Nutrient‐specific proteomic analysis of the mucin degrading bacterium Akkermansia muciniphila

Abstract Akkermansia muciniphila is a prominent mucin‐degrading bacterium that acts as a keystone species in regulating the human gut microbiota. Despite recently increasing research into this bacterium and its relevance to human health, a high‐resolution database of its functional proteins remains scarce. Here, we provide a proteomic overview of A. muciniphila grown in different nutrient conditions ranging from defined to complex. Of 2318 protein‐coding genes in the genome, we identified 841 (40%) that were expressed at the protein level. Overall, proteins involved in energy production and carbohydrate metabolism indicate that A. muciniphila relies mainly on the Embden‐Meyerhof‐Parnas pathway, and produces short‐chain fatty acids through anaerobic fermentation in a nutrient‐specific manner. Moreover, this bacterium possesses a broad repertoire of glycosyl hydrolases, together with putative peptidases and sulfatases, to cleave O ‐glycosylated mucin. Of them, putative mucin‐degrading enzymes (Amuc_1220, Amuc_1120, Amuc_0052, Amuc_0480, and Amuc_0060) are highly abundant in the mucin‐supplemented media. Furthermore, A. muciniphila uses mucin‐derived monosaccharides as sources of energy and cell wall biogenesis. Our dataset provides nutrient‐dependent global proteomes of A. muciniphila ATCC BAA‐835 to offer insights into its metabolic functions that shape the composition of the human gut microbiota via mucin degradation.