ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and...

Chitin is a highly abundant biopolymer of bioeconomic, biochemical and commercial importance. This carbohydrate is a source of nutrients for chitinolytic bacteria and can influence natural competence, surface adsorption and other fundamental aspects of prokaryote physiology. Bacterial enzymatic degradation of chitin is mediated by a well-studied set of hydrolytic enzymes, transcriptional regulators and carbohydrate transport proteins. Many of these gene products have been functionally characterized in vitro or in vivo, but there is a reliance on in silico genomic approaches to study the variation of these metabolic components amongst diverse bacteria. Computational surveys of bacterial genomes to date have tended to focus on determining the presence and absence of chitin metabolism genes in diverse genomes, but not on the diversity of sequences amongst these gene families. To enable future research into chitin metabolism variation in vibrios and other bacteria, we present ChiVariARIBA, a workflow for extracting chitin metabolism genes from published genome sequences of chitinolytic Vibrio species and their relatives, compatible with the rapid gene-finding and variant-characterizing tool ARIBA, with which to describe the presence of chitin-metabolising genes in genomes of interest and to characterize the sequence variation of these genes across diverse bacteria.