├── .gitignore ├── .gitattributes ├── Example_Outputs ├── ATCC.diamond_megan.kreport.txt ├── ATCC.bugseq.kreport.txt ├── ATCC.centrifuge500.kreport.txt ├── ATCC.bracken.kreport.txt ├── ATCC.centrifuge.kreport.txt └── ATCC.mmseqs.kreport.txt ├── README.md └── LICENSE /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | -------------------------------------------------------------------------------- /Example_Outputs/ATCC.diamond_megan.kreport.txt: -------------------------------------------------------------------------------- 1 | 88.41 2138742 193618 K 2 Bacteria 2 | 0.16 3852 818 P 201174 Actinobacteria 3 | 0.13 3034 0 C 1760 Actinomycetia 4 | 0.13 3034 45 O 85009 Propionibacteriales 5 | 0.12 2989 1847 F 31957 Propionibacteriaceae 6 | 0.05 1142 352 G 1912216 Cutibacterium 7 | 0.03 790 790 S 1747 Cutibacterium acnes 8 | 10.07 243594 9919 P 976 Bacteroidetes 9 | 9.66 233675 996 C 200643 Bacteroidia 10 | 9.62 232679 65248 O 171549 Bacteroidales 11 | 6.92 167431 1059 F 171551 Porphyromonadaceae 12 | 6.88 166372 36434 G 836 Porphyromonas 13 | 5.37 129938 129938 S 837 Porphyromonas gingivalis 14 | 0.01 324 0 P 1297 Deinococcus-Thermus 15 | 0.01 324 8 C 188787 Deinococci 16 | 0.01 316 0 O 118964 Deinococcales 17 | 0.01 316 0 F 183710 Deinococcaceae 18 | 0.01 316 316 G 1298 Deinococcus 19 | 20.33 491765 8913 P 1239 Firmicutes 20 | 18.88 456762 24779 C 91061 Bacilli 21 | 9.28 224443 14275 O 1385 Bacillales 22 | 1.83 44293 1191 F 186817 Bacillaceae 23 | 1.78 43102 39900 G 1386 Bacillus 24 | 0.13 3202 3202 S 1396 Bacillus cereus 25 | 6.86 165875 205 F 90964 Staphylococcaceae 26 | 6.85 165670 86104 G 1279 Staphylococcus 27 | 0.46 11022 11022 S 1280 Staphylococcus aureus 28 | 2.83 68544 68544 S 1282 Staphylococcus epidermidis 29 | 8.58 207540 8196 O 186826 Lactobacillales 30 | 0.05 1180 101 F 33958 Lactobacillaceae 31 | 0.04 1079 609 G 1578 Lactobacillus 32 | 0.02 470 470 S 1596 Lactobacillus gasseri 33 | 8.19 198164 1816 F 1300 Streptococcaceae 34 | 8.12 196348 102054 G 1301 Streptococcus 35 | 0.34 8266 8266 S 1311 Streptococcus agalactiae 36 | 3.56 86028 86028 S 1309 Streptococcus mutans 37 | 1.08 26090 64 C 186801 Clostridia 38 | 1.08 26026 773 O 186802 Eubacteriales 39 | 1.04 25253 157 F 31979 Clostridiaceae 40 | 1.04 25096 7814 G 1485 Clostridium 41 | 0.71 17282 17282 S 1520 Clostridium beijerinckii 42 | 49.84 1205589 104927 P 1224 Proteobacteria 43 | 25.96 628020 120727 C 28211 Alphaproteobacteria 44 | 20.97 507293 22873 O 204455 Rhodobacterales 45 | 20.03 484420 133914 F 31989 Rhodobacteraceae 46 | 7.02 169849 0 G 1653176 Cereibacter 47 | 7.02 169849 169849 S 1063 Cereibacter sphaeroides 48 | 7.47 180657 180657 G 1060 Rhodobacter 49 | 0.1 2393 101 C 28216 Betaproteobacteria 50 | 0.09 2292 9 O 206351 Neisseriales 51 | 0.09 2283 75 F 481 Neisseriaceae 52 | 0.09 2208 1825 G 482 Neisseria 53 | 0.02 383 383 S 487 Neisseria meningitidis 54 | 0.06 1458 0 C 29547 Epsilonproteobacteria 55 | 0.06 1458 32 O 213849 Campylobacterales 56 | 0.06 1426 1 F 72293 Helicobacteraceae 57 | 0.06 1425 69 G 209 Helicobacter 58 | 0.06 1356 1356 S 210 Helicobacter pylori 59 | 19.38 468791 18599 C 1236 Gammaproteobacteria 60 | 15.03 363645 19776 O 91347 Enterobacterales 61 | 14.22 343869 236529 F 543 Enterobacteriaceae 62 | 4.44 107340 14712 G 561 Escherichia 63 | 3.83 92628 92628 S 562 Escherichia coli 64 | 0.15 3629 0 O 2887326 Moraxellales 65 | 0.15 3629 16 F 468 Moraxellaceae 66 | 0.15 3613 2087 G 469 Acinetobacter 67 | 0.06 1526 1526 S 470 Acinetobacter baumannii 68 | 3.43 82918 7388 O 72274 Pseudomonadales 69 | 3.12 75530 85 F 135621 Pseudomonadaceae 70 | 3.12 75445 13972 G 286 Pseudomonas 71 | 2.54 61473 61473 S 287 Pseudomonas aeruginosa 72 | 0.03 766 766 K 2759 Eukaryota 73 | -------------------------------------------------------------------------------- /Example_Outputs/ATCC.bugseq.kreport.txt: -------------------------------------------------------------------------------- 1 | 17.2 415977 415977 U 0 unclassified 2 | 0.07 1768 1768 S 210 Helicobacter pylori 3 | 0.07 1768 0 G 209 Helicobacter 4 | 0.07 1768 0 F 72293 Helicobacteraceae 5 | 0.07 1768 0 O 213849 Campylobacterales 6 | 0.07 1768 0 C 29547 Epsilonproteobacteria 7 | 0.07 1768 0 - 68525 delta/epsilon subdivisions 8 | 48.92 1183357 0 P 1224 Proteobacteria 9 | 82.8 2003060 0 D 2 Bacteria 10 | 82.8 2003060 0 - 131567 cellular organisms 11 | 82.8 2003060 0 R 1 root 12 | 4.75 114841 114841 S 287 Pseudomonas aeruginosa 13 | 4.75 114841 0 - 136841 Pseudomonas aeruginosa group 14 | 4.75 114841 0 G 286 Pseudomonas 15 | 4.75 114841 0 F 135621 Pseudomonadaceae 16 | 4.99 120619 0 O 72274 Pseudomonadales 17 | 27.23 658584 0 C 1236 Gammaproteobacteria 18 | 0.24 5778 63 S 470 Acinetobacter baumannii 19 | 0.24 5778 0 - 909768 Acinetobacter calcoaceticus/baumannii complex 20 | 0.24 5778 0 G 469 Acinetobacter 21 | 0.24 5778 0 F 468 Moraxellaceae 22 | 22.24 537965 271 S 562 Escherichia coli 23 | 22.24 537965 0 G 561 Escherichia 24 | 22.24 537965 0 F 543 Enterobacteriaceae 25 | 22.24 537965 0 O 91347 Enterobacterales 26 | 11.08 268073 159446 S 837 Porphyromonas gingivalis 27 | 11.08 268073 0 G 836 Porphyromonas 28 | 11.08 268073 0 F 171551 Porphyromonadaceae 29 | 11.08 268099 0 O 171549 Bacteroidales 30 | 11.08 268099 0 C 200643 Bacteroidia 31 | 11.08 268099 0 P 976 Bacteroidetes 32 | 11.08 268099 0 - 68336 Bacteroidetes/Chlorobi group 33 | 11.08 268099 0 - 1783270 FCB group 34 | 9.3 224995 555 G 1279 Staphylococcus 35 | 9.3 224995 0 F 90964 Staphylococcaceae 36 | 11.83 286072 0 O 1385 Bacillales 37 | 21.9 529835 0 C 91061 Bacilli 38 | 22.61 546884 0 P 1239 Firmicutes 39 | 22.8 551605 0 - 1783272 Terrabacteria group 40 | 0.43 10311 468 S 1280 Staphylococcus aureus 41 | 8.85 214128 8539 S 1282 Staphylococcus epidermidis 42 | 0.62 15032 28 S 1311 Streptococcus agalactiae 43 | 10.03 242557 0 G 1301 Streptococcus 44 | 10.03 242557 0 F 1300 Streptococcaceae 45 | 10.08 243763 0 O 186826 Lactobacillales 46 | 0.7 17049 538 S 1520 Clostridium beijerinckii 47 | 0.7 17049 0 G 1485 Clostridium 48 | 0.7 17049 0 F 31979 Clostridiaceae 49 | 0.7 17049 0 O 186802 Clostridiales 50 | 0.7 17049 0 C 186801 Clostridia 51 | 2.52 61077 6 - 86661 Bacillus cereus group 52 | 2.52 61077 0 G 1386 Bacillus 53 | 2.52 61077 0 F 186817 Bacillaceae 54 | 0.13 3168 3168 S1 122586 Neisseria meningitidis MC58 55 | 0.13 3168 0 S1 491 Neisseria meningitidis serogroup B 56 | 0.13 3168 0 S 487 Neisseria meningitidis 57 | 0.13 3168 0 G 482 Neisseria 58 | 0.13 3168 0 F 481 Neisseriaceae 59 | 0.13 3168 0 O 206351 Neisseriales 60 | 0.13 3168 0 C 28216 Betaproteobacteria 61 | 8.5 205590 205590 S1 176280 Staphylococcus epidermidis ATCC 12228 62 | 0.62 15004 15004 S1 208435 Streptococcus agalactiae 2603V/R 63 | 0.62 15004 0 S1 216466 Streptococcus agalactiae serogroup V 64 | 2.52 61071 61071 S1 222523 Bacillus cereus ATCC 10987 65 | 2.52 61071 0 S 1396 Bacillus cereus 66 | 0 15 15 S1 243230 Deinococcus radiodurans R1 67 | 0 15 0 S 1299 Deinococcus radiodurans 68 | 0 15 0 G 1298 Deinococcus 69 | 0 15 0 F 183710 Deinococcaceae 70 | 0 15 0 O 118964 Deinococcales 71 | 0 15 0 C 188787 Deinococci 72 | 0 15 0 P 1297 Deinococcus-Thermus 73 | 0.68 16511 16511 S1 290402 Clostridium beijerinckii NCIMB 8052 74 | 0.05 1206 1206 S1 324831 Lactobacillus gasseri ATCC 33323 = JCM 1131 75 | 0.05 1206 0 S 1596 Lactobacillus gasseri 76 | 0.05 1206 0 G 1578 Lactobacillus 77 | 0.05 1206 0 F 33958 Lactobacillaceae 78 | 21.49 519838 519838 S1 349101 Rhodobacter sphaeroides ATCC 17029 79 | 21.49 519838 0 S 1063 Rhodobacter sphaeroides 80 | 21.49 519838 0 G 1060 Rhodobacter 81 | 21.49 519838 0 F 31989 Rhodobacteraceae 82 | 21.49 519838 0 O 204455 Rhodobacterales 83 | 21.49 519838 0 C 28211 Alphaproteobacteria 84 | 0.41 9844 18 S1 367830 Staphylococcus aureus subsp. aureus USA300 85 | 0.24 5715 5715 S1 400667 Acinetobacter baumannii ATCC 17978 86 | 4.49 108627 108627 S1 431947 Porphyromonas gingivalis ATCC 33277 87 | 0 25 25 S1 435590 Bacteroides vulgatus ATCC 8482 88 | 0 25 0 S 821 Phocaeicola vulgatus 89 | 0 25 0 G 909656 Phocaeicola 90 | 0 25 0 - 333046 Bacteroidales incertae sedis 91 | 0.41 9826 9826 S1 451516 Staphylococcus aureus subsp. aureus USA300_TCH1516 92 | 22.23 537694 537694 S1 511145 Escherichia coli str. K-12 substr. MG1655 93 | 22.23 537694 0 S1 83333 Escherichia coli K-12 94 | 0.19 4705 4705 S1 1091045 Cutibacterium acnes subsp. defendens ATCC 11828 95 | 0.19 4705 0 S1 1905725 Cutibacterium acnes subsp. defendens 96 | 0.19 4705 0 S 1747 Cutibacterium acnes 97 | 0.19 4705 0 G 1912216 Cutibacterium 98 | 0.19 4705 0 F 31957 Propionibacteriaceae 99 | 0.19 4705 0 O 85009 Propionibacteriales 100 | 0.19 4705 0 C 1760 Actinobacteria 101 | 0.19 4705 0 P 201174 Actinobacteria 102 | 9.41 227525 227525 S1 1437447 Streptococcus mutans UA159-FR 103 | 9.41 227525 0 S 1309 Streptococcus mutans -------------------------------------------------------------------------------- /Example_Outputs/ATCC.centrifuge500.kreport.txt: -------------------------------------------------------------------------------- 1 | 3.83 92684 92684 U 0 unclassified 2 | 96.17 2326353 0 - 1 root 3 | 96.17 2326353 0 - 131567 cellular organisms 4 | 96.17 2326353 85 D 2 Bacteria 5 | 61.53 1488321 775 P 1224 Proteobacteria 6 | 32.12 777098 0 C 28211 Alphaproteobacteria 7 | 32.12 777098 0 O 204455 Rhodobacterales 8 | 32.12 777098 0 F 31989 Rhodobacteraceae 9 | 32.12 777098 0 G 1060 Rhodobacter 10 | 32.12 777098 777098 S 1063 Rhodobacter sphaeroides 11 | 29.14 704837 0 C 1236 Gammaproteobacteria 12 | 24.62 595583 40 O 91347 Enterobacterales 13 | 24.62 595500 182538 F 543 Enterobacteriaceae 14 | 16.83 407010 10 G 561 Escherichia 15 | 16.81 406594 406594 S 562 Escherichia coli 16 | 0.02 388 388 S 564 Escherichia fergusonii 17 | 0.00 11 11 S 1499973 Escherichia marmotae 18 | 0.00 7 7 S 208962 Escherichia albertii 19 | 0.24 5865 64 G 620 Shigella 20 | 0.13 3100 3100 S 1813821 Shigella sp. PAMC 28760 21 | 0.06 1387 1387 S 622 Shigella dysenteriae 22 | 0.05 1314 1314 S 623 Shigella flexneri 23 | 0.00 33 0 G 590 Salmonella 24 | 0.00 33 33 S 28901 Salmonella enterica 25 | 0.00 28 0 G 544 Citrobacter 26 | 0.00 23 0 S 1344959 Citrobacter freundii complex 27 | 0.00 15 15 S 546 Citrobacter freundii 28 | 0.00 7 7 S 2077147 Citrobacter freundii complex sp. CFNIH3 29 | 0.00 1 1 S 2077149 Citrobacter freundii complex sp. CFNIH9 30 | 0.00 5 5 S 545 Citrobacter koseri 31 | 0.00 24 0 G 570 Klebsiella 32 | 0.00 19 19 S 571 Klebsiella oxytoca 33 | 0.00 5 5 S 1134687 Klebsiella michiganensis 34 | 0.00 2 0 G 547 Enterobacter 35 | 0.00 1 0 S 354276 Enterobacter cloacae complex 36 | 0.00 1 1 S 1915310 Enterobacter cloacae complex sp. ECNIH7 37 | 0.00 1 1 S 1166130 Enterobacter sp. R4-368 38 | 0.00 43 0 F 1903414 Morganellaceae 39 | 0.00 27 0 G 581 Morganella 40 | 0.00 27 27 S 582 Morganella morganii 41 | 0.00 16 0 G 583 Proteus 42 | 0.00 16 16 S 584 Proteus mirabilis 43 | 4.52 109246 0 O 72274 Pseudomonadales 44 | 4.28 103594 0 F 135621 Pseudomonadaceae 45 | 4.28 103594 0 G 286 Pseudomonas 46 | 4.27 103412 0 S 136841 Pseudomonas aeruginosa group 47 | 4.27 103412 103412 S 287 Pseudomonas aeruginosa 48 | 0.01 130 130 S 1898684 Pseudomonas sp. LPH1 49 | 0.00 52 52 S 1338689 Pseudomonas sp. JY-Q 50 | 0.23 5652 0 F 468 Moraxellaceae 51 | 0.23 5652 1 G 469 Acinetobacter 52 | 0.23 5651 35 S 909768 Acinetobacter calcoaceticus/baumannii complex 53 | 0.22 5395 5395 S 470 Acinetobacter baumannii 54 | 0.01 217 217 S 471 Acinetobacter calcoaceticus 55 | 0.00 2 2 S 48296 Acinetobacter pittii 56 | 0.00 2 2 S 106654 Acinetobacter nosocomialis 57 | 0.00 5 0 O 135624 Aeromonadales 58 | 0.00 5 0 F 84642 Aeromonadaceae 59 | 0.00 5 0 G 642 Aeromonas 60 | 0.00 5 5 S 1758179 Aeromonas sp. ASNIH5 61 | 0.00 3 0 O 135614 Xanthomonadales 62 | 0.00 3 0 F 32033 Xanthomonadaceae 63 | 0.00 3 0 G 68 Lysobacter 64 | 0.00 3 3 S 69 Lysobacter enzymogenes 65 | 0.17 4012 0 C 28216 Betaproteobacteria 66 | 0.13 3041 0 O 206351 Neisseriales 67 | 0.13 3041 0 F 481 Neisseriaceae 68 | 0.13 3041 1 G 482 Neisseria 69 | 0.13 3035 3035 S 487 Neisseria meningitidis 70 | 0.00 5 5 S 485 Neisseria gonorrhoeae 71 | 0.04 971 208 O 80840 Burkholderiales 72 | 0.03 633 324 F 119060 Burkholderiaceae 73 | 0.01 285 0 G 106589 Cupriavidus 74 | 0.01 285 285 S 119219 Cupriavidus metallidurans 75 | 0.00 22 0 G 32008 Burkholderia 76 | 0.00 22 0 S 87882 Burkholderia cepacia complex 77 | 0.00 22 22 S 95486 Burkholderia cenocepacia 78 | 0.00 2 0 G 48736 Ralstonia 79 | 0.00 1 1 S 329 Ralstonia pickettii 80 | 0.00 1 1 S 190721 Ralstonia insidiosa 81 | 0.01 127 46 F 506 Alcaligenaceae 82 | 0.00 45 0 G 517 Bordetella 83 | 0.00 45 45 S 463040 Bordetella genomosp. 13 84 | 0.00 36 0 G 222 Achromobacter 85 | 0.00 36 36 S 217203 Achromobacter spanius 86 | 0.00 3 0 F 80864 Comamonadaceae 87 | 0.00 3 0 G 47420 Hydrogenophaga 88 | 0.00 3 3 S 795665 Hydrogenophaga sp. PBC 89 | 0.07 1599 0 - 68525 delta/epsilon subdivisions 90 | 0.07 1592 0 C 29547 Epsilonproteobacteria 91 | 0.07 1592 0 O 213849 Campylobacterales 92 | 0.07 1592 0 F 72293 Helicobacteraceae 93 | 0.07 1592 0 G 209 Helicobacter 94 | 0.07 1592 1592 S 210 Helicobacter pylori 95 | 0.00 7 0 C 28221 Deltaproteobacteria 96 | 0.00 7 0 O 213118 Desulfobacterales 97 | 0.00 7 0 F 213121 Desulfobulbaceae 98 | 0.00 7 0 G 109168 Desulfotalea 99 | 0.00 7 7 S 84980 Desulfotalea psychrophila 100 | 23.47 567729 13 - 1783272 Terrabacteria group 101 | 23.25 562388 65 P 1239 Firmicutes 102 | 22.09 534257 42 C 91061 Bacilli 103 | 12.10 292604 0 O 1385 Bacillales 104 | 9.64 233304 4 F 90964 Staphylococcaceae 105 | 9.64 233300 2639 G 1279 Staphylococcus 106 | 8.82 213389 213389 S 1282 Staphylococcus epidermidis 107 | 0.67 16093 16093 S 1280 Staphylococcus aureus 108 | 0.02 414 414 S 283734 Staphylococcus pseudintermedius 109 | 0.02 404 404 S 1283 Staphylococcus haemolyticus 110 | 0.01 261 261 S 1286 Staphylococcus simulans 111 | 0.00 40 40 S 985002 Staphylococcus argenteus 112 | 0.00 28 28 S 70255 Staphylococcus condimenti 113 | 0.00 13 13 S 985762 Staphylococcus agnetis 114 | 0.00 12 12 S 29388 Staphylococcus capitis 115 | 0.00 7 7 S 1295 Staphylococcus schleiferi 116 | 2.45 59300 0 F 186817 Bacillaceae 117 | 2.45 59300 522 G 1386 Bacillus 118 | 2.39 57889 520 S 86661 Bacillus cereus group 119 | 2.35 56803 56803 S 1396 Bacillus cereus 120 | 0.02 545 545 S 1428 Bacillus thuringiensis 121 | 0.00 18 18 S 1392 Bacillus anthracis 122 | 0.00 2 2 S 155322 Bacillus toyonensis 123 | 0.00 1 1 S 1405 Bacillus mycoides 124 | 0.02 506 506 S 1892404 Bacillus sp. ABP14 125 | 0.02 379 379 S 2053832 Bacillus sp. HBCD-sjtu 126 | 0.00 3 3 S 658666 Bacillus bombysepticus 127 | 0.00 1 1 S 1839798 Bacillus sp. FDAARGOS_235 128 | 9.99 241611 21 O 186826 Lactobacillales 129 | 9.92 240006 0 F 1300 Streptococcaceae 130 | 9.92 240006 420 G 1301 Streptococcus 131 | 9.22 223093 223093 S 1309 Streptococcus mutans 132 | 0.57 13710 13710 S 1311 Streptococcus agalactiae 133 | 0.10 2519 2519 S 1319 Streptococcus sp. 