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

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/Shigella^a

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