Table 1 Datasets with bacterial genomes used for TaxPhlAn benchmarking.

From: A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

Taxon Name

Taxonomy Level of Input

Gram-Staining

Human Niche

# Genomes selected

Average ± SD

Genome Size (Mb)

Average ± SD

Genome GC-content (%)

Bifidobacterium

genus

positive

gut

261

2.30 ± 0.27

60.1 ± 2.0

Escherichia/Shigella

supra-genus

negative

gut

200

4.91 ± 0.35

50.6 ± 1.1

Propionibacterium acnes

species

positive

skin

123

2.50 ± 0.03

60.1 ± 0.1

Staphylococcus

genus

positive

skin

200

2.59 ± 0.20

33.0 ± 1.4

  1. For benchmarking we selected four bacterial taxa that are associated with the two clinically relevant human microbial niches of gut and skin. The datasets represent both Gram-positive and Gram-negative bacteria from different taxonomical levels, and with variable genome sizes and GC-content. See Suppl. Tables S1–S4 for more details. SD: standard deviation; Mb: mega base pairs.
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