'group B' 134 | 0.01 246 0 S 119603 Streptococcus dysgalactiae group 135 | 0.01 246 246 S 1334 Streptococcus dysgalactiae 136 | 0.00 9 9 S 45634 Streptococcus cristatus 137 | 0.00 5 5 S 1304 Streptococcus salivarius 138 | 0.00 3 0 S 671232 Streptococcus anginosus group 139 | 0.00 3 3 S 76860 Streptococcus constellatus 140 | 0.00 1 1 S 1307 Streptococcus suis 141 | 0.06 1401 0 F 33958 Lactobacillaceae 142 | 0.06 1401 0 G 1578 Lactobacillus 143 | 0.06 1399 1399 S 1596 Lactobacillus gasseri 144 | 0.00 2 2 S 1599 Lactobacillus sakei 145 | 0.01 166 0 F 81852 Enterococcaceae 146 | 0.01 166 0 G 1350 Enterococcus 147 | 0.01 166 166 S 1351 Enterococcus faecalis 148 | 0.00 17 0 F 186827 Aerococcaceae 149 | 0.00 17 0 G 1375 Aerococcus 150 | 0.00 17 17 S 87541 Aerococcus christensenii 151 | 1.16 28066 0 C 186801 Clostridia 152 | 1.16 28066 0 O 186802 Clostridiales 153 | 1.16 28066 0 F 31979 Clostridiaceae 154 | 1.16 28066 2 G 1485 Clostridium 155 | 1.16 28064 28064 S 1520 Clostridium beijerinckii 156 | 0.20 4784 0 P 201174 Actinobacteria 157 | 0.20 4784 0 C 1760 Actinobacteria 158 | 0.19 4689 0 O 85009 Propionibacteriales 159 | 0.19 4689 0 F 31957 Propionibacteriaceae 160 | 0.19 4675 0 G 1912216 Cutibacterium 161 | 0.19 4675 4675 S 1747 Cutibacterium acnes 162 | 0.00 14 0 G 1743 Propionibacterium 163 | 0.00 14 14 S 671223 Propionibacterium sp. oral taxon 193 164 | 0.00 95 0 O 85004 Bifidobacteriales 165 | 0.00 95 0 F 31953 Bifidobacteriaceae 166 | 0.00 95 0 G 1678 Bifidobacterium 167 | 0.00 94 94 S 1680 Bifidobacterium adolescentis 168 | 0.00 1 1 S 1686 Bifidobacterium catenulatum 169 | 0.02 534 0 P 1297 Deinococcus-Thermus 170 | 0.02 534 0 C 188787 Deinococci 171 | 0.02 534 0 O 118964 Deinococcales 172 | 0.02 534 0 F 183710 Deinococcaceae 173 | 0.02 534 0 G 1298 Deinococcus 174 | 0.02 534 534 S 1299 Deinococcus radiodurans 175 | 0.00 10 0 P 544448 Tenericutes 176 | 0.00 10 0 C 31969 Mollicutes 177 | 0.00 10 0 O 2085 Mycoplasmatales 178 | 0.00 10 0 F 2092 Mycoplasmataceae 179 | 0.00 10 0 G 2093 Mycoplasma 180 | 0.00 10 0 S 656088 Mycoplasma mycoides group 181 | 0.00 10 10 S 2102 Mycoplasma mycoides 182 | 11.17 270218 0 - 1783270 FCB group 183 | 11.17 270218 0 - 68336 Bacteroidetes/Chlorobi group 184 | 11.17 270218 0 P 976 Bacteroidetes 185 | 11.17 270218 0 C 200643 Bacteroidia 186 | 11.17 270218 16 O 171549 Bacteroidales 187 | 11.14 269560 0 F 171551 Porphyromonadaceae 188 | 11.14 269560 0 G 836 Porphyromonas 189 | 11.14 269560 269560 S 837 Porphyromonas gingivalis 190 | 0.03 639 0 F 815 Bacteroidaceae 191 | 0.03 639 0 G 816 Bacteroides 192 | 0.03 639 639 S 821 Bacteroides vulgatus 193 | 0.00 2 0 F 2005525 Tannerellaceae 194 | 0.00 2 0 G 195950 Tannerella 195 | 0.00 2 2 S 28112 Tannerella forsythia 196 | 0.00 1 0 F 171552 Prevotellaceae 197 | 0.00 1 0 G 838 Prevotella 198 | 0.00 1 1 S 28131 Prevotella intermedia 199 | -------------------------------------------------------------------------------- /Example_Outputs/ATCC.bracken.kreport.txt: -------------------------------------------------------------------------------- 1 | 100.00 2418044 0 R 1 root 2 | 100.00 2418032 0 R1 131567 cellular organisms 3 | 100.00 2418004 0 D 2 Bacteria 4 | 63.88 1544751 0 P 1224 Proteobacteria 5 | 33.36 806711 0 C 28211 Alphaproteobacteria 6 | 33.36 806631 0 O 204455 Rhodobacterales 7 | 33.36 806631 0 F 31989 Rhodobacteraceae 8 | 33.36 806631 0 G 1653176 Cereibacter 9 | 33.36 806631 806631 S 1063 Cereibacter sphaeroides 10 | 0.00 80 0 O 356 Hyphomicrobiales 11 | 0.00 80 0 F 41294 Bradyrhizobiaceae 12 | 0.00 80 0 G 374 Bradyrhizobium 13 | 0.00 80 0 G1 2631580 unclassified Bradyrhizobium 14 | 0.00 80 80 S 2715960 Bradyrhizobium sp. PSBB068 15 | 30.31 733022 0 C 1236 Gammaproteobacteria 16 | 25.22 609808 0 O 91347 Enterobacterales 17 | 25.22 609808 0 F 543 Enterobacteriaceae 18 | 25.08 606526 0 G 561 Escherichia 19 | 25.03 605201 605201 S 562 Escherichia coli 20 | 0.02 502 502 S 564 Escherichia fergusonii 21 | 0.01 296 296 S 208962 Escherichia albertii 22 | 0.01 273 273 S 1499973 Escherichia marmotae 23 | 0.01 253 0 G1 2608889 unclassified Escherichia 24 | 0.01 253 253 S 2044467 Escherichia sp. E4742 25 | 0.04 947 0 G 547 Enterobacter 26 | 0.03 672 0 G1 2608935 unclassified Enterobacter 27 | 0.03 672 672 S 2724468 Enterobacter sp. JUb54 28 | 0.01 274 0 G1 354276 Enterobacter cloacae complex 29 | 0.01 143 143 S 550 Enterobacter cloacae 30 | 0.00 77 77 S 1812935 Enterobacter roggenkampii 31 | 0.00 53 53 S 158836 Enterobacter hormaechei 32 | 0.03 827 0 G 620 Shigella 33 | 0.02 376 376 S 622 Shigella dysenteriae 34 | 0.01 256 256 S 621 Shigella boydii 35 | 0.01 194 194 S 623 Shigella flexneri 36 | 0.03 684 0 G 544 Citrobacter 37 | 0.02 601 0 G1 1344959 Citrobacter freundii complex 38 | 0.02 386 386 S 67827 Citrobacter werkmanii 39 | 0.01 215 215 S 546 Citrobacter freundii 40 | 0.00 82 0 G1 2644389 unclassified Citrobacter 41 | 0.00 82 82 S 2742624 Citrobacter sp. RHB25-C09 42 | 0.02 435 0 G 2815296 Jejubacter 43 | 0.02 435 435 S 2579935 Jejubacter calystegiae 44 | 0.01 206 0 G 590 Salmonella 45 | 0.01 206 206 S 28901 Salmonella enterica 46 | 0.01 181 0 G 570 Klebsiella 47 | 0.00 84 84 S 2153354 Klebsiella huaxiensis 48 | 0.00 97 97 S 573 Klebsiella pneumoniae 49 | 5.10 123214 0 O 72274 Pseudomonadales 50 | 4.85 117382 0 F 135621 Pseudomonadaceae 51 | 4.85 117382 0 G 286 Pseudomonas 52 | 4.85 117382 0 G1 136841 Pseudomonas aeruginosa group 53 | 4.85 117382 117382 S 287 Pseudomonas aeruginosa 54 | 0.24 5831 0 F 468 Moraxellaceae 55 | 0.24 5831 0 G 469 Acinetobacter 56 | 0.24 5831 0 G1 909768 Acinetobacter calcoaceticus/baumannii complex 57 | 0.24 5831 5831 S 470 Acinetobacter baumannii 58 | 0.14 3356 0 C 28216 Betaproteobacteria 59 | 0.13 3159 0 O 206351 Neisseriales 60 | 0.13 3159 0 F 481 Neisseriaceae 61 | 0.13 3159 0 G 482 Neisseria 62 | 0.13 3159 3159 S 487 Neisseria meningitidis 63 | 0.01 197 0 O 80840 Burkholderiales 64 | 0.01 155 0 F 119060 Burkholderiaceae 65 | 0.01 124 0 G 48736 Ralstonia 66 | 0.01 124 124 S 305 Ralstonia solanacearum 67 | 0.00 31 0 G 106589 Cupriavidus 68 | 0.00 31 0 G1 2640874 unclassified Cupriavidus 69 | 0.00 31 31 S 876364 Cupriavidus sp. USMAA2-4 70 | 0.00 41 0 F 80864 Comamonadaceae 71 | 0.00 41 0 G 238749 Diaphorobacter 72 | 0.00 41 41 S 1288495 Diaphorobacter aerolatus 73 | 0.07 1661 0 P1 68525 delta/epsilon subdivisions 74 | 0.07 1661 0 C 29547 Epsilonproteobacteria 75 | 0.07 1661 0 O 213849 Campylobacterales 76 | 0.07 1661 0 F 72293 Helicobacteraceae 77 | 0.07 1661 0 G 209 Helicobacter 78 | 0.07 1661 1661 S 210 Helicobacter pylori 79 | 24.58 594393 0 D1 1783272 Terrabacteria group 80 | 24.35 588804 0 P 1239 Firmicutes 81 | 23.12 559155 0 C 91061 Bacilli 82 | 12.91 312074 0 O 1385 Bacillales 83 | 10.29 248928 0 F 90964 Staphylococcaceae 84 | 10.29 248928 0 G 1279 Staphylococcus 85 | 9.58 231617 231617 S 1282 Staphylococcus epidermidis 86 | 0.70 17025 17025 S 1280 Staphylococcus aureus 87 | 0.00 84 84 S 1283 Staphylococcus haemolyticus 88 | 0.00 69 69 S 1290 Staphylococcus hominis 89 | 0.00 49 49 S 29388 Staphylococcus capitis 90 | 0.00 45 45 S 1654388 Staphylococcus schweitzeri 91 | 0.00 38 38 S 308354 Staphylococcus simiae 92 | 2.61 63146 0 F 186817 Bacillaceae 93 | 2.61 63146 0 G 1386 Bacillus 94 | 2.61 63146 0 G1 86661 Bacillus cereus group 95 | 2.44 58896 58896 S 1396 Bacillus cereus 96 | 0.06 1540 1540 S 1428 Bacillus thuringiensis 97 | 0.03 721 721 S 1392 Bacillus anthracis 98 | 0.02 466 466 S 2026191 Bacillus luti 99 | 0.02 438 438 S 2026187 Bacillus pacificus 100 | 0.01 309 309 S 2026186 Bacillus paranthracis 101 | 0.01 231 231 S 2026189 Bacillus albus 102 | 0.01 207 207 S 1890302 Bacillus wiedmannii 103 | 0.01 127 127 S 580165 Bacillus cytotoxicus 104 | 0.00 112 112 S 64104 Bacillus pseudomycoides 105 | 0.00 78 78 S 1405 Bacillus mycoides 106 | 0.00 18 0 G2 2750818 unclassified Bacillus cereus group 107 | 0.00 18 18 S 1892404 Bacillus sp. ABP14 108 | 10.22 247081 0 O 186826 Lactobacillales 109 | 10.15 245436 0 F 1300 Streptococcaceae 110 | 10.15 245436 0 G 1301 Streptococcus 111 | 9.49 229434 229434 S 1309 Streptococcus mutans 112 | 0.52 12638 12638 S 1311 Streptococcus agalactiae 113 | 0.08 1818 0 G1 2608887 unclassified Streptococcus 114 | 0.03 823 823 S 2420310 Streptococcus sp. FDAARGOS_522 115 | 0.03 794 794 S 2420309 Streptococcus sp. FDAARGOS_521 116 | 0.01 131 131 S 2420308 Streptococcus sp. FDAARGOS_520 117 | 0.00 69 69 S 1940319 Streptococcus sp. DAT741 118 | 0.01 306 306 S 1314 Streptococcus pyogenes 119 | 0.01 287 0 G1 119603 Streptococcus dysgalactiae group 120 | 0.01 287 287 S 1334 Streptococcus dysgalactiae 121 | 0.01 154 154 S 1307 Streptococcus suis 122 | 0.01 130 130 S 1329 Streptococcus canis 123 | 0.00 96 96 S 1349 Streptococcus uberis 124 | 0.00 83 83 S 361101 Streptococcus pseudoporcinus 125 | 0.00 78 78 S 1340 Streptococcus porcinus 126 | 0.00 64 64 S 1335 Streptococcus equinus 127 | 0.00 64 64 S 1305 Streptococcus sanguinis 128 | 0.00 49 49 S 1304 Streptococcus salivarius 129 | 0.00 43 43 S 400065 Streptococcus merionis 130 | 0.00 37 37 S 1111760 Streptococcus troglodytae 131 | 0.00 30 30 S 150055 Streptococcus lutetiensis 132 | 0.00 23 23 S 45634 Streptococcus cristatus 133 | 0.00 22 22 S 102684 Streptococcus infantarius 134 | 0.00 18 18 S 1345 Streptococcus ferus 135 | 0.00 17 0 G1 671232 Streptococcus anginosus group 136 | 0.00 17 17 S 1338 Streptococcus intermedius 137 | 0.00 14 14 S 1302 Streptococcus gordonii 138 | 0.00 14 14 S 1308 Streptococcus thermophilus 139 | 0.00 14 14 S 1348 Streptococcus parauberis 140 | 0.06 1428 0 F 33958 Lactobacillaceae 141 | 0.06 1428 0 G 1578 Lactobacillus 142 | 0.06 1428 1428 S 1596 Lactobacillus gasseri 143 | 0.01 217 0 F 81852 Enterococcaceae 144 | 0.01 217 0 G 1350 Enterococcus 145 | 0.01 217 217 S 1351 Enterococcus faecalis 146 | 1.23 29648 0 C 186801 Clostridia 147 | 1.23 29648 0 O 186802 Eubacteriales 148 | 1.22 29617 0 F 31979 Clostridiaceae 149 | 1.22 29617 0 G 1485 Clostridium 150 | 1.22 29568 29568 S 1520 Clostridium beijerinckii 151 | 0.00 28 28 S 223919 Clostridium diolis 152 | 0.00 21 21 S 1491 Clostridium botulinum 153 | 0.00 31 0 F 186804 Peptostreptococcaceae 154 | 0.00 31 0 G 1870884 Clostridioides 155 | 0.00 31 31 S 1496 Clostridioides difficile 156 | 0.21 5047 0 P 201174 Actinobacteria 157 | 0.21 5047 0 C 1760 Actinomycetia 158 | 0.20 4796 0 O 85009 Propionibacteriales 159 | 0.20 4796 0 F 31957 Propionibacteriaceae 160 | 0.20 4796 0 G 1912216 Cutibacterium 161 | 0.20 4796 4796 S 1747 Cutibacterium acnes 162 | 0.01 142 0 O 2037 Actinomycetales 163 | 0.01 142 0 F 2049 Actinomycetaceae 164 | 0.01 142 0 G 2529408 Schaalia 165 | 0.01 142 142 S 1660 Schaalia odontolytica 166 | 0.00 108 0 O 85004 Bifidobacteriales 167 | 0.00 108 0 F 31953 Bifidobacteriaceae 168 | 0.00 108 0 G 1678 Bifidobacterium 169 | 0.00 108 108 S 1680 Bifidobacterium adolescentis 170 | 0.02 542 0 P 1297 Deinococcus-Thermus 171 | 0.02 542 0 C 188787 Deinococci 172 | 0.02 542 0 O 118964 Deinococcales 173 | 0.02 542 0 F 183710 Deinococcaceae 174 | 0.02 542 0 G 1298 Deinococcus 175 | 0.02 542 542 S 1299 Deinococcus radiodurans 176 | 11.53 278860 0 D1 1783270 FCB group 177 | 11.53 278860 0 D2 68336 Bacteroidetes/Chlorobi group 178 | 11.53 278860 0 P 976 Bacteroidetes 179 | 11.53 278860 0 C 200643 Bacteroidia 180 | 11.53 278860 0 O 171549 Bacteroidales 181 | 11.51 278215 0 F 171551 Porphyromonadaceae 182 | 11.51 278215 0 G 836 Porphyromonas 183 | 11.51 278215 278215 S 837 Porphyromonas gingivalis 184 | 0.03 645 0 O1 333046 Bacteroidales incertae sedis 185 | 0.03 645 0 G 909656 Phocaeicola 186 | 0.03 645 645 S 821 Phocaeicola vulgatus 187 | 0.00 28 0 D 2759 Eukaryota 188 | 0.00 28 0 D1 33154 Opisthokonta 189 | 0.00 28 0 K 33208 Metazoa 190 | 0.00 28 0 K1 6072 Eumetazoa 191 | 0.00 28 0 K2 33213 Bilateria 192 | 0.00 28 0 K3 33511 Deuterostomia 193 | 0.00 28 0 P 7711 Chordata 194 | 0.00 28 0 P1 89593 Craniata 195 | 0.00 28 0 P2 7742 Vertebrata 196 | 0.00 28 0 P3 7776 Gnathostomata 197 | 0.00 28 0 P4 117570 Teleostomi 198 | 0.00 28 0 P5 117571 Euteleostomi 199 | 0.00 28 0 P6 8287 Sarcopterygii 200 | 0.00 28 0 C 1338369 Dipnotetrapodomorpha 201 | 0.00 28 0 C1 32523 Tetrapoda 202 | 0.00 28 0 C2 32524 Amniota 203 | 0.00 28 0 C 40674 Mammalia 204 | 0.00 28 0 C1 32525 Theria 205 | 0.00 28 0 C2 9347 Eutheria 206 | 0.00 28 0 C3 1437010 Boreoeutheria 207 | 0.00 28 0 C4 314146 Euarchontoglires 208 | 0.00 28 0 O 9443 Primates 209 | 0.00 28 0 O1 376913 Haplorrhini 210 | 0.00 28 0 O2 314293 Simiiformes 211 | 0.00 28 0 O3 9526 Catarrhini 212 | 0.00 28 0 O4 314295 Hominoidea 213 | 0.00 28 0 F 9604 Hominidae 214 | 0.00 28 0 F1 207598 Homininae 215 | 0.00 28 0 G 9605 Homo 216 | 0.00 28 28 S 9606 Homo sapiens 217 | 0.00 12 0 D 10239 Viruses 218 | 0.00 12 0 D1 2731341 Duplodnaviria 219 | 0.00 12 0 D2 2731360 Heunggongvirae 220 | 0.00 12 0 P 2731618 Uroviricota 221 | 0.00 12 0 C 2731619 Caudoviricetes 222 | 0.00 12 0 O 28883 Caudovirales 223 | 0.00 12 0 F 10699 Siphoviridae 224 | 0.00 12 0 G 1623274 Biseptimavirus 225 | 0.00 12 0 G1 1955180 unclassified Biseptimavirus 226 | 0.00 12 12 S 1505027 Staphylococcus phage 23MRA 227 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Taxonomic profiling for long-read shotgun metagenomics datasets 2 | 3 | ## **Table of Contents** 4 | 5 | **Overview** 6 | + [**Introduction**](#INTRO) 7 | + [**Example Dataset**](#EXDA) 8 | 9 | **Analyses** 10 | + [**Kraken2 & Bracken**](#KRBR) 11 | + [**Centrifuge**](#CENT) 12 | + [**MMSeqs2**](#MMSEQ) 13 | + [**BugSeq**](#BS) <- top performing method 14 | + [**Diamond & MEGAN-LR**](#MEG) <- top performing method 15 | 16 | **Summary** 17 | + [**Comparative Analysis**](#COMP) 18 | 19 | 20 | ## Introduction 21 | 22 | This tutorial was created for the [**Long Read Sequencing Workshop**](https://www.jax.org/education-and-learning/education-calendar/2022/may/long-read-sequencing-workshop) (2022) at The Jackson Laboratory for Genomic Medicine. It is an introduction to several methods that can be used to identify the number of species and associated relative abundances from a long-read metagenomic dataset. The analyses covered here are a subset of those performed in the following benchmarking study: 23 | 24 | [**Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets**](https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1) 25 | 26 | The above study evaluated a total of 9 methods using four mock community datasets. To keep the tutorial simple, I will demonstrate how to use 6 of these methods to analyze one mock community dataset: 27 | 28 | + **Kraken2** 29 | + **Bracken** 30 | + **Centrifuge** 31 | + **MMseqs2** 32 | + **BugSeq** <- top performing method 33 | + **Diamond + MEGAN-LR** <- top performing method 34 | 35 | The top-performing methods were **BugSeq** and **Diamond + MEGAN-LR**, both in terms of precision/recall and relative abundance estimates. **MMSeqs2** performed moderately well, whereas **Kraken2**, **Bracken**, and **Centrifuge** performed less well. There is plenty of room for the development of newer and better tools for profiling long-read datasets. However, these existing tools serve an important function and provide a baseline for future improvements. 36 | 37 | A small tutorial is provided for each of the 6 methods above. Each tutorial includes instructions for installing the program and associated reference database, and the commands to run the program. 