Table S8: Percentage of conserved neighboring gene pairs within significant clusters Group 1: Acidobacteria Bacteria Percentage Solibacter usitatus Ellin6076 92.3% Subtotal 92.3% Group 2: Actinobacteria Bacteria Percentage Corynebacterium diphtheriae NCTC 13129 89.1% Corynebacterium efficiens YS-314 92.8% Corynebacterium glutamicum ATCC 13032 98.6% Corynebacterium jeikeium K411 98.5% Mycobacterium sp. KMS 88.3% Mycobacterium sp. MCS 86.9% Mycobacterium avium 104 91.3% Mycobacterium avium subsp. paratuberculosis K-10 89.2% Mycobacterium bovis AF2122/97 87.7% Mycobacterium bovis BCG str. Pasteur 1173P2 87.7% Mycobacterium tuberculosis CDC1551 87.6% Mycobacterium tuberculosis H37Rv 87.7% Mycobacterium leprae TN 92.1% Mycobacterium smegmatis str. MC2 155 88.3% Mycobacterium ulcerans Agy99 84.6% Mycobacterium vanbaalenii PYR-1 84.4% Nocardia farcinica IFM 10152 89.9% Rhodococcus sp. RHA1 86.9% Acidothermus cellulolyticus 11B 93.4% Frankia sp. CcI3 92.4% Frankia alni ACN14a 87.8% Tropheryma whipplei str. Twist 89.3% Tropheryma whipplei TW08/27 89.1% Leifsonia xyli subsp. xyli str. CTCB07 98.0% Arthrobacter sp. FB24 85.6% Arthrobacter aurescens TC1 85.4% Nocardioides sp. JS614 91.9% Propionibacterium acnes KPA171202 90.1% Streptomyces avermitilis MA-4680 92.1% Streptomyces coelicolor A3(2) 89.3% Thermobifida fusca YX 91.8% Bifidobacterium adolescentis ATCC 15703 92.5% Bifidobacterium longum NCC2705 98.0% Rubrobacter xylanophilus DSM 9941 88.5% Subtotal 89.6% Group 3: Alphaproteobacteria Bacteria Percentage Caulobacter crescentus CB15 88.8% Bartonella bacilliformis KC583 91.2% Bartonella henselae str. Houston-1 92.6% Bartonella quintana str. Toulouse 95.3% Bradyrhizobium japonicum USDA 110 88.8% Nitrobacter hamburgensis X14 88.9% Nitrobacter winogradskyi Nb-255 89.5% Rhodopseudomonas palustris BisA53 92.1% Rhodopseudomonas palustris BisB18 90.5% Rhodopseudomonas palustris BisB5 91.1% Rhodopseudomonas palustris CGA009 89.1% Rhodopseudomonas palustris HaA2 87.0% Brucella abortus biovar 1 str. 9-941 90.2% Brucella melitensis biovar Abortus 2308 90.5% Brucella melitensis 16M 90.4% Brucella suis 1330 90.8% Mesorhizobium sp. BNC1 83.7% Mesorhizobium loti MAFF303099 84.0% Agrobacterium tumefaciens str. C58 84.8% Rhizobium etli CFN 42 84.5% Rhizobium leguminosarum bv. viciae 3841 85.2% Sinorhizobium meliloti 1021 80.0% Hyphomonas neptunium ATCC 15444 86.2% Maricaulis maris MCS10 86.0% Jannaschia sp. CCS1 86.2% Paracoccus denitrificans PD1222 90.4% Rhodobacter sphaeroides 2.4.1 88.3% Roseobacter denitrificans OCh 114 94.3% Silicibacter sp. TM1040 94.1% Silicibacter pomeroyi DSS-3 82.4% Gluconobacter oxydans 621H 92.6% Granulibacter bethesdensis CGDNIH1 93.1% Magnetospirillum magneticum AMB-1 90.8% Rhodospirillum rubrum ATCC 11170 88.6% Anaplasma phagocytophilum HZ 100.0% Anaplasma marginale str. St. Maries 100.0% Ehrlichia canis str. Jake 100.0% Ehrlichia chaffeensis str. Arkansas 100.0% Ehrlichia ruminantium str. Gardel 100.0% Ehrlichia ruminantium str. Welgevonden 100.0% Neorickettsia sennetsu str. Miyayama 100.0% Rickettsia conorii str. Malish 7 97.5% Rickettsia felis URRWXCal2 97.6% Rickettsia prowazekii str. Madrid E 95.2% Rickettsia typhi str. Wilmington 100.0% Rickettsia bellii RML369-C 97.6% Wolbachia endosymbiont strain TRS of Brugia malayi 100.0% Wolbachia endosymbiont of Drosophila melanogaster 100.0% Erythrobacter