Department of Internal Medicine, University of Turku, Turku, Finland.
Finnish Institute for Health and Welfare, Helsinki, Finland.
Environ Microbiol. 2021 May;23(5):2374-2388. doi: 10.1111/1462-2920.15462. Epub 2021 Mar 24.
Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.
微生物群落由于与环境的持续相互作用和扩散限制，在不同尺度上表现出空间结构。虽然这种空间结构在关注自由生活环境群落的研究中经常被考虑，但在宿主相关微生物群落或微生物组的背景下，它受到的关注较少。更广泛地采用考虑这些群落中空间变化的方法将有助于解决基础微生物生态学中的开放性问题，并充分发挥微生物组辅助医学的潜力。在这里，我们首先概述了已知的影响不同宿主类型和不同尺度下微生物组组成的因素，重点关注人类肠道作为研究最活跃的微生物组之一。我们概述了该领域与空间变化和模式相关的一些当前开放性问题。然后，我们回顾了用于微生物组空间建模的现有方法。我们认为，来自相关领域的方法，如系统生物学和宏观生物生态学，可以进行调整，以获得更准确的空间结构模型。我们进一步假设，在微生物组的空间建模和分析方法的发展反过来又可以广泛有益于理论和应用生态学，并有助于开发新的工业和临床应用。
