Profiling Vaginal Microbiome Diversity

DNA extraction, PCR amplification and sequencing of 16S rRNA gene amplicons from the vaginal tract of study participants were conducted in a prior study^{30 (link)}. Briefly, the V1-V3 region of the 16S rRNA gene was PCR amplified using the primers 27F-YM + 3^{107 (link)} and 534R^{57 (link)} and pyrosequenced using a Roche 454 FLX instrument. Species level assignments of Lactobacillus were performed using higher order Markov Chain models using the software speciateIT (speciateIT.sourceforge.net)^{33 (link)}. For each sample, community state types (CSTs) were assigned to individual samples based on diversity and relative abundances of different phylotypes as defined in the work of Gajer and Brotman et al.^{108 (link)}. The vaginal microbiota samples were categorized into CST-I (L. crispatus-dominated), CST-III (L. iners-dominated) and CST-IV (low-Lactobacillus/high strict and facultative anaerobes) (Table 2) Two other well-documented CSTs, CST-II (L. gasseri-dominated) and CST-V (L. jensenii-dominated) were not identified in this limited sample and are less commonly found even in larger surveys of women^{33 (link)}.