Recent progress in analyzing the spatial structure of the human microbiome: distinguishing biogeography and architecture in the oral and gut communities

Abstract

Fueled by technological advances in methods for sample collection and preservation in sequencing studies, and in advances in computational analyses of high content image data, the spatial structure of the human microbiome is coming to light. In this mini-review, we summarize recent developments in our understanding of the structure of two human microbiomes: the lower gut and the oral cavity. We focus on only the most recent literature and we make an important distinction between two forms of spatial structure, governed by scale: biogeography and architecture. By segmenting the study of microbiome spatial structure into two categories, we demonstrate the potential to greatly advance our understanding of the mechanistic principles that link structure and function in the microbiome.

Figure 1:. Architectural features of the microbiome are governed both by ecological and cell biological principles.

A. FISH-labeled image of murine gut community in an animal fed a low MAC diet. DAPI labels all bacteria, Bac303 labels Bacteroidales and Muc1437 labels Akkermansia. Compared to control animals, low MAC condition microbiota are located closer to the host epithelium (cyan mark) due to reduced mucus thickness. Monophyletic clusters of microbes are present (inset), suggesting functional interaction mediated by close spatial proximity in the face of lumenal mixing forces. Reprinted with permission from Earle, et al., 2015. Cell Host Microbe[27]. B. FISH-labeled image of a human tongue dorsum community on a shed epithelial cell. Probes for 10 abundant and prevalent taxa in the human tongue dorsum community show patchy distributions, nucleated around a shed host epithelial cell. The architectural arrangements of the different taxa are hypothesized to result from population founder effects and subsequent growth dynamics as well as inter-taxon physical and chemical interactions. Reprinted with permission from Wilbert, et al., 2020. Cell Host Microbe[58].