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Table 1 Number of plasma ASVs that met each decontamination criterion separately and in combination

From: Detection of cell-free microbial DNA using a contaminant-controlled analysis framework

  All ASVs (%) Low abundance ASVs (%) Med. abundance ASVs (%) High abundance ASVs (%)
Total 1506 (100) 1384 (100) 110 (100) 12 (100)
Criterion (i)
 No batch effect by sequencing run 612 (40.64) 582 (42.05) 25 (22.73) 5 (41.67)
 No batch effect by DEB 277 (18.39) 260 (18.79) 12 (10.91) 5 (41.67)
 No batch effect by DNA ext. day 1113 (73.9) 1069 (77.24) 38 (34.55) 6 (50)
 No batch effect by any tech. var. 239 (15.87) 227 (16.4) 8 (7.27) 4 (33.33)
Criterion (ii)
 Decontam in DEB A 183 (12.15) 144 (10.4) 36 (32.73) 3 (25)
 Decontam in DEB B 364 (24.17) 307 (22.18) 51 (46.36) 6 (50)
 Decontam in DEB C 573 (38.05) 504 (36.42) 68 (61.82) 1 (8.33)
 Decontam in DEB D 431 (28.62) 385 (27.82) 45 (40.91) 1 (8.33)
 Decontam in DEB E 452 (30.01) 395 (28.54) 55 (50) 2 (16.67)
 Decontam across DEBs 329 (21.85) 313 (22.62) 16 (14.55) 0 (0)
Criterion (iii)
 Sample association 20 (1.33) 14 (1.01) 6 (5.45) 0 (0)
 Complete bioinformatics decontamination strategy 38 (2.52) 38 (2.75) 0 (0) 0 (0)
 Final list after literature-based filter 31 (2.06) 31 (2.24) 0 (0) 0 (0)
  1. Low abundance, < 0.1%; med abundance, 0.1–1%; high abundance, > 1%; DNA ext. day, DNA extraction day; tech. var., technical variable