Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota

The gut microbiota is the largest and most complex microbial community in the human body. Host-gut microbiota interactions have significant implications on health and disease. The development of genome-sequencing technologies, especially the application of next-generation sequencing (NGS), has accelerated the study of the gut microbiota. Most gut microbiota studies rely on 16S rRNA sequencing, metagenomics, and metatranscriptomics, but metaproteomics, based on mass spectrometry (MS), provides functional information on the signaling and metabolic pathways in the gut microbiota. This review is intended to introduce different research methods to study the gut microbiota, with a specific focus on the current progress and application of metaproteomics. The gut microbiota plays a key role in human health and disease. In this review, different research methods are described and compared in the field of the gut microbiota. Among these research methods, metaproteomics reveals the taxonomy and functionality of the gut microbiota, especially the functional pathways associated with diseases. Thus, the current progress and application of metaproteomics are summarized, in order to enhance a comprehensive depiction of metaproteomics. [Display omitted] •Metaproteomics reveals the taxonomy, function, and metabolic pathway of the gut microbiota.•Metaproteomics develops rapidly owing to the progresses of sample processing, MS analysis, and bioinformatics tools.•Through metaproteomics, researchers can monitor the gut microbiota and assess the impact of diet and drug on them.•Integration of multiple meta-omic techniques facilitates understanding the human-microbiome interactions.