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Table 1 Sampling depth and biodiversity found by amplicon 454 pyrosequencing V1V2 and V6 region from urine

From: Alterations of microbiota in urine from women with interstitial cystitis

  Combined sequence pool from HF urine 1 Combined sequence pool from IC urine 2
V1V2 V6 V1V2 V6
Preprocessing
  Total reads 78346 74067 74211 98720
  Length cutoff 3 48861 45382 46272 62325
  Denoised4 48860 45136 46267 62173
  Cleaned5 48452 44760 46138 62032
Taxonomy analysis
  Phyla6 10 8 5 7
  Genera6 35 28 23 25
OTU and Diversity indices
  Cleaned5 48452 44760 46138 62032
  Silva 16S alignment7 46001 44146 44594 61170
  Unique OTUs 974 2045 514 1432
  OTUs8 (3%) 724 1537 344 1008
  OTUs8 (6%) 615 1265 292 786
  Chao19 (3%) 1435 3936 357 2485
  Chao1 LCI95 1261 3521 675 2172
  Caho1 HCI95 1664 4437 1137 2883
  Shannon index10 (3%) 2.62 3.02 1.67 1.95
  Inverse Simpson index11 (3%) 6.97 7.03 3.57 3.72
  1. 1Combined sequence data from eight healthy female (HF) urine samples, sequences generated in prior study (Siddiqui et al. (2011)[16]).
  2. 2Combined sequence data from eight interstitial cystitis (IC) urine samples.
  3. 3Length cutoff at minimum 218 nt for V1V2 and 235 nt for V6 reads.
  4. 4Total number of sequences after processing the dataset through Pyronoise[21].
  5. 5The number of reads per dataset after removal of sequences that could be from the same source as those in the contamination control dataset as described in Siddiqui et al. (2011)[16].
  6. 6Number of phyla and genera based on taxonomic classification by MEGAN V3.4[23, 24].
  7. 7The number of total reads after Silva 16S alignment as recommended by MOTHUR[29].
  8. 8OTUs: Operational Taxonomic Units at 3% or 6% nucleotide difference.
  9. 9Chao1 is an estimator of the minimum richness and is based on the number of rare OTUs (singletons and doublets) within a sample.
  10. 10The Shannon index combines estimates of richness (total number of OTUs) and evenness (relative abundance).
  11. 11Inverse Simpson index (1/D) is an indication of the richness a community with uniform evenness would have at the same level of diversity. It takes into account the number of OTUs present, as well as the abundance of each OTU.