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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)

From: Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

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