Table 1. Comparison of main signals using metagenomics (MG) with 16S rRNA amplicon sequencing.
| Species | Positive signals MG and 16S (79 = max) |
Avg. no. of MG reads in positive samples | Avg. % of 16S reads in positive samples* | Concordance MG and 16S kappa score (P value)† | Part of an MG batch effect‡ | Presence 16S in neg. controls Absent/Weak/Strong (n=5)t§ | |||
|---|---|---|---|---|---|---|---|---|---|
| Both* | MG only | 16S only* | Neither | ||||||
| Salmonella bongori | 79 | 0 | 0 | 0 | 178 | 54 % | N/A | No | 5/0/0 |
| Escherichia coli | 1 | 78 | 0 | 0 | 18602 | 1.2 % | 0 (-) | Gr. 1&2 | 4/1/0 |
| Shigella (genus) | 0 | 75 | 0 | 4 | 254 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Salmonella enterica | 0 | 75 | 0 | 4 | 33 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Cronobacter sakazakii | 0 | 65 | 0 | 14 | 21 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Bacillus subtilis | 0 | 63 | 0 | 16 | 13 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Y. pseudotuberculosis | 0 | 59 | 0 | 20 | 3 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Neisseria meningitidis | 0 | 44 | 0 | 35 | 2 | N/A | 0 (-) | Gr. 1&2 | 5/0/0 |
| Bradyrhizobium (genus) | 0 | 79 | 0 | 0 | 125 | N/A | 0 (-) | Gr. 2 | 5/0/0 |
| R. palustris | 0 | 79 | 0 | 0 | 45 | N/A | 0 (-) | Gr. 2 | 5/0/0 |
| Caulobacter (genus) | 12 | 67 | 0 | 0 | 14 | 1.4 % | 0 (-) | Gr. 2 | 1/3/1 |
| Methylobacterium (genus) | 9 | 69 | 0 | 1 | 8 | 2.4 % | 0.003 (0.36) | Gr. 2 | 1/4/0 |
| Burkholderia (genus) | 21 | 57 | 0 | 1 | 7 | 1.9 % | 0.009 (0.27) | Gr. 2 | 1/4/0 |
| Propionibacterium acnes | 66 | 13 | 0 | 0 | 20 | 4.8 % | 0 (-) | No | 0/3/2 |
| S. pneumoniae | 0 | 11 | 0 | 68 | 115 | N/A | 0 (-) | No | 5/0/0 |
| Vibrio cholerae | 0 | 14 | 0 | 65 | 46 | N/A | 0 (-) | No | 5/0/0 |
| Thiohalocapsa halophila | 0 | 0 | 71 | 8 | N/A | 4.2 % | 0 (-) | No | 0/0/5 |
| S. maltophilia | 5 | 51 | 1 | 22 | 2 | 1.9 % | 0.03 (0.24) | No | 2/3/0 |
| Acinetobacter baumanii | 1 | 26 | 0 | 52 | 2 | 2.4 % | 0.05 (0.08) | No | 4/1/0 |
| Micrococcus luteus | 1 | 46 | 0 | 32 | 15 | 2.0 % | 0.02 (0.20) | No | 4/1/0 |
| Gardnerella vaginalis | 0 | 5 | 0 | 74 | 1 | N/A | 0 (-) | No | 4/1/0 |
| Lactobacillus crispatus | 0 | 4 | 0 | 75 | 1 | N/A | 0 (-) | No | 5/0/0 |
| Deinococcus geothermalis | 1 | 1 | 0 | 77 | 68 | 33 % | 0.66 (<0.0001) | No | 5/0/0 |
| Streptococcus agalactiae | 3 | 4 | 0 | 72 | 8 | 13 % | 0.58 (<0.0001) | No | 5/0/0 |
*
16S rRNA amplicon sequencing signals higher than 1% are defined as positive.
†
One-sided P values
‡
See Fig. 1 for definition of groups 1 and 2.
§
Strong signals are defined as more than 1%