Comparative metagenomic analysis of the vaginal microbiome in healthy women

Abstract

The composition of these vaginal microbiome has a significant impact on women's health. However, few studies have characterized the vaginal microbiome of healthy Chinese women using metagenomic sequencing. Here, we carried out a comparative metagenomic analysis to survey taxonomic, functional levels, and microbial communities' genome content in healthy women's vaginal microbiome. Overall, we observed a total of 111 species, including all dominant vaginal Lactobacillus species, such as L. iners, L. crispatus, L. gasseri, and L. jensenii . Unlike microbial taxa, several pathways were ubiquitous and prevalent across individuals, including adenosine ribonucleotides de novo biosynthesis and pyruvate fermentation to acetate and lactate II. Notably, our diversity analysis confirmed a significant difference in healthy women from different ethnic groups. Moreover, we binned vaginal assemblies into 62 high-quality genomes, including 9 L. iners , 7 A. vaginae, 5 L. jensenii, and 5 L. crispatus . We identified the pan and core genomes of L. iners and A. vaginae and revealed the genetic diversity. Primary differences between strains were the hypothetical genes and mobile element-like genes. Our results provide a framework for understanding the implications of the female reproductive tract's composition and functional potential and highlight the importance of genome-resolved metagenomic analysis to further understand the human vaginal microbiome.

Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis

“…Nevertheless, shotgun metagenomics and circularizing probes-based RNA (ciRNA) sequencing targeted approaches with species-level resolution can provide in-depth insights into cervicovaginal microbiome. A growing number studies have employed shotgun sequencing of the vaginal metagenome 41 , 81 – 84 , metatranscriptome 85 , 86 and ciRNA 87 , 88 . Liu et al 84 have observed a total of 111 species in vaginal microbiome of healthy Chinese women, including all dominant vaginal Lactobacillus species, such as L. iners , L. crispatus , L. gasseri , and L. jensenii .…”

“…A growing number studies have employed shotgun sequencing of the vaginal metagenome 41 , 81 – 84 , metatranscriptome 85 , 86 and ciRNA 87 , 88 . Liu et al 84 have observed a total of 111 species in vaginal microbiome of healthy Chinese women, including all dominant vaginal Lactobacillus species, such as L. iners , L. crispatus , L. gasseri , and L. jensenii . It has been reported that L. crispatus , L. iners and G. vaginalis were the top three species in both HPV16-positive and control groups 83 .…”

Longitudinal cervicovaginal microbiome and virome alterations during ART and discordant shedding in women living with HIV

“…The vaginal microbiomes of reproductive-aged women typically consist mainly of Lactobacillus or diverse anaerobes including Gardnerella, Prevotella, Sneathia, Fannyhessea, Megasphaera, Dialister, Mobiluncus, Peptonophilus, Shuttleworthia, Parvimonas and other genera [11][12][13][14][15] . Lactobacilli contribute to vaginal health by producing lactic acid, which lowers vaginal pH and creates a less favorable environment for pathogenic bacteria, and by competing with pathogens for space 11 .…”

Orally administrated Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 can restore the vaginal health of patients recovering from bacterial vaginosis

“…However, 16S rRNA amplicon sequencing has low species resolution and functional information of microorganisms cannot be directly obtained from sequence data. Since metagenomic shotgun sequencing is able to identify microbial categories with high resolution and characterize their biological functions (16,17), it has been wildly used in explaining the structure and function of the vaginal microbiome (18,19). It's no doubt that metagenomic shotgun sequencing is a better tool to study the mechanisms of vaginal microbiome involvement in pathogenesis of BV.…”