The 46 preliminary targets identified from literature and available clinical tests are comprised of 15 genera and 31 species. To optimize the bioinformatics pipeline for accurate detection of the maximum number of targets, the following performance metrics were evaluated based on the number of true positives (TP), true negatives (TN), false positives (FP), and false negatives (FN) detected in a manually curated amplicon database (described in S1 Doc): specificity = TN / (TN + FP); sensitivity = TP / (TP + FN); precision = TP / (TP + FP); and negative predictive value (NPV) = TN / (TN + FN). After optimization, 28/46 preliminary targets passed our stringent threshold of 90% (red vertical line) for each of the parameters, resulting in the accurate detection of all genera (light blue) except for Pseudoflavonifractor, and 14/31 species (dark blue).