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Table 2 The eHOMD training set is superior for assigning species/supraspecies-level taxonomy to short- and long-read human aerodigestive tract datasets

From: Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

 

V1V3_hADT_CL

V1V3_HMPnares_ ASVb

FL_sinonasal_SMRT_ASV

(% reads)

(% ASVs)

(% reads)

(% ASVs)

(% reads)

eHOMD

Genus

100.0

95.5

98.9

99.5

100.0

Species

100.0

93.9

98.5

95.1

99.0

SILVA

Genus

96.1

94.7

97.6

96.6

98.9

Species

44.7a

4.1a

29.9a

18.6a

71.9a

RDP

Genus

93.2

90.2

92.2

94.1

98.5

Species

38.5a

3.1a

27.5a

13.2a

60.6a

  1. aExact match algorithm
  2. bASVs derived from the HMP nares V1–V3 dataset, as described in [20], constitute the V1V3_HMPnares_ASV dataset (Additional file 10)