Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.
Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America.
PeerJ. 2022 Jun 7;10:e13479. doi: 10.7717/peerj.13479. eCollection 2022.
Antimicrobial and antifungal species are essential members of the healthy human microbiota. Several different species of lactobacilli that naturally inhabit the human body have been explored for their probiotic capabilities including strains of the species . However, (identified by 16S rRNA gene sequencing) has been associated with urogenital symptoms. Recently a new sister taxon of was described: . is also posited to have probiotic qualities.
Here, we present a genomic investigation of all ( = 79) publicly available genome assemblies for both species. These strains include isolates from the vaginal tract, gastrointestinal tract, urinary tract, oral cavity, wounds, and lungs.
The two species cannot be distinguished from short-read sequencing of the 16S rRNA as the full-length gene sequences differ only by two nucleotides. Based upon average nucleotide identity (ANI), we identified 20 strains deposited as that are in fact representatives of . Investigation of the genic content of the strains of these two species suggests recent divergence and/or frequent gene exchange between the two species. The genomes frequently harbored intact prophage sequences, including prophages identified in strains of both species. To further explore the antimicrobial potential associated with both species, genome assemblies were examined for biosynthetic gene clusters. Gassericin T and S were identified in 46 of the genome assemblies, with all strains including one or both bacteriocins. This suggests that the properties once ascribed to may better represent the species.
抗菌和抗真菌物种是健康人体微生物群的重要成员。已经探索了几种不同的乳杆菌物种，这些物种天然存在于人体中，具有益生菌能力，包括该物种的菌株。然而，（通过 16S rRNA 基因测序鉴定）与泌尿生殖系统症状有关。最近，描述了该物种的一个新姐妹分类群：。也被认为具有益生菌特性。
在这里，我们对这两个物种的所有（= 79）公开可用的基因组组装进行了基因组研究。这些菌株包括来自阴道、胃肠道、泌尿道、口腔、伤口和肺部的分离株。
由于 16S rRNA 的全长基因序列仅相差两个核苷酸，因此无法通过短读测序区分这两个物种。根据平均核苷酸同一性（ANI），我们确定了 20 株被 deposited 为 实际上是 的代表。对这两个物种的菌株的基因含量的研究表明，这两个物种之间最近发生了分化和/或频繁的基因交换。这些基因组经常含有完整的噬菌体序列，包括在两个物种的菌株中鉴定出的噬菌体。为了进一步探索与这两个物种相关的抗菌潜力，检查了基因组组装的生物合成基因簇。在 46 个基因组组装中鉴定出了气杆菌素 T 和 S，所有 菌株都包括一种或两种细菌素。这表明曾经归因于 的特性可能更好地代表 物种。
