Ecology and functions of small SCIFF proteins in the gut microbiome

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Despite the major interest for intestinal microbiomes and their impact on host health, research on microbe-microbe and microbe-host interactions at the molecular level is in its infancy. We previously studied biosynthetic gene clusters (BGCs) in cultured bacteria from the intestine of pigs, which are important animals in both biomedical research and agriculture. Whilst the overall number of BGCs in the 38 novel taxa analyzed was relatively low for prokaryotic organisms, there was an enrichment for ribosomal peptide BGCs containing SCIFF-type (six cysteines in forty-five residues) small proteins pointing at the production of novel sactipeptides, which were detected in 24 strains (63% prevalence) compared with <1% in publicly available genomes. This widespread occurrence and the antibacterial potential of known sactipeptides suggest an important role of the encoded molecules in shaping the intestinal ecosystem. In this project, we combine our expertise in anaerobic cultivation, metagenomics, and biomolecular natural products chemistry to (i) study the processing of the small SCIFF proteins, (ii) structurally characterize their matured products, and (iii) functionally study their roles within gut microbiomes. The products will be investigated via synthetic biology techniques for pathway interception, recombination and heterologous expression combined with state-of-the-art chemical analytics for isolation and characterization. Cultured strains from the pig intestine and simplified communities thereof will be used in batch and continuous culture systems to assess luminal factors that regulate production of the target small proteins. In parallel, the impact of these small proteins on native microbial communities in vivo will be tested in pigs using shotgun molecular analyses. Samples from both in vitro and in vivo experiments will be analyzed in collaboration with the Z-projects. In summary, this interdisciplinary project will provide detailed functional insights into the biology of novel small proteins of relevance for microbe-host interactions in the gut. It strengthens current expertise within the consortium thanks to a unique combination of approaches dealing with microbial communities, new model systems, synthetic biology, and chemical analytics.