Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota

Abstract

Background A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus ) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus- dominated vaginal microbiota (LVM) are pheno- or genotypically distinct from L. crispatus strains isolated from vaginal samples with dysbiotic vaginal microbiota (DVM). Results We studied 33 L. crispatus strains ( n = 16 from LVM; n = 17 from DVM). Comparison of these two groups of strains showed that, although strain differences existed, both groups degraded various carbohydrates, produced similar amounts of organic acids, inhibited Neisseria gonorrhoeae growth, and did not produce biofilms. Comparative genomics analyses of 28 strains ( n = 12 LVM; n = 16 DVM) revealed a novel, 3-fragmented glycosyltransferase gene that was more prevalent among strains isolated from DVM. Most L. crispatus strains showed growth on glycogen-supplemented growth media. Strains that showed less-efficient ( n = 6) or no ( n = 1) growth on glycogen all carried N-terminal deletions (respectively, 29 and 37 amino acid deletions) in a putative pullulanase type I protein. Discussion L. crispatus strains isolated from LVM were not phenotypically distinct from L. crispatus strains isolated from DVM; however, the finding that the latter were more likely to carry a 3-fragmented glycosyltransferase gene may indicate a role for cell surface glycoconjugates, which may shape vaginal microbiota-host interactions. Furthermore, the observation that variation in the pullulanase type I gene is associated with growth on glycogen discourages previous claims that L. crispatus cannot directly utilize glycogen. Electronic supplementary material The online version of this article (10.1186/s40168-019-0667-9) contains supplementary material, which is available to authorized users.

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

“…Pullulanase is an enzyme that breaks down glycogen [14]. In the vagina, glycogen is the main source of carbohydrates for microorganisms [47].…”

“…The vaginal niche in a dysbiotic state was under some immune pressure. The GTs regulated the surface glycogen of L. crispatus through a phase change, helping it escape immunity [14].…”

Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts

“…The human vaginal tract, lined with multiple layers of stratified squamous epithelial cells (Anderson et al, 2014) and heavily regulated by the fluctuation of estrogen hormones (Farage and Maibach, 2006), is acidified to pH 3.5-4.5 mainly by lactic acid produced by the commensal microbiota (Boskey et al, 2001). With secretion of α-amylase from the host, the commensal bacteria in the vaginal tract are presumably able to utilize glycogen as a carbon source, the main carbohydrate stored in the superficial and intermediate layer of the epithelial cells and released when epithelial cells die and slough off (Anderson et al, 2014;Spear et al, 2014;van der Veer et al, 2019). On the other hand, the human GI tract is comprised of a single layer of columnar epithelial cells coated by a thick layer of mucus secreted by goblet cells (Turner, 2009).…”

“…O'Flaherty et al (2018 reported that lactobacilli containing bile salt hydrolase (BSH) proteins are usually associated with vertebrate-adapted lifestyle rather than environmental and plant-associated lifestyle. Possible mechanism for L. crispatus to dominate vaginal tract has been suggested as the presence of glycogen degradation genes in their genomes (van der Veer et al, 2019). Others have investigated if specific proteins exist among vaginal species allowing vaginal specialization (Mendes-Soares et al, 2014).…”

The Need to Focus on Therapy Instead of Associations

“…Indeed, selection of candidate probiotic strains seems to be their ability to adhere to vaginal cells and produce lactic acid and hydrogen peroxide (Hemmerling et al, 2009). Genomic and metabolomic studies have shown that there are significant differences between L. crispatus strains (van der Veer et al, 2019; Watson et al, unpublished), so some selection criterion is needed before expecting a strain to be effective. If the species is so protective, why is it apparently readily displaced by anaerobes?…”