Table S1: Percentage of occurrences of the 123 E. coli K12 operons that are significant Group 1: Acidobacteria Bacteria Percentage Solibacter usitatus Ellin6076 20.3% Group 2: Actinobacteria Bacteria Percentage Corynebacterium diphtheriae NCTC 13129 16.3% Corynebacterium efficiens YS-314 13.8% Corynebacterium glutamicum ATCC 13032 13.0% Corynebacterium jeikeium K411 10.6% Mycobacterium sp. KMS 26.0% Mycobacterium sp. MCS 25.2% Mycobacterium avium 104 19.5% Mycobacterium avium subsp. paratuberculosis K-10 22.0% Mycobacterium bovis AF2122/97 22.8% Mycobacterium bovis BCG str. Pasteur 1173P2 22.8% Mycobacterium tuberculosis CDC1551 22.8% Mycobacterium tuberculosis H37Rv 22.8% Mycobacterium leprae TN 14.6% Mycobacterium smegmatis str. MC2 155 19.5% Mycobacterium ulcerans Agy99 18.7% Mycobacterium vanbaalenii PYR-1 27.6% Nocardia farcinica IFM 10152 23.6% Rhodococcus sp. RHA1 23.6% Acidothermus cellulolyticus 11B 21.1% Frankia sp. CcI3 19.5% Frankia alni ACN14a 23.6% Tropheryma whipplei str. Twist 10.6% Tropheryma whipplei TW08/27 10.6% Leifsonia xyli subsp. xyli str. CTCB07 8.9% Arthrobacter sp. FB24 17.9% Arthrobacter aurescens TC1 14.6% Nocardioides sp. JS614 22.0% Propionibacterium acnes KPA171202 17.9% Streptomyces avermitilis MA-4680 22.8% Streptomyces coelicolor A3(2) 17.1% Thermobifida fusca YX 17.1% Bifidobacterium adolescentis ATCC 15703 8.9% Bifidobacterium longum NCC2705 8.9% Rubrobacter xylanophilus DSM 9941 23.6% Group 3: Alphaproteobacteria Bacteria Percentage Caulobacter crescentus CB15 23.6% Bartonella bacilliformis KC583 19.5% Bartonella henselae str. Houston-1 18.7% Bartonella quintana str. Toulouse 18.7% Bradyrhizobium japonicum USDA 110 39.8% Nitrobacter hamburgensis X14 28.5% Nitrobacter winogradskyi Nb-255 26.8% Rhodopseudomonas palustris BisA53 30.1% Rhodopseudomonas palustris BisB18 30.9% Rhodopseudomonas palustris BisB5 30.9% Rhodopseudomonas palustris CGA009 33.3% Rhodopseudomonas palustris HaA2 27.6% Brucella abortus biovar 1 str. 9-941 21.1% Brucella melitensis biovar Abortus 2308 22.0% Brucella melitensis 16M 23.6% Brucella suis 1330 22.8% Mesorhizobium sp. BNC1 24.4% Mesorhizobium loti MAFF303099 27.6% Agrobacterium tumefaciens str. C58 23.6% Rhizobium etli CFN 42 24.4% Rhizobium leguminosarum bv. viciae 3841 26.8% Sinorhizobium meliloti 1021 23.6% Hyphomonas neptunium ATCC 15444 25.2% Maricaulis maris MCS10 25.2% Jannaschia sp. CCS1 22.8% Paracoccus denitrificans PD1222 26.0% Rhodobacter sphaeroides 2.4.1 24.4% Roseobacter denitrificans OCh 114 22.0% Silicibacter sp. TM1040 20.3% Silicibacter pomeroyi DSS-3 22.8% Gluconobacter oxydans 621H 17.9% Granulibacter bethesdensis CGDNIH1 17.1% Magnetospirillum magneticum AMB-1 30.9% Rhodospirillum rubrum ATCC 11170 25.2% Anaplasma phagocytophilum HZ 6.5% Anaplasma marginale str. St. Maries 5.7% Ehrlichia canis str. Jake 5.7% Ehrlichia chaffeensis str. Arkansas 5.7% Ehrlichia ruminantium str. Gardel 5.7% Ehrlichia ruminantium str. Welgevonden 5.7% Neorickettsia sennetsu str. Miyayama 6.5% Rickettsia conorii str. Malish 7 8.1% Rickettsia felis URRWXCal2 8.9% Rickettsia prowazekii str. Madrid E 8.1% Rickettsia typhi str. Wilmington 6.5% Rickettsia bellii RML369-C 7.3% Wolbachia endosymbiont strain TRS of Brugia malayi 4.1% Wolbachia endosymbiont of Drosophila