Table S9: Percentage of conserved neighboring cluster pairs Group 1: Acidobacteria Bacteria Percentage Solibacter usitatus Ellin6076 20.0% Subtotal 20.0% Group 2: Actinobacteria Bacteria Percentage Corynebacterium diphtheriae NCTC 13129 15.0% Corynebacterium efficiens YS-314 17.6% Corynebacterium glutamicum ATCC 13032 25.0% Corynebacterium jeikeium K411 30.8% Mycobacterium sp. KMS 18.8% Mycobacterium sp. MCS 22.6% Mycobacterium avium 104 20.8% Mycobacterium avium subsp. paratuberculosis K-10 22.2% Mycobacterium bovis AF2122/97 10.7% Mycobacterium bovis BCG str. Pasteur 1173P2 10.7% Mycobacterium tuberculosis CDC1551 17.9% Mycobacterium tuberculosis H37Rv 10.7% Mycobacterium leprae TN 22.2% Mycobacterium smegmatis str. MC2 155 20.8% Mycobacterium ulcerans Agy99 26.1% Mycobacterium vanbaalenii PYR-1 23.5% Nocardia farcinica IFM 10152 20.7% Rhodococcus sp. RHA1 17.2% Acidothermus cellulolyticus 11B 19.2% Frankia sp. CcI3 25.0% Frankia alni ACN14a 13.8% Tropheryma whipplei str. Twist 30.8% Tropheryma whipplei TW08/27 38.5% Leifsonia xyli subsp. xyli str. CTCB07 36.4% Arthrobacter sp. FB24 18.2% Arthrobacter aurescens TC1 22.2% Nocardioides sp. JS614 11.1% Propionibacterium acnes KPA171202 31.8% Streptomyces avermitilis MA-4680 14.3% Streptomyces coelicolor A3(2) 28.6% Thermobifida fusca YX 28.6% Bifidobacterium adolescentis ATCC 15703 36.4% Bifidobacterium longum NCC2705 54.5% Rubrobacter xylanophilus DSM 9941 20.7% Subtotal 21.2% Group 3: Alphaproteobacteria Bacteria Percentage Caulobacter crescentus CB15 17.2% Bartonella bacilliformis KC583 25.0% Bartonella henselae str. Houston-1 13.0% Bartonella quintana str. Toulouse 17.4% Bradyrhizobium japonicum USDA 110 10.2% Nitrobacter hamburgensis X14 14.3% Nitrobacter winogradskyi Nb-255 18.2% Rhodopseudomonas palustris BisA53 16.2% Rhodopseudomonas palustris BisB18 7.9% Rhodopseudomonas palustris BisB5 15.8% Rhodopseudomonas palustris CGA009 14.6% Rhodopseudomonas palustris HaA2 17.6% Brucella abortus biovar 1 str. 9-941 21.4% Brucella melitensis 16M 19.4% Brucella melitensis biovar Abortus 2308 17.2% Brucella suis 1330 20.0% Mesorhizobium sp. BNC1 16.7% Mesorhizobium loti MAFF303099 17.6% Agrobacterium tumefaciens str. C58 17.2% Rhizobium etli CFN 42 16.7% Rhizobium leguminosarum bv. viciae 3841 11.8% Sinorhizobium meliloti 1021 20.7% Hyphomonas neptunium ATCC 15444 16.1% Maricaulis maris MCS10 9.7% Jannaschia sp. CCS1 14.3% Paracoccus denitrificans PD1222 11.8% Rhodobacter sphaeroides 2.4.1 26.7% Roseobacter denitrificans OCh 114 11.1% Silicibacter sp. TM1040 16.0% Silicibacter pomeroyi DSS-3 17.9% Gluconobacter oxydans 621H 18.2% Granulibacter bethesdensis CGDNIH1 33.3% Magnetospirillum magneticum AMB-1 26.3% Rhodospirillum rubrum ATCC 11170 22.6% Anaplasma phagocytophilum HZ 50.0% Anaplasma marginale str. St. Maries 71.4% Ehrlichia canis str. Jake 57.1% Ehrlichia chaffeensis str. Arkansas 57.1% Ehrlichia ruminantium str. Gardel 57.1% Ehrlichia ruminantium str. Welgevonden 57.1% Neorickettsia sennetsu str. Miyayama 62.5% Rickettsia conorii str. Malish 7 40.0% Rickettsia felis URRWXCal2 36.4% Rickettsia prowazekii str. Madrid E 40.0% Rickettsia typhi str. Wilmington 75.0% Rickettsia bellii RML369-C 55.6% Wolbachia endosymbiont strain TRS of Brugia malayi 80.0% Wolbachia endosymbiont of Drosophila melanogaster 80.0% Erythrobacter litoralis HTCC2594 