litoralis HTCC2594 93.1% Novosphingobium aromaticivorans DSM 12444 92.1% Sphingopyxis alaskensis RB2256 89.6% Zymomonas mobilis subsp. mobilis ZM4 97.6% Subtotal 89.9% Group 4: Betaproteobacteria Bacteria Percentage Bordetella bronchiseptica RB50 95.7% Bordetella parapertussis 12822 96.6% Bordetella pertussis Tohama I 95.8% Burkholderia sp. 383 92.5% Burkholderia cenocepacia AU 1054 94.8% Burkholderia cenocepacia HI2424 93.9% Burkholderia cepacia AMMD 95.0% Burkholderia mallei ATCC 23344 93.0% Burkholderia mallei SAVP1 93.8% Burkholderia pseudomallei 1710b 93.2% Burkholderia pseudomallei K96243 93.3% Burkholderia thailandensis E264 94.4% Burkholderia xenovorans LB400 91.7% Ralstonia eutropha H16 91.0% Ralstonia eutropha JMP134 93.8% Ralstonia metallidurans CH34 93.0% Ralstonia solanacearum GMI1000 96.9% Acidovorax sp. JS42 94.9% Acidovorax avenae subsp. citrulli AAC00-1 96.2% Polaromonas sp. JS666 94.1% Polaromonas naphthalenivorans CJ2 94.3% Rhodoferax ferrireducens T118 95.4% Verminephrobacter eiseniae EF01-2 93.3% Thiobacillus denitrificans ATCC 25259 94.3% Methylobacillus flagellatus KT 93.4% Chromobacterium violaceum ATCC 12472 95.8% Neisseria gonorrhoeae FA 1090 94.5% Neisseria meningitidis FAM18 93.8% Neisseria meningitidis MC58 93.8% Neisseria meningitidis Z2491 92.9% Nitrosomonas europaea ATCC 19718 96.2% Nitrosomonas eutropha C91 94.3% Nitrosospira multiformis ATCC 25196 94.9% Azoarcus sp. BH72 94.6% Azoarcus sp. EbN1 95.4% Dechloromonas aromatica RCB 92.5% Subtotal 94.1% Group 5: Deltaproteobacteria Bacteria Percentage Bdellovibrio bacteriovorus HD100 96.4% Desulfotalea psychrophila LSv54 92.9% Desulfovibrio desulfuricans G20 93.8% Desulfovibrio vulgaris subsp. vulgaris DP4 89.4% Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough 90.3% Lawsonia intracellularis PHE/MN1-00 100.0% Geobacter metallireducens GS-15 94.6% Geobacter sulfurreducens PCA 96.3% Pelobacter carbinolicus DSM 2380 94.2% Pelobacter propionicus DSM 2379 94.0% Anaeromyxobacter dehalogenans 2CP-C 88.6% Myxococcus xanthus DK 1622 91.9% Syntrophus aciditrophicus SB 93.7% Syntrophobacter fumaroxidans MPOB 89.2% Subtotal 93.0% Group 6: Epsilonproteobacteria Bacteria Percentage Campylobacter fetus subsp. fetus 82-40 95.8% Campylobacter jejuni RM1221 91.8% Campylobacter jejuni subsp. jejuni 81-176 89.7% Campylobacter jejuni subsp. jejuni NCTC 11168 91.8% Helicobacter acinonychis str. Sheeba 90.3% Helicobacter hepaticus ATCC 51449 87.1% Helicobacter pylori 26695 89.2% Helicobacter pylori HPAG1 87.9% Helicobacter pylori J99 87.3% Wolinella succinogenes DSM 1740 95.8% Thiomicrospira denitrificans ATCC 33889 87.7% Subtotal 90.6% Group 7: Gammaproteobacteria Bacteria Percentage Aeromonas hydrophila subsp. hydrophila ATCC 7966 97.4% Marinobacter aquaeolei VT8 94.6% Saccharophagus degradans 2-40 96.8% Colwellia psychrerythraea 34H 95.3% Idiomarina loihiensis L2TR 98.6% Pseudoalteromonas atlantica T6c 97.8% Pseudoalteromonas haloplanktis TAC125 97.2% Psychromonas ingrahamii 37 94.4% Shewanella sp. ANA-3 97.1% Shewanella sp. MR-4 97.6% Shewanella sp. MR-7 97.6% Shewanella sp. W3-18-1 98.4% Shewanella amazonensis SB2B 97.5% Shewanella denitrificans OS217 97.8% Shewanella frigidimarina NCIMB 400 97.1% Shewanella oneidensis MR-1 95.0% Nitrosococcus oceani ATCC 19707 96.3% Alkalilimnicola ehrlichei MLHE-1 97.5% Halorhodospira halophila SL1 