melanogaster 4.1% Erythrobacter litoralis HTCC2594 18.7% Novosphingobium aromaticivorans DSM 12444 19.5% Sphingopyxis alaskensis RB2256 22.0% Zymomonas mobilis subsp. mobilis ZM4 14.6% Group 4: Betaproteobacteria Bacteria Percentage Bordetella bronchiseptica RB50 32.5% Bordetella parapertussis 12822 31.7% Bordetella pertussis Tohama I 29.3% Burkholderia sp. 383 43.1% Burkholderia cenocepacia AU 1054 38.2% Burkholderia cenocepacia HI2424 39.0% Burkholderia cepacia AMMD 43.1% Burkholderia mallei ATCC 23344 36.6% Burkholderia mallei SAVP1 39.8% Burkholderia pseudomallei 1710b 39.8% Burkholderia pseudomallei K96243 40.7% Burkholderia thailandensis E264 41.5% Burkholderia xenovorans LB400 48.8% Ralstonia eutropha H16 43.1% Ralstonia eutropha JMP134 43.9% Ralstonia metallidurans CH34 45.5% Ralstonia solanacearum GMI1000 29.3% Acidovorax sp. JS42 31.7% Acidovorax avenae subsp. citrulli AAC00-1 29.3% Polaromonas sp. JS666 27.6% Polaromonas naphthalenivorans CJ2 32.5% Rhodoferax ferrireducens T118 34.1% Verminephrobacter eiseniae EF01-2 29.3% Thiobacillus denitrificans ATCC 25259 33.3% Methylobacillus flagellatus KT 31.7% Chromobacterium violaceum ATCC 12472 38.2% Neisseria gonorrhoeae FA 1090 17.1% Neisseria meningitidis FAM18 17.9% Neisseria meningitidis MC58 17.9% Neisseria meningitidis Z2491 17.9% Nitrosomonas europaea ATCC 19718 26.8% Nitrosomonas eutropha C91 26.8% Nitrosospira multiformis ATCC 25196 30.1% Azoarcus sp. BH72 35.8% Azoarcus sp. EbN1 27.6% Dechloromonas aromatica RCB 35.8% Group 5: Deltaproteobacteria Bacteria Percentage Bdellovibrio bacteriovorus HD100 14.6% Desulfotalea psychrophila LSv54 24.4% Desulfovibrio desulfuricans G20 20.3% Desulfovibrio vulgaris subsp. vulgaris DP4 22.0% Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough 22.0% Lawsonia intracellularis PHE/MN1-00 11.4% Geobacter metallireducens GS-15 29.3% Geobacter sulfurreducens PCA 23.6% Pelobacter carbinolicus DSM 2380 23.6% Pelobacter propionicus DSM 2379 19.5% Anaeromyxobacter dehalogenans 2CP-C 22.8% Myxococcus xanthus DK 1622 28.5% Syntrophus aciditrophicus SB 22.0% Syntrophobacter fumaroxidans MPOB 22.8% Group 6: Epsilonproteobacteria Bacteria Percentage Campylobacter fetus subsp. fetus 82-40 12.2% Campylobacter jejuni RM1221 17.1% Campylobacter jejuni subsp. jejuni 81-176 17.1% Campylobacter jejuni subsp. jejuni NCTC 11168 17.1% Helicobacter acinonychis str. Sheeba 11.4% Helicobacter hepaticus ATCC 51449 12.2% Helicobacter pylori 26695 11.4% Helicobacter pylori HPAG1 11.4% Helicobacter pylori J99 8.9% Wolinella succinogenes DSM 1740 13.0% Thiomicrospira denitrificans ATCC 33889 11.4% Group 7: Gammaproteobacteria Bacteria Percentage Aeromonas hydrophila subsp. hydrophila ATCC 7966 56.9% Marinobacter aquaeolei VT8 39.8% Saccharophagus degradans 2-40 34.1% Colwellia psychrerythraea 34H 43.1% Idiomarina loihiensis L2TR 37.4% Pseudoalteromonas atlantica T6c 39.8% Pseudoalteromonas haloplanktis TAC125 39.0% Psychromonas ingrahamii 37 43.9% Shewanella sp. ANA-3 43.1% Shewanella sp. MR-4 47.2% Shewanella sp. MR-7 47.2% Shewanella sp. W3-18-1 47.2% Shewanella amazonensis SB2B 46.3% Shewanella denitrificans OS217 40.7% Shewanella frigidimarina NCIMB 400 43.9% Shewanella oneidensis MR-1 48.0% Nitrosococcus oceani ATCC 19707 27.6% Alkalilimnicola ehrlichei MLHE-1 