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An optimized 16S rRNA sequencing protocol for vaginal microbiome to avoid biased abundance estimation

By Qiongqiong Zhang, Lei Zhang, Ying Wang, Meng Zhao, Rui Chen, Zhi Tao, Tao Lyu, Zhenyu Huang, Qinping Liao

Posted 27 Nov 2019
bioRxiv DOI: 10.1101/857052

We applied three 16S rRNA sequencing protocols on vaginal microbiome samples, to evaluate whether they produce unbiased estimation of vaginal microbiome composition.We modified the 27F primer (hereafter denoted as 27F’). Using vaginal samples from 28 healthy women and 10 women with bacterial vaginosis, we sequenced three 16S rRNA sequencing protocols, i.e., 27F-338R, 27F’-338R and 341F-806R protocols, naming after their PCR primer sets, to test whether the sequencing results are consistent with the clinical diagnostics, morphologyand qPCR results.First,the 27F primer would not align with Gardnerlla vaginalis very well, leading to poor amplification of such species. Bymodifying the primer sequences, the modified 27F primer (27F') was able to amplify Gardnerlla vaginalis very well.Second, the DNA sequence of characteristic species Lactobacillus crispatus is identical with Lactobacillus garrinarum , leading to biased estimation of abundance of Lactobacillus crispatus when using V3-V4 as PCR target region; in contrast, such bias did not occur when using V1-V2 as a target region. Third, optimized 27F'-338R avoided above-mentioned biases and restored the well-established community state types (CSTs) clustering.

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