TABLE 2

Performance of eHOMD and comparable databases for species-level taxonomic assignment to 16S rRNA gene data sets from sites throughout the human aerodigestive tract

Data set16S
region
16S
primers
Sequencing
technique
Sample
type
No. of samplesNo. of reads
analyzed
DatabaseNo. of reads
identifieda
% reads
identifieda
Laufer-
Pettigrew (21)
V1-V227F, 338RRoche/454Nostril
swab
108 children
(108 samples)
120,274eHOMDv15.196,23380.0
SILVA12897,23380.8
RDP1697,46481.0
NCBI 16S87,08272.4
Allen-
Sale (22)
V1-V327F, 534R454-FLXNasal
lavage
fluid
10 adults
(97 samples)
75,310eHOMDv15.168,59491.1
SILVA12869,08291.7
RDP1665,02886.4
NCBI 16S63,89284.8
Pei-Blaser
(25, 26)
CLb318F, 1519R,
8F, 1513R
CLEsophageal
biopsies
4 adults (10 libraries
each)
7,414eHOMDv15.17,27698.1
SILVA1287,01994.7
RDP166,84792.4
NCBI 16S6,68690.2
Harris-Pace
(27)
CL27F, 907RCLBrochial
alveola
lavage fluid
57 children
(50 libraries
CF and 19
control)c
3,203eHOMDv15.12,68483.8
SILVA1282,63382.2
RDP162,50078.1
NCBI 16S2,42775.8
HMPnV1-V3 (23, 24)V1-V327F, 534RRoche/454Nostril
swab
227 adults
(363 samples)d
2,338,563eHOMDv15.12,133,08391.2
SILVA1282,035,88287.1
RDP161,965,61184.1
NCBI 16S1,932,73282.6
van der Gast-
Bruce (40)
CL7F, 1510RCLExpectorated
sputa
14 adults (CF)2,137eHOMDv15.12,12399.3
SILVA1282,08497.5
RDP162,05796.3
NCBI 16S2,04595.7
Flanagan-
Bristow (38)
CL27F, 1492RCLEndotracheal
tube aspirate
6 adults, 1 child
(2 to 5 samples
each)
3,278eHOMDv15.13,19397.4
SILVA1283,19997.6
RDP163,19397.4
NCBI 16S3,18697.2
Perkins-
Angenent (39)
CL8F, 1391RCLExtubated
endotracheal
tube
8 adults1,263eHOMDv15.11,00879.8
SILVA1281,00079.2
RDP1691672.5
NCBI 16S83265.9
  • a Reads identified via blastn search at 98.5% identity and 98% coverage.

  • b CL, clone library.

  • c CF, cystic fibrosis.

  • d See Text S1 in the supplemental material.