33.3% Halorhodospira halophila SL1 30.1% Buchnera aphidicola str. APS (Acyrthosiphon pisum) 17.9% Buchnera aphidicola str. Bp (Baizongia pistaciae) 19.5% Buchnera aphidicola str. Cc (Cinara cedri) 11.4% Buchnera aphidicola str. Sg (Schizaphis graminum) 17.9% Candidatus Blochmannia floridanus 21.1% Candidatus Blochmannia pennsylvanicus str. BPEN 22.0% Escherichia coli 536 91.9% Escherichia coli APEC O1 91.1% Escherichia coli CFT073 91.1% Escherichia coli O157:H7 EDL933 95.1% Escherichia coli O157:H7 str. Sakai 95.1% Escherichia coli UTI89 91.9% Escherichia coli W3110 99.2% Erwinia carotovora subsp. atroseptica SCRI1043 69.9% Photorhabdus luminescens subsp. laumondii TTO1 65.0% Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 81.3% Salmonella enterica subsp. enterica serovar Typhi str. CT18 84.6% Salmonella enterica subsp. enterica serovar Typhi Ty2 84.6% Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 82.1% Salmonella typhimurium LT2 86.2% Shigella boydii Sb227 78.9% Shigella dysenteriae Sd197 72.4% Shigella flexneri 2a str. 2457T 81.3% Shigella flexneri 2a str. 301 82.1% Shigella flexneri 5 str. 8401 81.3% Shigella sonnei Ss046 87.8% Sodalis glossinidius str. 'morsitans' 42.3% Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis 17.9% Yersinia pestis Antiqua 59.3% Yersinia pestis biovar Microtus str. 91001 58.5% Yersinia pestis CO92 57.7% Yersinia pestis KIM 60.2% Yersinia pestis Nepal516 59.3% Yersinia pseudotuberculosis IP 32953 60.2% Coxiella burnetii RSA 493 22.8% Legionella pneumophila str. Lens 26.0% Legionella pneumophila str. Paris 27.6% Legionella pneumophila subsp. pneumophila str. Philadelphia 1 25.2% Methylococcus capsulatus str. Bath 25.2% Alcanivorax borkumensis SK2 30.1% Hahella chejuensis KCTC 2396 46.3% Chromohalobacter salexigens DSM 3043 39.0% Haemophilus ducreyi 35000HP 22.8% Haemophilus influenzae 86-028NP 31.7% Haemophilus influenzae Rd KW20 31.7% Haemophilus somnus 129PT 34.1% Mannheimia succiniciproducens MBEL55E 32.5% Pasteurella multocida subsp. multocida str. Pm70 34.1% Acinetobacter sp. ADP1 27.6% Psychrobacter arcticus 273-4 26.8% Psychrobacter cryohalolentis K5 27.6% Pseudomonas aeruginosa PAO1 44.7% Pseudomonas aeruginosa UCBPP-PA14 42.3% Pseudomonas fluorescens Pf-5 41.5% Pseudomonas fluorescens PfO-1 43.9% Pseudomonas putida KT2440 42.3% Pseudomonas syringae pv. phaseolicola 1448A 41.5% Pseudomonas syringae pv. tomato str. DC3000 43.1% Pseudomonas syringae pv. syringae B728a 39.8% Pseudomonas entomophila L48 47.2% Francisella tularensis subsp. holarctica 15.4% Francisella tularensis subsp. holarctica OSU18 16.3% Francisella tularensis subsp. novicida U112 20.3% Francisella tularensis subsp. tularensis FSC 198 16.3% Francisella tularensis subsp. tularensis SCHU S4 16.3% Thiomicrospira crunogena XCL-2 26.0% Photobacterium profundum SS9 56.1% Vibrio cholerae O1 biovar eltor str. N16961 46.3% Vibrio fischeri ES114 48.8% Vibrio parahaemolyticus RIMD 2210633 51.2% Vibrio vulnificus CMCP6 54.5% Vibrio vulnificus YJ016 56.1% Xanthomonas axonopodis pv. citri str. 306 30.9% Xanthomonas campestris pv. campestris str. 8004 29.3% Xanthomonas campestris pv. campestris str. ATCC 33913 28.5% Xanthomonas campestris pv. vesicatoria str. 85-10 28.5% Xanthomonas oryzae pv. oryzae MAFF 311018 30.1% Xylella