96.1% Buchnera aphidicola str. APS (Acyrthosiphon pisum) 93.8% Buchnera aphidicola str. Bp (Baizongia pistaciae) 95.3% Buchnera aphidicola str. Cc (Cinara cedri) 97.4% Buchnera aphidicola str. Sg (Schizaphis graminum) 95.9% Candidatus Blochmannia floridanus 96.6% Candidatus Blochmannia pennsylvanicus str. BPEN 96.6% Escherichia coli 536 99.8% Escherichia coli APEC O1 99.8% Escherichia coli CFT073 99.8% Escherichia coli O157:H7 EDL933 99.3% Escherichia coli O157:H7 str. Sakai 98.5% Escherichia coli UTI89 99.6% Escherichia coli W3110 99.8% Erwinia carotovora subsp. atroseptica SCRI1043 98.2% Photorhabdus luminescens subsp. laumondii TTO1 97.0% Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 98.5% Salmonella enterica subsp. enterica serovar Typhi str. CT18 98.3% Salmonella enterica subsp. enterica serovar Typhi Ty2 99.2% Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 98.7% Salmonella typhimurium LT2 99.0% Shigella boydii Sb227 99.3% Shigella dysenteriae Sd197 99.3% Shigella flexneri 2a str. 2457T 98.9% Shigella flexneri 2a str. 301 98.9% Shigella flexneri 5 str. 8401 99.3% Shigella sonnei Ss046 99.4% Sodalis glossinidius str. 'morsitans' 97.6% Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis 98.3% Yersinia pestis Antiqua 97.9% Yersinia pestis biovar Microtus str. 91001 97.3% Yersinia pestis CO92 97.8% Yersinia pestis KIM 97.5% Yersinia pestis Nepal516 97.9% Yersinia pseudotuberculosis IP 32953 98.0% Coxiella burnetii RSA 493 95.6% Legionella pneumophila str. Lens 95.4% Legionella pneumophila str. Paris 95.5% Legionella pneumophila subsp. pneumophila str. Philadelphia 1 95.3% Methylococcus capsulatus str. Bath 95.8% Alcanivorax borkumensis SK2 96.5% Hahella chejuensis KCTC 2396 96.0% Chromohalobacter salexigens DSM 3043 93.1% Haemophilus ducreyi 35000HP 98.2% Haemophilus influenzae 86-028NP 94.5% Haemophilus influenzae Rd KW20 94.0% Haemophilus somnus 129PT 97.1% Mannheimia succiniciproducens MBEL55E 97.2% Pasteurella multocida subsp. multocida str. Pm70 97.9% Acinetobacter sp. ADP1 91.2% Psychrobacter arcticus 273-4 92.9% Psychrobacter cryohalolentis K5 92.4% Pseudomonas aeruginosa PAO1 94.9% Pseudomonas aeruginosa UCBPP-PA14 95.2% Pseudomonas fluorescens Pf-5 92.6% Pseudomonas fluorescens PfO-1 94.4% Pseudomonas putida KT2440 94.1% Pseudomonas syringae pv. phaseolicola 1448A 94.9% Pseudomonas syringae pv. tomato str. DC3000 92.9% Pseudomonas syringae pv. syringae B728a 91.8% Pseudomonas entomophila L48 94.0% Francisella tularensis subsp. holarctica 95.8% Francisella tularensis subsp. holarctica OSU18 94.8% Francisella tularensis subsp. novicida U112 93.8% Francisella tularensis subsp. tularensis FSC 198 95.9% Francisella tularensis subsp. tularensis SCHU S4 95.9% Thiomicrospira crunogena XCL-2 93.4% Photobacterium profundum SS9 96.3% Vibrio cholerae O1 biovar eltor str. N16961 96.4% Vibrio fischeri ES114 97.4% Vibrio parahaemolyticus RIMD 2210633 97.3% Vibrio vulnificus CMCP6 95.8% Vibrio vulnificus YJ016 95.1% Xanthomonas axonopodis pv. citri str. 306 93.7% Xanthomonas campestris pv. campestris str. 8004 94.2% Xanthomonas campestris pv. campestris str. ATCC 33913 94.7% Xanthomonas campestris pv. vesicatoria str. 85-10 95.3% Xanthomonas oryzae pv. oryzae MAFF 311018 94.8% Xylella fastidiosa 9a5c 94.1% Xylella fastidiosa Temecula1 94.0% Subtotal 97.1% Group 8: Aquificae Bacteria Percentage Aquifex