Rocha Sofia T, Shah Dhara D, Zhu Qiyun, Shrivastava Abhishek
Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
Microbiol Spectr. 2025 Jan 7;13(1):e0126424. doi: 10.1128/spectrum.01264-24. Epub 2024 Dec 9.
The human oral and nasal microbiota contains approximately 770 cultivable bacterial species. More than 2,000 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 type 9 secretion system (T9SS)-driven gliding motility, flagellar motility, and type IV pilus-driven twitching 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 β-barrel protein SprA of human oral bacteria underwent horizontal evolution. Overall, we catalog motile bacteria 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 the shaping of the human oral microbiota.IMPORTANCEThe human oral microbiota has been extensively studied, and many of the isolated bacteria have genome sequences stored on the human oral microbiome database (eHOMD). Spatial distribution and polymicrobial biofilms are observed in the oral microbiota, but little is understood on how they are influenced by motility. To bridge this gap, we developed a software tool to identify motile bacteria from eHOMD. The results enabled the cataloging of motile bacteria present in the oral microbiota but also provided insight into their evolutionary relationships. This information can guide future research to better understand how bacterial motility shapes 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9型分泌系统（T9SS）驱动的滑行运动、鞭毛运动和IV型菌毛驱动的颤动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，人类口腔细菌的T9SS外膜β桶蛋白SprA经历了水平进化。总体而言，我们对栖息于人类口腔微生物群中的运动细菌进行了编目，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。
人类口腔微生物群已得到广泛研究，许多分离出的细菌的基因组序列存储在人类口腔微生物组数据库（eHOMD）中。在口腔微生物群中观察到了空间分布和多微生物生物膜，但对于它们如何受到运动性的影响却知之甚少。为了弥补这一差距，我们开发了一种软件工具，用于从eHOMD中识别运动细菌。这些结果不仅能够对口腔微生物群中存在的运动细菌进行编目，还能深入了解它们的进化关系。这些信息可以指导未来的研究，以更好地理解细菌运动性如何塑造人类口腔微生物群。
