Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment
- 1 April 2021
- journal article
- research article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 87 (8)
- https://doi.org/10.1128/AEM.02899-20
Abstract
The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxon composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results, we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated 15 L. crispatus strains from different environments in which this species abounds, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study revealed a genetic adaptation of strains to their respective ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains, together with a synthetic vaginal microbiota, reveal how this species is able to modulate the composition of the vaginal microbial consortia at the strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. IMPORTANCE The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus strains is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genomes of new L. crispatus strains from different environments, and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.Keywords
Funding Information
- Science Foundation Ireland (SFI/12/RC/2273-P1)
- Science Foundation Ireland (SFI/12/RC/2273-P2)
This publication has 103 references indexed in Scilit:
- BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptidesNucleic Acids Research, 2013
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology, 2012
- Garvieacin Q, a Novel Class II Bacteriocin from Lactococcus garvieae BCC 43578Applied and Environmental Microbiology, 2012
- PGAP: pan-genomes analysis pipelineBioinformatics, 2011
- Randomized, Placebo-Controlled Phase 2 Trial of a Lactobacillus crispatus Probiotic Given Intravaginally for Prevention of Recurrent Urinary Tract InfectionClinical Infectious Diseases, 2011
- Vaginal microbiome of reproductive-age womenProceedings of the National Academy of Sciences of the United States of America, 2010
- Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics, 2010
- Shifting the genomic gold standard for the prokaryotic species definitionProceedings of the National Academy of Sciences of the United States of America, 2009
- Evolution of Mammals and Their Gut MicrobesScience, 2008
- Multiple sequence alignment with the Clustal series of programsNucleic Acids Research, 2003