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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