Deep Metaproteomics Approach for the Study of Human Microbiomes

Host–microbiome
interactions have been shown to play important
roles in human health and diseases. Most of the current studies of
the microbiome have been performed by genomic approaches through next-generation
sequencing. Technologies, such as metaproteomics, for functional analysis
of the microbiome are needed to better understand the intricate host–microbiome
interactions. However, significant efforts to improve the depth and
resolution of gut metaproteomics are still required. In this study,
we combined an efficient sample preparation technique, high resolution
mass spectrometry, and metaproteomic bioinformatics tools to perform
ultradeep metaproteomic analysis of human gut microbiome from stool.
We reported the deepest analysis of the microbiome to date with an
average of 20 558 protein groups identified per sample analysis.
Moreover, strain resolution taxonomic and pathway analysis using deep
metaproteomics revealed strain level variations, in particular for Faecalibacterium prausnitzii, in the microbiome from the
different individuals. We also reported that the human proteins identified
in stool samples are functionally enriched in extracellular region
pathways and in particular those proteins involved in defense response
against microbial organisms. Deep metaproteomics is a promising approach
to perform in-depth microbiome analysis and simultaneously reveals
both human and microbial changes that are not readily apparent using
the standard genomic approaches.