38 | 39 | The simplest way to install programs and their dependencies into a single environment is to use [Anaconda](https://docs.anaconda.com/anaconda/)/[Conda](https://docs.conda.io/projects/conda/en/latest/index.html). Instructions for conda installation are therefore provided for each program. Manual installation is also possible; links to the program sources are provided. Databases will also need to be obtained for each program. 40 | 41 | The main objective is to obtain a kraken-style report (kreport) for each method. This format is highly useful because it contains cumulative counts and level counts across the complete hierarchical taxonomy for each taxon assigned. The level count is the number of reads specifically assigned to a taxon, whereas the cumulative count is the sum of the level counts for a taxon plus its descendants. For example, the cumulative count of a genus is the level count for that genus plus the level counts of all species and strains contained in that genus. The following columns are present in the kreport format: 42 | 43 | + `Percent Reads Contained in Taxon`: The cumulative percentage of reads for this taxon and all descendants. 44 | + `Number of Reads Contained in Taxon`: The cumulative number of reads for this taxon and all descendants. 45 | + `Number of Reads Assigned to Taxon`: The number of reads assigned directly to this taxon (not a cumulative count of all descendants). 46 | + `Rank Code`: (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. 47 | + `NCBI Taxon ID`: Numerical ID from the NCBI taxonomy database. 48 | + `Scientific Name`: The scientific name of the taxon. 49 | 50 | Example contents of a kreport: 51 | 52 | ``` 53 | 88.41 2138742 193618 K 2 Bacteria 54 | 0.16 3852 818 P 201174 Actinobacteria 55 | 0.13 3034 0 C 1760 Actinomycetia 56 | 0.13 3034 45 O 85009 Propionibacteriales 57 | 0.12 2989 1847 F 31957 Propionibacteriaceae 58 | 0.05 1142 352 G 1912216 Cutibacterium 59 | 0.03 790 790 S 1747 Cutibacterium acnes 60 | 10.07 243594 9919 P 976 Bacteroidetes 61 | 9.66 233675 996 C 200643 Bacteroidia 62 | 9.62 232679 65248 O 171549 Bacteroidales 63 | 6.92 167431 1059 F 171551 Porphyromonadaceae 64 | 6.88 166372 36434 G 836 Porphyromonas 65 | 5.37 129938 129938 S 837 Porphyromonas gingivalis 66 | ``` 67 | 68 | You are welcome to run some or all of the analyses. Outputs from each analysis are provided in the [**Example_Outputs**](https://github.com/dportik/LRSW-Taxonomic-Profiling-Tutorial/tree/main/Example_Outputs), and can be used to run the comparative analysis. 69 | 70 | [**Back to top**](#TOP) 71 | 72 | ## Example Dataset 73 | 74 | For this section we will use [**seqtk**](https://github.com/lh3/seqtk) for file format conversion. It can be installed using the following options: 75 | 76 | conda 77 | ``` 78 | $ conda create --name seqtk-env -c bioconda seqtk 79 | 80 | # activate the environment 81 | $ conda activate seqtk-env 82 | ``` 83 | 84 | github 85 | ``` 86 | $ git clone https://github.com/lh3/seqtk.git 87 | $ cd seqtk; make 88 | ``` 89 | 90 | The example dataset used for the tutorial is [**ATCC MSA-1003**](https://www.atcc.org/products/msa-1003), sequencing with PacBio HiFi. The ATCC MSA-1003 mock community contains 20 bacteria species with the following staggered design: 91 | 92 | |Number of species| Relative abundance| 93 | |----:|----:| 94 | |5|18.00%| 95 | |5|1.80%| 96 | |5|0.18%| 97 | |5|0.02%| 98 | 99 | The dataset was generated using the Sequel II System and contains 2.4 million HiFi reads with a median length of 8.3 kb, for a total of 20.5 Gbp of data. 100 | 101 | This dataset is available on NCBI ([**SRR9328980**](https://www.ncbi.nlm.nih.gov/sra/SRR9328980)). We can download it as a `fastq.gz` file that is ~15 Gb in size. We will need to convert this to `fasta` format for several programs. The following commands can be used to download the data, rename the file, and convert to fasta format: 102 | 103 | ``` 104 | # make directory for data 105 | $ mkdir data 106 | $ cd data 107 | 108 | # download from NCBI 109 | $ wget https://sra-pub-src-1.s3.amazonaws.com/SRR9328980/m64015_190521_115634.Q20.fastq.gz.1 110 | 111 | # rename file 112 | $ mv m64015_190521_115634.Q20.fastq.gz.1 ATCC.fastq.gz 113 | 114 | # convert to fasta using seqtk 115 | $ seqtk seq -a ATCC.fastq.gz > ATCC.fasta 116 | 117 | $ cd .. 118 | ``` 119 | 120 | The directory should now contain the following files: 121 | 122 | ``` 123 | 124 | ├── data/ 125 | │ ├── ATCC.fasta 126 | │ └── ATCC.fastq.gz 127 | ``` 128 | 129 | [**Back to top**](#TOP) 130 | 131 | 132 | ## Kraken2 & Bracken 133 | 134 | [**Kraken2**](https://ccb.jhu.edu/software/kraken2/) is a kmer-based approach, and [**Bracken**](https://github.com/jenniferlu717/Bracken) is a companion program that provides Bayesian refinement of abundance estimates. 135 | 136 | ### Program & Database Installation 137 | 138 | We will first install **Kraken2** and **Bracken**, and then obtain a suitable database. 139 | 140 | Conda installation: 141 | 142 | ``` 143 | $ conda create --name krakenbracken-env -c bioconda kraken2 bracken 144 | 145 | # activate the environment 146 | $ conda activate krakenbracken-env 147 | ``` 148 | 149 | For manual installation, follow instructions for **Kraken2** ([**here**](https://github.com/DerrickWood/kraken2)) and for **Bracken** ([**here**](https://github.com/jenniferlu717/Bracken)). 150 | 151 | **Kraken2** and **Bracken** rely on the same style of database. Several pre-compiled databases are available [**here**](https://benlangmead.github.io/aws-indexes/k2). We will use the `PlusPF` database from 2021, which contains archaea, bacteria, viral, plasmid, human, UniVec_Core, protozoa & fungi sequences. It has all files required for both **Kraken2** and **Bracken**. The unzipped size is roughly ~58 Gb. 152 | 153 | ``` 154 | # create a directory for the analysis 155 | $ mkdir krakenbracken_analysis 156 | $ cd krakenbracken_analysis 157 | 158 | # make a directory to hold the database files 159 | $ mkdir kraken_db 160 | $ cd kraken_db 161 | 162 | # download and unpack the database 163 | $ wget https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_20210517.tar.gz 164 | $ tar -xvzf k2_pluspf_20210517.tar.gz 165 | $ rm k2_pluspf_20210517.tar.gz 166 | $ cd .. 167 | ``` 168 | 169 | The directory should now contain the following: 170 | 171 | ``` 172 | ├── data/ 173 | │ ├── ATCC.fasta 174 | │ └── ATCC.fastq.gz 175 | │ 176 | ├── krakenbracken_analysis/ 177 | │ │ 178 | │ └── kraken_db/ 179 | │ ├── hash.k2d 180 | │ ├── opts.k2d 181 | │ ├── taxo.k2d 182 | │ ├── seqid2taxid.map 183 | │ ├── inspect.txt 184 | │ ├── database100mers.kmer_distrib 185 | │ ├── database150mers.kmer_distrib 186 | │ ├── database200mers.kmer_distrib 187 | │ ├── database250mers.kmer_distrib 188 | │ ├── database300mers.kmer_distrib 189 | │ ├── database50mers.kmer_distrib 190 | │ └── database75mers.kmer_distrib 191 | ``` 192 | 193 | 194 | ### Analysis Instructions 195 | 196 | From the `krakenbracken_analysis/` directory, run **Kraken2** the following general command to generate the kreport file. Change the number of threads and path to fasta file as necessary. This analysis should take <30 min. 197 | 198 | ``` 199 | $ kraken2 --db kraken_db --threads 12 --output ATCC.kraken --report ATCC.kraken.kreport.txt /data/ATCC.fasta 200 | ``` 201 | 202 | We can then run **Bracken** to generate the refined kreport. Change the number of threads as necessary. This analysis will be nearly instantaneous. 203 | 204 | ``` 205 | $ bracken -d kraken_db -t 12 -i ATCC.kraken.kreport.txt -o ATCC.bracken -l S 206 | 207 | # rename output 208 | $ mv ATCC.kreport_bracken_species.txt ATCC.bracken.kreport.txt 209 | ``` 210 | 211 | The directory should now contain two kreport files with the taxonomic profiles for the sample, one from Kraken2 and one from Bracken: 212 | 213 | ``` 214 | ├── data/ 215 | │ ├── ATCC.fasta 216 | │ └── ATCC.fastq.gz 217 | │ 218 | ├── krakenbracken_analysis/ 219 | │ ├── ATCC.bracken 220 | │ ├── ATCC.bracken.kreport.txt <- kreport from Bracken 221 | │ ├── ATCC.kraken 222 | │ ├── ATCC.kraken.kreport.txt <- kreport from Kraken2 223 | │ └── kraken_db/ 224 | ``` 225 | 226 | [**Back to top**](#TOP) 227 | 228 | ## Centrifuge 229 | 230 | [**Centrifuge**](http://www.ccb.jhu.edu/software/centrifuge/index.shtml) is a kmer-based profiling approach. 231 | 232 | ### Program & Database Installation 233 | 234 | We will first install **Centrifuge**, and then obtain a suitable database. 235 | 236 | Conda installation: 237 | 238 | ``` 239 | $ conda create --name centrifuge-env -c bioconda centrifuge 240 | 241 | # activate the environment 242 | $ conda activate centrifuge-env 243 | ``` 244 | 245 | For manual installation, follow instructions for **Centrifuge** on github [**here**](https://github.com/DaehwanKimLab/centrifuge) or on the website [**here**](http://www.ccb.jhu.edu/software/centrifuge/manual.shtml#obtaining-centrifuge). 246 | 247 | For **Centrifuge**, a few older pre-compiled databases are available [**here**](https://benlangmead.github.io/aws-indexes/k2). We will use a pre-compiled database from 2018 (`Refseq: bacteria, archaea (compressed)`) which contains archaea and bacteria sequences. Note that this database is quite outdated. Creating a new database is essential for real analysis - instructions for doing so are [**here**](http://www.ccb.jhu.edu/software/centrifuge/manual.shtml#database-download-and-index-building). However, the process is problematic as many scripts are outdated, which is why we use a pre-compiled database for the tutorial. The unzipped database size is roughly ~8.5 Gb. 248 | 249 | ``` 250 | # create a directory for the analysis 251 | $ mkdir centrifuge_analysis 252 | $ cd centrifuge_analysis 253 | 254 | # download and unpack the database 255 | $ wget https://genome-idx.s3.amazonaws.com/centrifuge/p_compressed_2018_4_15.tar.gz 256 | $ tar -xvzf p_compressed_2018_4_15.tar.gz 257 | $ rm p_compressed_2018_4_15.tar.gz 258 | ``` 259 | 260 | The directory should contain the following: 261 | 262 | ``` 263 | ├── data/ 264 | │ ├── ATCC.fasta 265 | │ └── ATCC.fastq.gz 266 | │ 267 | ├── centrifuge_analysis/ 268 | │ ├── p_compressed.1.cf 269 | │ ├── p_compressed.2.cf 270 | │ ├── p_compressed.3.cf 271 | │ └── p_compressed.4.cf 272 | ``` 273 | 274 | 275 | ### Analysis Instructions 276 | 277 | From the `centrifuge_analysis/` directory, run the following general command for **Centrifuge**. Change the number of threads and path to fasta file as necessary. This analysis should take <30 min. 278 | 279 | ``` 280 | $ centrifuge --threads 12 -f -k 20 -t -x p_compressed -U /data/ATCC.fasta -S ATCC.txt --report-file ATCC.centrifuge.tsv 281 | ``` 282 | 283 | We can then generate the kreport format: 284 | ``` 285 | $ centrifuge-kreport -x p_compressed ATCC.txt > ATCC.centrifuge.kreport.txt 286 | ``` 287 | 288 | In the benchmarking study we explored "long read" settings in **Centrifuge**. Note that this did not produce particularly good results. 289 | To run this, simply include the parameter `--min-hitlen 500`: 290 | ``` 291 | $ centrifuge --threads 12 --min-hitlen 500 -f -k 20 -t -x p_compressed -U /data/ATCC.fasta -S ATCC.500.txt --report-file ATCC.500.centrifuge.tsv 292 | $ centrifuge-kreport -x p_compressed ATCC.500.txt > ATCC.centrifuge500.kreport.txt 293 | ``` 294 | 295 | 296 | The directory should now contain a kreport file with the taxonomic profile for the sample, for each parameter set used: 297 | 298 | ``` 299 | ├── data/ 300 | │ ├── ATCC.fasta 301 | │ └── ATCC.fastq.gz 302 | │ 303 | ├── centrifuge_analysis/ 304 | │ ├── ATCC.500.centrifuge.tsv 305 | │ ├── ATCC.500.txt 306 | │ ├── ATCC.centrifuge.kreport.txt <- kreport; default settings 307 | │ ├── ATCC.centrifuge.tsv 308 | │ ├── ATCC.centrifuge500.kreport.txt <- kreport; "long read" settings 309 | │ ├── ATCC.txt 310 | │ ├── p_compressed.1.cf 311 | │ ├── p_compressed.2.cf 312 | │ ├── p_compressed.3.cf 313 | │ └── p_compressed.4.cf 314 | ``` 315 | 316 | [**Back to top**](#TOP) 317 | 318 | 319 | ## MMSeqs2 320 | 321 | [**MMSeqs2**](https://github.com/soedinglab/mmseqs2) is a protein alignment approach. 322 | 323 | ### Program & Database Installation 324 | 325 | We will first install **MMSeqs2**, and then obtain a suitable database. 326 | 327 | Conda installation: 328 | 329 | ``` 330 | $ conda create --name mmseqs-env -c bioconda mmseqs2 331 | 332 | # activate the environment 333 | $ conda activate mmseqs-env 334 | ``` 335 | 336 | For manual installation, follow instructions for **MMSeqs2** on github [**here**](https://github.com/soedinglab/MMseqs2/wiki). 337 | 338 | **MMSeqs2** has a module that can be used to download a number of different databases, which is explained [**here**](https://github.com/soedinglab/MMseqs2/wiki#downloading-databases). For the sake of time and space we will use the UniRef50 protein database (requires ~25 Gb space), but in the benchmarking study the NR database was used (requires ~215 Gb space). 339 | 340 | ``` 341 | # create a directory for the analysis 342 | $ mkdir mmseqs2_analysis 343 | $ cd mmseqs2_analysis 344 | 345 | # download & prepare database (adjust threads as necessary) 346 | $ mmseqs databases UniRef50 db_uniref50 tmp --threads 24 347 | 348 | # remove the temporary directory 349 | $ rm tmp 350 | 351 | # to download NCBI NR instead, you could use the following commands: 352 | $ mkdir ncbi_nr 353 | $ mmseqs databases NR ncbi_nr tmp --threads 24 354 | $ rm tmp 355 | ``` 356 | 357 | The directory should contain the following: 358 | 359 | ``` 360 | ├── data/ 361 | │ ├── ATCC.fasta 362 | │ └── ATCC.fastq.gz 363 | │ 364 | ├── mmseqs2_analysis/ 365 | │ ├── db_uniref50 366 | │ ├── db_uniref50.dbtype 367 | │ ├── db_uniref50_h 368 | │ ├── db_uniref50_h.dbtype 369 | │ ├── db_uniref50_h.index 370 | │ ├── db_uniref50.index 371 | │ ├── db_uniref50.lookup 372 | │ ├── db_uniref50_mapping 373 | │ ├── db_uniref50.source 374 | │ ├── db_uniref50_taxonomy 375 | │ └── db_uniref50.version 376 | ``` 377 | 378 | [**Back to top**](#TOP) 379 | 380 | ### Analysis Instructions 381 | 382 | From the `mmseqs2_analysis/` directory, run the following general command for **MMSeqs2**. Change the number of threads and path to fasta file as necessary. Note that the `tmp` directory specifies the temporary directory to write to, and this can be changed to another location if needed. This analysis will take ~5-10 hrs depending on resources available. 383 | 384 | ``` 385 | $ mmseqs easy-taxonomy /data/ATCC.fasta db_uniref50 ATCC tmp --threads 48 386 | ``` 387 | 388 | After completion, we will rename the relevant output file: 389 | 390 | ``` 391 | $ mv ATCC_report ATCC.mmseqs.kreport.txt 392 | ``` 393 | 394 | The directory will contain a kreport file with the taxonomic profile for the sample: 395 | 396 | ``` 397 | ├── data/ 398 | │ ├── ATCC.fasta 399 | │ └── ATCC.fastq.gz 400 | │ 401 | ├── mmseqs2_analysis/ 402 | │ ├── ATCC_lca.tsv 403 | │ ├── ATCC.mmseqs.kreport.txt <- kreport from mmseqs2 404 | │ ├── ATCC_tophit_aln 405 | │ ├── ATCC_tophit_report 406 | │ ├── db_uniref50 407 | │ ├── db_uniref50.dbtype 408 | │ ├── db_uniref50_h 409 | │ ├── db_uniref50_h.dbtype 410 | │ ├── db_uniref50_h.index 411 | │ ├── db_uniref50.index 412 | │ ├── db_uniref50.lookup 413 | │ ├── db_uniref50_mapping 414 | │ ├── db_uniref50.source 415 | │ ├── db_uniref50_taxonomy 416 | │ ├── db_uniref50.version 417 | │ └── tmp/ 418 | ``` 419 | 420 | [**Back to top**](#TOP) 421 | 422 | ## BugSeq 423 | 424 | [**BugSeq**](https://bugseq.com) is a cloud-based analysis platform that relies on nucleotide alignments for matching. 