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Home , Acidicapsa, Acinetobacter apis, Acinetobacter variabilis, Acrocarpospora, Actinobacillus, Actinokineospora

+ Gammaproteobacteria +Pasteurales+Orbales Enterobacterales +Erwiniaceae 30 enterica subsp. enterica 13 Klebsiella indica 8 Escherichia fergusonii 25 10 Escherichia marmotae 100 Escherichia albertii 8 Citrobacter amalonaticus 43 Citrobacter sedlakii Escherichia hermannii 10 subsp. pneumoniae 100 45 Klebsiella variicola subsp. variicola subsp. cloacae 100 Enterobacter cloacae subsp. dissolvens 100 Kosakonia radicincitans Kosakonia oryzae 5 100 Kosakonia sacchari Kosakonia quasisacchari Metakosakonia massiliensis 3 33 Phytobacter palmae 20 Cronobacter muytjensii 40 Cronobacter condimenti 28 Cronobacter sakazakii 70 Cronobacter malonaticus 18 Franconibacter daqui 5 Shimwellia blattae 35 Erwinia amylovora 100 Erwinia tasmaniensis Erwinia aphidicola 8 38 Erwinia rhapontici Erwinia mallotivora 100 Erwinia psidii 10 23 Mixta intestinalis 100 Erwinia oleae 100 Izhakiella australiensis 100 Erwinia iniecta Enterobacter quasihormaechei 10038 Enterobacter hormaechei subsp. hoffmannii Enterobacter hormaechei subsp. oharae 100 25 Enterobacter hormaechei subsp. steigerwaltii Enterobacter hormaechei subsp. xiangfangensis Enterobacter ludwigii Enterobacter wuhouensis 8 Enterobacter chuandaensis 25 Enterobacter tabaci Enterobacter quasiroggenkampii Cedecea davisae 10018 Enterobacter roggenkampii Enterobacter sichuanensis 20 Enterobacter chengduensis 53 Citrobacter braakii Citrobacter murliniae 28 Citrobacter portucalensis 13 Citrobacter werkmanii 5 Citrobacter gillenii 18 Yokenella regensburgei 10 Klebsiella pasteurii 48 Klebsiella spallanzanii 100 Enterobacter aerogenes 100 45 Pantoea allii Pantoea rodasii 100 Tatumella morbirosei 100 Tatumella punctata 30 100 Rosenbergiella collisarenosi Rosenbergiella epipactidis 100 Rosenbergiella australiborealis 8 Buttiauxella warmboldiae 33 Buttiauxella noackiae 100 Buttiauxella gaviniae 35 Buttiauxella izardii Scandinavium goeteborgense 100 Kluyvera ascorbata 10 Pseudocitrobacter vendiensis Serratia nematodiphila Pectobacteriaceae 30 Pectobacterium wasabiae 5 28 Pectobacterium betavasculorum 85 Pectobacterium atrosepticum 35 Pectobacterium parmentieri Brenneria alni 100 Pectobacterium punjabense 48 Pectobacterium odoriferum 63 Pectobacterium versatile 15 Pectobacterium carotovorum 43 100 Pectobacterium brasiliense 100 Pectobacterium polaris Pectobacterium actinidiae Pectobacterium aroidearum 35 8 Pectobacterium fontis 48 Dickeya dadantii subsp. dadantii Dickeya fangzhongdai Dickeya chrysanthemi 1008 Dickeya lacustris Dickeya undicola 28 Dickeya oryzae 38 Dickeya poaceiphila

Yersiniaceae+Budviciaceae 45 100 13 Yersinia thracica 13 Yersinia occitanica 20 Yersinia canariae Yersinia hibernica 20 Yersinia artesiana 40 60 Yersinia proxima Yersinia alsatica 25 45 100 Yersinia vastinensis Serratia oryzae 18 Ewingella americana 35 Rahnella inusitata Rouxiella silvae 18 13 Rouxiella badensis Serratia liquefaciens 43 Serratia grimesii Serratia quinivorans 1002370 Serratia proteamaculans Serratia fonticola Serratia microhaemolytica 30 Serratia ficaria 18 Serratia entomophila 8 3100 Serratia plymuthica 83 Serratia inhibens 100 Serratia odorifera Budvicia diplopodorum Chimaeribacter californicus 75 Chimaeribacter coloradensis

Pasteurellaceae 75 aphrophilus 78 Aggregatibacter kilianii 23 Aggregatibacter segnis 100 pittmaniae 13 Rodentibacter heidelbergensis 100 Rodentibacter ratti 100 dagmatis 35 8 Haemophilus massiliensis 100 Haemophilus aegyptius succinogenes 18 20 Actinobacillus minor Actinobacillus pleuropneumoniae 100 Actinobacillus ureae 15 15 63 Mannheimia haemolytica Mannheimia ruminalis 100 Mannheimia varigena 100 60 Mannheimia granulomatis Haemophilus parainfluenzae 68 63 Haemophilus sputorum Chelonobacter oris 38 Gilliamella apis 100 Gilliamella apicola Thorsellia anophelis Morganellaceae~1 100 Photorhabdus laumondii subsp. laumondii 100 Photorhabdus akhurstii 100 Photorhabdus luminescens subsp. luminescens 18 57 Photorhabdus temperata 100 Xenorhabdus beddingii 23 Xenorhabdus griffiniae 3 100 23 Xenorhabdus eapokensis Xenorhabdus szentirmaii 100 Xenorhabdus bovienii 53 Xenorhabdus ehlersii Xenorhabdus budapestensis 100 35 Xenorhabdus innexi 100 30 100 Proteus hauseri

Morganellacaeae 57 Providencia huaxiensis 70 Providencia vermicola 38 10 38 Providencia sneebia 68 Providencia alcalifaciens 88 65 Providencia rustigianii Providencia heimbachae 30 Moellerella wisconsensis 100 Morganella morganii subsp. morganii

57 Edwardsiella ictaluri Sodalis praecaptivus 33 Buchnera aphidicola Pragia fontium 85 Limnobaculum parvum 48 Chania multitudinisentens Gibbsiella dentisursi 20 Leminorella richardii

Aeromonadaceae_Aeromonadales Aeromonas bestiarum 100 Haemophilus piscium 100 Aeromonas salmonicida subsp. achromogenes 35 Aeromonas molluscorum Aeromonas rivuli 35 Aeromonas salmonicida subsp. salmonicida 50 35 Aeromonas bivalvium 13 Aeromonas encheleia Aeromonas popoffii 28 Aeromonas sobria Aeromonas eucrenophila Aeromonas jandaei 10 Aeromonas ichthiosmia Aeromonas tecta Aeromonas fluvialis 4015 Aeromonas allosaccharophila 100 subsp. hydrophila Aeromonas media 68 Aeromonas sanarellii 93100 Aeromonas taiwanensis Aeromonas punctata subsp. punctata 100 Aeromonas enteropelogenes Aeromonas diversa 100 Aeromonas schubertii 30 Aeromonas simiae Tolumonas auensis 100 Tolumonas lignilytica

Vibrionaceae_Vibrionales 23 Listonella pelagia 23 Vibrio nigripulchritudo 25 Vibrio caribbeanicus Vibrio coralliilyticus 10 95 Vibrio quintilis 100 Vibrio zhugei Vibrio viridaestus 20 8 Vibrio furnissii 60 Vibrio fluvialis 53 Vibrio superstes 30 25 Vibrio ezurae Vibrio penaeicida 18 100 18 28 33 Vibrio campbellii 5 Vibrio ouci 3 100 Vibrio ponticus Vibrio alfacsensis 5 Vibrio orientalis 5 25 Vibrio tubiashii subsp. europaeus Vibrio bivalvicida Vibrio agarivorans Vibrio hispanicus 13 18 Vibrio coralliirubri Vibrio atlanticus 100 Vibrio lentus 100 23 Vibrio echinoideorum 15 Vibrio artabrorum 5 Vibrio gallaecicus 15 Vibrio algicola Vibrio tapetis subsp. britannicus 100 23 Vibrio tapetis subsp. tapetis 13 33 Vibrio ordalii Vibrio salilacus 100 Vibrio sinensis 55 8 Vibrio renipiscarius Aliivibrio wodanis 100 Aliivibrio finisterrensis 100 Photobacterium carnosum 100 Photobacterium frigidiphilum 28 Photobacterium alginatilyticum Photobacterium jeanii 3 100 Photobacterium aphoticum 43 100 Photobacterium ganghwense 13 Photobacterium galatheae 100 Photobacterium sanctipauli Paraphotobacterium marinum Grimontia marina 13 85 Enterovibrio nigricans 50 100 Enterovibrio pacificus Salinivibrio kushneri 100 Salinivibrio costicola subsp. alcaliphilus 40 Salinivibrio socompensis 50 98 Salinivibrio costicola subsp. vallismortis Thaumasiovibrio occultus Photobacterium damselae subsp. damselae

