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

Abstract

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.

Keywords: ARIBA; bacterial genomics; chitin; chitin metabolism; gene database; natural competence.

Fig. 3.. Distribution of putative chitin metabolism genes across the genus-level phylogeny presented in Fig. 1. This figure displays the presence and absence of all annotated gene families in the Panaroo pangenome linked to chitin metabolism (see the ‘Methods’ section), minus those families which contained genes known to be involved in chitin metabolism and the distribution of which was visualized in Fig. 2, in the 241 isolates used in this study. Gene families are ordered by frequency from left to right; the most frequently observed families are presented to the left of the figure. Gene family names are reported on the X-axis. The code to reproduce this figure is available in File S7.

Fig. 1.. A maximum-likelihood phylogenetic tree of 241 publicly available Vibrio spp. genomes, computed as described in the ‘Methods’ section. The tree is rooted on ‘Candidatus Enterovibrio escicola’ (GCA_002464935.1 [100]). Species names as recorded in GenBank for each sample are reported (the top 15 most frequent species names are reported; all other species have been collapsed into ‘other’). FastBAPS level 1 clusters are indicated, calculated from parsimony-informative SNVs as described in the ‘Methods’ section. A horizontal black bar has been added to the bottom of this image to aid interpretation and alignment of FastBAPS cluster labels with the base of the phylogeny. This tree has been reproduced with a scale bar in, and the original tree file is available in File S4.

Fig. 2.. The distribution of chitin metabolism gene families across the phylogeny presented in Fig. 1. Gene family presence in a given isolate is indicated in blue; the absence of a gene family is indicated by white. Gene families are ordered by frequency from left to right; the most frequently observed families are presented to the left of the figure. Gene families are reported on the X-axis. These names can be matched to locus ID numbers using Tables 1 and S2. The code to reproduce this figure is available in File S7.