425 | 426 | ### Program & Database Installation 427 | 428 | No installation required! **BugSeq** is a cloud-based web service. 429 | 430 | ### Analysis Instructions 431 | 432 | Create a free account with **BugSeq**: https://bugseq.com/app/register 433 | 434 | Start a `New Analysis`. 435 | 436 | Upload the `ATCC.fastq.gz` file. 437 | 438 | Select the following options: 439 | 440 | + `Platform`: PacBio 441 | + `Device & Chemistry`: HiFi 442 | + `Metagenomic Database`: NCBI nt 443 | + `Sample Type`: Generic 444 | + `Sequenced Material`: DNA 445 | 446 | Submit the analysis and wait for the results by email (typically <24 hrs). 447 | 448 | [**Back to top**](#TOP) 449 | 450 | ## Diamond + MEGAN-LR 451 | 452 | [**Diamond**](https://github.com/bbuchfink/diamond) is used to perform translation alignments to a protein database and [**MEGAN-LR**](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/) is used to interpret the alignments to make taxonomic assignments. 453 | 454 | Unlike the other programs listed above, there is a PacBio workflow available for this method. It is called `Taxonomic-Functional-Profiling-Protein` and is available on github in the [**pb-metagenomics-tools**](https://github.com/PacificBiosciences/pb-metagenomics-tools) repo. 455 | 456 | You will need access to an HPC to successfully run the analysis, because it requires substantial resources to run. This analysis can take multiple days to finish running. For complete instructions on how to run the workflow, please see the tutorial [**here**](https://github.com/PacificBiosciences/pb-metagenomics-tools/blob/master/docs/Tutorial-Taxonomic-Functional-Profiling-Protein.md). The NCBI nr database must be downloaded and indexed by **Diamond**, and you must download **MEGAN-LR** and the associated mapping file before beginning. Instructions for doing this are included in the tutorial. 457 | 458 | Following completion of the workflow, the `MEGAN-RMA-Summary` workflow can be used to generate a taxonomic report. Complete instructions for running this workflow are available [**here**](https://github.com/PacificBiosciences/pb-metagenomics-tools/blob/master/docs/Tutorial-MEGAN-RMA-summary.md). This workflow could be run locally, as it is not as resource intensive. 459 | 460 | **NOTE**: The PacBio profiling pipeline is under development and is expected to change into a single workflow over the next couple months. 461 | 462 | [**Back to top**](#TOP) 463 | 464 | 465 | ## Comparative Analysis 466 | 467 | Outputs from each analysis are provided in the [**Example_Outputs**](https://github.com/dportik/LRSW-Taxonomic-Profiling-Tutorial/tree/main/Example_Outputs). 468 | The results from the different methods can be compared using the **Jupyter** notebook available from: https://osf.io/uzk64/ 469 | 470 | This notebook will produce: 471 | + read utilization metrics (how many reads are assigned, and to which taxonomic rank) 472 | + precision, recall, F-measures at the species and genus level 473 | + visualizations for dataset characteristics 474 | 475 | To use the notebook, you will need to have **Jupyter** installed. Installation instructions can be found [**here**](https://jupyter.org/install). The notebook also requires having the following Python libraries installed: `pandas`, `seaborn`, and `matplotlib`. These could be installed in a conda environment or using `pip` (as in the jupyter installation). 476 | 477 | Then, run the following to start a session: 478 | ``` 479 | $ jupyter notebook 480 | ``` 481 | Navigate to the downloaded notebook location and select it to begin the session. 482 | 483 | Within the notebook, you will only need to change the locations for the kreport files and the contents of the file list. This notebook can be used to replicate the analyses from the benchmarking study. However, keep in mind that the results are expected to be different because we used reference databases that differ from those in the paper. 484 | 485 | 486 | [**Back to top**](#TOP) -------------------------------------------------------------------------------- /Example_Outputs/ATCC.centrifuge.kreport.txt: -------------------------------------------------------------------------------- 1 | 0.01 128 128 U 0 unclassified 2 | 99.99 2418909 0 - 1 root 3 | 99.99 2418909 0 - 131567 cellular organisms 4 | 99.99 2418908 12 D 2 Bacteria 5 | 63.88 1545317 350 P 1224 Proteobacteria 6 | 33.35 806806 1 C 28211 Alphaproteobacteria 7 | 33.35 806687 0 O 204455 Rhodobacterales 8 | 33.35 806687 0 F 31989 Rhodobacteraceae 9 | 33.35 806687 0 G 1060 Rhodobacter 10 | 33.35 806687 806687 S 1063 Rhodobacter sphaeroides 11 | 0.00 116 0 O 356 Rhizobiales 12 | 0.00 77 0 F 41294 Bradyrhizobiaceae 13 | 0.00 76 0 G 374 Bradyrhizobium 14 | 0.00 66 66 S 2057741 Bradyrhizobium sp. SK17 15 | 0.00 3 3 S 288000 Bradyrhizobium sp. BTAi1 16 | 0.00 2 2 S 375 Bradyrhizobium japonicum 17 | 0.00 2 2 S 335659 Bradyrhizobium sp. S23321 18 | 0.00 2 2 S 1274631 Bradyrhizobium icense 19 | 0.00 1 1 S 1223566 Bradyrhizobium sp. CCGE-LA001 20 | 0.00 1 0 G 1073 Rhodopseudomonas 21 | 0.00 1 1 S 1076 Rhodopseudomonas palustris 22 | 0.00 37 0 F 82115 Rhizobiaceae 23 | 0.00 37 37 - 227290 Rhizobium/Agrobacterium group 24 | 0.00 1 0 F 118882 Brucellaceae 25 | 0.00 1 0 G 528 Ochrobactrum 26 | 0.00 1 1 S 529 Ochrobactrum anthropi 27 | 0.00 1 0 F 119045 Methylobacteriaceae 28 | 0.00 1 0 G 407 Methylobacterium 29 | 0.00 1 0 S 578822 Methylobacterium extorquens group 30 | 0.00 1 1 S 408 Methylobacterium extorquens 31 | 0.00 2 0 O 204457 Sphingomonadales 32 | 0.00 2 0 F 41297 Sphingomonadaceae 33 | 0.00 1 0 G 13687 Sphingomonas 34 | 0.00 1 1 S 160791 Sphingomonas wittichii 35 | 0.00 1 0 G 165695 Sphingobium 36 | 0.00 1 1 S 13690 Sphingobium yanoikuyae 37 | 30.26 731961 0 C 1236 Gammaproteobacteria 38 | 25.21 609762 1 O 91347 Enterobacterales 39 | 25.21 609744 27400 F 543 Enterobacteriaceae 40 | 23.90 578205 0 G 561 Escherichia 41 | 23.89 577881 577881 S 562 Escherichia coli 42 | 0.01 321 321 S 564 Escherichia fergusonii 43 | 0.00 3 3 S 1499973 Escherichia marmotae 44 | 0.17 4110 8 G 620 Shigella 45 | 0.11 2741 2741 S 1813821 Shigella sp. PAMC 28760 46 | 0.03 735 735 S 622 Shigella dysenteriae 47 | 0.03 626 626 S 623 Shigella flexneri 48 | 0.00 16 0 G 570 Klebsiella 49 | 0.00 9 9 S 573 Klebsiella pneumoniae 50 | 0.00 6 6 S 571 Klebsiella oxytoca 51 | 0.00 1 1 S 1134687 Klebsiella michiganensis 52 | 0.00 10 0 G 590 Salmonella 53 | 0.00 10 10 S 28901 Salmonella enterica 54 | 0.00 2 1 G 544 Citrobacter 55 | 0.00 1 0 S 1344959 Citrobacter freundii complex 56 | 0.00 1 1 S 546 Citrobacter freundii 57 | 0.00 1 0 - 191675 unclassified Enterobacteriaceae 58 | 0.00 1 0 - 36866 unclassified Enterobacteriaceae (miscellaneous) 59 | 0.00 1 1 S 2066051 Enterobacteriaceae bacterium ENNIH1 60 | 0.00 17 0 F 1903414 Morganellaceae 61 | 0.00 13 0 G 583 Proteus 62 | 0.00 13 13 S 584 Proteus mirabilis 63 | 0.00 4 0 G 581 Morganella 64 | 0.00 4 4 S 582 Morganella morganii 65 | 5.05 122064 0 O 72274 Pseudomonadales 66 | 4.80 116227 0 F 135621 Pseudomonadaceae 67 | 4.80 116227 17 G 286 Pseudomonas 68 | 4.78 115745 0 S 136841 Pseudomonas aeruginosa group 69 | 4.78 115744 115744 S 287 Pseudomonas aeruginosa 70 | 0.00 1 1 S 53408 Pseudomonas citronellolis 71 | 0.01 348 348 S 1898684 Pseudomonas sp. LPH1 72 | 0.00 54 54 S 1338689 Pseudomonas sp. JY-Q 73 | 0.00 37 0 S 136846 Pseudomonas stutzeri group 74 | 0.00 29 0 S 578833 Pseudomonas stutzeri subgroup 75 | 0.00 29 29 S 316 Pseudomonas stutzeri 76 | 0.00 8 8 S 74829 Pseudomonas balearica 77 | 0.00 17 2 S 136845 Pseudomonas putida group 78 | 0.00 11 11 S 70775 Pseudomonas plecoglossicida 79 | 0.00 3 3 S 303 Pseudomonas putida 80 | 0.00 1 1 S 78327 Pseudomonas mosselii 81 | 0.00 4 4 S 69328 Pseudomonas sp. VLB120 82 | 0.00 2 0 S 136842 Pseudomonas chlororaphis group 83 | 0.00 2 2 S 296 Pseudomonas fragi 84 | 0.00 2 2 S 157782 Pseudomonas parafulva 85 | 0.00 1 1 S 219572 Pseudomonas antarctica 86 | 0.24 5837 0 F 468 Moraxellaceae 87 | 0.24 5837 0 G 469 Acinetobacter 88 | 0.24 5837 5 S 909768 Acinetobacter calcoaceticus/baumannii complex 89 | 0.23 5622 5622 S 470 Acinetobacter baumannii 90 | 0.01 206 206 S 471 Acinetobacter calcoaceticus 91 | 0.00 3 3 S 106654 Acinetobacter nosocomialis 92 | 0.00 1 1 S 48296 Acinetobacter pittii 93 | 0.00 66 0 O 135619 Oceanospirillales 94 | 0.00 66 0 F 28256 Halomonadaceae 95 | 0.00 66 0 G 2745 Halomonas 96 | 0.00 65 65 S 1897729 Halomonas aestuarii 97 | 0.00 1 1 S 475662 Halomonas beimenensis 98 | 0.00 56 0 O 135614 Xanthomonadales 99 | 0.00 56 0 F 32033 Xanthomonadaceae 100 | 0.00 52 0 G 40323 Stenotrophomonas 101 | 0.00 51 51 S 128780 Stenotrophomonas acidaminiphila 102 | 0.00 1 0 - 995085 Stenotrophomonas maltophilia group 103 | 0.00 1 1 S 40324 Stenotrophomonas maltophilia 104 | 0.00 3 0 G 68 Lysobacter 105 | 0.00 3 3 S 69 Lysobacter enzymogenes 106 | 0.00 1 1 G 338 Xanthomonas 107 | 0.00 12 0 O 135624 Aeromonadales 108 | 0.00 12 0 F 84642 Aeromonadaceae 109 | 0.00 12 0 G 642 Aeromonas 110 | 0.00 12 12 S 1758179 Aeromonas sp. ASNIH5 111 | 0.00 1 0 O 135618 Methylococcales 112 | 0.00 1 0 F 403 Methylococcaceae 113 | 0.00 1 0 G 416 Methylomonas 114 | 0.00 1 1 S 1538553 Methylomonas denitrificans 115 | 0.18 4442 1 C 28216 Betaproteobacteria 116 | 0.13 3158 0 O 206351 Neisseriales 117 | 0.13 3155 0 F 481 Neisseriaceae 118 | 0.13 3155 0 G 482 Neisseria 119 | 0.13 3153 3153 S 487 Neisseria meningitidis 120 | 0.00 2 2 S 485 Neisseria gonorrhoeae 121 | 0.00 3 0 F 1499392 Chromobacteriaceae 122 | 0.00 3 0 G 168470 Laribacter 123 | 0.00 3 3 S 168471 Laribacter hongkongensis 124 | 0.05 1283 252 O 80840 Burkholderiales 125 | 0.04 848 257 F 119060 Burkholderiaceae 126 | 0.02 511 0 G 106589 Cupriavidus 127 | 0.02 511 511 S 119219 Cupriavidus metallidurans 128 | 0.00 78 0 G 32008 Burkholderia 129 | 0.00 71 0 S 87882 Burkholderia cepacia complex 130 | 0.00 68 68 S 95486 Burkholderia cenocepacia 131 | 0.00 3 3 S 488732 Burkholderia diffusa 132 | 0.00 7 0 S 111527 pseudomallei group 133 | 0.00 6 6 S 28450 Burkholderia pseudomallei 134 | 0.00 1 1 S 342113 Burkholderia oklahomensis 135 | 0.00 2 0 G 48736 Ralstonia 136 | 0.00 1 1 S 329 Ralstonia pickettii 137 | 0.00 1 1 S 190721 Ralstonia insidiosa 138 | 0.01 151 26 F 506 Alcaligenaceae 139 | 0.00 80 0 G 517 Bordetella 140 | 0.00 77 77 S 463040 Bordetella genomosp. 13 141 | 0.00 3 3 S 123899 Bordetella trematum 142 | 0.00 45 0 G 222 Achromobacter 143 | 0.00 42 42 S 217203 Achromobacter spanius 144 | 0.00 2 2 S 85698 Achromobacter xylosoxidans 145 | 0.00 1 1 S 1758194 Achromobacter sp. AONIH1 146 | 0.00 17 0 F 75682 Oxalobacteraceae 147 | 0.00 10 0 G 149698 Massilia 148 | 0.00 10 10 S 1678028 Massilia sp. NR 4-1 149 | 0.00 7 0 G 202907 Collimonas 150 | 0.00 6 6 S 279058 Collimonas arenae 151 | 0.00 1 1 S 158899 Collimonas fungivorans 152 | 0.00 14 0 F 80864 Comamonadaceae 153 | 0.00 8 0 G 12916 Acidovorax 154 | 0.00 6 6 S 232721 Acidovorax sp. JS42 155 | 0.00 2 2 S 1662456 Acidovorax sp. NA2 156 | 0.00 4 0 G 47420 Hydrogenophaga 157 | 0.00 4 4 S 795665 Hydrogenophaga sp. PBC 158 | 0.00 1 0 G 283 Comamonas 159 | 0.00 1 1 S 285 Comamonas testosteroni 160 | 0.00 1 0 G 80865 Delftia 161 | 0.00 1 1 S 80866 Delftia acidovorans 162 | 0.00 1 0 - 119065 unclassified Burkholderiales 163 | 0.00 1 0 - 224471 Burkholderiales Genera incertae sedis 164 | 0.00 1 0 G 88 Leptothrix 165 | 0.00 1 1 S 34029 Leptothrix cholodnii 166 | 0.07 1758 0 - 68525 delta/epsilon subdivisions 167 | 0.07 1661 0 C 29547 Epsilonproteobacteria 168 | 0.07 1661 0 O 213849 Campylobacterales 169 | 0.07 1661 0 F 72293 Helicobacteraceae 170 | 0.07 1661 0 G 209 Helicobacter 171 | 0.07 1661 1661 S 210 Helicobacter pylori 172 | 0.00 97 0 C 28221 Deltaproteobacteria 173 | 0.00 96 0 O 29 Myxococcales 174 | 0.00 95 0 - 80812 Sorangiineae 175 | 0.00 95 0 F 49 Polyangiaceae 176 | 0.00 95 0 G 39643 Sorangium 177 | 0.00 95 95 S 56 Sorangium cellulosum 178 | 0.00 1 0 - 80811 Cystobacterineae 179 | 0.00 1 0 F 39 Archangiaceae 180 | 0.00 1 0 G 47 Archangium 181 | 0.00 1 1 S 48 Archangium gephyra 182 | 0.00 1 0 O 213118 Desulfobacterales 183 | 0.00 1 0 F 213121 Desulfobulbaceae 184 | 0.00 1 0 G 109168 Desulfotalea 185 | 0.00 1 1 S 84980 Desulfotalea psychrophila 186 | 24.59 594733 6 - 1783272 Terrabacteria group 187 | 24.35 589132 20 P 1239 Firmicutes 188 | 23.13 559429 45 C 91061 Bacilli 189 | 12.90 312176 0 O 1385 Bacillales 190 | 10.29 248987 0 F 90964 Staphylococcaceae 191 | 10.29 248987 270 G 1279 Staphylococcus 192 | 9.51 230036 230036 S 1282 Staphylococcus epidermidis 193 | 0.70 17024 17024 S 1280 Staphylococcus aureus 194 | 0.03 734 734 S 28035 Staphylococcus lugdunensis 195 | 0.02 461 461 S 283734 Staphylococcus pseudintermedius 196 | 0.01 238 238 S 1283 Staphylococcus haemolyticus 197 | 0.00 109 109 S 1286 Staphylococcus simulans 198 | 0.00 49 49 S 985002 Staphylococcus argenteus 199 | 0.00 40 40 S 70255 Staphylococcus condimenti 200 | 0.00 13 13 S 29388 Staphylococcus capitis 201 | 0.00 7 7 S 1295 Staphylococcus schleiferi 202 | 0.00 5 5 S 985762 Staphylococcus agnetis 203 | 0.00 1 1 S 61015 Staphylococcus succinus 204 | 2.61 63188 0 F 186817 Bacillaceae 205 | 2.61 63185 20 G 1386 Bacillus 206 | 2.58 62477 174 S 86661 Bacillus cereus group 207 | 2.55 61636 61636 S 1396 Bacillus cereus 208 | 0.03 648 648 S 1428 Bacillus thuringiensis 209 | 0.00 15 15 S 1392 Bacillus anthracis 210 | 0.00 3 3 S 155322 Bacillus toyonensis 211 | 0.00 1 1 S 1405 Bacillus mycoides 212 | 0.01 342 342 S 1892404 Bacillus sp. ABP14 213 | 0.01 342 342 S 2053832 Bacillus sp. HBCD-sjtu 214 | 0.00 4 4 S 658666 Bacillus bombysepticus 215 | 0.00 2 0 G 400634 Lysinibacillus 216 | 0.00 2 2 S 1145276 Lysinibacillus varians 217 | 0.00 1 0 G 45667 Halobacillus 218 | 0.00 1 1 S 402384 Halobacillus mangrovi 219 | 0.00 1 0 F 186820 Listeriaceae 220 | 0.00 1 0 G 1637 Listeria 221 | 0.00 1 1 S 1639 Listeria monocytogenes 222 | 10.22 247208 13 O 186826 Lactobacillales 223 | 10.15 245534 0 F 1300 Streptococcaceae 224 | 10.15 245534 46 G 1301 Streptococcus 225 | 9.43 228009 228009 S 1309 Streptococcus mutans 226 | 0.60 14618 14618 S 1311 Streptococcus agalactiae 227 | 0.11 2606 2606 S 1319 Streptococcus sp. 