Aeromonadaceae~2_Aeromonadales~1 100 Zobellella denitrificans 70 Zobellella taiwanensis 50 Oceanimonas marisflavi 83 Oceanisphaera arctica Oceanisphaera avium 40 100 Oceanisphaera profunda Dongshaea marina

Alteromonadales~1 Colwelliaceae 100 Thalassotalea piscium 100 Thalassotalea atypica 5 Thalassotalea euphylliae 73 Colwellia beringensis Colwellia meonggei 13 18 Thalassotalea litorea 100 Thalassotalea mangrovi 85 Thalassomonas viridans Colwellia maris 25 57 Colwellia echini Colwellia asteriadis 20100 Colwellia psychrerythraea Litorilituus lipolyticus

Idiomarinaceae 38 Idiomarina indica 35 23 Pseudidiomarina donghaiensis 83 Pseudidiomarina woesei 100 15 Pseudidiomarina gelatinasegens 38 Pseudidiomarina insulisalsae 33 Pseudidiomarina halophila 73 Pseudidiomarina atlantica 63 100 65 Pseudidiomarina salinarum 100 Pseudidiomarina planktonica Idiomarina xiamenensis 100 Idiomarina loihiensis Idiomarina tyrosinivorans

Alteromonadaceae~1 Agarivorans aestuarii 90 Alginatibacterium sediminis

Pseudoalteromonadaceae Pseudoalteromonas antarctica 60 Pseudoalteromonas arctica 13 Pseudoalteromonas elyakovii 35 Pseudoalteromonas paragorgicola 20 Pseudoalteromonas distincta 63 Pseudoalteromonas agarivorans 38 Pseudoalteromonas tetraodonis Pseudoalteromonas donghaensis 40 Pseudoalteromonas lipolytica 100 Pseudoalteromonas arabiensis 18 33 Pseudoalteromonas gelatinilytica 85 100 Pseudoalteromonas profundi 48 Pseudoalteromonas ruthenica Pseudoalteromonas amylolytica 100 Pseudoalteromonas phenolica 13 Pseudoalteromonas tunicata Corallincola holothuriorum 15 Psychromonas ingrahamii 50 Motilimonas pumila Moritellaceae 45 Moritella abyssi 38 Moritella dasanensis 40 Moritella profunda Moritella japonica 100100 Moritella viscosa Moritella marina

Shewanellaceae 15 pealeana 45 Shewanella halifaxensis 38 Shewanella pneumatophori 48 Shewanella violacea 30 Shewanella kaireitica Shewanella surugensis 33 Shewanella fidelis 100 13 10 100 Shewanella indica 100 Parashewanella curva 50 Parashewanella tropica 50 Shewanella mangrovi 57 Shewanella amazonensis 100 100 Shewanella khirikhana Shewanella loihica 73 Shewanella colwelliana 53 Shewanella marisflavi Shewanella sediminis 98 Shewanella woodyi 100 Shewanella vesiculosa 60 40 Shewanella polaris 57 Shewanella denitrificans 43 Shewanella aestuarii 50 Shewanella gaetbuli Shewanella inventionis 75 10 Shewanella oneidensis 100 Shewanella xiamenensis 20 55 3023 Shewanella profunda Shewanella baltica Shewanella gelidii

Ferrimonadaceae 100 Ferrimonas balearica Ferrimonas gelatinilytica 65 Paraferrimonas haliotis

Chromatiaceae~1_Chromatiales~1 60 Rheinheimera mesophila 45 Rheinheimera sediminis 100 65 Rheinheimera soli Rheinheimera chironomi 45 30 Rheinheimera riviphila 28 Rheinheimera japonica 40 Rheinheimera baltica Rheinheimera aquimaris 78 Rheinheimera nanhaiensis 33 40 aestuarii 78 Alishewanella jeotgali 100 Alishewanella fetalis 57 43 Alishewanella agri 57 Alishewanella solinquinati Alishewanella alkalitolerans 20 83 Arsukibacterium ikkense Rheinheimera perlucida 23 100 Rheinheimera tuosuensis Rheinheimera salexigens Alkalimonas amylolytica 93 Alkalimonas collagenimarina Alteromonadaceae_Alteromonadales 33 Alteromonas australica 40 Alteromonas mediterranea 100 Alteromonas stellipolaris 23 15 Salinimonas sediminis Salinimonas iocasae Marisediminitalea mangrovi 100 Paraglaciecola chathamensis 100 45 Paraglaciecola polaris 100 Paraglaciecola hydrolytica 73 33 Paraglaciecola psychrophila 100 Paraglaciecola marina 33 Glaciecola nitratireducens Pseudobowmanella zhangzhouensis Bowmanella pacifica 90 88 Bowmanella dokdonensis Saliniradius amylolyticus 53 Planctobacterium marinum

Oceanospirillales~1 Halomonadaceae Halomonas aquamarina 28 100 Halomonas meridiana 100 Halomonas piezotolerans 13 Halomonas alkaliphila 100 Halomonas venusta Halomonas janggokensis 100 Halomonas titanicae 20 100 Halomonas variabilis 100 Halomonas alkaliantarctica 100 Halomonas boliviensis 38 Halomonas nanhaiensis 33 Halomonas rituensis 38 100 Halomonas zhuhanensis 43 Halomonas malpeensis 100 Halomonas subglaciescola 15 Halomonas montanilacus Halomonas urumqiensis Halomonas pellis 88 Halomonas elongata 100 Halomonas halmophila 8 33 Halomonas salina 70 Halomonas borealis 10 Halomonas stenophila 3 Halomonas aestuarii 20 35 Halomonas denitrificans Halomonas alimentaria 100 18 Halomonas litopenaei Halomonas tabrizica 30 100 Halomonas urmiana Halomonas tibetensis 50 Halomonas pantelleriensis Halomonas socia 848 Halomonas qiaohouensis 100 Chromohalobacter canadensis 100 Chromohalobacter japonicus 8 40 Chromohalobacter israelensis Salinicola halophilus 38 3318 Salinicola tamaricis Halomonas niordiana 45 Halomonas anticariensis Halomonas xianhensis 80 Kushneria konosiri 18 70 Cobetia pacifica Cobetia marina 100 38 Cobetia amphilecti 80 Cobetia litoralis Marinospirillum perlucidum

Alteromonadales~2+Oceanospirillales Oceanospirillaceae_Oceanospirillales 23 Marinomonas profundi 38 Marinomonas profundimaris 45 Marinomonas arenicola 53 Marinomonas pontica Marinomonas posidonica 100100 Marinomonas epiphytica 45 Marinomonas mediterranea 50 Marinomonas algicida 100 100 Marinomonas blandensis Marinomonas piezotolerans 73 Marinomonas aquimarina 78 Marinomonas communis Thalassolituus oleivorans 28 100 Amphritea opalescens 35 Neptunomonas antarctica 100 25 Neptunomonas japonica Oceanospirillum sanctuarii Motiliproteus coralliicola 40 Neptuniibacter caesariensis 33 Pontibacterium granulatum 25 Oceanospirillaceae~1 100 Nitrincola tibetensis 98 Nitrincola alkalisediminis 40 Nitrincola iocasae 100 Nitrincola tapanii 53 100 Nitrincola alkalilacustris

100 Marinobacterium aestuarii Marinobacterium iners ~1 45 Marinobacterium zhoushanense Marinobacterium litorale 100 Marinobacterium mangrovicola 28

Oceanospirillales~2 100 Reinekea blandensis 100 Reinekea aestuarii 100 Reinekea marinisedimentorum 78 Saccharospirillum impatiens Natronospirillum operosum

