Resolving glycogen and related enzymes reveals correlates of Lactobacillus crispatus dominance in a cohort of young African women

Abstract Background: A healthy vaginal microbiome is dominated by Lactobacillus species that produce lactic acid, lowering vaginal pH and limiting colonization by pathogens. Lactobacillus dominance (LD) is established during puberty, but many women, especially those of Black race, lose LD during their reproductive years. Glycogen is thought to be a key host nutrient that supports vaginal lactobacilli and their fermentative lactic acid production, but mechanisms of glycogen utilization by Lactobacillus species are incompletely understood. By partitioning glycogen and glycogen-derived maltodextrin, as well as the activity of glycogen-degrading amylase and pullulanase enzymes (targeting glycogen α-1,4 and α-1,6 linkages, respectively) in vivo, this work refines understanding of vaginal glycogen catabolism and identifies correlates of LD. Results: Vaginal swab samples were collected from a cohort of young women with limited sexual experience in Thika, Kenya (N=17, ages 16–21). Metagenomic profiling of the vaginal microbiome revealed that most samples exhibited LD, particularly dominant Lactobacillus crispatus. Glycogen and pullulanase activity, but not maltodextrin and amylase activity correlated with lactic acid levels. Amylase activity showed a positive correlation with glycogen-derived maltodextrin, but no relationship with L. crispatus dominance. In contrast, pullulanase activity was 3-fold higher in L. crispatus-dominated samples. Metagenomics and targeted PCR revealed that 36% of L. crispatus-dominated metagenomes from our African cohort lacked a functional L. crispatus pullulanase (pulA) gene, a 3-fold higher frequency of gene loss than that seen in metagenomes from European and North American women. Our findings suggest pulA gene loss or inactivation may correspond with reductions in pullulanase activity, lactic acid, and L. crispatus abundance compared to samples dominated by pulA-competent L. crispatus. Conclusions: Our results indicate that although amylase activity drives the accumulation of glycogen catabolites in vaginal fluid, pullulanase appears to specifically contribute to maximal D-lactic acid production by L. crispatus. However, this is only possible when a functional pulA gene is present, which was not the case in a substantial proportion of young African women with dominant L. crispatus. Scaling this analysis to a larger cohort will address whether genomic and enzymatic indicators of L. crispatus pullulanase activity are predictive of sustained LD and vaginal health.