'group B' 228 | 0.01 227 0 S 119603 Streptococcus dysgalactiae group 229 | 0.01 227 227 S 1334 Streptococcus dysgalactiae 230 | 0.00 12 12 S 45634 Streptococcus cristatus 231 | 0.00 10 10 S 1304 Streptococcus salivarius 232 | 0.00 5 0 S 671232 Streptococcus anginosus group 233 | 0.00 5 5 S 76860 Streptococcus constellatus 234 | 0.00 1 1 S 1307 Streptococcus suis 235 | 0.06 1435 0 F 33958 Lactobacillaceae 236 | 0.06 1435 0 G 1578 Lactobacillus 237 | 0.06 1435 1435 S 1596 Lactobacillus gasseri 238 | 0.01 201 0 F 81852 Enterococcaceae 239 | 0.01 201 0 G 1350 Enterococcus 240 | 0.01 201 201 S 1351 Enterococcus faecalis 241 | 0.00 25 0 F 186827 Aerococcaceae 242 | 0.00 25 0 G 1375 Aerococcus 243 | 0.00 25 25 S 87541 Aerococcus christensenii 244 | 1.23 29682 0 C 186801 Clostridia 245 | 1.23 29682 0 O 186802 Clostridiales 246 | 1.23 29671 0 F 31979 Clostridiaceae 247 | 1.23 29671 0 G 1485 Clostridium 248 | 1.23 29671 29671 S 1520 Clostridium beijerinckii 249 | 0.00 10 0 F 186803 Lachnospiraceae 250 | 0.00 10 0 G 207244 Anaerostipes 251 | 0.00 10 10 S 649756 Anaerostipes hadrus 252 | 0.00 1 0 F 541000 Ruminococcaceae 253 | 0.00 1 0 G 1263 Ruminococcus 254 | 0.00 1 1 S 1264 Ruminococcus albus 255 | 0.00 1 0 C 526524 Erysipelotrichia 256 | 0.00 1 0 O 526525 Erysipelotrichales 257 | 0.00 1 0 F 128827 Erysipelotrichaceae 258 | 0.00 1 0 - 433334 unclassified Erysipelotrichaceae 259 | 0.00 1 0 - 544447 unclassified Erysipelotrichaceae (miscellaneous) 260 | 0.00 1 1 S 1834207 Erysipelotrichaceae bacterium I46 261 | 0.21 5043 0 P 201174 Actinobacteria 262 | 0.21 5043 3 C 1760 Actinobacteria 263 | 0.20 4799 0 O 85009 Propionibacteriales 264 | 0.20 4798 0 F 31957 Propionibacteriaceae 265 | 0.20 4785 0 G 1912216 Cutibacterium 266 | 0.20 4785 4785 S 1747 Cutibacterium acnes 267 | 0.00 12 0 G 1743 Propionibacterium 268 | 0.00 12 12 S 671223 Propionibacterium sp. oral taxon 193 269 | 0.00 1 0 G 1912217 Pseudopropionibacterium 270 | 0.00 1 1 S 1750 Pseudopropionibacterium propionicum 271 | 0.00 1 0 F 85015 Nocardioidaceae 272 | 0.00 1 0 G 2040 Aeromicrobium 273 | 0.00 1 1 S 2041 Aeromicrobium erythreum 274 | 0.00 110 0 O 85004 Bifidobacteriales 275 | 0.00 110 0 F 31953 Bifidobacteriaceae 276 | 0.00 110 0 G 1678 Bifidobacterium 277 | 0.00 108 108 S 1680 Bifidobacterium adolescentis 278 | 0.00 1 1 S 35760 Bifidobacterium choerinum 279 | 0.00 1 1 S 216816 Bifidobacterium longum 280 | 0.00 91 0 O 2037 Actinomycetales 281 | 0.00 91 0 F 2049 Actinomycetaceae 282 | 0.00 91 0 G 1654 Actinomyces 283 | 0.00 81 81 S 52773 Actinomyces meyeri 284 | 0.00 4 4 S 1852377 Actinomyces pacaensis 285 | 0.00 2 2 S 544580 Actinomyces oris 286 | 0.00 2 2 S 712122 Actinomyces sp. oral taxon 414 287 | 0.00 1 1 S 111015 Actinomyces radicidentis 288 | 0.00 1 1 S 2081702 Actinomyces sp. oral taxon 897 289 | 0.00 18 0 O 85006 Micrococcales 290 | 0.00 5 0 F 1268 Micrococcaceae 291 | 0.00 5 0 G 32207 Rothia 292 | 0.00 4 4 S 43675 Rothia mucilaginosa 293 | 0.00 1 1 S 2047 Rothia dentocariosa 294 | 0.00 5 0 F 85023 Microbacteriaceae 295 | 0.00 3 0 G 33882 Microbacterium 296 | 0.00 1 1 S 2033 Microbacterium testaceum 297 | 0.00 1 1 S 1714373 Microbacterium sp. No. 7 298 | 0.00 1 1 S 1906742 Microbacterium sp. BH-3-3-3 299 | 0.00 1 0 G 69578 Cryobacterium 300 | 0.00 1 1 S 670052 Cryobacterium arcticum 301 | 0.00 1 0 G 110932 Leifsonia 302 | 0.00 1 1 S 1575 Leifsonia xyli 303 | 0.00 4 0 F 85020 Dermabacteraceae 304 | 0.00 4 0 G 43668 Brachybacterium 305 | 0.00 2 2 S 1903186 Brachybacterium sp. P6-10-X1 306 | 0.00 1 1 S 43669 Brachybacterium faecium 307 | 0.00 1 1 S 1331682 Brachybacterium ginsengisoli 308 | 0.00 2 0 F 85016 Cellulomonadaceae 309 | 0.00 2 0 G 1707 Cellulomonas 310 | 0.00 1 1 S 1708 Cellulomonas fimi 311 | 0.00 1 1 S 2003551 Cellulomonas sp. PSBB021 312 | 0.00 1 0 F 85017 Promicromonosporaceae 313 | 0.00 1 0 G 157920 Cellulosimicrobium 314 | 0.00 1 1 S 1980001 Cellulosimicrobium sp. TH-20 315 | 0.00 1 0 F 145357 Dermacoccaceae 316 | 0.00 1 0 G 745364 Luteipulveratus 317 | 0.00 1 1 S 571913 Luteipulveratus mongoliensis 318 | 0.00 12 0 O 85011 Streptomycetales 319 | 0.00 12 0 F 2062 Streptomycetaceae 320 | 0.00 12 2 G 1883 Streptomyces 321 | 0.00 4 4 S 1783515 Streptomyces sp. S10(2016) 322 | 0.00 1 1 S 1889 Streptomyces ambofaciens 323 | 0.00 1 1 S 1901 Streptomyces clavuligerus 324 | 0.00 1 1 S 33903 Streptomyces avermitilis 325 | 0.00 1 1 S 1725411 Streptomyces sp. CdTB01 326 | 0.00 1 1 S 1837283 Streptomyces sp. S8 327 | 0.00 1 1 S 1964449 Streptomyces sp. 3211 328 | 0.00 5 0 O 85007 Corynebacteriales 329 | 0.00 2 0 F 1653 Corynebacteriaceae 330 | 0.00 2 0 G 1716 Corynebacterium 331 | 0.00 1 1 S 35757 Corynebacterium cystitidis 332 | 0.00 1 1 S 42817 Corynebacterium argentoratense 333 | 0.00 2 0 F 1762 Mycobacteriaceae 334 | 0.00 2 1 G 1763 Mycobacterium 335 | 0.00 1 0 S 120793 Mycobacterium avium complex (MAC) 336 | 0.00 1 1 S 339268 Mycobacterium colombiense 337 | 0.00 1 0 F 85025 Nocardiaceae 338 | 0.00 1 0 G 1827 Rhodococcus 339 | 0.00 1 1 S 1805827 Rhodococcus sp. MTM3W5.2 340 | 0.00 3 0 O 85012 Streptosporangiales 341 | 0.00 2 0 F 83676 Nocardiopsaceae 342 | 0.00 2 0 G 2013 Nocardiopsis 343 | 0.00 2 2 S 280236 Nocardiopsis gilva 344 | 0.00 1 0 F 2004 Streptosporangiaceae 345 | 0.00 1 0 G 83681 Nonomuraea 346 | 0.00 1 1 S 1909395 Nonomuraea sp. ATCC 55076 347 | 0.00 1 0 O 85010 Pseudonocardiales 348 | 0.00 1 0 F 2070 Pseudonocardiaceae 349 | 0.00 1 0 G 65496 Actinoalloteichus 350 | 0.00 1 1 S 2072503 Actinoalloteichus sp. AHMU CJ021 351 | 0.00 1 0 O 414714 Catenulisporales 352 | 0.00 1 0 F 414877 Catenulisporaceae 353 | 0.00 1 0 G 414878 Catenulispora 354 | 0.00 1 1 S 304895 Catenulispora acidiphila 355 | 0.02 542 0 P 1297 Deinococcus-Thermus 356 | 0.02 542 0 C 188787 Deinococci 357 | 0.02 542 0 O 118964 Deinococcales 358 | 0.02 542 0 F 183710 Deinococcaceae 359 | 0.02 542 0 G 1298 Deinococcus 360 | 0.02 542 542 S 1299 Deinococcus radiodurans 361 | 0.00 7 0 P 200795 Chloroflexi 362 | 0.00 7 0 C 301297 Dehalococcoidia 363 | 0.00 7 0 G 670486 Dehalogenimonas 364 | 0.00 7 7 S 1839801 Dehalogenimonas formicexedens 365 | 0.00 2 0 P 544448 Tenericutes 366 | 0.00 2 0 C 31969 Mollicutes 367 | 0.00 2 0 O 2085 Mycoplasmatales 368 | 0.00 2 0 F 2092 Mycoplasmataceae 369 | 0.00 2 0 G 2093 Mycoplasma 370 | 0.00 2 0 S 656088 Mycoplasma mycoides group 371 | 0.00 1 1 S 2095 Mycoplasma capricolum 372 | 0.00 1 1 S 2102 Mycoplasma mycoides 373 | 0.00 1 0 - 1798711 Cyanobacteria/Melainabacteria group 374 | 0.00 1 0 P 1117 Cyanobacteria 375 | 0.00 1 0 O 1890424 Synechococcales 376 | 0.00 1 0 F 1213 Prochloraceae 377 | 0.00 1 0 G 1218 Prochlorococcus 378 | 0.00 1 1 S 1501269 Prochlorococcus sp. MIT 0801 379 | 11.53 278846 0 - 1783270 FCB group 380 | 11.53 278846 0 - 68336 Bacteroidetes/Chlorobi group 381 | 11.53 278846 0 P 976 Bacteroidetes 382 | 11.53 278841 0 C 200643 Bacteroidia 383 | 11.53 278841 0 O 171549 Bacteroidales 384 | 11.50 278192 0 F 171551 Porphyromonadaceae 385 | 11.50 278192 0 G 836 Porphyromonas 386 | 11.50 278192 278192 S 837 Porphyromonas gingivalis 387 | 0.03 648 0 F 815 Bacteroidaceae 388 | 0.03 648 0 G 816 Bacteroides 389 | 0.03 648 648 S 821 Bacteroides vulgatus 390 | 0.00 1 0 F 171552 Prevotellaceae 391 | 0.00 1 0 G 838 Prevotella 392 | 0.00 1 1 S 28131 Prevotella intermedia 393 | 0.00 4 0 C 768503 Cytophagia 394 | 0.00 4 0 O 768507 Cytophagales 395 | 0.00 4 0 F 1853232 Hymenobacteraceae 396 | 0.00 3 0 G 1379908 Rufibacter 397 | 0.00 3 3 S 512763 Rufibacter tibetensis 398 | 0.00 1 0 G 89966 Hymenobacter 399 | 0.00 1 1 S 1484118 Hymenobacter sp. PAMC 26628 400 | 0.00 1 0 C 117747 Sphingobacteriia 401 | 0.00 1 0 O 200666 Sphingobacteriales 402 | 0.00 1 0 F 84566 Sphingobacteriaceae 403 | 0.00 1 0 G 84567 Pedobacter 404 | 0.00 1 1 S 430522 Pedobacter steynii 405 | 0.00 1 0 D 2157 Archaea 406 | 0.00 1 0 P 28890 Euryarchaeota 407 | 0.00 1 0 C 183963 Halobacteria 408 | 0.00 1 0 O 2235 Halobacteriales 409 | 0.00 1 0 F 1963268 Haloarculaceae 410 | 0.00 1 0 G 146825 Halorhabdus 411 | 0.00 1 1 S 430914 Halorhabdus tiamatea 412 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /Example_Outputs/ATCC.mmseqs.kreport.txt: -------------------------------------------------------------------------------- 1 | 0.0041 99 99 no rank 0 unclassified 2 | 99.9959 2418862 745205 no rank 1 root 3 | 69.1890 1673655 2688 no rank 131567 cellular organisms 4 | 69.0699 1670774 665668 superkingdom 2 Bacteria 5 | 26.1196 631822 166356 phylum 1224 Proteobacteria 6 | 11.7123 283317 134842 class 28211 Alphaproteobacteria 7 | 6.1329 148353 66815 order 204455 Rhodobacterales 8 | 3.3652 81404 68032 family 31989 Rhodobacteraceae 9 | 0.5474 13242 5280 genus 1653176 Cereibacter 10 | 0.3276 7925 5740 species 1063 Cereibacter sphaeroides 11 | 0.0855 2068 2068 strain 349101 Cereibacter sphaeroides ATCC 17029 12 | 0.0044 106 106 subspecies 418630 [Luteovulum] sphaeroides subsp. megalophilum 13 | 0.0004 9 9 strain 557760 Cereibacter sphaeroides KD131 14 | 0.0001 2 2 strain 349102 Cereibacter sphaeroides ATCC 17025 15 | 0.0013 31 30 species 402884 Cereibacter changlensis 16 | 0.0000 1 1 strain 1188249 Cereibacter changlensis JA139 17 | 0.0001 3 3 species 445629 Cereibacter johrii 18 | 0.0001 2 2 species 43057 Cereibacter azotoformans 19 | 0.0000 1 1 species 439529 Cereibacter ovatus 20 | 0.0024 59 6 no rank 58840 unclassified Rhodobacteraceae 21 | 0.0016 39 39 species 1904441 Rhodobacteraceae bacterium 22 | 0.0005 12 12 species 1666915 Rhodobacteraceae bacterium HLUCCA09 23 | 0.0000 1 1 species 388401 Rhodobacteraceae bacterium HTCC2150 24 | 0.0000 1 1 species 2719011 Rhodobacteraceae bacterium R_SAG9 25 | 0.0008 19 1 genus 1060 Rhodobacter 26 | 0.0007 16 1 no rank 196779 unclassified Rhodobacter 27 | 0.0003 7 7 species 1408890 Rhodobacter sp. CACIA14H1 28 | 0.0003 7 7 species 2033869 Rhodobacter sp. CZR27 29 | 0.0000 1 1 species 1062 Rhodobacter sp. 30 | 0.0000 1 1 species 1061 Rhodobacter capsulatus 31 | 0.0000 1 1 species 453582 Rhodobacter aestuarii 32 | 0.0004 9 0 genus 2211638 Limimaricola 33 | 0.0004 9 7 species 1125964 Limimaricola cinnabarinus 34 | 0.0001 2 2 strain 1337093 Limimaricola cinnabarinus LL-001 35 | 0.0002 6 3 genus 265 Paracoccus 36 | 0.0001 2 0 no rank 2688777 unclassified Paracoccus (in: Bacteria) 37 | 0.0001 2 2 species 579490 Paracoccus sp. S4493 38 | 0.0000 1 1 species 59779 Paracoccus marcusii 39 | 0.0002 6 0 genus 238783 Pseudorhodobacter 40 | 0.0001 3 3 species 1120568 Pseudorhodobacter wandonensis 41 | 0.0001 3 0 no rank 2644082 unclassified Pseudorhodobacter 42 | 0.0001 3 3 species 1934400 Pseudorhodobacter sp. 43 | 0.0002 5 0 genus 1233054 Oceanicella 44 | 0.0002 5 5 species 1189325 Oceanicella actignis 45 | 0.0002 4 0 genus 204456 Gemmobacter 46 | 0.0001 2 2 species 2169400 Gemmobacter aquarius 47 | 0.0000 1 1 species 875041 Gemmobacter tilapiae 48 | 0.0000 1 1 species 2652247 Gemmobacter serpentinus 49 | 0.0002 4 4 genus 34008 Rhodovulum 50 | 0.0001 3 0 genus 366614 Haematobacter 51 | 0.0001 3 3 species 366616 Haematobacter missouriensis 52 | 0.0001 3 0 genus 1775705 Frigidibacter 53 | 0.0001 2 2 species 1335048 Frigidibacter mobilis 54 | 0.0000 1 1 species 2487129 Frigidibacter oleivorans 55 | 0.0001 3 0 genus 2201383 Mangrovicoccus 56 | 0.0001 3 3 species 1911570 Mangrovicoccus ximenensis 57 | 0.0001 2 0 genus 2831925 Pukyongiella 58 | 0.0001 2 2 species 2605946 Pukyongiella litopenaei 59 | 0.0001 2 0 genus 2911684 Rhabdonatronobacter 60 | 0.0001 2 2 species 2743469 Rhabdonatronobacter sediminivivens 61 | 0.0000 1 0 genus 121820 Roseinatronobacter 62 | 0.0000 1 1 species 121821 Roseinatronobacter thiooxidans 63 | 0.0000 1 0 genus 1617805 Amylibacter 64 | 0.0000 1 1 species 1889778 Amylibacter kogurei 65 | 0.0000 1 0 genus 56999 Amaricoccus 66 | 0.0000 1 0 no rank 2633320 unclassified Amaricoccus 67 | 0.0000 1 1 species 1985299 Amaricoccus sp. HAR-UPW-R2A-40 68 | 0.0000 1 0 genus 1658781 Aliiroseovarius 69 | 0.0000 1 0 no rank 2623558 unclassified Aliiroseovarius 70 | 0.0000 1 1 species 1872442 Aliiroseovarius sp. 71 | 0.0000 1 0 genus 2824145 Antarcticimicrobium 72 | 0.0000 1 1 species 2547397 Antarcticimicrobium luteum 73 | 0.0051 124 78 family 2854170 Roseobacteraceae 74 | 0.0005 11 4 genus 295418 Rubellimicrobium 75 | 0.0001 3 0 no rank 543077 environmental samples 76 | 0.0001 3 3 species 543078 uncultured Rubellimicrobium sp. 77 | 0.0001 2 0 species 295419 Rubellimicrobium thermophilum 78 | 0.0001 2 2 strain 1123069 Rubellimicrobium thermophilum DSM 16684 79 | 0.0001 2 0 species 1123067 Rubellimicrobium mesophilum 80 | 0.0001 2 2 strain 442562 Rubellimicrobium mesophilum DSM 19309 81 | 0.0002 6 0 genus 188905 Jannaschia 82 | 0.0002 6 6 species 313367 Jannaschia seosinensis 83 | 0.0002 6 2 genus 653686 Wenxinia 84 | 0.0001 3 3 species 1447782 Wenxinia saemankumensis 85 | 0.0000 1 0 species 390641 Wenxinia marina 86 | 0.0000 1 1 strain 1123501 Wenxinia marina DSM 24838 87 | 0.0002 6 0 genus 1158296 Poseidonocella 88 | 0.0002 6 6 species 871652 Poseidonocella sedimentorum 89 | 0.0001 2 0 genus 74030 Roseovarius 90 | 0.0000 1 0 species 314263 Roseovarius nubinhibens 91 | 0.0000 1 1 strain 89187 Roseovarius nubinhibens ISM 92 | 0.0000 1 1 species 337701 Roseovarius pacificus 93 | 0.0001 2 0 genus 97050 Ruegeria 94 | 0.0001 2 2 species 1715692 Ruegeria denitrificans 95 | 0.0001 2 0 genus 404235 Maritimibacter 96 | 0.0001 2 0 species 404236 Maritimibacter alkaliphilus 97 | 0.0001 2 2 strain 314271 Maritimibacter alkaliphilus HTCC2654 98 | 0.0001 2 0 genus 436357 Thalassococcus 99 | 0.0001 2 2 species 2282382 Thalassococcus profundi 100 | 0.0001 2 0 genus 599652 Tropicimonas 101 | 0.0001 2 2 species 441112 Tropicimonas isoalkanivorans 102 | 0.0001 2 0 genus 1434019 Mameliella 103 | 0.0001 2 2 species 561184 Mameliella alba 104 | 0.0000 1 0 genus 58842 Sagittula 105 | 0.0000 1 1 species 52603 Sagittula stellata 106 | 0.0000 1 0 genus 263377 Salipiger 107 | 0.0000 1 1 species 1229727 Salipiger profundus 108 | 0.0000 1 0 genus 302485 Phaeobacter 109 | 0.0000 1 0 no rank 2621772 unclassified Phaeobacter 110 | 0.0000 1 1 species 1317111 Phaeobacter sp. 22II1-1F12B 111 | 0.0000 1 0 genus 573139 Shimia 112 | 0.0000 1 1 species 321267 Shimia marina 113 | 0.0000 1 0 genus 1400062 Tranquillimonas 114 | 0.0000 1 1 species 641238 Tranquillimonas rosea 115 | 0.0004 10 0 no rank 285892 unclassified Rhodobacterales 116 | 0.0002 5 5 species 1970556 Rhodobacterales bacterium 17-64-5 117 | 0.0001 2 2 species 1970555 Rhodobacterales bacterium 12-65-15 118 | 0.0000 1 1 species 1970558 Rhodobacterales bacterium 32-66-7 119 | 0.0000 1 1 species 1970559 Rhodobacterales bacterium 32-66-9 120 | 0.0000 1 1 species 1970561 Rhodobacterales bacterium 34-62-10 121 | 0.0038 91 41 order 356 Hyphomicrobiales 122 | 0.0012 28 1 family 69277 Phyllobacteriaceae 123 | 0.0009 22 5 genus 68287 Mesorhizobium 124 | 0.0007 17 7 no rank 325217 unclassified Mesorhizobium 125 | 0.0003 8 8 species 1871066 Mesorhizobium sp. 126 | 0.0001 2 2 species 2496754 Mesorhizobium sp. M4A.F.Ca.ET.050.02.1.1 127 | 0.0002 4 0 genus 2911176 Aquibium 128 | 0.0002 4 4 species 675281 Aquibium microcysteis 129 | 0.0000 1 0 genus 245876 Nitratireductor 130 | 0.0000 1 1 species 1670619 Nitratireductor soli 131 | 0.0005 11 0 family 82115 Rhizobiaceae 132 | 0.0005 11 1 no rank 227290 Rhizobium/Agrobacterium group 133 | 0.0004 10 0 genus 379 Rhizobium 134 | 0.0003 8 8 species 1764550 Rhizobium aegyptiacum 135 | 0.0000 1 0 species 29449 Rhizobium etli 136 | 0.0000 1 1 strain 993047 Rhizobium etli CNPAF512 137 | 0.0000 1 0 species 1353277 Rhizobium freirei 138 | 0.0000 1 1 strain 363754 Rhizobium freirei PRF 81 139 | 0.0003 7 0 family 41294 Bradyrhizobiaceae 140 | 