Pseudomonadaceae+ 13 lurida Pseudomonas paralactis 100 Pseudomonas poae 15 Pseudomonas trivialis Pseudomonas tolaasii 100 Pseudomonas lactis 20 Pseudomonas costantinii Pseudomonas edaphica 100 55 Pseudomonas cedrina subsp. fulgida 25 Pseudomonas cedrina subsp. cedrina Pseudomonas orientalis Pseudomonas fluorescens 1013 Pseudomonas meridiana 60 Pseudomonas antarctica Pseudomonas libanensis 5 Pseudomonas veronii 43 Pseudomonas fildesensis 100 Pseudomonas grimontii 100 Pseudomonas extremaustralis Pseudomonas haemolytica 10 25 Pseudomonas rhodesiae Pseudomonas gessardii 28 Pseudomonas proteolytica Pseudomonas karstica 15 Pseudomonas spelaei Pseudomonas viciae 1810 Pseudomonas lini Pseudomonas kilonensis 10 Pseudomonas migulae Pseudomonas prosekii Pseudomonas viridiflava 48 Pseudomonas asturiensis Pseudomonas chlororaphis subsp. aurantiaca 13 25 Pseudomonas chlororaphis subsp. aureofaciens 38 Pseudomonas helleri 15 Pseudomonas weihenstephanensis Pseudomonas saxonica 100 Pseudomonas versuta 28 20 Pseudomonas congelans Pseudomonas avellanae 2023 Pseudomonas cannabina Pseudomonas cichorii 25 Pseudomonas tremae 13 Pseudomonas silesiensis Pseudomonas mandelii 10 40 18 Pseudomonas frederiksbergensis Pseudomonas protegens 18 Pseudomonas vancouverensis 1318 Pseudomonas laurylsulfatiphila 100 Pseudomonas laurylsulfativorans 100 Pseudomonas reinekei 13 Pseudomonas baetica 10 Pseudomonas moraviensis Pseudomonas agarici 25 Pseudomonas rhizosphaerae 13 Pseudomonas graminis 50 100 Pseudomonas lutea Pseudomonas bohemica Pseudomonas kuykendallii 25 Pseudomonas tructae 13 Pseudomonas wadenswilerensis Pseudomonas donghuensis 100 Pseudomonas huaxiensis 18 Pseudomonas vranovensis 10 Pseudomonas defluvii 18 100 Pseudomonas japonica Pseudomonas asplenii 100 100 Pseudomonas mosselii Pseudomonas sichuanensis Pseudomonas inefficax 57 3 Pseudomonas plecoglossicida Pseudomonas monteilii Pseudomonas asiatica 15 5 8 23 Pseudomonas fulva Pseudomonas parafulva 50 Pseudomonas juntendi 18 Pseudomonas cremoricolorata 30 Pseudomonas oryzihabitans Pseudomonas reidholzensis 100 100 Pseudomonas glareae Pseudomonas taeanensis 100 65 Pseudomonas guineae Pseudomonas leptonychotis 100 Pseudomonas peli Pseudomonas punonensis 38 68 Pseudomonas argentinensis Pseudomonas straminea 1825 Pseudomonas flavescens Pseudomonas benzenivorans Azotobacter salinestris 100 38 Pseudomonas tarimensis 38 Pseudomonas urumqiensis Pseudomonas matsuisoli 25 13 100 Pseudomonas balearica 50 20 Pseudomonas otitidis 38 Pseudomonas resinovorans 100 Pseudomonas citronellolis 5 Pseudomonas knackmussii 90 Pseudomonas nitroreducens 5 Pseudomonas luteola 40 Pseudomonas rhizoryzae 38 Pseudomonas hussainii 5 Pseudomonas mangrovi 33 Pseudomonas guguanensis Pseudomonas sagittaria 90 Pseudomonas guangdongensis 100 Pseudomonas hydrolytica 100 100 100 Pseudomonas khazarica 18 Pseudomonas chengduensis Pseudomonas tianjinensis 25 Pseudomonas stutzeri Pseudomonas kunmingensis 55 Pseudomonas xanthomarina 55 Pseudomonas formosensis 40 Pseudomonas pertucinogena 45 Pseudomonas xiamenensis 85 33 Pseudomonas bauzanensis 50 Pseudomonas pelagia 100 Pseudomonas salina 40 Pseudomonas profundi 68 Pseudomonas xinjiangensis Pseudomonas sabulinigri 4528 Pseudomonas oceani Pseudomonas phragmitis 35 Pseudomonas salegens Entomomonas moraniae

Alteromonadales~3+Oceanospirillales~3 Alteromonadaceae~2 90 Marinobacter algicola 55 Marinobacter salarius 53 Marinobacter denitrificans 25 Marinobacter salsuginis 30 Marinobacter lacisalsi 53 Marinobacter flavimaris 8 Marinobacter adhaerens 43 Marinobacter maroccanus 100 Marinobacter changyiensis 15 8 Marinobacter gudaonensis 15 Marinobacter sediminum 70 Marinobacter similis 23 Marinobacter lipolyticus 20 Marinobacter guineae 100 Marinobacter psychrophilus 100 Marinobacter aromaticivorans 100 Marinobacter salinus 33 Marinobacter nauticus 33 Marinobacter excellens 78 Marinobacter fuscus 53 Marinobacter salinexigens 73 100 Marinobacter nitratireducens 75 Marinobacter santoriniensis 70 Marinobacter fonticola Marinobacter lutaoensis 60 Hydrocarboniclastica marina 23 Mangrovitalea sediminis 10 Zooshikella ganghwensis 8 Hahella chejuensis 100 Hahella ganghwensis 8 Pseudohongiella nitratireducens Endozoicomonadaceae 13 100 Endozoicomonas ascidiicola 45 Endozoicomonas elysicola 85 Endozoicomonas arenosclerae Endozoicomonas euniceicola 100 100 Endozoicomonas montiporae 18 Kistimonas asteriae

Cellvibrionales Cellvibrionaceae 100 Cellvibrio fibrivorans 85 Cellvibrio fontiphilus 73 Cellvibrio japonicus 40 Cellvibrio gandavensis 15 Simiduia litorea 33 Saccharophagus degradans 28 Teredinibacter turnerae Marinagarivorans algicola 28 30 Gilvimarinus chinensis 70 Gilvimarinus polysaccharolyticus Maricurvus nonylphenolicus 10 Umboniibacter marinipuniceus

Halieaceae 28 28 Parahaliea mediterranea 30 Luminiphilus syltensis 30 Kineobactrum sediminis 55 Haliea atlantica 68 Haliea salexigens Halioglobus japonicus 38 Marimicrobium arenosum

60 Spongiibacteraceae 53 Spongiibacter marinus Spongiibacter tropicus 5 33 100 100 Zhongshania aliphaticivorans Zhongshania antarctica 100 Zhongshania guokunii

Microbulbiferaceae 35 Microbulbifer epialgicus Microbulbifer marinus 5757 Microbulbifer taiwanensis 100 Microbulbifer gwangyangensis Microbulbifer pacificus 33 78 Microbulbifer aggregans Microbulbifer mangrovi 73 Microbulbifer flavimaris 30 Microbulbifer yueqingensis

Alcanivoracaceae_Oceanospirillales~4 Alcanivorax dieselolei 35 93 Alcanivorax marinus 40 Alcanivorax venustensis 68 Alcanivorax mobilis 100 Alcanivorax pacificus 80 Alcanivorax indicus 68 63 Alcanivorax borkumensis 40 Alcanivorax jadensis 30 Alcanivorax profundi 83 38 Alcanivorax nanhaiticus 88 Alcanivorax sediminis Alcanivorax hongdengensis 20 Ketobacter alkanivorans 100 Ketobacter nezhaii Pelagibaculum spongiae

Legionellaceae_Legionellales 60 100 Legionella qingyii Legionella saoudiensis 100 100 35 100 Legionella tunisiensis 33100

30 Francisellaceae+Fastidiosibacteraceae_Thiotrichales~1 90 Francisella halioticida 57 Francisella philomiragia 78 subsp. mediasiatica 100 13 100 Francisella tularensis subsp. novicida Francisella hispaniensis 93 Francisella persica Fastidiosibacter lacustris

5 Piscirickettsia salmonis Kangiellaceae_Oceanospirillales~5 90 Kangiella profundi Kangiella aquimarina 100 Kangiella taiwanensis 3 75 Kangiella japonica

Chromatiaceae_Chromatiales Allochromatium vinosum 18 100 Marichromatium purpuratum 100 Marichromatium gracile Imhoffiella purpurea 38 100 Phaeobacterium nitratireducens 100 Thiocapsa roseopersicina 40 Thiocapsa marina 48 Thiodictyon bacillosum 53 70 Thiodictyon elegans Lamprocystis purpurea Caldichromatium japonicum

10 Piscirickettsiaceae~1_Thiotrichales~2 100 Thiomicrorhabdus indica 100 Hydrogenovibrio halophilus 100 Thiomicrospira cyclica Thioprofundum hispidum 13 Chromatiales~2 20 Granulosicoccus coccoides Sedimenticola selenatireducens 100 Endothiovibrio diazotrophicus

