Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics
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Published Version
Date
2025
Authors
Nori, Sai Ravi Chandra
Walsh, Calum J.
McAuliffe, Fionnuala M.
Moore, Rebecca L.
Van Sinderen, Douwe
Feehily, Conor
Cotter, Paul D.
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
Published Version
Abstract
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. © The Author(s) 2025.
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Keywords
Amino acid , Carbohydrate , Glycan , Mucin , Accessory genome
Citation
Nori, S. R. C., Walsh, C. J., McAuliffe, F. M., Moore, R. L., Van Sinderen, Douwe, Feehily, C. and Cotter, Paul D. (2025) 'Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics', npj Biofilms and Microbiomes, 11(1), p.49. https://doi.org/10.1038/s41522-025-00682-1