0.0002 4 3 genus 374 Bradyrhizobium 141 | 0.0000 1 0 no rank 2631580 unclassified Bradyrhizobium 142 | 0.0000 1 1 species 1230476 Bradyrhizobium sp. DFCI-1 143 | 0.0001 3 0 genus 1073 Rhodopseudomonas 144 | 0.0001 3 3 species 1513892 Rhodopseudomonas pseudopalustris 145 | 0.0001 2 2 family 119045 Methylobacteriaceae 146 | 0.0001 2 0 family 255475 Aurantimonadaceae 147 | 0.0001 2 0 genus 414371 Aureimonas 148 | 0.0001 2 0 no rank 2615206 unclassified Aureimonas 149 | 0.0001 2 2 species 1736381 Aureimonas sp. Leaf454 150 | 0.0005 13 3 order 204441 Rhodospirillales 151 | 0.0002 5 0 family 2829815 Azospirillaceae 152 | 0.0001 3 0 genus 204447 Skermanella 153 | 0.0001 3 3 species 1817965 Skermanella rosea 154 | 0.0001 2 0 genus 191 Azospirillum 155 | 0.0001 2 0 no rank 2630922 unclassified Azospirillum 156 | 0.0001 2 2 species 652740 Azospirillum sp. TSH64 157 | 0.0001 3 0 family 41295 Rhodospirillaceae 158 | 0.0001 2 0 genus 13134 Magnetospirillum 159 | 0.0001 2 0 no rank 2617991 unclassified Magnetospirillum 160 | 0.0001 2 2 species 2681467 Magnetospirillum sp. UT-4 161 | 0.0000 1 0 genus 1612157 Pararhodospirillum 162 | 0.0000 1 0 species 1084 Pararhodospirillum photometricum 163 | 0.0000 1 1 strain 1150469 Pararhodospirillum photometricum DSM 122 164 | 0.0001 2 0 family 433 Acetobacteraceae 165 | 0.0000 1 0 genus 125216 Roseomonas 166 | 0.0000 1 0 no rank 2617492 unclassified Roseomonas 167 | 0.0000 1 1 species 1926319 Roseomonas sp. TAS13 168 | 0.0000 1 0 genus 2870713 Falsiroseomonas 169 | 0.0000 1 0 species 484882 Falsiroseomonas stagni 170 | 0.0000 1 1 strain 1123062 Roseomonas stagni DSM 19981 171 | 0.0005 12 0 order 204457 Sphingomonadales 172 | 0.0003 8 0 family 2820280 Sphingosinicellaceae 173 | 0.0003 8 0 genus 335405 Sphingosinicella 174 | 0.0003 8 8 species 333708 Sphingosinicella soli 175 | 0.0001 3 3 family 41297 Sphingomonadaceae 176 | 0.0000 1 0 family 335929 Erythrobacteraceae 177 | 0.0000 1 0 no rank 2800788 Erythrobacter/Porphyrobacter group 178 | 0.0000 1 0 genus 1041 Erythrobacter 179 | 0.0000 1 1 species 35811 Erythrobacter ramosus 180 | 0.0002 6 0 no rank 33807 unclassified Alphaproteobacteria 181 | 0.0002 5 5 species 1913988 Alphaproteobacteria bacterium 182 | 0.0000 1 1 species 2013668 Alphaproteobacteria bacterium HGW-Alphaproteobacteria-5 183 | 7.4160 179391 65558 class 1236 Gammaproteobacteria 184 | 3.9418 95350 26719 order 91347 Enterobacterales 185 | 2.8371 68629 66557 family 543 Enterobacteriaceae 186 | 0.0574 1389 135 genus 561 Escherichia 187 | 0.0518 1254 1254 species 562 Escherichia coli 188 | 0.0262 634 394 genus 620 Shigella 189 | 0.0095 231 231 species 624 Shigella sonnei 190 | 0.0004 9 9 species 623 Shigella flexneri 191 | 0.0014 34 0 no rank 2890311 Klebsiella/Raoultella group 192 | 0.0012 28 22 genus 570 Klebsiella 193 | 0.0002 5 2 species 1463165 Klebsiella quasipneumoniae 194 | 0.0001 3 3 subspecies 1463164 Klebsiella quasipneumoniae subsp. similipneumoniae 195 | 0.0000 1 1 species 573 Klebsiella pneumoniae 196 | 0.0002 6 0 genus 160674 Raoultella 197 | 0.0002 6 6 species 54291 Raoultella ornithinolytica 198 | 0.0003 7 0 genus 590 Salmonella 199 | 0.0003 7 2 species 28901 Salmonella enterica 200 | 0.0002 5 1 subspecies 59201 Salmonella enterica subsp. enterica 201 | 0.0002 4 4 no rank 58097 Salmonella enterica subsp. enterica serovar Bovismorbificans 202 | 0.0002 5 3 genus 547 Enterobacter 203 | 0.0001 2 0 species group 354276 Enterobacter cloacae complex 204 | 0.0000 1 1 species 158836 Enterobacter hormaechei 205 | 0.0000 1 1 species 299767 Enterobacter ludwigii 206 | 0.0001 2 0 genus 413496 Cronobacter 207 | 0.0001 2 1 species 28141 Cronobacter sakazakii 208 | 0.0000 1 1 strain 290339 Cronobacter sakazakii ATCC BAA-894 209 | 0.0000 1 0 genus 544 Citrobacter 210 | 0.0000 1 0 species group 1344959 Citrobacter freundii complex 211 | 0.0000 1 1 species 546 Citrobacter freundii 212 | 0.0000 1 0 family 1903411 Yersiniaceae 213 | 0.0000 1 0 genus 613 Serratia 214 | 0.0000 1 1 species 82996 Serratia plymuthica 215 | 0.0000 1 0 family 1903412 Hafniaceae 216 | 0.0000 1 0 genus 635 Edwardsiella 217 | 0.0000 1 1 species 1263550 Edwardsiella piscicida 218 | 0.7440 17998 506 order 72274 Pseudomonadales 219 | 0.7231 17492 3384 family 135621 Pseudomonadaceae 220 | 0.5832 14108 10559 genus 286 Pseudomonas 221 | 0.1457 3524 138 species group 136841 Pseudomonas aeruginosa group 222 | 0.1400 3386 3381 species 287 Pseudomonas aeruginosa 223 | 0.0002 5 5 strain 1407059 Pseudomonas aeruginosa PA38182 224 | 0.0005 13 10 species group 136849 Pseudomonas syringae group 225 | 0.0000 1 0 species 53409 Pseudomonas coronafaciens 226 | 0.0000 1 1 no rank 251700 Pseudomonas coronafaciens pv. zizaniae 227 | 0.0000 1 0 species subgroup 251695 Pseudomonas syringae group genomosp. 1 228 | 0.0000 1 0 species 317 Pseudomonas syringae 229 | 0.0000 1 1 no rank 663959 Pseudomonas syringae pv. avii 230 | 0.0000 1 0 species subgroup 251698 Pseudomonas syringae group genomosp. 2 231 | 0.0000 1 0 species 29438 Pseudomonas savastanoi 232 | 0.0000 1 1 no rank 360920 Pseudomonas savastanoi pv. savastanoi 233 | 0.0002 6 0 species group 136843 Pseudomonas fluorescens group 234 | 0.0002 6 6 species 294 Pseudomonas fluorescens 235 | 0.0001 3 1 no rank 196821 unclassified Pseudomonas 236 | 0.0000 1 1 species 1844093 Pseudomonas sp. 22 E 5 237 | 0.0000 1 1 species 2772300 Pseudomonas sp. OF001 238 | 0.0000 1 0 species group 136842 Pseudomonas chlororaphis group 239 | 0.0000 1 1 species 587753 Pseudomonas chlororaphis 240 | 0.0000 1 0 species group 136845 Pseudomonas putida group 241 | 0.0000 1 0 species 303 Pseudomonas putida 242 | 0.0000 1 1 strain 1218169 Pseudomonas putida S11 243 | 0.0000 1 1 species 2816993 Pseudomonas schmalbachii 244 | 0.0188 454 1 order 2887326 Moraxellales 245 | 0.0187 453 138 family 468 Moraxellaceae 246 | 0.0130 315 276 genus 469 Acinetobacter 247 | 0.0015 37 23 species group 909768 Acinetobacter calcoaceticus/baumannii complex 248 | 0.0006 14 14 species 470 Acinetobacter baumannii 249 | 0.0000 1 1 no rank 196816 unclassified Acinetobacter 250 | 0.0000 1 1 species 1148157 Acinetobacter oleivorans 251 | 0.0007 18 0 order 135614 Xanthomonadales 252 | 0.0007 18 1 family 32033 Xanthomonadaceae 253 | 0.0006 15 0 genus 338 Xanthomonas 254 | 0.0006 15 0 no rank 2643310 unclassified Xanthomonas 255 | 0.0006 15 15 species 1591157 Xanthomonas sp. LMG 8992 256 | 0.0001 2 2 genus 68 Lysobacter 257 | 0.0003 8 0 no rank 118884 Gammaproteobacteria incertae sedis 258 | 0.0003 8 8 genus 582472 Wohlfahrtiimonas 259 | 0.0001 3 0 order 135613 Chromatiales 260 | 0.0001 3 0 family 1046 Chromatiaceae 261 | 0.0001 3 0 genus 85078 Thiococcus 262 | 0.0001 3 3 species 1057 Thiococcus pfennigii 263 | 0.0000 1 0 order 135625 Pasteurellales 264 | 0.0000 1 0 family 712 Pasteurellaceae 265 | 0.0000 1 0 genus 1855419 Ursidibacter 266 | 0.0000 1 1 species 1331689 Ursidibacter maritimus 267 | 0.0000 1 0 order 1240482 Orbales 268 | 0.0000 1 0 family 1240483 Orbaceae 269 | 0.0000 1 1 genus 1193503 Gilliamella 270 | 0.0667 1614 214 class 28216 Betaproteobacteria 271 | 0.0572 1383 168 order 206351 Neisseriales 272 | 0.0502 1215 655 family 481 Neisseriaceae 273 | 0.0232 560 487 genus 482 Neisseria 274 | 0.0030 73 73 species 487 Neisseria meningitidis 275 | 0.0005 12 0 order 80840 Burkholderiales 276 | 0.0002 6 1 family 119060 Burkholderiaceae 277 | 0.0002 4 0 genus 32008 Burkholderia 278 | 0.0001 3 0 species group 87882 Burkholderia cepacia complex 279 | 0.0001 2 2 species 60552 Burkholderia vietnamiensis 280 | 0.0000 1 1 species 95486 Burkholderia cenocepacia 281 | 0.0000 1 0 species group 111527 pseudomallei group 282 | 0.0000 1 1 species 28450 Burkholderia pseudomallei 283 | 0.0000 1 1 genus 93217 Pandoraea 284 | 0.0001 2 0 family 80864 Comamonadaceae 285 | 0.0000 1 0 genus 34072 Variovorax 286 | 0.0000 1 0 no rank 663243 unclassified Variovorax 287 | 0.0000 1 1 species 207745 Variovorax sp. WDL1 288 | 0.0000 1 0 genus 174951 Ramlibacter 289 | 0.0000 1 0 no rank 260754 environmental samples 290 | 0.0000 1 1 species 260755 uncultured Ramlibacter sp. 291 | 0.0001 2 0 no rank 224471 Burkholderiales genera incertae sedis 292 | 0.0000 1 0 genus 28067 Rubrivivax 293 | 0.0000 1 0 species 316997 Rubrivivax benzoatilyticus 294 | 0.0000 1 1 strain 987059 Rubrivivax benzoatilyticus JA2 = ATCC BAA-35 295 | 0.0000 1 0 genus 316612 Methylibium 296 | 0.0000 1 0 no rank 2633235 unclassified Methylibium 297 | 0.0000 1 1 species 1430884 Methylibium sp. T29 298 | 0.0000 1 0 family 506 Alcaligenaceae 299 | 0.0000 1 0 genus 222 Achromobacter 300 | 0.0000 1 1 species 2069367 Achromobacter veterisilvae 301 | 0.0000 1 0 family 75682 Oxalobacteraceae 302 | 0.0000 1 0 no rank 2895353 Massilia group 303 | 0.0000 1 0 genus 75654 Duganella 304 | 0.0000 1 0 no rank 2636909 unclassified Duganella 305 | 0.0000 1 1 species 1781067 Duganella sp. HH105 306 | 0.0002 5 0 no rank 119066 Betaproteobacteria incertae sedis 307 | 0.0002 5 0 genus 327159 Candidatus Accumulibacter 308 | 0.0002 5 0 no rank 2619054 unclassified Candidatus Accumulibacter 309 | 0.0002 5 5 species 1454000 Candidatus Accumulibacter sp. SK-11 310 | 0.0473 1144 31 subphylum 68525 delta/epsilon subdivisions 311 | 0.0460 1113 45 class 29547 Epsilonproteobacteria 312 | 0.0442 1068 128 order 213849 Campylobacterales 313 | 0.0388 939 119 family 72293 Helicobacteraceae 314 | 0.0339 820 595 genus 209 Helicobacter 315 | 0.0093 225 225 species 210 Helicobacter pylori 316 | 0.0000 1 0 family 72294 Campylobacteraceae 317 | 0.0000 1 0 genus 194 Campylobacter 318 | 0.0000 1 1 species 197 Campylobacter jejuni 319 | 8.6140 208370 263 clade 1783270 FCB group 320 | 8.6031 208106 530 clade 68336 Bacteroidetes/Chlorobi group 321 | 8.5812 207576 18261 phylum 976 Bacteroidetes 322 | 7.8257 189300 4414 class 200643 Bacteroidia 323 | 7.6432 184886 54820 order 171549 Bacteroidales 324 | 5.3731 129972 42426 family 171551 Porphyromonadaceae 325 | 3.6192 87546 79082 genus 836 Porphyromonas 326 | 0.3465 8382 8268 species 837 Porphyromonas gingivalis 327 | 0.0031 75 75 strain 1227270 Porphyromonas gingivalis F0569 328 | 0.0011 27 27 strain 431947 Porphyromonas gingivalis ATCC 33277 329 | 0.0002 6 6 strain 242619 Porphyromonas gingivalis W83 330 | 0.0001 2 2 strain 1227271 Porphyromonas gingivalis F0570 331 | 0.0001 2 2 strain 1321822 Porphyromonas gingivalis F0566 332 | 0.0000 1 1 strain 1195243 Porphyromonas gingivalis JCVI SC001 333 | 0.0000 1 1 strain 1297565 Porphyromonas gingivalis SJD5 334 | 0.0015 37 37 species 1884669 Porphyromonas loveana 335 | 0.0009 21 21 species 28114 Porphyromonas levii 336 | 0.0005 11 11 species 111105 Porphyromonas gulae 337 | 0.0003 7 7 species 393921 Porphyromonas crevioricanis 338 | 0.0001 3 3 species 28115 Porphyromonas macacae 339 | 0.0001 2 1 no rank 2645799 unclassified Porphyromonas 340 | 0.0000 1 0 species 712437 Porphyromonas sp. oral taxon 278 341 | 0.0000 1 1 strain 1227272 Porphyromonas sp. oral taxon 278 str. W7784 342 | 0.0000 1 1 species 41976 Porphyromonas catoniae 343 | 0.0026 63 46 family 815 Bacteroidaceae 344 | 0.0005 11 2 genus 816 Bacteroides 345 | 0.0004 9 5 no rank 139043 environmental samples 346 | 0.0000 1 1 species 1262736 Bacteroides sp. CAG:144 347 | 0.0000 1 1 species 1262744 Bacteroides sp. CAG:633 348 | 0.0000 1 1 species 1263044 Bacteroides faecis CAG:32 349 | 0.0000 1 1 species 1263046 Bacteroides fragilis CAG:47 350 | 0.0002 6 5 genus 909656 Phocaeicola 351 | 0.0000 1 1 species 821 Phocaeicola vulgatus 352 | 0.0006 15 0 family 171552 Prevotellaceae 353 | 0.0006 15 5 genus 838 Prevotella 354 | 0.0003 8 0 no rank 84374 environmental samples 355 | 0.0002 6 6 species 1262920 Prevotella sp. CAG:1124 356 | 0.0000 1 1 species 1262926 Prevotella sp. CAG:474 357 | 0.0000 1 1 species 1262932 Prevotella sp. CAG:604 358 | 0.0000 1 0 species 28131 Prevotella intermedia 359 | 0.0000 1 1 strain 1347790 Prevotella intermedia ZT 360 | 0.0000 1 0 species 439703 Prevotella maculosa 361 | 0.0000 1 1 strain 999422 Prevotella maculosa OT 289 362 | 0.0005 12 0 no rank 185291 unclassified Bacteroidales 363 | 0.0003 7 7 species 1497953 Bacteroidales bacterium KA00251 364 | 0.0002 4 4 species 1633200 Bacteroidales bacterium Barb4 365 | 0.0000 1 1 species 1497954 Bacteroidales bacterium KA00344 366 | 0.0002 4 0 family 2005525 Tannerellaceae 367 | 0.0001 2 0 genus 195950 Tannerella 368 | 0.0001 2 2 no rank 2620507 unclassified Tannerella 369 | 0.0001 2 0 genus 375288 Parabacteroides 370 | 0.0001 2 0 no rank 2649774 unclassified Parabacteroides 371 | 0.0001 2 2 species 1917887 Parabacteroides sp. Marseille-P3160 372 | 0.0006 14 0 no rank 37452 unclassified Bacteroidetes 373 | 0.0004 10 10 species 1898104 Bacteroidetes bacterium 374 | 0.0001 2 2 species 1852803 Bacteroidetes bacterium ADurb.Bin090 375 | 0.0001 2 2 species 1852814 Bacteroidetes bacterium ADurb.Bin416 376 | 0.0000 1 0 class 117747 Sphingobacteriia 377 | 0.0000 1 0 order 200666 Sphingobacteriales 378 | 0.0000 1 0 family 84566 Sphingobacteriaceae 379 | 0.0000 1 0 genus 28453 Sphingobacterium 380 | 0.0000 1 1 species 1796905 Sphingobacterium humi 381 | 0.0000 1 0 phylum 142187 Candidatus Hydrogenedentes 382 | 0.0000 1 0 no rank 1046981 unclassified Candidatus Hydrogenedentes 383 | 0.0000 1 1 species 2030809 Candidatus Hydrogenedentes bacterium 384 | 6.8166 164891 2196 clade 1783272 Terrabacteria group 385 | 6.6057 159789 22460 phylum 1239 Firmicutes 386 | 5.2031 125860 20250 class 91061 Bacilli 387 | 2.8082 67930 20031 order 186826 Lactobacillales 388 | 1.9431 47003 2838 family 1300 Streptococcaceae 389 | 1.8258 44165 40413 genus 1301 Streptococcus 390 | 0.1464 3542 3524 species 1309 Streptococcus mutans 391 | 0.0007 18 18 strain 210007 Streptococcus mutans UA159 392 | 0.0023 56 56 species 1311 Streptococcus agalactiae 393 | 0.0015 37 37 species 1111760 Streptococcus troglodytae 394 | 0.0010 23 22 species 1313 Streptococcus pneumoniae 395 | 0.0000 1 1 strain 516950 Streptococcus pneumoniae CGSP14 396 | 0.0008 20 20 species 1310 Streptococcus sobrinus 397 | 0.0008 19 1 no rank 2608887 unclassified Streptococcus 398 | 0.0005 13 13 species 1316409 Streptococcus sp. HSISB1 399 | 0.0001 3 3 species 2866599 Streptococcus sp. Marseille-Q5112 400 | 0.0000 1 1 species 1777879 Streptococcus sp. DD11 401 | 0.0000 1 1 species 1777881 Streptococcus sp. DD13 402 | 0.0006 15 11 species 380397 Streptococcus ictaluri 403 | 0.0002 4 4 strain 764299 Streptococcus ictaluri 707-05 404 | 0.0003 7 7 species 1343 Streptococcus vestibularis 405 | 0.0002 6 6 species 1307 Streptococcus suis 406 | 0.0002 4 4 species 315405 Streptococcus gallolyticus 407 | 0.0001 3 0 species 1339 Streptococcus macacae 408 | 0.0001 3 3 strain 764298 Streptococcus macacae NCTC 11558 409 | 0.0001 3 3 species 1348 Streptococcus parauberis 410 | 0.0001 3 2 species 1308 Streptococcus thermophilus 411 | 0.0000 1 1 strain 1042404 Streptococcus thermophilus CNCM I-1630 412 | 0.0001 2 0 species 1333 Streptococcus criceti 413 | 0.0001 2 2 strain 873449 Streptococcus criceti HS-6 414 | 0.0001 2 2 species 1345 Streptococcus ferus 415 | 0.0001 2 0 species group 119603 Streptococcus dysgalactiae group 416 | 0.0001 2 0 