21.7% Novosphingobium aromaticivorans DSM 12444 16.7% Sphingopyxis alaskensis RB2256 25.9% Zymomonas mobilis subsp. mobilis ZM4 16.7% Subtotal 20.6% Group 4: Betaproteobacteria Bacteria Percentage Bordetella bronchiseptica RB50 17.5% Bordetella parapertussis 12822 15.4% Bordetella pertussis Tohama I 22.2% Burkholderia sp. 383 18.3% Burkholderia cenocepacia AU 1054 18.4% Burkholderia cenocepacia HI2424 24.0% Burkholderia cepacia AMMD 21.3% Burkholderia mallei ATCC 23344 16.7% Burkholderia mallei SAVP1 19.2% Burkholderia pseudomallei 1710b 16.1% Burkholderia pseudomallei K96243 18.3% Burkholderia thailandensis E264 19.7% Burkholderia xenovorans LB400 12.2% Ralstonia eutropha H16 8.6% Ralstonia eutropha JMP134 10.5% Ralstonia metallidurans CH34 20.0% Ralstonia solanacearum GMI1000 16.7% Acidovorax sp. JS42 7.7% Acidovorax avenae subsp. citrulli AAC00-1 11.1% Polaromonas sp. JS666 8.8% Polaromonas naphthalenivorans CJ2 15.0% Rhodoferax ferrireducens T118 14.3% Verminephrobacter eiseniae EF01-2 13.9% Thiobacillus denitrificans ATCC 25259 19.5% Methylobacillus flagellatus KT 20.5% Chromobacterium violaceum ATCC 12472 17.0% Neisseria gonorrhoeae FA 1090 33.3% Neisseria meningitidis FAM18 18.2% Neisseria meningitidis MC58 18.2% Neisseria meningitidis Z2491 18.2% Nitrosomonas europaea ATCC 19718 12.1% Nitrosomonas eutropha C91 18.2% Nitrosospira multiformis ATCC 25196 13.5% Azoarcus sp. BH72 15.9% Azoarcus sp. EbN1 11.8% Dechloromonas aromatica RCB 13.6% Subtotal 16.4% Group 5: Deltaproteobacteria Bacteria Percentage Bdellovibrio bacteriovorus HD100 11.1% Desulfotalea psychrophila LSv54 10.0% Desulfovibrio desulfuricans G20 16.0% Desulfovibrio vulgaris subsp. vulgaris DP4 22.2% Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough 22.2% Lawsonia intracellularis PHE/MN1-00 42.9% Geobacter metallireducens GS-15 8.3% Geobacter sulfurreducens PCA 13.8% Pelobacter carbinolicus DSM 2380 20.7% Pelobacter propionicus DSM 2379 8.3% Anaeromyxobacter dehalogenans 2CP-C 14.3% Myxococcus xanthus DK 1622 14.3% Syntrophus aciditrophicus SB 22.2% Syntrophobacter fumaroxidans MPOB 17.9% Subtotal 16.4% Group 6: Epsilonproteobacteria Bacteria Percentage Campylobacter fetus subsp. fetus 82-40 40.0% Campylobacter jejuni RM1221 9.5% Campylobacter jejuni subsp. jejuni 81-176 9.5% Campylobacter jejuni subsp. jejuni NCTC 11168 9.5% Helicobacter acinonychis str. Sheeba 28.6% Helicobacter hepaticus ATCC 51449 33.3% Helicobacter pylori 26695 35.7% Helicobacter pylori HPAG1 28.6% Helicobacter pylori J99 36.4% Wolinella succinogenes DSM 1740 12.5% Thiomicrospira denitrificans ATCC 33889 35.7% Subtotal 23.3% Group 7: Gammaproteobacteria Bacteria Percentage Aeromonas hydrophila subsp. hydrophila ATCC 7966 15.7% Marinobacter aquaeolei VT8 16.3% Saccharophagus degradans 2-40 19.0% Colwellia psychrerythraea 34H 13.2% Idiomarina loihiensis L2TR 19.6% Pseudoalteromonas atlantica T6c 12.2% Pseudoalteromonas haloplanktis TAC125 12.5% Psychromonas ingrahamii 37 9.3% Shewanella sp. ANA-3 22.6% Shewanella sp. MR-4 19.0% Shewanella sp. MR-7 19.0% Shewanella sp. W3-18-1 15.5% Shewanella amazonensis SB2B 22.8% Shewanella denitrificans OS217 20.0% Shewanella frigidimarina NCIMB 400 24.1% Shewanella oneidensis MR-1 27.1% Nitrosococcus oceani ATCC 19707 14.7% Alkalilimnicola ehrlichei MLHE-1 19.5% Halorhodospira halophila SL1 18.9% Buchnera aphidicola