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.