species 1336 Streptococcus equi 417 | 0.0001 2 2 subspecies 40041 Streptococcus equi subsp. zooepidemicus 418 | 0.0001 2 1 species 1314 Streptococcus pyogenes 419 | 0.0000 1 0 serotype 301452 Streptococcus pyogenes serotype M49 420 | 0.0000 1 1 strain 471876 Streptococcus pyogenes NZ131 421 | 0.0001 2 2 species 2740579 Streptococcus vicugnae 422 | 0.0000 1 1 species 1326 Streptococcus acidominimus 423 | 0.0000 1 1 species 29389 Streptococcus alactolyticus 424 | 0.0000 1 1 species 1080071 Streptococcus orisasini 425 | 0.0000 1 1 species 1303 Streptococcus oralis 426 | 0.0359 868 717 family 33958 Lactobacillaceae 427 | 0.0060 146 134 genus 1578 Lactobacillus 428 | 0.0003 7 6 species 1596 Lactobacillus gasseri 429 | 0.0000 1 1 strain 1380360 Lactobacillus gasseri DSM 14869 430 | 0.0001 2 2 species 33959 Lactobacillus johnsonii 431 | 0.0000 1 1 species 147802 Lactobacillus iners 432 | 0.0000 1 1 species 1819254 Lactobacillus colini 433 | 0.0000 1 1 species 2107999 Lactobacillus paragasseri 434 | 0.0001 2 0 genus 2742598 Limosilactobacillus 435 | 0.0001 2 0 species 1613 Limosilactobacillus fermentum 436 | 0.0001 2 2 strain 575599 Limosilactobacillus fermentum 28-3-CHN 437 | 0.0001 2 0 genus 2767887 Ligilactobacillus 438 | 0.0000 1 1 species 1606 Ligilactobacillus aviarius 439 | 0.0000 1 1 species 1808352 Ligilactobacillus salitolerans 440 | 0.0000 1 0 genus 46254 Oenococcus 441 | 0.0000 1 1 species 1247 Oenococcus oeni 442 | 0.0010 23 6 family 81852 Enterococcaceae 443 | 0.0005 11 7 genus 1350 Enterococcus 444 | 0.0002 4 4 species 1351 Enterococcus faecalis 445 | 0.0002 5 0 genus 51668 Tetragenococcus 446 | 0.0002 5 0 species 64642 Tetragenococcus muriaticus 447 | 0.0002 5 5 strain 1302649 Tetragenococcus muriaticus PMC-11-5 448 | 0.0000 1 0 genus 33969 Melissococcus 449 | 0.0000 1 0 no rank 2644359 unclassified Melissococcus 450 | 0.0000 1 1 species 2293110 Melissococcus sp. OM08-11BH 451 | 0.0001 3 0 no rank 263855 unclassified Lactobacillales 452 | 0.0001 3 3 species 2291323 Lactobacillaceae bacterium 453 | 0.0000 1 0 family 186827 Aerococcaceae 454 | 0.0000 1 0 genus 1375 Aerococcus 455 | 0.0000 1 1 species 1377 Aerococcus viridans 456 | 0.0000 1 0 family 186828 Carnobacteriaceae 457 | 0.0000 1 0 genus 2747 Carnobacterium 458 | 0.0000 1 1 species 2748 Carnobacterium divergens 459 | 1.5577 37680 13125 order 1385 Bacillales 460 | 0.5097 12330 5382 family 90964 Staphylococcaceae 461 | 0.2872 6947 5364 genus 1279 Staphylococcus 462 | 0.0386 933 930 species 1282 Staphylococcus epidermidis 463 | 0.0001 3 3 strain 176280 Staphylococcus epidermidis ATCC 12228 464 | 0.0226 547 545 species 1280 Staphylococcus aureus 465 | 0.0000 1 1 strain 585160 Staphylococcus aureus subsp. aureus WBG10049 466 | 0.0000 1 1 strain 585161 Staphylococcus aureus subsp. aureus WW2703/97 467 | 0.0016 38 38 species 29380 Staphylococcus caprae 468 | 0.0010 23 23 species 33028 Staphylococcus saccharolyticus 469 | 0.0004 9 9 species 1290 Staphylococcus hominis 470 | 0.0003 7 7 species 28035 Staphylococcus lugdunensis 471 | 0.0002 6 0 no rank 91994 unclassified Staphylococcus 472 | 0.0001 3 3 species 1715206 Staphylococcus sp. HMSC077H01 473 | 0.0001 2 2 species 1403935 Staphylococcus sp. DORA_6_22 474 | 0.0000 1 1 species 2653174 Staphylococcus sp. 8AQ 475 | 0.0002 5 5 species 1283 Staphylococcus haemolyticus 476 | 0.0001 3 3 species 1293 Staphylococcus gallinarum 477 | 0.0001 3 3 species 45972 Staphylococcus pasteuri 478 | 0.0001 2 2 species 1288 Staphylococcus xylosus 479 | 0.0001 2 2 species 29388 Staphylococcus capitis 480 | 0.0000 1 1 species 985002 Staphylococcus argenteus 481 | 0.0000 1 0 species 308354 Staphylococcus simiae 482 | 0.0000 1 1 strain 911238 Staphylococcus simiae CCM 7213 = CCUG 51256 483 | 0.0000 1 1 species 46127 Staphylococcus felis 484 | 0.0000 1 1 species 29379 Staphylococcus auricularis 485 | 0.0000 1 1 species 1295 Staphylococcus schleiferi 486 | 0.0000 1 1 genus 227979 Jeotgalicoccus 487 | 0.5043 12199 8909 family 186817 Bacillaceae 488 | 0.1357 3282 1979 genus 1386 Bacillus 489 | 0.0537 1298 1082 species group 86661 Bacillus cereus group 490 | 0.0073 177 161 species 1396 Bacillus cereus 491 | 0.0002 5 5 strain 526975 Bacillus cereus BDRD-ST26 492 | 0.0001 3 3 strain 526983 Bacillus cereus Rock3-28 493 | 0.0001 2 0 no rank 1179100 Bacillus cereus biovar anthracis 494 | 0.0001 2 2 strain 637380 Bacillus cereus biovar anthracis str. CI 495 | 0.0000 1 1 strain 361100 Bacillus cereus Q1 496 | 0.0000 1 1 strain 526969 Bacillus cereus m1550 497 | 0.0000 1 1 strain 526985 Bacillus cereus Rock3-42 498 | 0.0000 1 1 strain 1053208 Bacillus cereus HuB13-1 499 | 0.0000 1 1 strain 1053233 Bacillus cereus VD133 500 | 0.0000 1 1 strain 1053249 Bacillus cereus VDM053 501 | 0.0012 29 10 species 1428 Bacillus thuringiensis 502 | 0.0005 12 0 no rank 1430 Bacillus thuringiensis serovar israelensis 503 | 0.0005 12 12 strain 339854 Bacillus thuringiensis serovar israelensis ATCC 35646 504 | 0.0002 4 0 no rank 29340 Bacillus thuringiensis serovar sotto 505 | 0.0002 4 4 strain 527026 Bacillus thuringiensis serovar sotto str. T04001 506 | 0.0000 1 1 strain 1195464 Bacillus thuringiensis MC28 507 | 0.0000 1 1 strain 1218175 Bacillus thuringiensis HD-771 508 | 0.0000 1 1 strain 1431339 Bacillus thuringiensis DB27 509 | 0.0002 5 5 species 1890302 Bacillus wiedmannii 510 | 0.0001 2 2 species 1405 Bacillus mycoides 511 | 0.0000 1 1 species 1392 Bacillus anthracis 512 | 0.0000 1 1 species 2026186 Bacillus paranthracis 513 | 0.0000 1 1 species 2026187 Bacillus pacificus 514 | 0.0001 2 0 species group 653685 Bacillus subtilis group 515 | 0.0001 2 2 species 1423 Bacillus subtilis 516 | 0.0000 1 0 no rank 185979 unclassified Bacillus (in: Bacteria) 517 | 0.0000 1 1 species 2499213 Bacillus sp. BD59S 518 | 0.0000 1 1 species 561879 Bacillus safensis 519 | 0.0000 1 1 species 2039284 Bacillus fungorum 520 | 0.0000 1 0 genus 45667 Halobacillus 521 | 0.0000 1 0 no rank 2636472 unclassified Halobacillus 522 | 0.0000 1 1 species 1543706 Halobacillus sp. BBL2006 523 | 0.0000 1 0 genus 129337 Geobacillus 524 | 0.0000 1 0 no rank 2642459 unclassified Geobacillus 525 | 0.0000 1 1 species 1547578 Geobacillus sp. BCO2 526 | 0.0000 1 0 genus 2675231 Mesobacillus 527 | 0.0000 1 0 species 308892 Mesobacillus boroniphilus 528 | 0.0000 1 1 strain 1294265 Mesobacillus boroniphilus JCM 21738 529 | 0.0000 1 0 genus 2675232 Neobacillus 530 | 0.0000 1 0 species 220686 Neobacillus vireti 531 | 0.0000 1 1 strain 1131730 Neobacillus vireti LMG 21834 532 | 0.0000 1 1 genus 2675234 Alkalihalobacillus 533 | 0.0000 1 1 genus 2800373 Priestia 534 | 0.0000 1 0 genus 2813788 Litchfieldia 535 | 0.0000 1 1 species 304268 Litchfieldia alkalitelluris 536 | 0.0000 1 0 genus 2837502 Ectobacillus 537 | 0.0000 1 1 species 363872 Ectobacillus panaciterrae 538 | 0.0005 11 2 family 186822 Paenibacillaceae 539 | 0.0004 9 3 genus 44249 Paenibacillus 540 | 0.0001 3 0 no rank 185978 unclassified Paenibacillus 541 | 0.0000 1 1 species 1472719 Paenibacillus sp. P1XP2 542 | 0.0000 1 1 species 1761880 Paenibacillus sp. yr247 543 | 0.0000 1 1 species 2691605 Paenibacillus sp. OT2-17 544 | 0.0000 1 1 species 59843 Paenibacillus glucanolyticus 545 | 0.0000 1 1 species 189691 Paenibacillus elgii 546 | 0.0000 1 1 species 379896 Paenibacillus fonticola 547 | 0.0004 10 0 family 186820 Listeriaceae 548 | 0.0004 10 0 genus 1637 Listeria 549 | 0.0004 10 10 species 1639 Listeria monocytogenes 550 | 0.0001 3 0 no rank 539002 Bacillales incertae sedis 551 | 0.0001 3 0 no rank 539742 Bacillales Family XII. Incertae Sedis 552 | 0.0001 3 0 genus 33986 Exiguobacterium 553 | 0.0001 3 3 species 307643 Exiguobacterium profundum 554 | 0.0000 1 0 family 186818 Planococcaceae 555 | 0.0000 1 0 genus 1569 Sporosarcina 556 | 0.0000 1 0 no rank 2647733 unclassified Sporosarcina 557 | 0.0000 1 1 species 2660747 Sporosarcina sp. A4 558 | 0.0000 1 0 family 186821 Sporolactobacillaceae 559 | 0.0000 1 1 genus 2077 Sporolactobacillus 560 | 0.4736 11455 400 class 186801 Clostridia 561 | 0.4569 11053 2616 order 186802 Eubacteriales 562 | 0.3476 8408 4829 family 31979 Clostridiaceae 563 | 0.1478 3576 2730 genus 1485 Clostridium 564 | 0.0288 697 697 species 1520 Clostridium beijerinckii 565 | 0.0018 44 7 no rank 2614128 unclassified Clostridium 566 | 0.0005 13 13 species 1523155 Clostridium sp. IBUN22A 567 | 0.0004 10 10 species 1506 Clostridium sp. 568 | 0.0002 5 5 species 1196322 Clostridium sp. Maddingley MBC34-26 569 | 0.0001 2 2 species 2698832 Clostridium sp. C2-6-12 570 | 0.0000 1 1 species 328398 Clostridium sp. IBUN 22A 571 | 0.0000 1 1 species 349938 Clostridium sp. BL-8 572 | 0.0000 1 1 species 641107 Clostridium sp. DL-VIII 573 | 0.0000 1 1 species 704125 Clostridium sp. C5S11 574 | 0.0000 1 1 species 1354301 Clostridium sp. BL8 575 | 0.0000 1 1 species 1761781 Clostridium sp. DSM 8431 576 | 0.0000 1 1 species 2843317 Clostridium sp. DSM 17811 577 | 0.0006 15 15 species 36745 Clostridium saccharoperbutylacetonicum 578 | 0.0005 13 13 species 1492 Clostridium butyricum 579 | 0.0005 12 12 species 169679 Clostridium saccharobutylicum 580 | 0.0005 12 12 species 225345 Clostridium chromiireducens 581 | 0.0002 5 5 species 1491 Clostridium botulinum 582 | 0.0002 5 5 species 1534 Clostridium kluyveri 583 | 0.0002 4 4 species 91623 Clostridium akagii 584 | 0.0002 4 0 no rank 59619 environmental samples 585 | 0.0001 2 2 species 1262780 Clostridium sp. CAG:221 586 | 0.0001 2 2 species 1262782 Clostridium sp. CAG:230 587 | 0.0001 3 3 species 205327 Clostridium frigoris 588 | 0.0001 3 3 species 137838 Clostridium neonatale 589 | 0.0001 3 0 species 76489 Clostridium acetireducens 590 | 0.0001 3 3 strain 1121290 Clostridium acetireducens DSM 10703 591 | 0.0001 3 3 species 394958 Clostridium taeniosporum 592 | 0.0001 3 3 species 1502 Clostridium perfringens 593 | 0.0001 2 2 species 319475 Clostridium lundense 594 | 0.0001 2 2 species 223919 Clostridium diolis 595 | 0.0001 2 2 species 1216932 Clostridium bornimense 596 | 0.0001 2 2 species 2794346 Clostridium thailandense 597 | 0.0001 2 0 species 36834 Clostridium celatum 598 | 0.0001 2 2 strain 545697 Clostridium celatum DSM 1785 599 | 0.0001 2 2 species 1533 Clostridium fallax 600 | 0.0001 2 2 species 1519 Clostridium tyrobutyricum 601 | 0.0000 1 0 species 84031 Clostridium sartagoforme 602 | 0.0000 1 1 strain 1202534 Clostridium sartagoforme AAU1 603 | 0.0000 1 1 species 238834 Clostridium estertheticum 604 | 0.0000 1 1 species 1548 Clostridium scatologenes 605 | 0.0000 1 1 species 360422 Clostridium tagluense 606 | 0.0000 1 1 species 1538 Clostridium ljungdahlii 607 | 0.0000 1 1 species 1509 Clostridium sporogenes 608 | 0.0000 1 0 genus 1649459 Hungatella 609 | 0.0000 1 0 species 154046 Hungatella hathewayi 610 | 0.0000 1 1 strain 566550 Hungatella hathewayi DSM 13479 611 | 0.0000 1 0 genus 1769729 Hathewaya 612 | 0.0000 1 0 species 29365 Hathewaya proteolytica 613 | 0.0000 1 1 strain 1121331 Hathewaya proteolytica DSM 3090 614 | 0.0000 1 0 genus 2018663 Marinisporobacter 615 | 0.0000 1 1 species 2018667 Marinisporobacter balticus 616 | 0.0004 10 5 family 186803 Lachnospiraceae 617 | 0.0001 2 0 genus 2383 Epulopiscium 618 | 0.0001 2 1 no rank 2628445 unclassified Epulopiscium 619 | 0.0000 1 1 species 2384 Epulopiscium sp. 620 | 0.0000 1 0 genus 28050 Lachnospira 621 | 0.0000 1 1 species 39485 Lachnospira eligens 622 | 0.0000 1 0 genus 33042 Coprococcus 623 | 0.0000 1 0 no rank 458252 environmental samples 624 | 0.0000 1 1 species 1262862 Coprococcus sp. CAG:131 625 | 0.0000 1 0 no rank 186928 unclassified Lachnospiraceae 626 | 0.0000 1 1 species 1898203 Lachnospiraceae bacterium 627 | 0.0002 6 0 family 216572 Oscillospiraceae 628 | 0.0001 2 0 no rank 473772 unclassified Oscillospiraceae 629 | 0.0001 2 2 species 2485925 Oscillospiraceae bacterium 630 | 0.0001 2 0 genus 1508657 Ruminiclostridium 631 | 0.0001 2 0 species 29362 Ruminiclostridium papyrosolvens 632 | 0.0001 2 2 strain 588581 Ruminiclostridium papyrosolvens DSM 2782 633 | 0.0000 1 0 genus 2304693 Pseudoclostridium 634 | 0.0000 1 1 species 84032 Pseudoclostridium thermosuccinogenes 635 | 0.0000 1 0 genus 2576755 Caproicibacter 636 | 0.0000 1 1 species 2576756 Caproicibacter fermentans 637 | 0.0002 5 0 family 186804 Peptostreptococcaceae 638 | 0.0002 5 0 genus 1870884 Clostridioides 639 | 0.0002 4 4 species 1496 Clostridioides difficile 640 | 0.0000 1 0 no rank 2635829 unclassified Clostridioides 641 | 0.0000 1 1 species 2770773 Clostridioides sp. ES-S-0108-01 642 | 0.0002 4 0 family 2937909 Desulfitobacteriaceae 643 | 0.0002 4 0 genus 79206 Desulfosporosinus 644 | 0.0002 4 1 no rank 2633794 unclassified Desulfosporosinus 645 | 0.0001 2 2 species 1617025 Desulfosporosinus sp. I2 646 | 0.0000 1 1 species 157907 Desulfosporosinus sp. 647 | 0.0001 2 0 family 186806 Eubacteriaceae 648 | 0.0001 2 0 genus 1730 Eubacterium 649 | 0.0001 2 0 no rank 2624479 unclassified Eubacterium 650 | 0.0001 2 2 species 142586 Eubacterium sp. 651 | 0.0001 2 0 family 2603322 Vallitaleaceae 652 | 0.0001 2 2 genus 1348611 Vallitalea 653 | 0.0000 1 0 order 53433 Halanaerobiales 654 | 0.0000 1 0 family 53434 Halobacteroidaceae 655 | 0.0000 1 0 genus 2017975 Candidatus Frackibacter 656 | 0.0000 1 0 no rank 2648818 unclassified Candidatus Frackibacter 657 | 0.0000 1 1 species 1785949 Candidatus Frackibacter sp. T328-2 658 | 0.0000 1 0 order 68295 Thermoanaerobacterales 659 | 0.0000 1 0 family 186814 Thermoanaerobacteraceae 660 | 0.0000 1 0 no rank 42857 Moorella group 661 | 0.0000 1 0 genus 1326739 Calderihabitans 662 | 0.0000 1 1 species 1246530 Calderihabitans maritimus 663 | 0.0002 6 0 class 909932 Negativicutes 664 | 0.0002 6 0 order 909929 Selenomonadales 665 | 0.0002 5 0 family 1843491 Selenomonadaceae 666 | 0.0002 4 0 genus 52225 Mitsuokella 667 | 0.0002 4 4 no rank 2637239 unclassified Mitsuokella 668 | 0.0000 1 0 genus 82373 Anaerovibrio 669 | 0.0000 1 1 species 82374 Anaerovibrio lipolyticus 670 | 0.0000 1 0 family 1843490 Sporomusaceae 671 | 0.0000 1 0 genus 2375 Sporomusa 672 | 0.0000 1 0 species 112900 Sporomusa acidovorans 673 | 0.0000 1 1 strain 1123286 Sporomusa acidovorans DSM 3132 674 | 0.0002 5 0 class 526524 Erysipelotrichia 675 | 0.0002 5 0 order 526525 Erysipelotrichales 676 | 0.0002 4 0 family 128827 Erysipelotrichaceae 677 | 0.0002 4 0 no rank 544447 unclassified Erysipelotrichaceae 678 | 0.0002 4 4 species 2049044 Erysipelotrichaceae bacterium 679 | 0.0000 1 0 family 2810281 Turicibacteraceae 680 | 0.0000 1 0 genus 191303 Turicibacter 681 | 0.0000 1 0 no rank 2638206 unclassified Turicibacter 682 | 0.0000 1 1 species 2304578 Turicibacter sp. TS3 683 | 0.0001 3 1 class 1737404 Tissierellia 684 | 0.0000 1 0 order 1737405 Tissierellales 685 | 0.0000 1 0 family 1570339 Peptoniphilaceae 686 | 0.0000 1 0 genus 150022 Finegoldia 687 | 0.0000 1 1 species 1260 Finegoldia magna 688 | 0.0000 1 0 no rank 1737408 unclassified Tissierellia 689 | 0.0000 1 1 species 2049431 Tissierellia bacterium 690 | 0.1033 2499 142 phylum 201174 Actinobacteria 691 | 0.0972 2352 858 class 1760 Actinomycetia 692 | 0.0586 1417 132 order 85009 Propionibacteriales 693 | 0.0530 1281 609 family 31957 