aeolicus VF5 82.6% Subtotal 82.6% Group 9: Bacteroidetes/Chlorobi Bacteria Percentage Bacteroides fragilis NCTC 9343 83.7% Bacteroides fragilis YCH46 83.3% Bacteroides thetaiotaomicron VPI-5482 80.9% Porphyromonas gingivalis W83 92.3% Gramella forsetii KT0803 94.4% Cytophaga hutchinsonii ATCC 33406 91.0% Chlorobium tepidum TLS 92.0% Chlorobium chlorochromatii CaD3 93.6% Chlorobium phaeobacteroides DSM 266 91.8% Pelodictyon luteolum DSM 273 90.2% Subtotal 89.1% Group 10: Chlamydiae/Verrucomicrobia Bacteria Percentage Chlamydia muridarum Nigg 97.2% Chlamydia trachomatis A/HAR-13 97.8% Chlamydia trachomatis D/UW-3/CX 97.8% Chlamydophila abortus S26/3 100.0% Chlamydophila caviae GPIC 93.8% Chlamydophila felis Fe/C-56 97.9% Chlamydophila pneumoniae AR39 97.7% Chlamydophila pneumoniae CWL029 97.7% Chlamydophila pneumoniae J138 97.7% Chlamydophila pneumoniae TW-183 97.7% Candidatus Protochlamydia amoebophila UWE25 91.2% Subtotal 96.5% Group 11: Chloroflexi Bacteria Percentage Dehalococcoides sp. CBDB1 86.0% Dehalococcoides ethenogenes 195 88.5% Subtotal 87.2% Group 12: Cyanobacteria Bacteria Percentage Gloeobacter violaceus PCC 7421 97.6% Synechococcus elongatus PCC 6301 90.7% Synechococcus elongatus PCC 7942 90.7% Synechococcus sp. CC9311 89.7% Synechococcus sp. CC9605 88.1% Synechococcus sp. CC9902 88.1% Synechococcus sp. JA-2-3B'a(2-13) 97.8% Synechococcus sp. JA-3-3Ab 95.1% Synechococcus sp. WH 8102 88.1% Synechocystis sp. PCC 6803 100.0% Thermosynechococcus elongatus BP-1 100.0% Anabaena variabilis ATCC 29413 90.0% Nostoc sp. PCC 7120 91.8% Trichodesmium erythraeum IMS101 90.4% Prochlorococcus marinus str. MIT 9312 89.5% Prochlorococcus marinus str. MIT 9313 90.7% Prochlorococcus marinus str. NATL2A 89.5% Prochlorococcus marinus subsp. marinus str. CCMP1375 94.4% Prochlorococcus marinus subsp. pastoris str. CCMP1986 94.7% Subtotal 92.2% Group 13: Deinococcus-Thermus Bacteria Percentage Deinococcus geothermalis DSM 11300 91.2% Deinococcus radiodurans R1 90.1% Thermus thermophilus HB27 93.7% Thermus thermophilus HB8 89.9% Subtotal 91.2% Group 14: Firmicutes Bacteria Percentage Bacillus anthracis str. 'Ames Ancestor' 88.7% Bacillus anthracis str. Ames 88.7% Bacillus anthracis str. Sterne 88.7% Bacillus cereus ATCC 10987 87.9% Bacillus cereus ATCC 14579 87.3% Bacillus cereus E33L 88.1% Bacillus thuringiensis serovar konkukian str. 97-27 88.1% Bacillus thuringiensis str. Al Hakam 90.1% Bacillus clausii KSM-K16 85.3% Bacillus halodurans C-125 88.3% Bacillus licheniformis ATCC 14580 90.9% Bacillus subtilis subsp. subtilis str. 168 82.5% Geobacillus kaustophilus HTA426 90.6% Oceanobacillus iheyensis HTE831 85.3% Listeria innocua Clip11262 95.8% Listeria monocytogenes EGD-e 96.8% Listeria monocytogenes str. 4b F2365 97.8% Listeria welshimeri serovar 6b str. SLCC5334 97.8% Staphylococcus aureus RF122 95.9% Staphylococcus aureus subsp. aureus COL 92.0% Staphylococcus aureus subsp. aureus MRSA252 93.9% Staphylococcus aureus subsp. aureus MSSA476 92.0% Staphylococcus aureus subsp. aureus Mu50 92.0% Staphylococcus aureus subsp. aureus MW2 92.0% Staphylococcus aureus subsp. aureus N315 92.0% Staphylococcus aureus subsp. aureus NCTC 8325 91.5% Staphylococcus aureus subsp. aureus USA300 92.0% Staphylococcus epidermidis ATCC 12228 96.7% Staphylococcus epidermidis RP62A 95.8% Staphylococcus haemolyticus JCSC1435 