Naughton Evan P, Dorman Matthew J
School of Mathematical and Statistical Sciences, College of Science and Engineering, University of Galway, Galway, H91 TK33, Ireland.
Present address: Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, D02 PN40, Ireland.
Microb Genom. 2025 Jul;11(7). doi: 10.1099/mgen.0.001439.
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 or , but there is a reliance on 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 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.
几丁质是一种具有生物经济、生物化学和商业重要性的高度丰富的生物聚合物。这种碳水化合物是几丁质分解细菌的营养来源，并且可以影响原核生物生理学的自然感受态、表面吸附及其他基本方面。几丁质的细菌酶促降解由一组经过充分研究的水解酶、转录调节因子和碳水化合物转运蛋白介导。这些基因产物中的许多已进行功能表征，但仍依赖基因组方法来研究这些代谢成分在不同细菌中的变异情况。迄今为止，对细菌基因组的计算调查往往侧重于确定不同基因组中几丁质代谢基因的有无，而不是这些基因家族中序列的多样性。为了推动未来对弧菌及其他细菌中几丁质代谢变异的研究，我们展示了ChiVariARIBA，这是一种从已发表的几丁质分解物种及其亲缘物种的基因组序列中提取几丁质代谢基因的工作流程，它与快速基因发现和变异表征工具ARIBA兼容，可用于描述目标基因组中几丁质代谢基因的存在情况，并表征这些基因在不同细菌中的序列变异。