str. APS (Acyrthosiphon pisum) 40.9% Buchnera aphidicola str. Bp (Baizongia pistaciae) 41.7% Buchnera aphidicola str. Cc (Cinara cedri) 57.1% Buchnera aphidicola str. Sg (Schizaphis graminum) 45.5% Candidatus Blochmannia floridanus 42.3% Candidatus Blochmannia pennsylvanicus str. BPEN 44.4% Escherichia coli 536 82.3% Escherichia coli APEC O1 88.4% Escherichia coli CFT073 88.4% Escherichia coli O157:H7 EDL933 93.2% Escherichia coli O157:H7 str. Sakai 89.7% Escherichia coli UTI89 84.1% Escherichia coli W3110 92.6% Erwinia carotovora subsp. atroseptica SCRI1043 37.2% Photorhabdus luminescens subsp. laumondii TTO1 32.5% Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 76.0% Salmonella enterica subsp. enterica serovar Typhi str. CT18 69.2% Salmonella enterica subsp. enterica serovar Typhi Ty2 69.2% Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 74.3% Salmonella typhimurium LT2 79.2% Shigella boydii Sb227 74.2% Shigella dysenteriae Sd197 62.9% Shigella flexneri 2a str. 2457T 81.0% Shigella flexneri 2a str. 301 84.2% Shigella flexneri 5 str. 8401 83.0% Shigella sonnei Ss046 83.3% Sodalis glossinidius str. 'morsitans' 46.2% Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis 31.8% Yersinia pestis Antiqua 35.6% Yersinia pestis biovar Microtus str. 91001 40.3% Yersinia pestis CO92 43.7% Yersinia pestis KIM 44.6% Yersinia pestis Nepal516 41.1% Yersinia pseudotuberculosis IP 32953 43.2% Coxiella burnetii RSA 493 21.4% Legionella pneumophila str. Lens 15.6% Legionella pneumophila str. Paris 11.8% Legionella pneumophila subsp. pneumophila str. Philadelphia 1 16.1% Methylococcus capsulatus str. Bath 16.1% Alcanivorax borkumensis SK2 18.9% Hahella chejuensis KCTC 2396 14.0% Chromohalobacter salexigens DSM 3043 18.8% Haemophilus ducreyi 35000HP 14.3% Haemophilus influenzae 86-028NP 7.7% Haemophilus influenzae Rd KW20 10.3% Haemophilus somnus 129PT 11.9% Mannheimia succiniciproducens MBEL55E 12.5% Pasteurella multocida subsp. multocida str. Pm70 11.9% Acinetobacter sp. ADP1 17.6% Psychrobacter arcticus 273-4 12.1% Psychrobacter cryohalolentis K5 8.8% Pseudomonas aeruginosa PAO1 16.4% Pseudomonas aeruginosa UCBPP-PA14 17.3% Pseudomonas fluorescens Pf-5 19.6% Pseudomonas fluorescens PfO-1 16.7% Pseudomonas putida KT2440 19.2% Pseudomonas syringae pv. phaseolicola 1448A 15.7% Pseudomonas syringae pv. tomato str. DC3000 17.0% Pseudomonas syringae pv. syringae B728a 20.4% Pseudomonas entomophila L48 15.5% Francisella tularensis subsp. holarctica 26.3% Francisella tularensis subsp. holarctica OSU18 30.0% Francisella tularensis subsp. novicida U112 16.0% Francisella tularensis subsp. tularensis FSC 198 30.0% Francisella tularensis subsp. tularensis SCHU S4 30.0% Thiomicrospira crunogena XCL-2 18.8% Photobacterium profundum SS9 19.2% Vibrio cholerae O1 biovar eltor str. N16961 22.4% Vibrio fischeri ES114 24.2% Vibrio parahaemolyticus RIMD 2210633 25.0% Vibrio vulnificus CMCP6 17.4% Vibrio vulnificus YJ016 16.4% Xanthomonas axonopodis pv. citri str. 306 21.1% Xanthomonas campestris pv. campestris str. 8004 16.7% Xanthomonas campestris pv. campestris str. ATCC 33913 17.1% Xanthomonas campestris pv. vesicatoria str. 85-10 17.1% Xanthomonas oryzae pv. oryzae MAFF 311018 24.3% Xylella fastidiosa 9a5c 13.8% Xylella fastidiosa Temecula1 10.7% Subtotal 42.9% Group 8: Aquificae Bacteria Percentage Aquifex aeolicus