TABLE 2

Sequence diversity, coverage, and taxonomic complexity by groups of patients

MeasurementH. pylori statusaProton pump inhibitor status
Positive (n = 9)Negative (n = 15)Treated (n = 12)Untreated (n = 12)Combined (n = 24)
No. of sequences
    Total95,94995,709103,91287,746191,658
    Assigned95,75893,854103,51986,093189,612
    Unassigned1911,8553931,6532,046
    Helicobacter sequences45,73999415,83430,89946,733
No. of OTUsb304479419378519
Chao1 estimator of species richness313.9479.6423.0387.5519.0
Shannon's index for diversity3.55.74.94.64.9
Simpson's index for diversity0.70.90.90.80.9
Evennessc0.40.60.60.50.5
Good's estimator of coverage (%)99.999.999.999.9100
Classification success (% [no. of identified taxa])
    Phylum70.6 (12)100 (17)94.1 (16)88.2 (15)100 (17)
    Family77.1 (64)94.0 (78)85.5 (71)91.6 (76)100 (83)
    Genus64.3 (74)94.8 (109)81.7 (94)82.6 (95)100 (115)
  • a As determined by conventional testing.

  • b OTU, operational taxonomic unit.

  • c The Shannon's index of evenness was calculated using the formula E = eD/N, where D is the Shannon diversity index.