fastidiosa 9a5c 23.6% Xylella fastidiosa Temecula1 22.8% Group 8: Aquificae Bacteria Percentage Aquifex aeolicus VF5 7.3% Group 9: Bacteroidetes/Chlorobi Bacteria Percentage Bacteroides fragilis NCTC 9343 16.3% Bacteroides fragilis YCH46 14.6% Bacteroides thetaiotaomicron VPI-5482 17.1% Porphyromonas gingivalis W83 8.1% Gramella forsetii KT0803 13.8% Cytophaga hutchinsonii ATCC 33406 16.3% Chlorobium tepidum TLS 15.4% Chlorobium chlorochromatii CaD3 13.8% Chlorobium phaeobacteroides DSM 266 17.9% Pelodictyon luteolum DSM 273 15.4% Group 10: Chlamydiae/Verrucomicrobia Bacteria Percentage Chlamydia muridarum Nigg 7.3% Chlamydia trachomatis A/HAR-13 8.9% Chlamydia trachomatis D/UW-3/CX 8.9% Chlamydophila abortus S26/3 8.1% Chlamydophila caviae GPIC 9.8% Chlamydophila felis Fe/C-56 9.8% Chlamydophila pneumoniae AR39 8.1% Chlamydophila pneumoniae CWL029 8.1% Chlamydophila pneumoniae J138 8.1% Chlamydophila pneumoniae TW-183 8.1% Candidatus Protochlamydia amoebophila UWE25 15.4% Group 11: Chloroflexi Bacteria Percentage Dehalococcoides sp. CBDB1 15.4% Dehalococcoides ethenogenes 195 13.0% Group 12: Cyanobacteria Bacteria Percentage Gloeobacter violaceus PCC 7421 9.8% Synechococcus elongatus PCC 6301 9.8% Synechococcus elongatus PCC 7942 9.8% Synechococcus sp. CC9311 7.3% Synechococcus sp. CC9605 8.1% Synechococcus sp. CC9902 8.1% Synechococcus sp. JA-2-3B'a(2-13) 8.9% Synechococcus sp. JA-3-3Ab 8.9% Synechococcus sp. WH 8102 8.1% Synechocystis sp. PCC 6803 6.5% Thermosynechococcus elongatus BP-1 5.7% Anabaena variabilis ATCC 29413 13.0% Nostoc sp. PCC 7120 15.4% Trichodesmium erythraeum IMS101 11.4% Prochlorococcus marinus str. MIT 9312 7.3% Prochlorococcus marinus str. MIT 9313 8.1% Prochlorococcus marinus str. NATL2A 7.3% Prochlorococcus marinus subsp. marinus str. CCMP1375 6.5% Prochlorococcus marinus subsp. pastoris str. CCMP1986 8.1% Group 13: Deinococcus-Thermus Bacteria Percentage Deinococcus geothermalis DSM 11300 11.4% Deinococcus radiodurans R1 13.0% Thermus thermophilus HB27 13.0% Thermus thermophilus HB8 13.0% Group 14: Firmicutes Bacteria Percentage Bacillus anthracis str. 'Ames Ancestor' 29.3% Bacillus anthracis str. Ames 29.3% Bacillus anthracis str. Sterne 29.3% Bacillus cereus ATCC 10987 28.5% Bacillus cereus ATCC 14579 30.9% Bacillus cereus E33L 29.3% Bacillus thuringiensis serovar konkukian str. 97-27 29.3% Bacillus thuringiensis str. Al Hakam 30.1% Bacillus clausii KSM-K16 26.8% Bacillus halodurans C-125 23.6% Bacillus licheniformis ATCC 14580 23.6% Bacillus subtilis subsp. subtilis str. 168 30.9% Geobacillus kaustophilus HTA426 26.8% Oceanobacillus iheyensis HTE831 23.6% Listeria innocua Clip11262 17.9% Listeria monocytogenes EGD-e 17.1% Listeria monocytogenes str. 4b F2365 17.1% Listeria welshimeri serovar 6b str. SLCC5334 16.3% Staphylococcus aureus RF122 20.3% Staphylococcus aureus subsp. aureus COL 20.3% Staphylococcus aureus subsp. aureus MRSA252 19.5% Staphylococcus aureus subsp. aureus MSSA476 20.3% Staphylococcus aureus subsp. aureus Mu50 20.3% Staphylococcus aureus subsp. aureus MW2 20.3% Staphylococcus aureus subsp. aureus N315 20.3% Staphylococcus aureus subsp. aureus NCTC 8325 19.5% Staphylococcus aureus subsp. aureus USA300 20.3% Staphylococcus epidermidis ATCC 12228 18.7% Staphylococcus epidermidis RP62A 