Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease

Abstract Background: Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn’s disease (CD) and ulcerative colitis (UC)) have not been investigated. Here, we explored the microbial proteolysis landscape using two public datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals using a semi-tryptic peptide centric mining approach. Results: Fecal metaproteome revealed a global alteration of gut microbial proteolysis signatures in IBD, while MLI metaproteome demonstrated remarkable disease-specific and location-specific alterations at taxonomic, functional, and cleavage site motif levels. The functional alterations in IBD mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease transcriptome, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, suggesting the inhibitory effects of these host factors on gut microbial proteolysis events. Conclusions: Our findings highlight the complex and diverse proteolytic alterations of gut microbiome in IBD, providing a unique layer of information beyond taxonomic and proteomic abundance.