VF5 11.1% Subtotal 11.1% Group 9: Bacteroidetes/Chlorobi Bacteria Percentage Bacteroides fragilis NCTC 9343 35.0% Bacteroides fragilis YCH46 22.2% Bacteroides thetaiotaomicron VPI-5482 33.3% Porphyromonas gingivalis W83 30.0% Gramella forsetii KT0803 17.6% Cytophaga hutchinsonii ATCC 33406 20.0% Chlorobium tepidum TLS 36.8% Chlorobium chlorochromatii CaD3 52.9% Chlorobium phaeobacteroides DSM 266 27.3% Pelodictyon luteolum DSM 273 36.8% Subtotal 31.1% Group 10: Chlamydiae/Verrucomicrobia Bacteria Percentage Chlamydia muridarum Nigg 33.3% Chlamydia trachomatis A/HAR-13 27.3% Chlamydia trachomatis D/UW-3/CX 27.3% Chlamydophila abortus S26/3 20.0% Chlamydophila caviae GPIC 41.7% Chlamydophila felis Fe/C-56 33.3% Chlamydophila pneumoniae AR39 40.0% Chlamydophila pneumoniae CWL029 40.0% Chlamydophila pneumoniae J138 40.0% Chlamydophila pneumoniae TW-183 40.0% Candidatus Protochlamydia amoebophila UWE25 15.8% Subtotal 31.5% Group 11: Chloroflexi Bacteria Percentage Dehalococcoides sp. CBDB1 15.8% Dehalococcoides ethenogenes 195 12.5% Subtotal 14.3% Group 12: Cyanobacteria Bacteria Percentage Gloeobacter violaceus PCC 7421 33.3% Synechococcus elongatus PCC 6301 33.3% Synechococcus elongatus PCC 7942 33.3% Synechococcus sp. CC9311 44.4% Synechococcus sp. CC9605 30.0% Synechococcus sp. CC9902 20.0% Synechococcus sp. JA-2-3B'a(2-13) 9.1% Synechococcus sp. JA-3-3Ab 36.4% Synechococcus sp. WH 8102 20.0% Synechocystis sp. PCC 6803 37.5% Thermosynechococcus elongatus BP-1 28.6% Anabaena variabilis ATCC 29413 31.2% Nostoc sp. PCC 7120 26.3% Trichodesmium erythraeum IMS101 21.4% Prochlorococcus marinus str. MIT 9312 44.4% Prochlorococcus marinus str. MIT 9313 40.0% Prochlorococcus marinus str. NATL2A 44.4% Prochlorococcus marinus subsp. marinus str. CCMP1375 50.0% Prochlorococcus marinus subsp. pastoris str. CCMP1986 50.0% Subtotal 32.4% Group 13: Deinococcus-Thermus Bacteria Percentage Deinococcus geothermalis DSM 11300 50.0% Deinococcus radiodurans R1 37.5% Thermus thermophilus HB27 31.2% Thermus thermophilus HB8 25.0% Subtotal 35.5% Group 14: Firmicutes Bacteria Percentage Bacillus anthracis str. 'Ames Ancestor' 16.7% Bacillus anthracis str. Ames 16.7% Bacillus anthracis str. Sterne 19.4% Bacillus cereus ATCC 10987 17.1% Bacillus cereus ATCC 14579 15.8% Bacillus cereus E33L 16.7% Bacillus thuringiensis serovar konkukian str. 97-27 16.7% Bacillus thuringiensis str. Al Hakam 16.2% Bacillus clausii KSM-K16 18.2% Bacillus halodurans C-125 17.2% Bacillus licheniformis ATCC 14580 20.7% Bacillus subtilis subsp. subtilis str. 168 10.5% Geobacillus kaustophilus HTA426 21.2% Oceanobacillus iheyensis HTE831 20.7% Listeria innocua Clip11262 27.3% Listeria monocytogenes EGD-e 33.3% Listeria monocytogenes str. 4b F2365 28.6% Listeria welshimeri serovar 6b str. SLCC5334 35.0% Staphylococcus aureus RF122 12.0% Staphylococcus aureus subsp. aureus COL 12.0% Staphylococcus aureus subsp. aureus MRSA252 12.5% Staphylococcus aureus subsp. aureus MSSA476 12.0% Staphylococcus aureus subsp. aureus Mu50 12.0% Staphylococcus aureus subsp. aureus MW2 12.0% Staphylococcus aureus subsp. aureus N315 12.0% Staphylococcus aureus subsp. aureus NCTC 8325 12.5% Staphylococcus aureus subsp. aureus USA300 12.0% Staphylococcus epidermidis ATCC 12228 13.0% Staphylococcus epidermidis RP62A 12.5% Staphylococcus haemolyticus JCSC1435 