Bohr Lindsey L, Mortimer Tatum D, Pepperell Caitlin S
Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
Front Cell Infect Microbiol. 2020 Jun 23;10:293. doi: 10.3389/fcimb.2020.00293. eCollection 2020.
spp. are pathognomonic for bacterial vaginosis, which increases the risk of preterm birth and the transmission of sexually transmitted infections. spp. are genetically diverse, comprising what have recently been defined as distinct species with differing functional capacities. Disease associations with spp. are not straightforward: patients with BV are usually infected with multiple species, and spp. are also found in the vaginal microbiome of healthy women. Genome comparisons of spp. show evidence of lateral gene transfer (LGT), but patterns of LGT have not been characterized in detail. Here we sought to define the role of LGT in shaping the genetic structure of spp. We analyzed whole genome sequencing data for 106 strains and used these data for pan genome analysis and to characterize LGT in the core and accessory genomes, over recent and remote timescales. In our diverse sample of strains, we found that both the core and accessory genomes are clearly differentiated in accordance with newly defined species designations. We identified putative competence and pilus assembly genes across most species; we also found them to be differentiated between species. Competence machinery has diverged in parallel with the core genome, with selection against deleterious mutations as a predominant influence on their evolution. By contrast, the virulence factor vaginolysin, which encodes a toxin, appears to be readily exchanged among species. We identified five distinct prophage clusters in genomes, two of which appear to be exchanged between species. Differences among species are apparent in their patterns of LGT, including their exchange with diverse gene pools. Despite frequent LGT and co-localization in the same niche, our results show that spp. are clearly genetically differentiated and yet capable of exchanging specific genetic material. This likely reflects complex interactions within bacterial communities associated with the vaginal microbiome. Our results provide insight into how such interactions evolve and are maintained, allowing these multi-species communities to colonize and invade human tissues and adapt to antibiotics and other stressors.
某些物种是细菌性阴道病的特征性标志，这会增加早产风险和性传播感染的传播几率。这些物种在基因上具有多样性，包含了最近被定义为具有不同功能能力的不同物种。与这些物种的疾病关联并不简单直接：患有细菌性阴道病的患者通常感染多种物种，而且在健康女性的阴道微生物群中也能发现这些物种。这些物种的基因组比较显示出横向基因转移（LGT）的证据，但LGT的模式尚未得到详细表征。在这里，我们试图确定LGT在塑造这些物种的遗传结构中所起的作用。我们分析了106株该物种的全基因组测序数据，并将这些数据用于泛基因组分析，以在近期和遥远的时间尺度上表征核心基因组和辅助基因组中的LGT。在我们多样的该物种样本中，我们发现核心基因组和辅助基因组都根据新定义的物种分类明显区分开来。我们在大多数物种中鉴定出了假定的感受态和菌毛组装基因；我们还发现它们在不同物种之间存在差异。感受态机制与核心基因组平行分化，对有害突变的选择是其进化的主要影响因素。相比之下，编码毒素的毒力因子阴道溶素似乎很容易在物种间交换。我们在该物种的基因组中鉴定出五个不同的前噬菌体簇，其中两个似乎在该物种之间交换。不同物种之间的LGT模式存在明显差异，包括它们与不同基因库的交换。尽管LGT频繁发生且在同一生态位中共定位，但我们的结果表明这些物种在基因上明显分化，但仍能够交换特定的遗传物质。这可能反映了与阴道微生物群相关的细菌群落内部的复杂相互作用。我们的结果为这些相互作用如何进化和维持提供了见解，使这些多物种群落能够定殖和侵入人体组织，并适应抗生素和其他应激源。