Thiotrichaceae_Thiotrichales 100 Thiothrix nivea Thiofilum flexile 18 Leucothrix mucor

Methylococcaceae_Methylococcales 100 Methylosarcina fibrata 40 Methylomicrobium lacus 100 Methylobacter tundripaludum 28 Methylicorpusculum oleiharenae Methylocucumis oryzae

23 Piscirickettsiaceae~2_Thiotrichales~3 88 Methylophaga nitratireducenticrescens Methylophaga frappieri 100 Methylophaga thalassica

Moraxellaceae_Pseudomonadales~1 45 calcoaceticus 8 Acinetobacter lactucae Acinetobacter ursingii 33 Acinetobacter tandoii 8 563 Acinetobacter johnsonii 15 Acinetobacter bouvetii 13 Acinetobacter haemolyticus Acinetobacter proteolyticus 8 43 Acinetobacter tjernbergiae 100 Acinetobacter dispersus 100 Acinetobacter parvus 55 Acinetobacter bereziniae 40 Acinetobacter guillouiae Acinetobacter wuhouensis 33 Acinetobacter defluvii 100 25 Acinetobacter chinensis 18 18 Acinetobacter sichuanensis Acinetobacter cumulans 25 80 Acinetobacter chengduensis Acinetobacter piscicola 5 Acinetobacter modestus 100 Acinetobacter rudis 68 Acinetobacter larvae 3 13 Acinetobacter gerneri Acinetobacter courvalinii 78 Acinetobacter vivianii 8 30 Acinetobacter baylyi Acinetobacter schindleri 8 Acinetobacter bohemicus 30 Acinetobacter pragensis 10 28 Acinetobacter lwoffii Acinetobacter pseudolwoffii 20 23 Acinetobacter albensis Acinetobacter equi Acinetobacter radioresistens 10033 Acinetobacter towneri 40 Acinetobacter variabilis 50 80 Acinetobacter nectaris Acinetobacter apis 88 Acinetobacter boissieri Perlucidibaca aquatica Psychrobacter cryohalolentis 63 Psychrobacter okhotskensis Psychrobacter glacincola 100 40 Psychrobacter cibarius 30 70 Psychrobacter urativorans 48 Psychrobacter glaciei Psychrobacter fozii 100 Psychrobacter arcticus Psychrobacter frigidicola 2345 Psychrobacter luti 65 Psychrobacter piscatorii 100 90 18 Psychrobacter adeliensis Psychrobacter nivimaris 73 30 Psychrobacter aquimaris 20 Psychrobacter namhaensis 45 Psychrobacter aquaticus 38 Psychrobacter vallis Psychrobacter maritimus 30 Psychrobacter alimentarius 83 Psychrobacter celer 35 Psychrobacter fulvigenes 100 Psychrobacter faecalis 50 Psychrobacter pulmonis 45 Psychrobacter arenosus 93 flava Moraxella nonliquefaciens 85 63 Moraxella lincolnii Leucothrix sargassi

Beggiotaceae_Thiotrichales~4 100 Beggiatoa leptomitoformis Beggiatoa alba

Nevskiales Nevskiaceae Nevskia ramosa 10 63 50 Hydrocarboniphaga effusa 100 Hydrocarboniphaga daqingensis Panacagrimonas perspica 100 90 Solimonas flava 100 Solimonas variicoloris Solimonas soli 100 100 Sinimarinibacterium flocculans Steroidobacter soli 3 100 Povalibacter uvarum

68 Ignatzschineria indica 100 Ignatzschineria ureiclastica 93 Ignatzschineria larvae 35 Wohlfahrtiimonas populi Chromatiales~3 Guyparkeria hydrothermalis 45 57 Halothiobacillus kellyi

Betaproteobacteria 100 lacustris 100 20 serinivorans 100 chironomi 100 100 Comamonas phosphati Comamonas terrigena 10 Comamonas badia 13 35 Comamonas nitrativorans 57 denitrificans 8 Melaminivora jejuensis 63 28 Pulveribacter suum nitroreducens 10 caeni 100 Giesbergeria giesbergeri 80 Giesbergeria sinuosa Giesbergeria anulus 28 3 Pseudacidovorax intermedius 13 Acidovorax avenae 100 13 Pseudomonas avenae subsp. konjaci Acidovorax wautersii 100 10 40 Simplicispira suum Simplicispira lacusdiani 15 48 Simplicispira metamorpha 13 48 Acidovorax carolinensis 1060 10 Acidovorax radicis Acidovorax kalamii "Verminephrobacter aporrectodeae subs. tuberculata 20 ferrireducens 13 aquaticus Rhodoferax saidenbachensis 13 35 Rhodoferax lacus 15 Rhodoferax bucti 45 Rhodoferax sediminis 10 Pseudorhodoferax soli ginsengisoli 10 100 100 Polaromonas naphthalenivorans 100 Limnohabitans australis Limnohabitans curvus 53 delicatus 100 85 boronicumulans 40 Variovorax robiniae 20 Variovorax rhizosphaerae Variovorax ureilyticus Variovorax humicola 53 Variovorax defluvii 8 40 Variovorax soli 70 8 spinosa 13 bisanensis 100 60 73 Hydrogenophaga atypica 5 28 Hydrogenophaga laconesensis 18 Hydrogenophaga soli 100 20 Hydrogenophaga aquatica thermarum 57 Tepidicella xavieri Tibeticola sediminis 80 oryzae 100 100 Ottowia flava 25 Ottowia beijingensis 33 Hylemonella gracilis 100 Ramlibacter humi 20 Ramlibacter tataouinensis Ramlibacter rhizophilus Ramlibacter monticola 100 Ramlibacter ginsenosidimutans 48 Mitsuaria chitosanitabida 53 45 saccharophila 25 Inhella inkyongensis 100 23 Inhella crocodyli lacunae discophora 23 subsp. natans 5 livida 5 Leptothrix mobilis 73 20 lata 33 Rubrivivax benzoatilyticus 100 100 Rhizobacter fulvus 100 Rhizobacter gummiphilus 35 Methylibium petroleiphilum 30 18 Pseudorivibacter rhizosphaerae Zhizhongheella caldifontis 18 Schlegelella thermodepolymerans 100 Calidifontimicrobium sediminis islandica secunda 100 putida Massilia neuiana 50 Massilia agri 35 38 Massilia arenae 100 Massilia timonae Massilia oculi 1028 63 Massilia terrae Massilia agilis 57 18 Massilia chloroacetimidivorans Massilia aquatica 48 Massilia armeniaca 33 Massilia namucuonensis 100 Massilia frigida 100 Massilia rubra Massilia violaceinigra 100 10 Massilia atriviolacea 30 Massilia guangdongensis 100 rivi Duganella fentianensis 53 100 Duganella qianjiadongensis 30 Duganella albus 100 Duganella aquatilis 25 Duganella pernnla 30 Rugamonas aquatica 65 Rugamonas rivuli Duganella levis 35 Massilia rivuli 285 35 Massilia arenosa Duganella guangzhouensis 13 Duganella flavida 43 Duganella lactea 100 15 35 violaceinigrum 38 Janthinobacterium aquaticum Janthinobacterium rivuli 43 90 Janthinobacterium agaricidamnosum arcticum 100 Herminiimonas arsenicoxydans 100 Herminiimonas saxobsidens 65 lusitanum Herbaspirillum rhizosphaerae 85 18 Herbaspirillum autotrophicum 60 Glaciimonas alpina 78 Glaciimonas frigoris 100 Glaciimonas immobilis 100 20 Glaciimonas soli 20 Glaciimonas singularis Lacisediminimonas profundi 53 Herbaspirillum frisingense 100 Herbaspirillum chlorophenolicum 60 Herbaspirillum seropedicae 100 Noviherbaspirillum autotrophicum Noviherbaspirillum massiliense 100 33 Noviherbaspirillum soli 90 Noviherbaspirillum aurantiacum 100 terreum 100 Undibacterium danionis 90 Undibacterium oligocarboniphilum 23 Undibacterium squillarum vibrioformis

