a homeostatic microbiome.

微生物组研究的一个中心目标是了解平衡肠道相关微生物群落的因素，从而在它们的组成和密度上产生纵向和横向的异质性。虽然饮食决定了类群的优势，但微生物群落通过消化和吸收功能与宿主生理密切相关，这些功能在营养供应方面产生纵向异质性。此外，宿主沿肠道纵轴差异控制电子受体的进入，以驱动微生物群落的发展，这些微生物群落以小肠中的兼性厌氧菌或大肠中的专性厌氧菌为主。通过分泌粘液和抗菌剂，宿主进一步构建微生境，在结肠微生物群组成中产生横截面异质性。在这里，我们将回顾了解参与产生纵向和横截面微生物群异质性的宿主因素如何帮助定义具有稳态微生物群特征或适合于稳态微生物群的生理状态。