Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation

Abstract

Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human feces (n = 11), and chicken feces (n = 9), and used comparative genomics to explore the genetic information of L. crispatus from the feces and vagina. No significant difference was found in the three sources of genomic features such as genome size, GC content, and number of protein coding sequences (CDS). However, in a phylogenetic tree constructed based on core genes, vagina-derived L. crispatus and feces-derived strains were each clustered separately. Therefore, the niche exerted an important impact on the evolution of L. crispatus. According to gene annotation, the L. crispatus derived from the vagina possessed a high abundance of genes related to acid tolerance, redox reactions, pullulanase, and carbohydrate-binding modules (CBMs). These genes helped L. crispatus to better adapt to the acidic environment of the vagina and obtain more nutrients, maintaining its dominance in the vagina in competition with other strains. In feces-derived bacteria, more genes encoding CRISPR/Cas system, glycoside hydrolases (GHs) family, and tetracycline/lincomycin resistance genes were found to adapt to the complex intestinal environment. This study highlights the evolutionary relationship of L. crispatus strains isolated from the vagina and feces, and the adaptation of L. crispatus to the host environment.

Variability of the response of human vaginal Lactobacillus crispatus to 17β-estradiol

“…Generally, the vaginal microbiota is composed of a single and almost clonal population of Lactobacillus and L. crispatus CIP104459 may be an exception. In addition, this strain was isolated in 1955 and is, thus, old, whereas bacteria, including L. crispatus , can rapidly evolve in response to host 23 and environmental 24 factors, especially by rearrangements within their genomic structure.…”

Novel insights in bacterial vaginosis etiology through genomic approaches

“…crispatus is a biomarker for vaginal health, and some strains are used as probiotics against BV (Almeida et al 2019, Cohen et al 2020. Due to its association with health promotion, its genetic diversity and mechanisms involved in the probiotic effects of L. crispatus have been investigated using genomics data and in vitro experiments (Ojala et al 2014, Abdelmaksoud et al 2016, France et al 2016, Van der veer et al 2019, Pan et al 2020, Petit & Read 2020, Zhang et al 2020).…”

“…Comparative genomics with a specific focus on vaginal isolates investigated the phylogeny, gene content, horizontal gene transfer, prophages, metabolism, and positive selection within strains (Ojala et al 2014, France et al 2016, Pan et al 2020, Petit & Read 2020, Zhang et al 2020. A comparison of strains from different hosts found that human vaginal isolates have a unique CRISPR Type II-A system, and a complete trehalose metabolism operon.…”

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil

“…Comparative genomic analyses have been performed to identify genomic features of L. crispatus associated with female urogenital tract using samples from North America, Europe and Asia ( Ojala et al, 2014 ; Abdelmaksoud et al, 2016 ; France, Mendes-Soares & Forney, 2016 ; Van der Veer et al, 2019 ; Pan, Hidalgo-Cantabrana & Barrangou, 2020 ; Petit & Read, 2020 ; Zhang et al, 2020 ). Analyses that searched for genomic features associated with lactobacilli-dominated (healthy) or BV microbiota were performed using samples isolated from the USA ( Abdelmaksoud et al, 2016 ) and Netherlands ( Van der Veer et al, 2019 ).…”