Table 1 Profiling of spike-in microbes with host-unmapped NGS reads
From: A systematic sequencing-based approach for microbial contaminant detection and functional inference
Assay (culture) | Antibiotics | Spike-ins | CFU | Input reads(host-mapped) | Sample-levelRPMHs | Genus-levelRPMHs | Uniq-genus-hit | Multi-genera-hit | Weighted | p value |
|---|---|---|---|---|---|---|---|---|---|---|
DNA-seq (0 day) | Yes | 60 × 6 species | 360 | 356,831,325 (354,374,295) | 2.85 |  | ||||
 Aspergillus | 60 |  |  | 0.023 | 8 | 1 | 8.00 | 7.93e−46 | ||
 Candida | 60 |  |  | 0.003 | 1 | 0 | 1.00 | 0.2 | ||
 Bacillus | 60 |  |  | 0.014 | 5 | 13 | 5.02 | 1.21e−10 | ||
 Clostridium | 60 |  |  | 0.006 | 1 | 26 | 2.07 | 0.439 | ||
 Pseudomonas | 60 |  |  | 0.144 | 50 | 8 | 50.98 | 0.0 | ||
 Staphylococcus | 60 |  |  | 0.015 | 4 | 13 | 5.32 | 2.57e−19 | ||
DNA-seq (0 day) | Yes | 1100 × 6 species | 6600 | 364,040,378 (353,592,879) | 7.31 |  | ||||
 Aspergillus | 1100 |  |  | 0.274 | 96 | 4 | 96.83 | 0.0 | ||
 Candida | 1100 |  |  | 0.249 | 88 | 0 | 88.00 | 0.0 | ||
 Bacillus | 1100 |  |  | 3.600 | 1272 | 16 | 1272.90 | 0.0 | ||
 Clostridium | 1100 |  |  | 0.019 | 6 | 14 | 6.59 | 0.108 | ||
 Pseudomonas | 1100 |  |  | 1.379 | 484 | 22 | 487.74 | 0.0 | ||
 Staphylococcus | 1100 |  |  | 0.257 | 90 | 16 | 90.90 | 0.0 | ||
DNA-seq (0 day) | Yes | 2000 × 7 species | 14,000 | 337,322,388 (326,833,300) | 167.27 |  | ||||
 Acholeplasma | 2000 |  |  | 70.632 | 23,075 | 52 | 23,084.88 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 94.750 | 30,957 | 49 | 30,967.52 | 0.0 | ||
DNA-seq (3 days) | No | 2000 × 7 species | 14,000 | 330,472,068 (322,510,723) | 4002.63 |  | ||||
 Acholeplasma | 2000 |  |  | 3493.819 | 1,126,497 | 2123 | 1,126,793.98 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 500.993 | 161,484 | 956 | 161,575.60 | 0.0 | ||
Yes | 2000 × 7 species | 14,000 | 366,225,114 (355,493,668) | 4.15 |  | |||||
 Acholeplasma | 2000 |  |  | 1.872 | 665 | 1 | 665.40 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 1.336 | 475 | 0 | 475.00 | 0.0 | ||
RNA-seq (3 days) | No | 2000 × 7 species | 14,000 | 293,731,220 (273,924,497) | 700.00 |  | ||||
 Acholeplasma | 2000 |  |  | 24.696 | 5949 | 3379 | 6764.96 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 20.636 | 3846 | 13,753 | 5652.74 | 0.0 | ||
Yes | 2000 × 7 species | 14,000 | 373,580,135 (343,111,904) | 64.75 |  | |||||
 Acholeplasma | 2000 |  |  | n/a | 0 | 0 | n/a | n/a | ||
 Mycoplasma | 12,000 |  |  | 0.153 | 11 | 346 | 52.66 | 0.387 | ||
ATAC-seq (3 days) | No | 2000 × 7 species | 14,000 | 155,464,170 (44,754,687) | 436,529.79 |  | ||||
 Acholeplasma | 2000 |  |  | 415,647.522 | 18,596,370 | 42,587 | 18,602,174.73 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 19,628.123 | 877,487 | 13,815 | 878,450.49 | 0.0 | ||
Yes | 2000 × 7 species | 14,000 | 115,413,203 (45,447,065) | 212.14 |  | |||||
 Acholeplasma | 2000 |  |  | 121.798 | 5533 | 14 | 5535.38 | 0.0 | ||
 Mycoplasma | 12,000 |  |  | 27.192 | 1234 | 7 | 1235.80 | 0.0 | ||