Introduction: Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.
Areas covered: This review summarizes the recent progress from a technical side and an application-related point of view.
Expert opinion: Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.
Keywords: Bioinformatics; analytic sample preparation methods; host–pathogen interactions; human microbiome; mass spectrometry; metaproteome; proteomics.