Metaproteomic analysis of human gut microbiota: where are we heading?

Abstract

The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss

“…Metabolomics is currently considered as the most appropriate omics technology to investigate complex, polygenic, and multifactorial diseases with a strong multisystemic metabolic nature which have been successfully used to investigate functional changes after RYGB [20][21][22]. Recently, several studies have shown that metaproteomics which involves the high-throughput characterisation of the entire constituent profile of microbial proteins provides promising insights of functional aspects in microbiome research [23][24][25].…”

Metagenomics for Gut Microbes

“…Moreover, about 1000 bacterial species were found and each individual in this study is estimated to contain at least 160 species, and in addition, 18 species of bacteria were common to 124 individuals [19]. Nevertheless, complementary approaches to metagenomic studies as well as integrative analysis are required to understand the complex and intrinsic interactions with gut microbiota and hosts, like metatranscriptomics, metaproteomics for studying the functional aspects of the microbiota and metabolomics [20,21].…”

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

“…The reasons for this have been discussed in depth elsewhere (Arnold et al 2016; Heyer et al 2017; Hettich et al 2012; Lee et al 2017). However, there are two major ABPP-related hurdles that are important to highlight here.…”