Separation and characterization of human microbiomes by metaproteomics

The surface of the human body, including the gastrointestinal tract, is occupied by trillions of microbial cells with diverse metabolic functions, constituting the human microbiome. The composition of the microbiome varies with body region and among individuals, and the majority of the microbiomes, their genes and protein products are poorly characterized. Recent studies have highlighted the importance of mass spectrometry-based omics approaches, and in particular metaproteomics, for deep functional characterization of the human microbiome. However, major analytical and bioinformatics challenges remain due to the enormous complexity, high dynamic range and large intra- and inter-individual variations in the human microbiome. Herein, we review the analytical approaches that have been implemented for metaproteomic studies of the microbiome and discuss the challenges in sample separation and instrument measurements. As well, we review the bioinformatics tools available for metaproteomic data processing, their challenges and their applications for deep characterizations of human microbiomes.