Abstract
The human gut microbiota (GM) is a community of microorganisms that
reside in the gastrointestinal tract. Recognized as a critical element
of human health, the functions of the GM extend beyond gastrointestinal
well-being to influence overall systemic health and susceptibility to
disease. Among the other omic sciences, metaproteomics highlights
additional facets that make it a highly valuable discipline in the study
of GM. Indeed, it allows the protein inventory of complex microbial
communities; peptides identified and quantified by liquid chromatography
coupled to mass spectrometry analyses and then are mapped to the most
likely proteins, taxa and functions by querying specific databases. The
aim of this review was to compile comprehensive information on
metaproteomic studies of the human GM, with a focus on the bacterial
component, to assist newcomers in understanding the methods and types of
research conducted in this field. The review outlines key steps in a
metaproteomic-based study, such as protein extraction, database
selection, and bioinformatic workflow. The importance of standardization
is emphasized. In addition, a list of previously published studies is
provided as hints for researchers interested in investigating the role
of GM in health and disease states.