Alcaligenaceae 55 insuavis 18 Achromobacter pulmonis 38 Achromobacter pestifer 100 Achromobacter mucicolens 10 Achromobacter animicus Achromobacter agilis 100 Achromobacter denitrificans 100 holmesii 25100 35 18 100 38 23 Bordetella pseudohinzii 18 10038 Bordetella bronchialis 100 Pigmentiphaga daeguensis 100 90 Pigmentiphaga kullae Pigmentiphaga litoralis 18 Orrella dioscoreae 50 Algicoccus marinus 25 Candidimonas bauzanensis 100 thiosulfatoxidans 100 endophyticus 30 fermenti 73 100 Castellaniella defragrans Pusillimonas noertemannii 63 mimigardefordensis 80 Advenella faeciporci 40 ureolytica Basilea psittacipulmonis

Burkholderiaceae 18 phytofirmans Paraburkholderia aromaticivorans Paraburkholderia telluris 43 Paraburkholderia pallidirosea Paraburkholderia sediminicola 55 Paraburkholderia elongata 100 Paraburkholderia agricolaris 20 Paraburkholderia fungorum Paraburkholderia solitsugae 1008 Paraburkholderia megapolitana 100 Paraburkholderia caledonica Paraburkholderia dilworthii 15 40 70 Paraburkholderia fynbosensis Paraburkholderia kirstenboschensis 35 Paraburkholderia rhynchosiae 18 Paraburkholderia terricola 10 Paraburkholderia caffeinilytica 55 Paraburkholderia phenoliruptrix Paraburkholderia ginsengiterrae 100 Paraburkholderia bannensis 100 Paraburkholderia unamae 33 Paraburkholderia sacchari 38 13 Paraburkholderia dinghuensis 100 45 Paraburkholderia silvatlantica 65 Paraburkholderia caseinilytica 55 Paraburkholderia silviterrae 43 30 Paraburkholderia ferrariae 100 Paraburkholderia pallida 100 100 Paraburkholderia caballeronis Paraburkholderia phosphatilytica Paraburkholderia acidipaludis 60 60 Paraburkholderia monticola 35 Paraburkholderia tuberum 60 Paraburkholderia sprentiae Paraburkholderia phymatum Paraburkholderia flava 100 arvi 100 Caballeronia hypogeia Caballeronia catudaia Caballeronia fortuita 10013 Caballeronia jiangsuensis 15 23 50 Caballeronia temeraria Caballeronia pedi Caballeronia calidae 28 33 Caballeronia glebae 20 Caballeronia peredens Caballeronia insecticola 18 48 Caballeronia ptereochthonis Caballeronia concitans 100 100 Caballeronia turbans Caballeronia mineralivorans 100 Caballeronia arationis 1315 Caballeronia telluris Caballeronia terrestris Mycetohabitans endofungorum 100 Trinickia soli 88 Trinickia diaoshuihuensis 40 Trinickia dinghuensis 20 Trinickia fusca Pararobbsia silviterrae 28 contaminans 28 100 3 Burkholderia aenigmatica Burkholderia catarinensis 100 100 100 100 Burkholderia vietnamiensis 15 35 8 5 13 Burkholderia oklahomensis 38 45 Burkholderia thailandensis 38 Burkholderia humptydooensis 18 13 Burkholderia singularis Chitinasiproducens palmae 40 apista Pandoraea soli 38 Pandoraea fibrosis Pandoraea terrigena Pandoraea cepalis 57 83 53 Pandoraea iniqua 45 33 Pandoraea pneumonica 38 Pandoraea bronchicola 50 Pandoraea communis Pandoraea horticolens Pandoraea eparura 55100 Pandoraea aquatica 45 45 Pandoraea anapnoica 100 Pandoraea captiosa 50 Pandoraea vervacti 28 Pandoraea anhela 88 Pandoraea morbifera 33 75 Pandoraea nosoerga Pandoraea thiooxydans mirabilis 83 litoralis 80 Limnobacter humi 13 necator 23 Cupriavidus pinatubonensis Cupriavidus taiwanensis 20 48 Cupriavidus alkaliphilus 100 Cupriavidus metallidurans 13 60 Cupriavidus agavae 8 Cupriavidus plantarum 38 Cupriavidus campinensis 23 Cupriavidus pampae pickettii 80 100 aenigmaticus 60 Polynucleobacter duraquae Polynucleobacter yangtzensis 100 Polynucleobacter sinensis 53 Polynucleobacter sphagniphilus 33 Polynucleobacter hirudinilacicola 83 Polynucleobacter paneuropaeus Polynucleobacter victoriensis 15 Ephemeroptericola cinctiostellae

Casimicrobium huifangae Neisseriales 48 35 25 65 53 Neisseria weixii 30 40 Eikenella halliae 100 38 Eikenella exigua 23 Eikenella longinqua 100 denitrificans 100 subsp. glycolytica 100 Bergeriella denitrificans 28 Simonsiella muelleri 40 35 50 Kingella negevensis 15 Kingella oralis 100 45 Neisseria wadsworthii 100 Neisseria zalophi Alysiella filiformis Snodgrassella alvi

100 Chromobacteriaceae sphagni 83 70 Chromobacterium phragmitis 18 75 Chromobacterium amazonense 100 28 Chromobacterium vaccinii 100 Chromobacterium haemolyticum Aquitalea magnusonii 100 Aquitalea pelogenes Crenobacter luteus 45 Chromobacteriaceae~1 48 rivuli 40 Chitinibacter tainanensis 93 Chitiniphilus eburneus 75 28 Chitiniphilus shinanonensis 33 Formivibrio citricus 75 Silvimonas terrae 100 Iodobacter arcticus

Chitinimonas koreensis Leeia oryzae 33 Thiobacillaceae_Nitrosomonadales~1 25 88 denitrificans 98 Thiobacillus thioparus Thiobacillus thiophilus 93 aquaesulis

Nitrosomonadales 83 Methylotenera mobilis 38 Methylotenera versatilis glycogenes 100 100 Methylovorus glucosotrophus 60 Sulfuricella denitrificans 53 Nitrosospira multiformis winogradskyi 35 Sterolibacteriaceae_Nitrosomonadales~2 100 Sulfuritalea hydrogenivorans 48 Rugosibacter aromaticivorans 90 Methyloversatilis discipulorum Methyloversatilis universalis 7557 denitrificans oestradiolicum

Rhodocyclales 3 Azonexaceae 85 denitrificans 38 100 100 limneticum caeni

55 53 dicarboxylicus Propionivibrio pelophilus 100

Zoogloeaceae_Rhodocyclales~1 78 dura 100 45 Zoogloeaceae~1_Rhodocyclales~2 aminoaromatica 38 Thauera phenylacetica 28 Thauera mechernichensis 45 Thauera propionica 40 68 Thauera sinica 85 Thauera humireducens 23 80 rhizosphaerae Thauera hydrothermalis 100 100 Azoarcus nasutitermitis 100 evansii 50 55 Aromatoleum petrolei Aromatoleum diolicum 55 43 Aromatoleum aromaticum 45 Aromatoleum buckelii Aromatoleum anaerobium 4855 Aromatoleum bremense Azoarcus halotolerans

Hydrogenophilaceae_Hydrogenophilales_Hydrogenophilalia 100 Hydrogenophilus hirschii Hydrogenophilus islandicus 100 Tepidiphilus olei

