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Table 1 Differences between expected and observed genus abundances in the mock communities (Nshotgun = 4, Namplicon = 3) via a one-sample t test (two-sided) of relative abundances (P values are adjusted via Hommel procedure)

From: Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

  Shotgun Amplicon
Members mock community MEGAN V1 V2 one-step V3 V4 one-step V1 V2 two-step V3 V4 two-step
Staphylococcus 0.00002 0.52446 0.09200 0.03994 0.21564
Listeria 0.00395 0.34964 0.53267 0.03003 0.00545
Bacillus 0.00006 0.21420 0.02818 0.29671 0.30589
Pseudomonas 0.13668 0.36721 0.05776 0.38147 0.59037
Escherichia/Shigellaa NA 0.00462 0.45612 0.00237 0.59037
Shigella a 4.6372 × 10−10 NA NA NA NA
Escherichia a 0.00001 NA NA NA NA
Enterobacteriaceae a NA 0.87898 0.00004 0.19274 0.00055
Salmonella 3.8092 × 10−6 0.34964 0.05838 0.09712 0.08851
Lactobacillus 0.00297 0.87898 0.53267 0.38147 0.59037
Enterococcus 0.00012 0.04816 0.03746 0.01159 0.00954
  1. aEscherichia/Shigella relatives counted as equivalent