Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

BackgroundBacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal FindingsBroad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/SignificanceThe human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in Black women. Tools developed in this project can be used to study microbial ecology in diverse settings at high resolution.

背景：细菌性阴道病（Bacterial vaginosis, BV）是一类高发病症，与多种不良健康结局相关，其病理特征为阴道菌群出现尚未完全阐明的改变。本研究旨在通过16S核糖体RNA（16S rRNA）基因深度测序结合物种级分类鉴定，系统描述细菌性阴道病患者阴道细菌群落的组成与多样性，并探究单个细菌物种的存在与BV临床诊断特征之间的关联。方法与主要结果：本研究对220名分别患有或未患有BV的女性的阴道拭子样本开展广谱16S rRNA基因聚合酶链式反应（PCR）及焦磷酸测序。BV的临床评估采用阿姆塞尔（Amsel）临床标准，并通过革兰氏染色予以确认。分类学鉴定采用系统发育定位工具，可将99%的查询序列读数精准分配至物种水平。结果显示，BV患者的阴道细菌群落呈现显著异质性，通常不存在单一优势类群。在未患BV的个体中，阴道菌群多以卷曲乳杆菌（Lactobacillus crispatus）或惰性乳杆菌（Lactobacillus iners）为优势菌。羊水弯杆菌（Leptotrichia amnionii）与埃格特菌属（Eggerthella sp.）是仅有的两种与四项Amsel标准均显著相关的BV相关细菌（BV-associated bacteria, BVABs）。共现分析揭示了多组BVAB亚群，提示这些细菌间存在代谢共依赖关系。在未患BV的黑人女性中，数种BVAB的丰度显著更高。结论与意义：人类阴道细菌群落具有显著异质性，BV患者的菌群物种丰富度与多样性均显著高于健康人群，且未发现普遍存在的单一优势细菌物种。不同细菌物种与四项临床诊断标准的关联模式存在差异，这或可解释Amsel标准与努根特（Nugent）革兰染色诊断标准之间常出现的不一致性。按BV状态分组分析后发现，数种BVAB的流行率存在种族差异，这可能是黑人女性BV发病率更高的潜在原因之一。本研究开发的分析工具可用于高分辨率下多样本环境中的微生物生态学研究。