Lysobacterales_Gammaproteobacteria~1 Lysobacteraceae 100 Xanthomonas alfalfae subsp. citrumelonis Xanthomonas euvesicatoria Xanthomonas perforans 100 Xanthomonas vasicola 100 Xanthomonas citri subsp. malvacearum Xanthomonas prunicola 100 Xanthomonas arboricola 23 Xanthomonas hortorum Xanthomonas cynarae Xanthomonas campestris 63 Stenotrophomonas terrae 20 78 Stenotrophomonas humi Stenotrophomonas acidaminiphila 48 53 Stenotrophomonas daejeonensis 100 Stenotrophomonas ginsengisoli 98 Stenotrophomonas koreensis Stenotrophomonas maltophilia 8 33 40 Stenotrophomonas indicatrix 50 Stenotrophomonas lactitubi Stenotrophomonas rhizophila 45 Pseudoxanthomonas dokdonensis 73 23 Pseudoxanthomonas sacheonensis Pseudoxanthomonas spadix 28 Xanthomonas translucens 100 Xanthomonas melonis 100 100 Pseudoxanthomonas suwonensis Pseudoxanthomonas taiwanensis 100 Pseudoxanthomonas mexicana Xylella fastidiosa subsp. fastidiosa 100 Xylella taiwanensis 98 Xylella fastidiosa subsp. multiplex 18 73 Luteimonas soli 100 Luteimonas notoginsengisoli 45 Luteimonas gilva 13 Luteimonas composti 100 Luteimonas chenhongjianii 100 Luteimonas rhizosphaerae 8 Luteimonas terricola 100 20 65 Luteimonas yindakuii Luteimonas huabeiensis 70 Lysobacter prati 100 Lysobacter soli 100 Lysobacter cavernae 3 68 Lysobacter tabacisoli 10053 Lysobacter antibioticus Lysobacter gummosus 28 Lysobacter firmicutimachus 8 75 Thermomonas brevis 35 Thermomonas carbonis Lysobacter caseinilyticus 15 Lysobacter lycopersici 65 Lysobacter solanacearum 13 Lysobacter oligotrophicus 28 Lysobacter ginsengisoli 100 Lysobacter segetis 73 Lysobacter mobilis 18 Lysobacter helvus 100 68 Vulcaniibacterium gelatinicum Vulcaniibacterium thermophilum 28 Vulcaniibacterium tengchongense Silanimonas lenta 100 40 Silanimonas mangrovi 100 Lysobacter spongiicola 100 Lysobacter concretionis Lysobacter olei 100 Lysobacter caeni 18 45 Luteimonas lumbrici 100 25 Lysobacter pocheonensis Luteimonas pelagia 15 Lysobacter profundi 55 Arenimonas oryziterrae 35 Arenimonas composti 15 Arenimonas malthae 100 Arenimonas metalli 70 Arenimonas caeni 6338 Arenimonas halophila Arenimonas donghaensis 8 13 Arenimonas aestuarii 30 Arenimonas soli Rehaibacterium terrae 100 Rhodanobacteraceae~1 Dokdonella ginsengisoli 43 Dokdonella immobilis Chiayiivirga flava Rhodanobacteraceae 100 Rhodanobacter spathiphylli 55 Rhodanobacter fulvus 50 Rhodanobacter soli 8 43 Rhodanobacter thiooxydans 100 Rhodanobacter terrae 100 Rhodanobacter hydrolyticus 28 Dyella tabacisoli 20 Dyella amyloliquefaciens 30 30 Dyella jiangningensis 23 Dyella japonica Dyella solisilvae 100 55 Dyella mobilis Dyella caseinilytica 100 Dyella psychrodurans 5 Dyella choica 10048 Dyella nitratireducens 13 Dyella monticola 100 Dyella humi 20 Frateuria terrea 75 Dyella ginsengisoli Frateuria defendens 100 Fulvimonas yonginensis Aerosticca soli

Methylococcaceae_Methylococcales_Gammaproteobacteria~2 83 Methylococcus capsulatus Methylococcus geothermalis 100 5 Methyloterricola oryzae

Gammaproteobacteria~3 Immundisolibacter cernigliae 8 Inmirania thermothiophila

Gammaproteobacteria~4 Ectothiorhodospiraceae_Chromatiales~4 100 Thioalkalivibrio thiocyanoxidans 50 Thiorhodospira sibirica Acidihalobacter ferrooxydans 100 25 Acidihalobacter aeolianus 100 Halorhodospira halophila Halorhodospira halochloris 10065 Spiribacter roseus Arhodomonas recens 8 48 100 Aquisalimonas halophila Marinicella rhabdoformis 43 Wenzhouxiangella limi

Salinisphaeraceae_Nevskiales~1_Gammaproteobacteria~5 90 Salinisphaera aquimarina Salinisphaera halophila 80 Abyssibacter profundi

Nitrosococcus oceani Acidithiobacillaceae_Acidithiobacillales_Acidithiobacillia 98 Acidithiobacillus albertensis 100 Acidithiobacillus thiooxidans 98 Acidithiobacillus ferrianus 88 Acidithiobacillus ferrooxidans 100 Acidithiobacillus sulfuriphilus Acidithiobacillus caldus

