Jones David T, Schulz Frederik, Roux Simon, Brown Steven D
Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand.
Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA.
Microorganisms. 2023 Sep 7;11(9):2253. doi: 10.3390/microorganisms11092253.
The review provides an overview of the current status of the solvent-producing clostridia. The origin and development of industrial clostridial species, as well as the history of the industrial Acetone Butanol Ethanol fermentation process, is reexamined, and the recent resurgence of interest in the production of biobutanol is reviewed. Over 300 fully sequenced genomes for solvent-producing and closely related clostridial species are currently available in public databases. These include 270 genomes sourced from the David Jones culture collection. These genomes were allocated arbitrary DJ codes, and a conversion table to identify the species and strains has now been provided. The expanded genomic database facilitated new comparative genomic and phylogenetic analysis. A synopsis of the common features, molecular taxonomy, and phylogeny of solvent-producing clostridia and the application of comparative phylogenomics are evaluated. A survey and analysis of resident prophages in solvent-producing clostridia are discussed, and the discovery, occurrence, and role of novel R-type tailocins are reported. Prophage genomes with R-type tailocin-like features were detected in all 12 species investigated. The widespread occurrence of tailocins in Gram-negative species is well documented; this survey has indicated that they may also be widespread in clostridia.
本综述概述了产溶剂梭菌的现状。重新审视了工业梭菌物种的起源和发展，以及工业丙酮丁醇乙醇发酵工艺的历史，并对近期对生物丁醇生产兴趣的复苏进行了综述。目前公共数据库中已有300多个产溶剂及密切相关梭菌物种的全序列基因组。其中包括来自大卫·琼斯培养物保藏中心的270个基因组。这些基因组被赋予了任意的DJ代码，现在已经提供了一个用于识别物种和菌株的转换表。扩展的基因组数据库促进了新的比较基因组学和系统发育分析。评估了产溶剂梭菌的共同特征、分子分类学和系统发育以及比较系统发育基因组学的应用概述。讨论了对产溶剂梭菌中常驻原噬菌体的调查和分析，并报告了新型R型尾丝菌素的发现、存在情况及其作用。在所研究的所有12个物种中均检测到具有R型尾丝菌素样特征的原噬菌体基因组。尾丝菌素在革兰氏阴性菌中的广泛存在已有充分记录；本次调查表明它们在梭菌中也可能广泛存在。
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