Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis

Background:Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens remain generally unexplored. Method:The vaginal bacterial composition of women with Trichomonas vaginalis (TV, N = 22) was compared to that of women with Chlamydia trachomatis (CT, N = 22), and controls (N =21) (women negative for both TV and CT). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit, of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women. QIIME and R package “Phyloseq” were used to assess the alpha and beta diversity and absolute abundance of the 16S rRNA gene per location in the three groups. Differences in taxa at various levels were determined using the independent T-test.Results:A total of 545 operational taxonomic units (OTUs) were identified in all the three groups of which 488 were the core OTUs. Bacterial a-diversity, by both Simpson's and Shannon's indices, was significantly higher, (p = 0.056) and (p = 0.001) respectively, among women with either TV or CT than among controls (median alpha diversity TV-infected > CT-infected > Controls). At the genus level, women infected with TV had significantly (p < 0.01) higher abundance of Parvimonas and Prevotella species compared to both controls and CT-infected women, whereas women infected with CT had significantly (p < 0.05) higher abundance of Anaerococcus, Collinsella, Corynebacterium and Dialister. Conclusion: The vaginal microbiomes of TV and CT-infected women were markedly different from each other and from women without TV and CT. Future studies should determine whether the altered microbiomes are merely markers of disease, or whether they actively contribute to the pathology of the two genital infections.

背景：尽管人类阴道微生物组（human vaginal microbiome）在健康与疾病中的重要性日益得到学界认可，但感染不同性传播病原体（sexually transmitted pathogens）后，阴道微生物组组成的差异仍未得到充分探究。
方法：本研究将阴道毛滴虫（Trichomonas vaginalis, TV）感染女性（n=22）、沙眼衣原体（Chlamydia trachomatis, CT）感染女性（n=22）以及对照组女性（n=21，TV与CT检测均为阴性）的阴道细菌组成进行对比分析。通过Ion 16S宏基因组试剂盒（Ion 16S metagenomics kit），对受试者阴道拭子DNA提取物中细菌16S核糖体RNA基因（16S ribosomal RNA gene）的V2、V4、V8可变区进行高通量测序（high throughput sequencing），以此确定阴道细菌组成。采用QIIME软件与R语言包"Phyloseq"评估三组受试者的α多样性（alpha diversity）、β多样性（beta diversity）以及各部位16S rRNA基因的绝对丰度；使用独立样本t检验（independent T-test）分析不同分类学层级的类群（taxa）差异。
结果：三组受试者共鉴定得到545个操作分类单元（operational taxonomic unit, OTU），其中488个为核心OTU。与对照组相比，TV或CT感染女性的细菌α多样性（以Simpson指数与Shannon指数计算）均显著更高，分别对应p=0.056与p=0.001；三组α多样性的中位数为TV感染组>CT感染组>对照组。在属水平上，与对照组及CT感染女性相比，TV感染女性的Parvimonas属与Prevotella属物种丰度显著更高（p<0.01）；而CT感染女性的Anaerococcus属、Collinsella属、Corynebacterium属及Dialister属物种丰度显著更高（p<0.05）。
结论：TV感染与CT感染女性的阴道微生物组彼此间差异显著，且均与未感染女性的阴道微生物组存在明显区别。未来研究需明确，这种发生改变的微生物组仅为疾病标志物，还是会主动参与这两种生殖道感染的病理进程。