BACKGROUND: The vaginal microbial community plays a vital role in maintaining women’s health. Understanding the
precise bacterial composition is challenging because of the diverse and difficult-to-culture nature of many bacterial
constituents, necessitating culture-independent methodology. During a natural menstrual cycle, physiological
changes could have an impact on bacterial growth, colonization, and community structure. The objective of this
study was to assess the stability of the vaginal microbiome of healthy Canadian women throughout a menstrual
cycle by using cpn60-based microbiota analysis. Vaginal swabs from 27 naturally cycling reproductive-age women
were collected weekly through a single menstrual cycle. Polymerase chain reaction (PCR) was performed to amplify
the universal target region of the cpn60 gene and generate amplicons representative of the microbial community.
Amplicons were pyrosequenced, assembled into operational taxonomic units, and analyzed. Samples were also
assayed for total 16S rRNA gene content and Gardnerella vaginalis by quantitative PCR and screened for the
presence of Mollicutes by using family and genus-specific PCR.
RESULTS: Overall, the vaginal microbiome of most women remained relatively stable throughout the menstrual
cycle, with little variation in diversity and only modest fluctuations in species richness. Microbiomes between
women were more different than were those collected consecutively from individual women. Clustering of
microbial profiles revealed the expected groupings dominated by Lactobacillus crispatus, Lactobacillus iners,
and Lactobacillus jensenii. Interestingly, two additional clusters were dominated by either Bifidobacterium breve
or a heterogeneous mixture of nonlactobacilli. Direct G. vaginalis quantification correlated strongly with its
pyrosequencing-read abundance, and Mollicutes, including Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma
urealyticum, were detected in most samples.
CONCLUSIONS: Our cpn60-based investigation of the vaginal microbiome demonstrated that in healthy women
most vaginal microbiomes remained stable through their menstrual cycle. Of interest in these findings was the
presence of Bifidobacteriales beyond just Gardnerella species. Bifidobacteriales are frequently underrepresented
in 16S rRNA gene-based studies, and their detection by cpn60-based investigation suggests that their significance in the
vaginal community may be underappreciated.