13.6% Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 9.5% Enterococcus faecalis V583 25.0% Lactobacillus acidophilus NCFM 50.0% Lactobacillus brevis ATCC 367 21.4% Lactobacillus casei ATCC 334 17.6% Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 50.0% Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 30.8% Lactobacillus gasseri ATCC 33323 18.8% Lactobacillus johnsonii NCC 533 33.3% Lactobacillus plantarum WCFS1 20.0% Lactobacillus sakei subsp. sakei 23K 50.0% Lactobacillus salivarius subsp. salivarius UCC118 21.4% Pediococcus pentosaceus ATCC 25745 13.3% Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 8.3% Oenococcus oeni PSU-1 18.8% Lactococcus lactis subsp. cremoris SK11 33.3% Lactococcus lactis subsp. lactis Il1403 30.8% Streptococcus agalactiae 2603V/R 44.4% Streptococcus agalactiae A909 54.5% Streptococcus agalactiae NEM316 62.5% Streptococcus mutans UA159 16.7% Streptococcus pneumoniae D39 25.0% Streptococcus pneumoniae R6 23.1% Streptococcus pneumoniae TIGR4 25.0% Streptococcus pyogenes M1 GAS 44.4% Streptococcus pyogenes MGAS10270 44.4% Streptococcus pyogenes MGAS10394 44.4% Streptococcus pyogenes MGAS10750 85.7% Streptococcus pyogenes MGAS2096 55.6% Streptococcus pyogenes MGAS315 44.4% Streptococcus pyogenes MGAS5005 44.4% Streptococcus pyogenes MGAS6180 44.4% Streptococcus pyogenes MGAS8232 62.5% Streptococcus pyogenes MGAS9429 44.4% Streptococcus pyogenes SSI-1 37.5% Streptococcus thermophilus CNRZ1066 44.4% Streptococcus thermophilus LMD-9 40.0% Streptococcus thermophilus LMG 18311 44.4% Clostridium acetobutylicum ATCC 824 15.4% Clostridium novyi NT 44.4% Clostridium perfringens ATCC 13124 14.3% Clostridium perfringens SM101 25.0% Clostridium perfringens str. 13 22.2% Clostridium tetani E88 15.8% Carboxydothermus hydrogenoformans Z-2901 18.9% Desulfitobacterium hafniense Y51 17.6% Syntrophomonas wolfei subsp. wolfei str. Goettingen 23.1% Moorella thermoacetica ATCC 39073 15.2% Thermoanaerobacter tengcongensis MB4 30.4% Aster yellows witches'-broom phytoplasma AYWB 28.6% Onion yellows phytoplasma OY-M 28.6% Mesoplasma florum L1 50.0% Mycoplasma capricolum subsp. capricolum ATCC 27343 50.0% Mycoplasma gallisepticum R 16.7% Mycoplasma genitalium G37 80.0% Mycoplasma hyopneumoniae 232 80.0% Mycoplasma hyopneumoniae 7448 60.0% Mycoplasma hyopneumoniae J 66.7% Mycoplasma mobile 163K 66.7% Mycoplasma mycoides subsp. mycoides SC str. PG1 50.0% Mycoplasma penetrans HF-2 62.5% Mycoplasma pneumoniae M129 80.0% Mycoplasma pulmonis UAB CTIP 83.3% Mycoplasma synoviae 53 75.0% Ureaplasma parvum serovar 3 str. ATCC 700970 75.0% Subtotal 24.0% Group 15: Fusobacteria Bacteria Percentage Fusobacterium nucleatum subsp. nucleatum ATCC 25586 14.3% Subtotal 14.3% Group 16: Planctomycetes Bacteria Percentage Rhodopirellula baltica SH 1 14.3% Subtotal 14.3% Group 17: Spirochaetes Bacteria Percentage Leptospira borgpetersenii serovar Hardjo-bovis JB197 20.0% Leptospira borgpetersenii serovar Hardjo-bovis L550 33.3% Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 18.8% Leptospira interrogans serovar Lai str. 56601 31.2% Borrelia afzelii PKo 33.3% Borrelia burgdorferi B31 62.5% Borrelia garinii PBi 33.3% Treponema denticola ATCC 35405 15.4% Treponema pallidum subsp. pallidum str. Nichols 57.1% Subtotal 30.6% Group 18: Thermotogae Bacteria Percentage Thermotoga maritima MSB8 31.6% Subtotal 31.6%