Fig. 1.

Structure and ecology of the MLI. A, Spatiotemporal dynamics of the MLI ecosystem. B, Cross-feeding mechanism between intestinal species: an example of Akkermansia. C, Comparison between host-microbiome homeostasis and dysbiosis. Site-specific sampling can be performed using colonoscopy. D, An example of studying the MLI using mathematical modeling approach (see supplemental Information for details). E, Different biological components of the MLI can be extracted using a series of isolation/enrichment techniques for proteomics/metarpteomics analysis. F, Tracking material flow can be achieved by combining metaproteomics with metabolic labeling approaches.