Propionibacteriaceae 694 | 0.0278 672 297 genus 1912216 Cutibacterium 695 | 0.0155 375 375 species 1747 Cutibacterium acnes 696 | 0.0002 4 1 family 85015 Nocardioidaceae 697 | 0.0001 2 0 genus 116071 Micropruina 698 | 0.0001 2 2 species 75385 Micropruina glycogenica 699 | 0.0000 1 0 genus 1839 Nocardioides 700 | 0.0000 1 0 no rank 198440 environmental samples 701 | 0.0000 1 1 species 198441 uncultured Nocardioides sp. 702 | 0.0021 51 4 order 85004 Bifidobacteriales 703 | 0.0019 47 8 family 31953 Bifidobacteriaceae 704 | 0.0016 39 33 genus 1678 Bifidobacterium 705 | 0.0002 4 4 species 1680 Bifidobacterium adolescentis 706 | 0.0000 1 0 species 1686 Bifidobacterium catenulatum 707 | 0.0000 1 0 subspecies 630129 Bifidobacterium catenulatum subsp. kashiwanohense 708 | 0.0000 1 1 strain 1150460 Bifidobacterium catenulatum subsp. kashiwanohense JCM 15439 = DSM 21854 709 | 0.0000 1 1 species 78448 Bifidobacterium pullorum 710 | 0.0004 10 0 order 2037 Actinomycetales 711 | 0.0004 10 6 family 2049 Actinomycetaceae 712 | 0.0001 3 1 genus 2529408 Schaalia 713 | 0.0001 2 2 species 1660 Schaalia odontolytica 714 | 0.0000 1 0 genus 1654 Actinomyces 715 | 0.0000 1 0 no rank 2609248 unclassified Actinomyces 716 | 0.0000 1 1 species 936549 Actinomyces sp. ICM54 717 | 0.0003 7 1 order 85007 Corynebacteriales 718 | 0.0002 6 0 family 1762 Mycobacteriaceae 719 | 0.0002 4 0 genus 1763 Mycobacterium 720 | 0.0001 3 0 species 1789 Mycobacterium xenopi 721 | 0.0001 3 3 strain 1299333 Mycobacterium xenopi 3993 722 | 0.0000 1 0 species group 77643 Mycobacterium tuberculosis complex 723 | 0.0000 1 1 species 1773 Mycobacterium tuberculosis 724 | 0.0001 2 0 genus 670516 Mycobacteroides 725 | 0.0001 2 0 species 36809 Mycobacteroides abscessus 726 | 0.0001 2 2 subspecies 1185650 Mycobacteroides abscessus subsp. abscessus 727 | 0.0002 5 0 order 85008 Micromonosporales 728 | 0.0002 5 5 family 28056 Micromonosporaceae 729 | 0.0001 3 0 order 85006 Micrococcales 730 | 0.0001 2 0 family 85023 Microbacteriaceae 731 | 0.0001 2 0 genus 33882 Microbacterium 732 | 0.0001 2 0 no rank 2609290 unclassified Microbacterium 733 | 0.0001 2 2 species 51671 Microbacterium sp. 734 | 0.0000 1 0 family 85016 Cellulomonadaceae 735 | 0.0000 1 0 genus 162491 Oerskovia 736 | 0.0000 1 1 species 43678 Oerskovia enterophila 737 | 0.0000 1 0 order 85011 Streptomycetales 738 | 0.0000 1 0 family 2062 Streptomycetaceae 739 | 0.0000 1 0 genus 1883 Streptomyces 740 | 0.0000 1 1 species 36818 Streptomyces subrutilus 741 | 0.0002 4 0 class 84998 Coriobacteriia 742 | 0.0002 4 0 order 1643822 Eggerthellales 743 | 0.0002 4 0 family 1643826 Eggerthellaceae 744 | 0.0002 4 0 genus 644652 Gordonibacter 745 | 0.0002 4 4 species 471189 Gordonibacter pamelaeae 746 | 0.0000 1 0 class 1497346 Thermoleophilia 747 | 0.0000 1 0 order 588673 Solirubrobacterales 748 | 0.0000 1 0 family 320599 Solirubrobacteraceae 749 | 0.0000 1 0 no rank 1162705 environmental samples 750 | 0.0000 1 1 species 1162706 uncultured Solirubrobacteraceae bacterium 751 | 0.0167 405 16 phylum 1297 Deinococcus-Thermus 752 | 0.0161 389 51 class 188787 Deinococci 753 | 0.0140 338 2 order 118964 Deinococcales 754 | 0.0139 336 151 family 183710 Deinococcaceae 755 | 0.0076 185 162 genus 1298 Deinococcus 756 | 0.0010 23 21 species 1299 Deinococcus radiodurans 757 | 0.0001 2 2 strain 243230 Deinococcus radiodurans R1 758 | 0.0001 2 0 phylum 200795 Chloroflexi 759 | 0.0001 2 0 no rank 189774 unclassified Chloroflexi 760 | 0.0000 1 1 species 1852860 Chloroflexi bacterium ADurb.Bin344 761 | 0.0000 1 1 species 2026724 Chloroflexi bacterium 762 | 0.0006 15 0 no rank 48479 environmental samples 763 | 0.0006 14 14 species 77133 uncultured bacterium 764 | 0.0000 1 1 species 1701365 uncultured bacterium 35i19 765 | 0.0001 3 0 no rank 2323 Bacteria incertae sedis 766 | 0.0001 3 0 clade 1783234 Bacteria candidate phyla 767 | 0.0001 2 0 phylum 422282 candidate division WWE3 768 | 0.0001 2 2 species 1619118 candidate division WWE3 bacterium GW2011_GWB2_43_22 769 | 0.0000 1 0 clade 1783273 Patescibacteria group 770 | 0.0000 1 0 clade 1794811 Parcubacteria group 771 | 0.0000 1 0 phylum 1752728 Candidatus Falkowbacteria 772 | 0.0000 1 1 species 1618634 Candidatus Falkowbacteria bacterium GW2011_GWA2_39_24 773 | 0.0001 2 0 phylum 40117 Nitrospirae 774 | 0.0001 2 0 class 203693 Nitrospira 775 | 0.0001 2 0 order 189778 Nitrospirales 776 | 0.0001 2 0 family 189779 Nitrospiraceae 777 | 0.0001 2 0 genus 995729 Candidatus Magnetoovum 778 | 0.0001 2 2 species 1609970 Candidatus Magnetoovum chiemensis 779 | 0.0001 2 0 phylum 508458 Synergistetes 780 | 0.0001 2 0 no rank 508677 unclassified Synergistetes 781 | 0.0001 2 2 species 1852915 Synergistetes bacterium ADurb.Bin520 782 | 0.0000 1 0 phylum 203691 Spirochaetes 783 | 0.0000 1 0 class 203692 Spirochaetia 784 | 0.0000 1 0 order 1643688 Leptospirales 785 | 0.0000 1 0 family 170 Leptospiraceae 786 | 0.0000 1 0 genus 171 Leptospira 787 | 0.0000 1 1 species 29506 Leptospira inadai 788 | 0.0079 192 39 superkingdom 2759 Eukaryota 789 | 0.0050 120 1 clade 33154 Opisthokonta 790 | 0.0048 115 0 kingdom 33208 Metazoa 791 | 0.0048 115 0 clade 6072 Eumetazoa 792 | 0.0048 115 1 clade 33213 Bilateria 793 | 0.0040 96 0 clade 33317 Protostomia 794 | 0.0040 96 0 clade 1206794 Ecdysozoa 795 | 0.0033 79 0 clade 88770 Panarthropoda 796 | 0.0033 79 8 phylum 6656 Arthropoda 797 | 0.0029 71 0 clade 197563 Mandibulata 798 | 0.0029 71 0 clade 197562 Pancrustacea 799 | 0.0029 70 0 subphylum 6960 Hexapoda 800 | 0.0029 70 0 class 50557 Insecta 801 | 0.0029 70 0 clade 85512 Dicondylia 802 | 0.0029 70 0 subclass 7496 Pterygota 803 | 0.0029 70 0 infraclass 33340 Neoptera 804 | 0.0021 51 0 cohort 33342 Paraneoptera 805 | 0.0021 51 5 order 7524 Hemiptera 806 | 0.0019 45 0 clade 33343 Prosorrhyncha 807 | 0.0019 45 0 suborder 33345 Heteroptera 808 | 0.0019 45 0 clade 33347 Euheteroptera 809 | 0.0019 45 0 clade 33349 Neoheteroptera 810 | 0.0019 45 0 clade 33351 Panheteroptera 811 | 0.0019 45 0 infraorder 33354 Cimicomorpha 812 | 0.0019 45 0 superfamily 33355 Cimicoidea 813 | 0.0019 45 0 family 30078 Cimicidae 814 | 0.0019 45 0 genus 30079 Cimex 815 | 0.0019 45 45 species 79782 Cimex lectularius 816 | 0.0000 1 0 suborder 33373 Sternorrhyncha 817 | 0.0000 1 0 infraorder 33380 Aphidomorpha 818 | 0.0000 1 0 superfamily 33385 Aphidoidea 819 | 0.0000 1 0 family 27482 Aphididae 820 | 0.0000 1 0 subfamily 133076 Aphidinae 821 | 0.0000 1 0 tribe 33386 Macrosiphini 822 | 0.0000 1 0 genus 7028 Acyrthosiphon 823 | 0.0000 1 1 species 7029 Acyrthosiphon pisum 824 | 0.0008 19 0 cohort 33392 Endopterygota 825 | 0.0005 12 0 superorder 85604 Amphiesmenoptera 826 | 0.0005 12 0 order 7088 Lepidoptera 827 | 0.0005 12 0 suborder 41191 Glossata 828 | 0.0005 12 0 infraorder 41196 Neolepidoptera 829 | 0.0005 12 0 parvorder 41197 Heteroneura 830 | 0.0005 12 0 clade 37567 Ditrysia 831 | 0.0005 12 0 clade 104431 Obtectomera 832 | 0.0005 12 0 superfamily 37570 Noctuoidea 833 | 0.0005 12 0 family 7100 Noctuidae 834 | 0.0005 12 0 subfamily 95182 Amphipyrinae 835 | 0.0005 12 0 genus 7106 Spodoptera 836 | 0.0005 12 12 species 7107 Spodoptera exigua 837 | 0.0003 7 0 order 7041 Coleoptera 838 | 0.0003 7 0 suborder 41084 Polyphaga 839 | 0.0003 7 0 infraorder 41087 Elateriformia 840 | 0.0003 7 0 superfamily 71193 Elateroidea 841 | 0.0003 7 0 family 7049 Lampyridae 842 | 0.0003 7 0 subfamily 433515 Luciolinae 843 | 0.0003 7 0 genus 2069291 Abscondita 844 | 0.0003 7 7 species 2069292 Abscondita terminalis 845 | 0.0000 1 0 subphylum 6657 Crustacea 846 | 0.0000 1 0 superclass 2172819 Oligostraca 847 | 0.0000 1 0 class 6670 Ostracoda 848 | 0.0000 1 0 subclass 43953 Podocopa 849 | 0.0000 1 0 order 84318 Podocopida 850 | 0.0000 1 0 suborder 84328 Cypridocopina 851 | 0.0000 1 0 superfamily 84329 Cypridoidea 852 | 0.0000 1 0 family 43954 Cyprididae 853 | 0.0000 1 0 genus 163713 Cyprideis 854 | 0.0000 1 1 species 163714 Cyprideis torosa 855 | 0.0007 17 0 phylum 6231 Nematoda 856 | 0.0006 14 0 class 119089 Chromadorea 857 | 0.0006 14 0 order 6236 Rhabditida 858 | 0.0005 11 0 suborder 6300 Tylenchina 859 | 0.0005 11 0 infraorder 2082223 Panagrolaimomorpha 860 | 0.0005 11 0 superfamily 2082224 Strongyloidoidea 861 | 0.0005 11 0 family 6246 Strongyloididae 862 | 0.0005 11 0 genus 131309 Parastrongyloides 863 | 0.0005 11 11 species 131310 Parastrongyloides trichosuri 864 | 0.0001 3 1 suborder 6274 Spirurina 865 | 0.0001 2 0 infraorder 6249 Ascaridomorpha 866 | 0.0001 2 0 superfamily 33256 Ascaridoidea 867 | 0.0001 2 0 family 33259 Toxocaridae 868 | 0.0001 2 0 genus 6264 Toxocara 869 | 0.0001 2 2 species 6265 Toxocara canis 870 | 0.0001 3 0 class 119088 Enoplea 871 | 0.0001 3 0 subclass 1457286 Dorylaimia 872 | 0.0001 3 0 order 6329 Trichinellida 873 | 0.0001 3 0 family 119093 Trichuridae 874 | 0.0001 3 0 genus 36086 Trichuris 875 | 0.0001 3 3 species 36087 Trichuris trichiura 876 | 0.0007 18 0 clade 33511 Deuterostomia 877 | 0.0007 18 0 phylum 7711 Chordata 878 | 0.0007 18 0 subphylum 89593 Craniata 879 | 0.0007 18 0 clade 7742 Vertebrata 880 | 0.0007 18 1 clade 7776 Gnathostomata 881 | 0.0007 16 0 clade 117570 Teleostomi 882 | 0.0007 16 1 clade 117571 Euteleostomi 883 | 0.0006 15 0 superclass 8287 Sarcopterygii 884 | 0.0006 15 0 clade 1338369 Dipnotetrapodomorpha 885 | 0.0006 15 0 clade 32523 Tetrapoda 886 | 0.0006 15 2 clade 32524 Amniota 887 | 0.0005 13 0 class 40674 Mammalia 888 | 0.0005 13 0 clade 32525 Theria 889 | 0.0005 13 0 clade 9347 Eutheria 890 | 0.0005 13 0 clade 1437010 Boreoeutheria 891 | 0.0004 9 0 superorder 314146 Euarchontoglires 892 | 0.0004 9 0 order 9443 Primates 893 | 0.0004 9 0 suborder 376913 Haplorrhini 894 | 0.0004 9 2 infraorder 314293 Simiiformes 895 | 0.0003 7 3 parvorder 9526 Catarrhini 896 | 0.0002 4 0 superfamily 314294 Cercopithecoidea 897 | 0.0002 4 0 family 9527 Cercopithecidae 898 | 0.0002 4 1 subfamily 9528 Cercopithecinae 899 | 0.0001 3 3 genus 9539 Macaca 900 | 0.0002 4 0 superorder 314145 Laurasiatheria 901 | 0.0002 4 0 order 91561 Artiodactyla 902 | 0.0002 4 0 suborder 9845 Ruminantia 903 | 0.0002 4 1 infraorder 35500 Pecora 904 | 0.0001 3 0 family 9895 Bovidae 905 | 0.0001 3 0 subfamily 27592 Bovinae 906 | 0.0001 3 3 genus 9903 Bos 907 | 0.0000 1 0 class 7777 Chondrichthyes 908 | 0.0000 1 0 subclass 7778 Elasmobranchii 909 | 0.0000 1 0 infraclass 119203 Selachii 910 | 0.0000 1 0 clade 119197 Galeomorphii 911 | 0.0000 1 0 superorder 119195 Galeoidea 912 | 0.0000 1 0 order 30503 Orectolobiformes 913 | 0.0000 1 0 family 40580 Hemiscylliidae 914 | 0.0000 1 0 genus 34767 Chiloscyllium 915 | 0.0000 1 1 species 137246 Chiloscyllium punctatum 916 | 0.0002 4 0 kingdom 4751 Fungi 917 | 0.0001 3 0 subkingdom 451864 Dikarya 918 | 0.0001 3 0 phylum 4890 Ascomycota 919 | 0.0001 3 0 clade 716545 saccharomyceta 920 | 0.0001 3 0 subphylum 147538 Pezizomycotina 921 | 0.0001 3 0 clade 716546 leotiomyceta 922 | 0.0001 3 0 clade 715989 sordariomyceta 923 | 0.0001 3 0 class 147550 Sordariomycetes 924 | 0.0001 3 0 subclass 222543 Hypocreomycetidae 925 | 0.0001 3 2 order 5125 Hypocreales 926 | 0.0000 1 0 family 474942 Ophiocordycipitaceae 927 | 0.0000 1 0 genus 1052105 Purpureocillium 928 | 0.0000 1 1 species 33203 Purpureocillium lilacinum 929 | 0.0000 1 0 no rank 112252 Fungi incertae sedis 930 | 0.0000 1 0 phylum 4761 Chytridiomycota 931 | 0.0000 1 0 no rank 2683659 Chytridiomycota incertae sedis 932 | 0.0000 1 0 class 451455 Neocallimastigomycetes 933 | 0.0000 1 0 order 29006 Neocallimastigales 934 | 0.0000 1 0 family 29007 Neocallimastigaceae 935 | 0.0000 1 0 genus 4821 Piromyces 936 | 0.0000 1 1 species 1754191 Piromyces finnis 937 | 0.0013 32 0 kingdom 33090 Viridiplantae 938 | 0.0013 32 0 phylum 35493 Streptophyta 939 | 0.0013 32 0 subphylum 131221 Streptophytina 940 | 0.0013 32 0 clade 3193 Embryophyta 941 | 0.0013 32 0 clade 58023 Tracheophyta 942 | 0.0013 32 0 clade 78536 Euphyllophyta 943 | 0.0013 32 0 clade 58024 Spermatophyta 944 | 0.0013 32 1 class 3398 Magnoliopsida 945 | 0.0013 31 1 clade 1437183 Mesangiospermae 946 | 0.0009 22 0 clade 71240 eudicotyledons 947 | 0.0009 22 0 clade 91827 Gunneridae 948 | 0.0009 22 6 clade 1437201 Pentapetalae 949 | 0.0006 15 0 clade 71275 rosids 950 | 0.0006 15 1 clade 91835 fabids 951 | 0.0005 13 0 order 72025 Fabales 952 | 0.0005 13 0 family 3803 Fabaceae 953 | 0.0005 13 0 subfamily 3814 Papilionoideae 954 | 0.0005 13 0 clade 2231393 50 kb inversion clade 955 | 0.0005 13 0 clade 2231384 genistoids sensu lato 956 | 0.0005 13 0 clade 2231385 core genistoids 957 | 0.0005 13 0 tribe 163729 Genisteae 958 | 0.0005 13 0 genus 3869 Lupinus 959 | 0.0005 13 13 species 3870 Lupinus albus 960 | 0.0000 1 0 order 3646 Malpighiales 961 | 0.0000 1 0 family 3977 Euphorbiaceae 962 | 0.0000 1 0 subfamily 235629 Acalyphoideae 963 | 0.0000 1 0 tribe 235880 Acalypheae 964 | 0.0000 1 0 genus 3987 Ricinus 965 | 0.0000 1 1 species 3988 Ricinus communis 966 | 0.0000 1 0 clade 71274 asterids 967 | 0.0000 1 0 clade 91882 campanulids 968 | 0.0000 1 0 order 4209 Asterales 969 | 0.0000 1 0 family 4210 Asteraceae 970 | 0.0000 1 0 subfamily 102804 Asteroideae 971 | 0.0000 1 0 tribe 102810 Anthemideae 972 | 0.0000 1 0 subtribe 886730 Anthemidinae 973 | 0.0000 1 0 genus 99105 Tanacetum 974 | 0.0000 1 1 species 118510 Tanacetum cinerariifolium 975 | 0.0003 8 0 clade 4447 Liliopsida 976 | 0.0003 8 0 subclass 1437197 Petrosaviidae 977 | 0.0003 8 0 clade 4734 commelinids 978 | 0.0003 8 0 order 38820 Poales 979 | 0.0003 8 0 family 4479 Poaceae 980 | 0.0003 7 0 clade 359160 BOP clade 981 | 0.0003 7 0 subfamily 147367 Oryzoideae 982 | 0.0003 7 0 tribe 147380 Oryzeae 983 | 0.0003 7 0 subtribe 1648021 Oryzinae 984 | 0.0003 7 3 genus 4527 Oryza 985 | 0.0001 2 2 species 4530 Oryza sativa 986 | 0.0000 1 1 species 40148 Oryza glumipatula 987 | 0.0000 1 1 species 40149 Oryza meridionalis 988 | 0.0000 1 0 clade 147370 PACMAD clade 989 | 0.0000 1 0 subfamily 147371 Chloridoideae 990 | 0.0000 1 0 tribe 147435 Cynodonteae 991 | 0.0000 1 0 subtribe 751762 Eleusininae 992 | 0.0000 1 0 genus 15437 Cynodon 993 | 0.0000 1 1 species 1920021 Cynodon dactylon x Cynodon transvaalensis 994 | 0.0000 1 0 clade 2698737 Sar 995 | 0.0000 1 0 clade 33630 Alveolata 996 | 0.0000 1 0 class 2864 Dinophyceae 997 | 0.0000 1 0 order 89954 Suessiales 998 | 0.0000 1 0 family 252141 Symbiodiniaceae 999 | 0.0000 1 0 genus 2949 Symbiodinium 1000 | 0.0000 1 1 species 2951 Symbiodinium microadriaticum 1001 | 0.0000 1 0 superkingdom 2157 Archaea 1002 | 0.0000 1 0 phylum 28890 Euryarchaeota 1003 | 0.0000 1 0 no rank 115531 unclassified Euryarchaeota 1004 | 0.0000 1 1 species 1852878 Euryarchaeota archaeon ADurb.Bin294 1005 | 0.0001 2 0 superkingdom 10239 Viruses 1006 | 0.0001 2 0 clade 2731341 Duplodnaviria 1007 | 0.0001 2 0 kingdom 2731360 Heunggongvirae 1008 | 0.0001 2 0 phylum 2731618 Uroviricota 1009 | 0.0001 2 0 class 2731619 Caudoviricetes 1010 | 0.0001 2 0 order 28883 Caudovirales 1011 | 0.0001 2 0 family 10699 Siphoviridae 1012 | 0.0001 2 0 no rank 196894 unclassified Siphoviridae 1013 | 0.0001 2 2 species 2548092 Streptococcus phage Javan28 1014 | --------------------------------------------------------------------------------