Alphaproteobacteria Rhodobacterceae_Rhodobacterales 100 Neptunicoccus sediminis 50 Amylibacter lutimaris 100 Profundibacter amoris 18 Planktotalea lamellibrachiae Aliiroseovarius marinus 100 100 Aliiroseovarius crassostreae 100 Litoreibacter janthinus Litoreibacter albidus 8 100 Litoreibacter arenae 50 Octadecabacter antarcticus 57 Octadecabacter ponticola 100 Thalassorhabdomicrobium marinisediminis 30 Planktomarina temperata 80 Thalassobius autumnalis Thalassobius mediterraneus 100 Thalassobius gelatinovorus 100 Phaeobacter piscinae Phaeobacter porticola 25 68 100 Leisingera methylohalidivorans Leisingera aquimarina 20 30 Parasedimentitalea marina 100 Sedimentitalea nanhaiensis 13 Tritonibacter horizontis 48 Leisingera aquaemixtae 28 Leisingera daeponensis 57 Leisingera caerulea Phaeobacter italicus 330 Puniceibacterium antarcticum Pseudooceanicola antarcticus 50 Pseudopuniceibacterium sediminis 33 Antarcticimicrobium sediminis 100 83 Antarcticimicrobium luteum 100 Ruegeria denitrificans 50 Ruegeria profundi 48 Ruegeria lacuscaerulensis 50 Ruegeria marisrubri 78 15 Ruegeria sediminis Ruegeria pomeroyi 3 Albibacillus kandeliae 18 Ruegeria mediterranea Tropicibacter naphthalenivorans 100 20 Pelagimonas phthalicica Shimia marina 100 Yoonia rosea 33 Yoonia maricola 100 100 Yoonia maritima Loktanella salsilacus 23 100 Yoonia vestfoldensis Poseidonocella pacifica 70 Poseidonocella sedimentorum 3 30 Tateyamaria armeniaca 100 Nereida ignava 33 30 Sulfitobacter salinus Loktanella sediminum 43 Marivita byunsanensis 100 Chachezhania antarctica 100 Cognatishimia activa Thalassobius activus 40 Litorivita pollutaquae 5 65 Celeribacter indicus 100 Celeribacter persicus 53 Celeribacter ethanolicus 88 Celeribacter neptunius Celeribacter arenosi 100 80 Lutimaribacter pacificus 40 Lutimaribacter saemankumensis 23 Thalassobius litoralis 18 Lutimaribacter marinistellae Pacificitalea manganoxidans 35 5 Lacimonas salitolerans Cribrihabitans pelagius 100 100 Cribrihabitans marinus 53 Salipiger mucosus 45 Carideicomes alvinocaridis 100 Aquicoccus porphyridii 100 Donghicola eburneus Donghicola tyrosinivorans 100 Pseudodonghicola xiamenensis 100 30 Youngimonas vesicularis 100 Salipiger marinus Paraphaeobacter pallidus 5 Sediminimonas qiaohouensis 53 Salinihabitans flavidus 48 Roseivivax marinus 100 40 Roseivivax sediminis 38 Roseivivax halodurans 100 Roseivivax isoporae 63 Allosediminivita pacifica 33 Roseivivax halotolerans Aestuariicoccus marinus 8 35 Pseudooceanicola batsensis Pseudooceanicola atlanticus 2375 Pseudooceanicola onchidii 8 Pseudooceanicola nanhaiensis 57 93 Oceanicola nanhaiensis 100 Pseudooceanicola pacificus Marimonas lutisalis Sagittula stellata 20 Ponticoccus marisrubri 65 Roseovarius ramblicola 100 100 Roseovarius nitratireducens 30 Roseovarius tibetensis Roseovarius salinarum 100 Roseovarius amoyensis Roseovarius pacificus 100 845 Roseovarius bejariae Roseovarius nubinhibens 8 Pseudoruegeria marinistellae 100 Psychromarinibacter halotolerans Tropicimonas arenosa 45 Roseibacterium elongatum 10015 Dinoroseobacter shibae Maritimibacter alkaliphilus 458 Maritimibacter lacisalsi Phycocomes zhengii 68 Rhodovulum sulfidophilum 38 Rhodovulum mangrovi 100 100 Actibacterium ureilyticum Palleronia soli 100 30 Actibacterium atlanticum 100 53 Actibacterium pelagium 100 Nioella sediminis 48 Nioella ostreopsis Rhodophyticola porphyridii 13 Roseicyclus mahoneyensis 100 Roseicyclus marinus Roseovarius arcticus 48 57 Pelagivirga sediminicola Pelagivirga dicentrarchi 38 100 15 Roseovarius spongiae 100 Oceaniglobus indicus 18 Kandeliimicrobium roseum 38 15 Oceaniglobus ichthyenteri 100 Pontibaca methylaminivorans Pukyongiella litopenaei 100 Primorskyibacter marinus Primorskyibacter sedentarius 100 10 Thalassococcus profundi Pseudaestuariivita atlantica 100 Pseudooceanicola lipolyticus 100 Sulfitobacter geojensis 38 Sulfitobacter noctilucae 100 Sulfitobacter noctilucicola Roseobacter litoralis 100 38 Sulfitobacter delicatus 40 Sulfitobacter dubius Sulfitobacter aestuarii 15 Sulfitobacter donghicola 35 100 Sulfitobacter pseudonitzschiae 100 Oceanicola granulosus 50 Roseisalinus antarcticus 13 Histidinibacterium lentulum 95 Rubellimicrobium roseum Rubellimicrobium rubrum 18 100 100 Rubellimicrobium thermophilum Aestuarium zhoushanense 100 Jannaschia seosinensis 100 Jannaschia rubra 100 Jannaschia donghaensis 100 Jannaschia cystaugens Tritonibacter scottomollicae 78 Paracoccus zeaxanthinifaciens 57 Paracoccus homiensis 57 Paracoccus seriniphilus Paracoccus sediminilitoris 63 Paracoccus carotinifaciens 100 Paracoccus marcusii Paracoccus haeundaensis 28 60 Paracoccus liaowanqingii 25 Paracoccus alkanivorans 25 Paracoccus caeni 10 Paracoccus alcaliphilus 8 Paracoccus subflavus 65 Paracoccus sediminis 25 Paracoccus suum Paracoccus luteus 100 13 Paracoccus endophyticus 100 Paracoccus aurantiacus 13 Paracoccus pacificus 73 Paracoccus aeridis Paracoccus marinus 48 30 8 Paracoccus contaminans 10 Paracoccus solventivorans 43 Paracoccus acridae 100 Paracoccus panacisoli 18 Paracoccus halophilus Paracoccus huijuniae 100 Paracoccus simplex 100 Paracoccus limosus 25 85 Paracoccus versutus 57 Paracoccus pantotrophus Paracoccus communis 63 10 Paracoccus denitrificans Paracoccus aminophilus 43 Paracoccus mangrovi 28 Paracoccus lutimaris 100 Paracoccus yeei Actibacterium naphthalenivorans 90 Rhodobaca bogoriensis 100 65 Roseinatronobacter monicus Rhodobaculum claviforme 8 55 Alkalilacustris brevis Pararhodobacter oceanensis 533 Pararhodobacter zhoushanensis 70 Allgaiera indica 8 Acidimangrovimonas sediminis 8 10 Acidimangrovimonas pyrenivorans 23 Solirhodobacter olei Roseicitreum antarcticum 100 Arenibacillus arenosus 50 Frigidibacter oleivorans Frigidibacter mobilis 63 Frigidibacter albus 18 Haematobacter massiliensis 80 Haematobacter missouriensis 100 Cereibacter sphaeroides 48 15 Rhodobacter megalophilus 70 Cereibacter alkalitolerans 35 Cereibacter johrii Rhodobacter sediminicola 100 Pseudorhodobacter antarcticus 20 85 Pseudorhodobacter ferrugineus Pseudorhodobacter aquimaris 40 75 Cypionkella psychrotolerans 80 Cypionkella collinsensis Cypionkella aquatica 70 33 Cypionkella sinensis Tabrizicola piscis 80 100 53 Tabrizicola alkalilacus 100 Gemmobacter aquatilis 88 Gemmobacter caeni Gemmobacter straminiformis 80100 Gemmobacter aquarius 45 Gemmobacter megaterium Gemmobacter aestuarii 90 35 53 Gemmobacter nectariphilus Rhodobacter flagellatus 25 45 Pseudogemmobacter bohemicus 63 Xinfangfangia soli 60 Rhodobacter sediminis Paenirhodobacter enshiensis 38 Sinirhodobacter huangdaonensis 100 Thioclava dalianensis 48 Thioclava indica 38 48 Thioclava sediminum 25 Thioclava nitratireducens Thioclava atlantica 18 43 Thioclava pacifica 88 Thioclava marina Defluviimonas nitratireducens Meinhardsimonia xiamenensis 73 Halovulum marinum 40 Halovulum dunhuangense 53 Oceanibium sediminis 25 Monaibacterium marinum Amaricoccus solimangrovi 65 Oceanicella actignis 57 Paroceanicella profunda Minwuia thermotolerans 55 intermedia 33 Brevundimonas mediterranea 55 Brevundimonas vesicularis 57 Brevundimonas nasdae 3 Brevundimonas aurantiaca 8 Brevundimonas aveniformis 43 Brevundimonas fluminis Brevundimonas kwangchunensis 15 Brevundimonas viscosa 18 100 Brevundimonas bacteroides 33 Brevundimonas variabilis Brevundimonas poindexterae 30 Brevundimonas bullata Brevundimonas humi 25 13 5 Brevundimonas staleyi Brevundimonas subvibrioides 45 Brevundimonas lenta 38 100 Brevundimonas diminuta 100 Brevundimonas terrae 63 40 Brevundimonas naejangsanensis Brevundimonas balnearis 38 Asticcacaulis benevestitus Asticcacaulis biprosthecium 80 Asticcacaulis excentricus 100 Asticcacaulis tiandongensis 78 Caulobacter henricii 80 60 Caulobacter rhizosphaerae 100 Caulobacter flavus 100 Caulobacter segnis 90 Caulobacter vibrioides Caulobacter fusiformis 80 Phenylobacterium soli 38 Phenylobacterium kunshanense 20 Phenylobacterium muchangponense 43 100 68 78 Phenylobacterium panacis Phenylobacterium terrae 35 Phenylobacterium immobile 100 Phenylobacterium koreense 100 Phenylobacterium falsum Caulobacter mirabilis

100 Vitreimonas flagellata Terricaulis silvestris 100 Aquidulcibacter paucihalophilus

Hyphomonadaceae_Caulobacterales~1 38 Hyphomonas atlantica 28 Hyphomonas beringensis Hyphomonas adhaerens 33 98 Hyphomonas jannaschiana Hyphomonas oceanitis 4818 Hyphomonas johnsonii 20 100 Hyphomonas hirschiana 73 Hyphomonas neptunium 100 Hyphomonas polymorpha 100 Henriciella marina 57 Henriciella pelagia 57 Ponticaulis koreensis 85 Hirschia maritima 100 Hirschia baltica Algimonas arctica 100 Hellea balneolensis 35 Parvularculaceae_Parvularculales 100 Parvularcula bermudensis 78 Parvularcula marina Aquisalinus flavus 78 100 Parvularcula flava Marinicaulis flavus 100 Hyphococcus flavus 23 Hyphomonadaceae~1_Caulobacterales~2 78 Marinicauda pacifica 73 Marinicauda salina 100 Oceanicaulis alexandrii Glycocaulis abyssi 90 75 Glycocaulis profundi Maricaulis maris 68 Hyphobacterium indicum

Sphingomonadales Sphingomonadaceae+Zymomonadaceae Sphingomonadaceae 100 Sphingomonas dokdonensis 38 Sphingomonas jeddahensis 38 Sphingomonas olei Sphingomonas xinjiangensis 8 45 Sphingomonas pituitosa 83 Sphingomonas trueperi Sphingomonas azotifigens 100 8 Sphingomonas gei 63 Sphingomonas naasensis 100 Sphingomonas echinoides Sphingomonas glacialis 5 80 Sphingomonas psychrolutea 23 Sphingomonas panacis 33 Sphingomonas aracearum 8 Sphingomonas turrisvirgatae 90 Sphingomonas suaedae 23 Sphingomonas asaccharolytica Sphingomonas soli 13 5 Sphingomonas hengshuiensis 100 Sphingomonas melonis 100 Sphingomonas aquatilis 18 Sphingomonas leidyi 50 Sphingomonas roseiflava 5 Sphingomonas metalli 35 100 Sphingomonas rubra Sphingomonas cynarae 18 Sphingomonas insulae 68 Sphingomonas hankookensis 5 Sphingomonas desiccabilis 5 Sphingomonas gilva 100 Sphingomonas yabuuchiae 28 Sphingomonas paucimobilis Sphingomonas phyllosphaerae 100 70 Sphingomonas morindae 13 Sphingomonas polyaromaticivorans 57 Sphingomonas difficilis 100 Sphingosinithalassobacter portus 23 Sphingosinithalassobacter tenebrarum 8 Sphingomonas floccifaciens 88 Sphingomonas spermidinifaciens Sphingomonas yantingensis 60 5 Sphingomonas japonica Sphingomonas aerophila 23 Sphingomonas lenta