19.5% Staphylococcus haemolyticus JCSC1435 17.9% Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 17.1% Enterococcus faecalis V583 16.3% Lactobacillus acidophilus NCFM 9.8% Lactobacillus brevis ATCC 367 11.4% Lactobacillus casei ATCC 334 13.8% Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 9.8% Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 10.6% Lactobacillus gasseri ATCC 33323 13.0% Lactobacillus johnsonii NCC 533 12.2% Lactobacillus plantarum WCFS1 16.3% Lactobacillus sakei subsp. sakei 23K 8.1% Lactobacillus salivarius subsp. salivarius UCC118 11.4% Pediococcus pentosaceus ATCC 25745 12.2% Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 19.5% Oenococcus oeni PSU-1 13.0% Lactococcus lactis subsp. cremoris SK11 9.8% Lactococcus lactis subsp. lactis Il1403 10.6% Streptococcus agalactiae 2603V/R 7.3% Streptococcus agalactiae A909 8.9% Streptococcus agalactiae NEM316 6.5% Streptococcus mutans UA159 14.6% Streptococcus pneumoniae D39 9.8% Streptococcus pneumoniae R6 10.6% Streptococcus pneumoniae TIGR4 9.8% Streptococcus pyogenes M1 GAS 7.3% Streptococcus pyogenes MGAS10270 7.3% Streptococcus pyogenes MGAS10394 7.3% Streptococcus pyogenes MGAS10750 5.7% Streptococcus pyogenes MGAS2096 7.3% Streptococcus pyogenes MGAS315 7.3% Streptococcus pyogenes MGAS5005 7.3% Streptococcus pyogenes MGAS6180 7.3% Streptococcus pyogenes MGAS8232 6.5% Streptococcus pyogenes MGAS9429 7.3% Streptococcus pyogenes SSI-1 6.5% Streptococcus thermophilus CNRZ1066 7.3% Streptococcus thermophilus LMD-9 8.1% Streptococcus thermophilus LMG 18311 7.3% Clostridium acetobutylicum ATCC 824 21.1% Clostridium novyi NT 14.6% Clostridium perfringens ATCC 13124 17.1% Clostridium perfringens SM101 13.0% Clostridium perfringens str. 13 14.6% Clostridium tetani E88 15.4% Carboxydothermus hydrogenoformans Z-2901 30.1% Desulfitobacterium hafniense Y51 27.6% Syntrophomonas wolfei subsp. wolfei str. Goettingen 21.1% Moorella thermoacetica ATCC 39073 26.8% Thermoanaerobacter tengcongensis MB4 18.7% Aster yellows witches'-broom phytoplasma AYWB 5.7% Onion yellows phytoplasma OY-M 5.7% Mesoplasma florum L1 4.9% Mycoplasma capricolum subsp. capricolum ATCC 27343 6.5% Mycoplasma gallisepticum R 4.9% Mycoplasma genitalium G37 4.1% Mycoplasma hyopneumoniae 232 4.1% Mycoplasma hyopneumoniae 7448 4.1% Mycoplasma hyopneumoniae J 4.9% Mycoplasma mobile 163K 2.4% Mycoplasma mycoides subsp. mycoides SC str. PG1 6.5% Mycoplasma penetrans HF-2 6.5% Mycoplasma pneumoniae M129 4.1% Mycoplasma pulmonis UAB CTIP 4.9% Mycoplasma synoviae 53 3.3% Ureaplasma parvum serovar 3 str. ATCC 700970 3.3% Group 15: Fusobacteria Bacteria Percentage Fusobacterium nucleatum subsp. nucleatum ATCC 25586 11.4% Group 16: Planctomycetes Bacteria Percentage Rhodopirellula baltica SH 1 11.4% Group 17: Spirochaetes Bacteria Percentage Leptospira borgpetersenii serovar Hardjo-bovis JB197 11.4% Leptospira borgpetersenii serovar Hardjo-bovis L550 11.4% Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 12.2% Leptospira interrogans serovar Lai str. 56601 12.2% Borrelia afzelii PKo 7.3% Borrelia burgdorferi B31 6.5% Borrelia garinii PBi 7.3% Treponema denticola ATCC 35405 10.6% Treponema pallidum subsp. pallidum str. Nichols 5.7% Group 18: Thermotogae Bacteria Percentage Thermotoga maritima MSB8 15.4%