Table 1 Accuracy of microbial identification using two in silico constructed simulated food mixtures.
From: Monitoring the microbiome for food safety and quality using deep shotgun sequencing
Mixture 1, no MF # GENERA | Mixture 1, MF # GENERA | Mixture 1, no MF # READS | Mixture 1, MF # READS | Mixture 2, no MF # GENERA | Mixture 2, MF # GENERA | Mixture 2, no MF # READS | Mixture 2, MF # READS | |
|---|---|---|---|---|---|---|---|---|
Bacteria in mixture (expected Content) | 14 | 14 | 15,000 | 15,000 | 14 | 14 | 15,000 | 15,000 |
Observed bacteria | 34 | 18 | 13,700 | 13,517 | 33 | 15 | 13,999 | 13,551 |
Observed viruses | 9 | 0 | 563 | 0 | 4 | 0 | 328 | 0 |
Observed archaea | 1 | 0 | 1 | 0 | 1 | 0 | 3 | 0 |
Observed Eukaryota | 4 | 0 | 104 | 0 | 4 | 0 | 799 | 0 |
Total observed (TO) | 48 | 18 | 14,368 | 13,517 | 42 | 15 | 15,129 | 13,551 |
True positives (TP) | 14 | 14 | 13,571 | 13,511 | 14 | 14 | 13,623 | 13,548 |
TP as % of TO | 29% | 78% | 94.45% | 99.96% | 33% | 93% | 90.05% | 99.98% |
False positives (FP) | 34 | 4 | 797 | 6 | 28 | 1 | 1506 | 3 |
FP as % of TO | 71% | 22% | 5.55% | 0.04% | 67% | 7% | 9.95% | 0.02% |
FP removed with MF | – | 30 | – | 791 | – | 27 | – | 1503 |
% FP removed with MF | – | 88.2% | – | 99.2% | – | 96.4% | – | 99.8% |
