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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.

microbiome

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