Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface

Abstract

Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.

Keywords: Microbiome; bacteria; ecology; exosomes; gastrointestinal disease; host-microbiome interaction; mathematical modeling; metaproteomics; proteomics; viruses.

Graphical abstract

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.

Fig. 2

Number of publications in the recent decade corresponding to different keywords (PubMed).