Rocha Sofia T, Shah Dhara D, Zhu Qiyun, Shrivastava Abhishek
bioRxiv. 2023 Jul 17:2023.07.17.549387. doi: 10.1101/2023.07.17.549387.
The human oral and nasal microbiota contains approximately 770 cultivable bacterial species. More than 2000 genome sequences of these bacteria can be found in the expanded Human Oral Microbiome Database (eHOMD). We developed HOMDscrape, a freely available Python software tool to programmatically retrieve and process amino acid sequences and sequence identifiers from BLAST results acquired from the eHOMD website. Using the data obtained through HOMDscrape, the phylogeny of proteins involved in bacterial flagellar motility, Type 4 pilus driven twitching motility, and Type 9 Secretion system (T9SS) driven gliding motility was constructed. A comprehensive phylogenetic analysis was conducted for all components of the rotary T9SS, a machinery responsible for secreting various enzymes, virulence factors, and enabling bacterial gliding motility. Results revealed that the T9SS outer membrane ß-barrel protein SprA of human oral microbes underwent horizontal evolution. Overall, we catalog motile microbes that inhabit the human oral microbiota and document their evolutionary connections. These results will serve as a guide for further studies exploring the impact of motility on shaping of the human oral microbiota.
人类口腔和鼻腔微生物群包含约770种可培养细菌物种。在扩展的人类口腔微生物组数据库（eHOMD）中可以找到这些细菌的2000多个基因组序列。我们开发了HOMDscrape，这是一个免费的Python软件工具，用于以编程方式从eHOMD网站获取的BLAST结果中检索和处理氨基酸序列及序列标识符。利用通过HOMDscrape获得的数据，构建了参与细菌鞭毛运动、IV型菌毛驱动的颤动运动和IX型分泌系统（T9SS）驱动的滑行运动的蛋白质系统发育树。对旋转T9SS的所有组件进行了全面的系统发育分析，该系统负责分泌各种酶、毒力因子并实现细菌的滑行运动。结果显示，人类口腔微生物的T9SS外膜β桶蛋白SprA经历了水平进化。总体而言，我们对居住在人类口腔微生物群中的运动性微生物进行了编目，并记录了它们的进化联系。这些结果将为进一步研究运动性对人类口腔微生物群形成的影响提供指导。
