Background: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease. Results: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 44) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential abundance analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential abundance analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes, and also supported the existence of motile vs. non-motile subgroups in the BV population. Conclusions: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets.

中文翻译：

---

阴道宏转录组荟萃分析揭示功能性 BV 亚群和新的定植策略

背景：应用“组学”技术研究细菌性阴道病 (BV)，发现健康人和 BV 患者的阴道微生物群在组成和规模上存在巨大差异。与专注于单一或少数物种的扩增子测序和鸟枪法宏基因组方法相比，在全系统水平上研究阴道微生物组的转录组可以深入了解活跃表达的功能以及健康与疾病状态之间的差异。结果：我们对三项研究的阴道宏转录组进行了荟萃分析，分为探索性数据集 (n = 44) 和验证数据集 (n = 297)，解释了测序数据的组成性质以及健康微生物组和细菌性阴道微生物组之间的规模差异。通过对探索性数据集进行差异丰度分析，我们确定了与健康状态和 BV 相关的微生物采用的多种策略来逃避宿主阳离子抗菌肽 (CAMP)； BV 相关物种抵抗和抵消阴道 pH 值低的假定机制；以及破坏阴道上皮完整性的潜在方法，以便建立粘附和生物膜形成的位点。此外，我们还确定了 BV 群体中几个不同的功能亚群，这些亚群以参与运动、趋化性、生物膜形成和辅因子生物合成的基因来区分。在使用 KEGG 直系同源术语而不是群落状态类型在验证数据集中定义健康和 BV 的分子状态后，差异丰度分析证实了早期关于健康和 BV 微生物组中 CAMP 抵抗和损害上皮屏障完整性的观察结果，并且还支持了运动与 BV 微生物组的存在BV 人群中的非运动亚群。结论：我们的研究结果强调，在考虑微生物组在疾病中的作用时，需要关注功能差异而不是分类差异，并确定进一步研究的途径作为潜在的 BV 治疗目标。