Oliveira de Almeida Marcelle, Carvalho Rodrigo, Figueira Aburjaile Flavia, Malcher Miranda Fabio, Canário Cerqueira Janaína, Brenig Bertram, Ghosh Preetam, Ramos Rommel, Kato Rodrigo Bentes, de Castro Soares Siomar, Silva Artur, Azevedo Vasco, Canário Viana Marcus Vinicius
Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany.
PeerJ. 2021 Mar 10;9:e11079. doi: 10.7717/peerj.11079. eCollection 2021.
is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome.
The four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain ( CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions.
Genes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes and . No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use.
是与健康相关的阴道微生物群中的优势物种，被认为是一种稳态生物标志物。有趣的是，一些菌株甚至被用作益生菌。然而， 参与控制阴道微生物群和预防细菌性阴道病（BV）的遗传机制尚不完全清楚。为了进一步研究这些机制，我们对来自巴西女性阴道样本的前四个 基因组进行了测序和表征，并使用全基因组关联研究（GWAS）和比较分析来确定参与健康或BV状况的遗传机制以及作用于阴道微生物群的选择压力。
对这四个基因组进行测序，使用十种不同策略进行组装并自动注释。通过与已知益生菌菌株比较的生物信息学工具进行功能表征。此外，选择了一个代表性菌株（CRI4）通过电子显微镜进行体外噬菌体检测。使用代表健康和BV状况的46个公共基因组菌株进行进化分析，包括系统发育、GWAS和正选择。
鉴定出参与益生菌作用的基因，如乳酸产生、过氧化氢、细菌素和黏附素。预测了三种溶血素和腐胺的产生，尽管这些特征也存在于其他益生菌菌株中。这四个基因组没有质粒，但检测到14个已知的插入序列家族和几个原噬菌体。然而，没有一个移动遗传元件含有抗微生物抗性基因。这些基因组含有一个CRISPR-Cas II-A亚型系统，可能由于基因 和 的片段化而失活。没有基因组特征与健康状况相关，可能是由于其多因素特征。鉴定出五个处于正选择下的基因，但选择压力仍有待发现。总之，本研究中调查的巴西菌株具有潜在的保护特性，尽管需要进行体外和体内研究以确认其有效性和安全性，才能考虑用于人类。
