TABLE 1.
Microbiome sampling characteristics of different body sites
| Body site or sample type | Avg (SD) DNA concn (ng/μl)a | Avg (SD) library concn (ng/μl) | Avg (SD) no. of reads (M)b | No. of microbial-positive samplesb | Avg (SD) no. of microbial reads (M)c | Avg (SD) percentage of microbial readsc | Avg (SD) microbial read length (bp)c |
|---|---|---|---|---|---|---|---|
| Axillary vault | <0.05 (0.04) | 1.48 (2.74) | 12.31 (14.58) | 9 | 7.87 (13.39) | 62.91 (34.01) | 116.84 (3.57) |
| Inguinal crease | <0.05 (0.03) | 0.64 (0.92) | 12.71 (18.94) | 12 | 9.17 (10.94) | 65.58 (27.50) | 119.25 (3.49) |
| Nares | 2.54 (4.14) | 2.79 (4.89) | 37.75 (27.05) | 14 | 5.45 (9.78) | 15.74 (27.98) | 119.03 (5.83) |
| Periumbilical | 0.27 (0.34) | 0.50 (0.42) | 10.66 (11.75) | 5 | 0.99 (0.76) | 17.75 (22.75) | 120.47 (5.41) |
| Upper chest | <0.10 (0.13) | 0.4 (0.35) | 14.71 (13.84) | 8 | 2.89 (3.77) | 21.65 (23.19) | 119.42 (6.97) |
| Skin combined | <0.80 (2.45) | 1.37 (3.02) | 21.06 (21.99) | 48 | 5.93 (9.74) | 38.24 (35.56) | 118.89 (5.03) |
| Stool | 7.91 (8.15) | 19.57 (11.41) | 22.76 (9.19) | 12 | 22.56 (9.05) | 99.23 (0.61) | 123.18 (5.90) |
a
Measured after concentration with sodium acetate-ethanol plus glycogen. Detection limit was 0.025 ng/μl.
b
Number of reads generated from Illumina NextSeq run.
c
After filtering reads with KneadData.