Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.
Arch Microbiol. 2021 Apr;203(3):1159-1166. doi: 10.1007/s00203-020-02114-4. Epub 2020 Nov 22.
The exploration of vaginal microbiota by using next-generation sequencing (NGS) of 16S ribosomal RNA (rRNA) gene is widely used. Up to now, different hypervariable regions have been selected to study vaginal microbiota by NGS and there is no standard method for analysis. The study aimed to characterize vaginal microbiota from clinical samples using NGS targeting the 16S rRNA gene and to determine the performance of individual and concatenated hypervariable region sequences to generate the taxonomic profiles of the vaginal microbiota. Fifty-one vaginal DNA samples were subjected to 16S rRNA gene NGS based on the Ion Torrent PGM platform with the use of two primer sets spanning seven hypervariable regions of the 16S rRNA gene. Our analysis revealed that the predominant bacterial genera were Lactobacillus, Gardnerella and Atopobium, which accounted for 78%, 14% and 2%, respectively, of sequences from all vaginal bacterial genera. At the species level, Lactobacillus iners, Gardnerella vaginalis and Atopobium vaginae accounted for 72%, 10% and 6%, respectively, of the bacterial cells present. Analyses using the V3 region generally indicated the highest bacterial diversity followed by the V6-V7 and V4 regions, while the V9 region gave the lowest bacterial resolution. NGS based on the 16S rRNA gene can give comprehensive estimates of the diversity of vaginal bacterial communities. Selection of sequences from appropriate hypervariable regions is necessary to provide reliable information on bacterial community diversity.
采用 16S 核糖体 RNA（rRNA）基因的下一代测序（NGS）技术广泛用于阴道微生物组的研究。到目前为止，已经选择了不同的高变区通过 NGS 来研究阴道微生物组，但是目前还没有标准的分析方法。本研究旨在通过靶向 16S rRNA 基因的 NGS 技术对临床样本中的阴道微生物组进行特征分析，并确定单条和串联高变区序列在生成阴道微生物组分类特征方面的性能。对 51 例阴道 DNA 样本进行 16S rRNA 基因 NGS 分析，该分析基于 Ion Torrent PGM 平台，使用两个跨越 16S rRNA 基因 7 个高变区的引物组。我们的分析结果表明，优势细菌属为乳杆菌属、加德纳菌属和阿托波菌属，分别占所有阴道细菌属序列的 78%、14%和 2%。在种水平上，阴道乳杆菌、阴道加德纳菌和阴道阿托波菌分别占存在细菌细胞的 72%、10%和 6%。V3 区分析通常表明细菌多样性最高，其次是 V6-V7 区和 V4 区，而 V9 区的细菌分辨率最低。基于 16S rRNA 基因的 NGS 可以全面估计阴道细菌群落的多样性。选择适当的高变区的序列是提供细菌群落多样性可靠信息的必要条件。