95.3% Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 96.6% Enterococcus faecalis V583 91.0% Lactobacillus acidophilus NCFM 90.4% Lactobacillus brevis ATCC 367 95.4% Lactobacillus casei ATCC 334 91.0% Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 100.0% Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 96.8% Lactobacillus gasseri ATCC 33323 87.7% Lactobacillus johnsonii NCC 533 88.1% Lactobacillus plantarum WCFS1 91.8% Lactobacillus sakei subsp. sakei 23K 95.7% Lactobacillus salivarius subsp. salivarius UCC118 98.4% Pediococcus pentosaceus ATCC 25745 95.7% Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 84.6% Oenococcus oeni PSU-1 96.9% Lactococcus lactis subsp. cremoris SK11 96.5% Lactococcus lactis subsp. lactis Il1403 93.5% Streptococcus agalactiae 2603V/R 93.5% Streptococcus agalactiae A909 91.7% Streptococcus agalactiae NEM316 95.5% Streptococcus mutans UA159 91.3% Streptococcus pneumoniae D39 92.5% Streptococcus pneumoniae R6 92.9% Streptococcus pneumoniae TIGR4 94.2% Streptococcus pyogenes M1 GAS 97.7% Streptococcus pyogenes MGAS10270 97.7% Streptococcus pyogenes MGAS10394 97.7% Streptococcus pyogenes MGAS10750 97.4% Streptococcus pyogenes MGAS2096 97.6% Streptococcus pyogenes MGAS315 97.7% Streptococcus pyogenes MGAS5005 97.7% Streptococcus pyogenes MGAS6180 97.7% Streptococcus pyogenes MGAS8232 97.6% Streptococcus pyogenes MGAS9429 97.7% Streptococcus pyogenes SSI-1 97.4% Streptococcus thermophilus CNRZ1066 100.0% Streptococcus thermophilus LMD-9 96.0% Streptococcus thermophilus LMG 18311 100.0% Clostridium acetobutylicum ATCC 824 86.8% Clostridium novyi NT 95.3% Clostridium perfringens ATCC 13124 93.4% Clostridium perfringens SM101 95.9% Clostridium perfringens str. 13 92.7% Clostridium tetani E88 92.9% Carboxydothermus hydrogenoformans Z-2901 88.8% Desulfitobacterium hafniense Y51 92.0% Syntrophomonas wolfei subsp. wolfei str. Goettingen 92.5% Moorella thermoacetica ATCC 39073 93.5% Thermoanaerobacter tengcongensis MB4 85.5% Aster yellows witches'-broom phytoplasma AYWB 94.3% Onion yellows phytoplasma OY-M 94.4% Mesoplasma florum L1 100.0% Mycoplasma capricolum subsp. capricolum ATCC 27343 94.7% Mycoplasma gallisepticum R 100.0% Mycoplasma genitalium G37 95.8% Mycoplasma hyopneumoniae 232 100.0% Mycoplasma hyopneumoniae 7448 100.0% Mycoplasma hyopneumoniae J 100.0% Mycoplasma mobile 163K 100.0% Mycoplasma mycoides subsp. mycoides SC str. PG1 94.4% Mycoplasma penetrans HF-2 90.9% Mycoplasma pneumoniae M129 96.3% Mycoplasma pulmonis UAB CTIP 96.6% Mycoplasma synoviae 53 91.3% Ureaplasma parvum serovar 3 str. ATCC 700970 100.0% Subtotal 92.3% Group 15: Fusobacteria Bacteria Percentage Fusobacterium nucleatum subsp. nucleatum ATCC 25586 91.2% Subtotal 91.2% Group 16: Planctomycetes Bacteria Percentage Rhodopirellula baltica SH 1 90.0% Subtotal 90.0% Group 17: Spirochaetes Bacteria Percentage Leptospira borgpetersenii serovar Hardjo-bovis JB197 92.2% Leptospira borgpetersenii serovar Hardjo-bovis L550 92.2% Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 92.5% Leptospira interrogans serovar Lai str. 56601 92.4% Borrelia afzelii PKo 100.0% Borrelia burgdorferi B31 100.0% Borrelia garinii PBi 100.0% Treponema denticola ATCC 35405 98.1% Treponema pallidum subsp. pallidum str. Nichols 100.0% Subtotal 95.7% Group 18: Thermotogae Bacteria Percentage Thermotoga maritima MSB8 89.5% Subtotal 89.5%