98% Lactobacillus crispatus on microbiome test, but wet mounts consistently show low lactobacilli

The microbiome test showed the following bacterial composition at the phylum level:
Bacillota: 99.2107%
Bacteroidota: 0.4746%
Verrucomicrobiota: 0.3146%

At the species level, the microbiome test showed:
Lactobacillus crispatus: 98.0792%
Limosilactobacillus fermentum: 0.5604%
Lacticaseibacillus rhamnosus: 0.4132%
Akkermansia muciniphila: 0.3146%

This really confused me because for the past six months, my vaginal swabs have consistently shown only a small amount of lactobacilli
Even one week before my microbiome test, it still showed low lactobacilli. So how can the microbiome test show 98% L. crispatus? Do sequencing and microscopy measure different things?
My symptoms are also confusing. I often get itching after sex and white discharge that looks like a yeast infection. Fluconazole usually helps, but Candida has never been detected in my vaginal swabs or cultures, even when I had a lot of discharge.
I always test positive for aerobic bacteria such as Enterococcus faecalis and E.coli However, my microbiome test did not provide any information about them

Also, my microbiome test detected Akkermansia muciniphila. I’ve never had this bacterium detected in any of my previous vaginal tests. What exactly is it? Could it be contributing to my vaginal symptoms, or is it more likely to be temporary colonization?