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Table 4 Bacterial species identified

From: Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

ID Species No. of contigs Total aligned length Total no. of associated PE reads Total no. of associated SE reads Sum of PE and SE reads MCRPM
BBC ctl        (sum/372)
  Acinetobacter johnsonii XBB1 17 5,428 69 30 99 0.27
  Bacillus cereus 2 708 6 35 41 0.11
  Mycobacterium sp. 4 2,124 73 70 143 0.38
  Ralstonia mannitolilytica 4 1,227 31 12 43 0.12
EJC ctl        (sum/389)
  Acinetobacter haemolyticus 12 4,345 59 30 89 0.23
  Acinetobacter johnsonii XBB1 231 99,403 1,719 616 2,335 6.00
  Acinetobacter junii 4 1,948 30 7 37 0.10
  Acinetobacter lwoffii 17 6,186 87 31 118 0.30
  Acinetobacter schindleri 4 1,770 43 16 59 0.15
  Bacillus cereus 4 1,314 31 51 82 0.21
  Corynebacterium pseudotuberculosis 2 588 2 48 50 0.13
  Methylobacterium populi 18 5,102 54 18 72 0.19
  Mycobacterium abscessus 4 2,238 53 14 67 0.17
  Mycobacterium avium 8 2,751 30 15 45 0.12
  Mycobacterium sp. 8 2,620 36 63 99 0.25
  Mycoplasma mycoides 1 276 17 28 45 0.12
  Porphyrobacter sp. 7 2,478 20 34 54 0.14
  Ralstonia mannitolilytica 8 2,899 37 40 77 0.20
  Sphingomonas sp. 11 3,533 27 28 55 0.14
BC 0145        (sum/375)
  Pannonibacter phragmitetus 714 230,779 1,999 1,309 3,308 8.82
  Pseudomonas aeruginosa 2 1,824 254 78 332 0.89
  Pseudomonas alcaliphila 6 5,093 896 170 1,066 2.84
  Pseudomonas mendocina ymp 1,675 2,678,493 918,733 109,787 1,028,520 2,742.72
  Pseudomonas sp. 3 1,195 41 36 77 0.21
  Pseudomonas stutzeri 3 1,717 220 21 241 0.64
  Rhizobium sp. 34 12,418 144 65 209 0.56
BC 0190        (sum/426)
  Acinetobacter baumannii 2 1,078 29 17 46 0.11
  Acinetobacter johnsonii XBB1 71 24,930 366 168 534 1.25
  Bacillus cereus 4 1,172 24 76 100 0.23
  Methylobacterium populi 38 10,970 123 72 195 0.46
  Mycobacterium abscessus 5 2,599 67 28 95 0.22
  Mycobacterium sp. 7 2,432 52 88 140 0.33
  Porphyrobacter sp. 6 2,195 38 31 69 0.16
  Ralstonia mannitolilytica 7 2,370 19 53 72 0.17
  Sphingomonas sp. 17 5,030 63 44 107 0.25
CGBC 025        (sum/579)
  Acinetobacter baumannii 24 6,818 118 48 166 0.29
  Bradyrhizobium sp. 7 2,059 41 16 57 0.10
  Enterobacter cloacae 8 3,140 108 33 141 0.24
  Sphingobium japonicum 8 5,088 262 43 305 0.53
  Sphingomonas melonis 336 157,346 5,397 2,503 7,900 13.64
  Sphingomonas panacis 4 1,261 36 30 66 0.11
  Sphingomonas sp. 51 21,410 720 271 991 1.71
  1. Only microbial species with MCRPM ≥ 0.1 are listed. Those with MCRPM ≥ 1 are listed in bold.
  2. Ctl control; MCRPM, microbial cfDNA per million quality PE reads; sp. (same as spp.), species with unspecified species name