Table 2 Expected and observed relative abundance (%) of genera in mock community sample HM-783D. Setup 1 (2-step PCR; V3 V4 region); Setup 2 (2-step PCR; V4 region); Setup 3 (1-step PCR; V4 region)
Genera | Expected | Setup 1 (I) | Setup 1 (II) | Setup 1 (III) | Setup 1 (IV) | Setup 2 | Setup 3 |
|---|---|---|---|---|---|---|---|
Escherichia | 21.91 | 27.68 | 23.99 | 25.20 | 26.65 | 22.54 | 32.90 |
Rhodobacter | 21.91 | 5.98 | 9.52 | 9.23 | 8.94 | 11.00 | 8.77 |
Staphylococcus | 24.10 | 29.02 | 29.27 | 29.66 | 30.56 | 29.88 | 24.98 |
Streptococcus | 24.12 | 28.51 | 27.39 | 27.03 | 25.38 | 26.20 | 25.81 |
Bacillus | 2.19 | 3.38 | 2.86 | 2.95 | 2.85 | 3.15 | 2.49 |
Clostridium | 2.19 | 2.18 | 3.28 | 2.19 | 1.88 | 2.64 | 1.69 |
Pseudomonas | 2.19 | 1.44 | 1.68 | 1.75 | 1.93 | 2.12 | 2.02 |
Acinetobacter | 0.22 | 0.32 | 0.29 | 0.33 | 0.30 | 0.29 | 0.12 |
Helicobacter | 0.22 | 0.36 | 0.49 | 0.44 | 0.38 | 0.61 | 0.26 |
Lactobacillus | 0.22 | 0.22 | 0.20 | 0.23 | 0.24 | 0.35 | 0.18 |
Listeria | 0.22 | 0.33 | 0.33 | 0.30 | 0.32 | 0.37 | 0.26 |
Neisseria | 0.22 | 0.24 | 0.31 | 0.30 | 0.27 | 0.43 | 0.39 |
Propionibacterium | 0.22 | 0.13 | 0.22 | 0.18 | 0.15 | 0.29 | 0.00 |
Actinomyces | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 |
Bacteroides | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 |
Deinococcus | 0.02 | 0.02 | 0.04 | 0.03 | 0.02 | 0.03 | 0.02 |
Enterococcus | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.02 | 0.00 |
Other | 0.00 | 0.13 | 0.11 | 0.10 | 0.09 | 0.03 | 0.08 |