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<p>The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by <i>Lactobacillus</i> spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with <i>Lactobacillus crispatus</i> and <i>Lactobacillus iners</i> being the most dominant. We found genes, including putative mucin-binding genes, distinct to <i>L. crispatus</i> subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in <i>L. crispatus</i> related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in <i>L. crispatus</i> but absent in <i>L. iners</i> and <i>Gardnerella vaginalis</i>. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.</p>

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Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月23日

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  • Sai Ravi Chandra Nori,
  • Calum J. Walsh,
  • Fionnuala M. McAuliffe,
  • Rebecca L. Moore,
  • Douwe Van Sinderen,
  • Conor Feehily,
  • Paul D. Cotter

摘要

The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.