Funding This work was supported by the National Institutes of Health (R01AI087409-01A1, R15DE021194-01), the Department of Defense (W81XWH1010870), and the TGen Foundation. The funders had no role in study design, data collection

and analysis, decision to publish, or preparation of the manuscript. Electronic supplementary material Additional file 1 : Figure S1. Figure S1 containing the in silico coverage analysis using the relaxed criteria. (DOC 160 KB) Additional file 2 : Figure S2A-E. Standard curve amplification plots using mixed templates. (TIFF 396 KB) Additional file 3 : Figure S3A-E. Amplification plots of the https://www.selleckchem.com/products/ml323.html non-perfect match targets, including C. trachomatis, C. pneumoniae, C. ATM/ATR cancer gilvus, B. burgdorferi, and E. vulneris. (TIFF 6 MB) Additional file 4 : Figure S4A-E. Coefficient of variance (CoV) distribution across assay dynamic range for mixed templates. (TIFF 4 MB) Additional file 5 : Supplemental File 1. Detailed results for BactQuant using the stringent criteria. (TIFF 715 KB) Additional file 6 : Supplemental File 2. Detailed results for BactQuant using the relaxed criteria. (XLSX 3 MB) Additional file 7 : Supplemental File 3. Detailed results for published assay using the stringent criteria. (XLSX 3 MB) Additional

file 8 : Supplemental File 4. Detailed results from published assay using the relaxed criteria. (XLSX 3 MB) 17DMAG cell line Additional file 9 : Table S1. Base distribution output used in primer and probe design, with the bolded base signifying the selected base(s) and incorporation of more than one allele at a given nucleotide position Carnitine palmitoyltransferase II was accomplished using degenerate bases. The alignment position information in the base distribution file contains many gaps as a result from the

sequence alignment and differs from the E. coli region information from Table 1. (XLSX 3 MB) References 1. Tringe SG, Hugenholtz P: A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 2008,11(5):442–446.PubMedCrossRef 2. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY: Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008,14(10):908–934.PubMedCrossRef 3. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, et al.: Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 2011,108(Suppl 1):4680–4687.PubMedCrossRef 4. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, et al.