Equal amounts of both amplicons (V1V2 and V6) for a single subject or contamination control were pooled and sequenced using GS FLX chemistry in the same lane of a PicoTiterPlate divided into 16 lanes. Each of the amplicons was pyrosequenced together, except for samples F1 and F3. 454 pyrosequencing was performed by the Norwegian Sequencing Centre (NSC) at the Department of Biology, University of Oslo, Norway. The initial sequence reads were split into two pools using the V1V2 and V6 primer sequences via the sfffile Tubastatin A program from 454 Life Sciences, thus reducing the CX-6258 cell line sequences to 152 413 urine reads (Table 2) due to the program splitting on exact match to primer. Table 2 Sampling depth and biodiversity

found by amplicon 454 pyrosequencing 4SC-202 order V1V2 and V6 regions from eight culture negative female urine samples   Sample   Combined sequence pool F1 F2 F3 F4 F5 F6 F7 F8   V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 V1V2 V6 Sampling depth                                   Total reads 78346 74067 14579 18362 12629 6565 4305 17474 9877 5005 12645 6586 8216 5692 7861 6986 8234 7397 Length cutoff1 48861 45382 8479 8039 8416 4752 2721 13066 6253 3467 10116 5074 4428 3047 3967 3495 4481

4442 Denoised 2 48860 45136 8479 7977 8416 4703 2721 13064 6253 3461 10116 5057 4427 3031 3967 3432 4481 4411 Cleaned 3 48452 44760 8476 7969 8353 4682 2720 13060 6242 3459 10109 5053 4361 2988 3711 3138 4480 4411 Unique OTUs 1354 2069 61 376 456 328 22 115 116 102 95 81 523 134 322 581 163 538 OTUs4 3% 1209 1435 52 240 411 254 20 81 101 85 73 63 504 116 300 499 130 338 OTUs4 6% 1092 1072 50 178 379 210 19 61 92 73 62 51 472 101 270 436 116 oxyclozanide 244 Phyla5 (11) 10 8 4 4 6 3 1 3 4 4 3 3 3 4 8 7 4 4 Genera5 (45) 35 28 8 8 15 10 1 8 10 5 6 4 4 4 19 17 9 8 Diversity indices Chao16 (3%) 1211 2469 64.75 456.36 412.62 410.33 24.5 128.83 104 195.5 86.04 108.76 504.11 130.6 324.6 1121.43 250.12 835.02 Chao1 LCI95 1209 2286 56.13 371.05 411.36 353.85 20.97 102.95 101.7 136.49 77.88 82.43 504 122.1 313.14 953.17 195.84 670.9 Caho1 HCI95 1216 2690 91.27 597.21 418.2 498.76 40.69 185.2 112.75 322.11 107.8 170.8 506.28 148.39 346.03 1352.03 349.14 1080.04 Shannon index7 (3%) 2.99 3.05 0.52 1.96 1.99 1.62 0.23 0.49 1.44 1.44 0.33 0.44 3.01 1.32 3.76 4.07 2.06 3.31 Normalized Shannon index (3%) 8     0.52 1.96 1.86 1.63 0.23 0.50 1.42 1.44 0.34 0.45 2.89 1.35 3.72 4.07 2.06 3.31 1Length cutoff at minimum 218 nt for V1V2 reads and 235 nt for V6 reads.