FIG 6.

Effect of taxonomy assignment strategy on the perceived taxonomic profile of each sample. Assigning taxonomy to shotgun metagenomic reads with various tools yields somewhat different community profiles. (a) Taxonomy for each pool assigned with Metaphlan, Metalign, or Kraken2 to its complete microbial database, Kraken2 to the OptiVag database, or VIRGO. (b) Same samples as in panel a, compared to qPCR results for Lactobacillus iners, Lactobacillus crispatus, and Gardnerella vaginalis. For each sample, the sum of these three taxa was normalized to 1, to make them comparable to the qPCR results in the triaxial plot. (c) Manhattan distance between each sample and method and its corresponding qPCR profile. In this three-dimensional structure, the Manhattan distance is strictly limited between 0 (identical profiles) and 3 (maximum distance for each of the three species considered).