90 Zymomonas mobilis subsp. mobilis 8 90 Zymomonas mobilis subsp. pomaceae 43 Zymomonas mobilis subsp. francensis 35 Sphingomonas profundi 50 Sphingomonas solaris 13 Sphingomonas formosensis 20 Sphingomonas fennica 57 Sphingomonas oleivorans Sphingomonas prati 28 88 Sphingomonas arantia 40 Rhizorhabdus argentea 25 Rhizorhabdus dicambivorans 100 Rhizorhabdus starnbergensis Sphingomonas crocodyli 100 63 Sphingomonas montanisoli Allosphingosinicella indica 15 35 Sphingomonas vulcanisoli

Sphingosinicellaceae~1 100 Polymorphobacter multimanifer Sandarakinorhabdus cyanobacteriorum 33 90 Sandarakinorhabdus limnophila

33 Sandaracinobacter neustonicus Sphingomonadaceae~2 Sphingomonas changbaiensis 90 10 Sphingomonas tabacisoli Sphingomonadaceae~3 25 100 Sphingomonas sanxanigenens Sphingomonas zeicaulis 48 15 Sphingomonas lacunae

Sphingomonadaceae~4 Sphingomonas gimensis 30 Sphingomonas flavalba

Sphingomonadaceae~5 100 Sphingomonas mesophila 25 100 Sphingomonas ginsengisoli 23 Sphingomonas segetis 70 Sphingomonas limnosediminicola Sphingomonas sediminicola 88 Sphingomonas kaistensis 50 Sphingomonas ginkgonis 100 Sphingosinicellaceae+Sphingonadaceae~6 78 Sphingosinicella humi Sphingomonas montis Stakelama algicida 1338 Sphingomonas colocasiae Sphingosinicella microcystinivorans

Sphingomonadaceae~7 100 Sphingobium indicum 13 Sphingobium chungbukense 15 Sphingobium quisquiliarum 1350 Sphingobium mellinum 20 Sphingobium amiense 3 Sphingobium limneticum 13 Sphingobium vermicomposti Sphingobium baderi 23 68 Sphingobium jiangsuense 33 Sphingobium qiguonii 28 Sphingobium fluviale 18 Sphingobium xanthum 10 Sphingobium herbicidovorans 15 38 Sphingobium pinisoli 28 Sphingobium fuliginis 33 Sphingobium ummariense 28 Sphingobium lactosutens 23 Sphingobium rhizovicinum 30 Sphingobium naphthae 100 Sphingobium algorifonticola Sphingobium phenoxybenzoativorans 43 Sphingobium subterraneum

Sphingomonadaceae~8 53 Blastomonas natatoria Blastomonas ursincola 100 Blastomonas fulva

Sphingomonadaceae~9 38 Sphingopyxis bauzanensis 23 Sphingopyxis fribergensis 28 Sphingopyxis alaskensis 8 45 Sphingopyxis chilensis 18 Sphingopyxis taejonensis 15 Sphingopyxis panaciterrae 28 Sphingopyxis lindanitolerans 85 Sphingopyxis witflariensis 20 Sphingopyxis granuli 23 80 Sphingopyxis ginsengisoli Sphingopyxis terrae subsp. terrae Sphingopyxis panaciterrulae 78 Sphingorhabdus planktonica 35 100 Sphingorhabdus rigui 100 Sphingorhabdus wooponensis 45 Sphingorhabdus pulchriflava Sphingorhabdus buctiana 23 38 90 Chakrabartia godavariana Aestuariisphingobium litorale 90 Aquisediminimonas profunda 53 Novosphingopyxis baekryungensis 28 Parasphingopyxis lamellibrachiae Blastomonas quesadae 35 15 Sphingorhabdus pacifica 95 Sphingomicrobium astaxanthinifaciens 50 Sphingomicrobium arenosum 80 Sphingomicrobium lutaoense 15 Sphingomicrobium marinum 33 100 Sphingomicrobium flavum Pacificimonas flava

Erythrobacteraceae~1 35 Novosphingobium aromaticivorans 43 Novosphingobium subterraneum 43 Novosphingobium meiothermophilum 18 Novosphingobium hassiacum Novosphingobium kunmingense 53 8 Caenibius tardaugens 100 Novosphingobium pokkalii 48 Novosphingobium acidiphilum 20 Novosphingobium ovatum 18 Novosphingobium flavum 33 Novosphingobium nitrogenifigens 15 Novosphingobium stygium 100 Novosphingobium arabidopsis 20 Novosphingobium naphthae 85 Novosphingobium fontis 100 Novosphingobium humi 28 Novosphingobium oryzae 20 Novosphingobium guangzhouense Novosphingobium lindaniclasticum 30 18 60 Novosphingobium silvae 3 Novosphingobium fluoreni 20 Novosphingobium colocasiae 3 Novosphingobium arvoryzae Novosphingobium chloroacetimidivorans 3 Novosphingobium pentaromativorans 100 Novosphingobium endophyticum Novosphingobium clariflavum 235 Novosphingobium soli Novosphingobium naphthalenivorans

Erythrobacteraceae~2 Altericroceibacterium spongiae 30 Novosphingobium malaysiense 57 Novosphingobium indicum

Erythrobacteraceae 48 Erythrobacter aquimaris 5 Erythrobacter longus 15 Erythrobacter seohaensis 33 Erythrobacter flavus Erythrobacter vulgaris 25 Erythrobacter pelagi 18 Porphyrobacter tepidarius 93 100 Porphyrobacter neustonensis Porphyrobacter colymbi 43 23 Porphyrobacter donghaensis 25 57 Porphyrobacter sanguineus 28 Erythromicrobium ramosum 53 Porphyrobacter dokdonensis Erythrobacter litoralis 100 Erythrobacter jejuensis 53 Erythrobacter xanthus 57 Erythrobacter atlanticus 70 Erythrobacter alti 100 Erythrobacter zhengii 43 55 Croceibacterium mercuriale 20 Altererythrobacter xixiisoli 30 Erythrobacter spongiae Parapontixanthobacter aurantiacus Altererythrobacter epoxidivorans 100 Altererythrobacter sediminis 40 Altererythrobacter gangjinensis Altererythrobacter aestiaquae 100 100 Pontixanthobacter luteolus 33 Altererythrobacter rigui 20 Altererythrobacter dongtanensis 25 Altererythrobacter soli Altererythrobacter xinjiangensis 1815 5 100 Altererythrobacter rhizovicinus Altererythrobacter marinus 90 Altererythrobacter lauratis 100 Altererythrobacter palmitatis 100 Altererythrobacter buctensis 40 Altererythrobacter salegens 30 5 25 Altererythrobacter flavus Altererythrobacter mangrovi 63 Croceicoccus pelagius Croceicoccus marinus 57 33 Croceicoccus mobilis Altererythrobacter fulvus

Hyphomicrobiales~1 Stappiaceae Roseibium aggregatum 100 3 43 Roseibium sediminis 70 Roseibium aestuarii 75 Roseibium aquae Pannonibacter phragmitetus 63 85 Pannonibacter carbonis 83 Pseudovibrio axinellae 65 Pseudovibrio denitrificans 90 Pseudovibrio hongkongensis 88 Pseudovibrio stylochi 23 Stappia indica Cohaesibacter intestini 30 Breoghania corrubedonensis 100 Parvibaculaceae_Hyphomicrobiales~2 100 Parvibaculum indicum Parvibaculum lavamentivorans 38 Pyruvatibacter mobilis

Hyphomicrobiales~3 Methylobacteriaceae 55 Methylorubrum populi 100 Methylorubrum rhodesianum 100 Methylorubrum aminovorans 73 Methylorubrum suomiense Methylorubrum rhodinum 43 68 Methylobacterium terricola 53 Methylobacterium currus 100 Methylobacterium nonmethylotrophicum Methylobacterium variabile 75 85 Methylobacterium nodulans Methylobacterium isbiliense 73 Methylobacterium oryzihabitans 33 100 Methylobacterium radiotolerans 88 Methylobacterium fujisawaense 25 Methylobacterium mesophilicum Methylobacterium goesingense 33100 Methylobacterium bullatum 57 100 Methylobacterium marchantiae 85 Methylobacterium gnaphalii 100 Methylobacterium brachythecii 83 Methylobacterium haplocladii Methylobacterium organophilum 100 Methylobacterium oxalidis Methylobacterium segetis 73 Methylobacterium durans 53 75 Microvirga zambiensis 100 Microvirga aerilata 45 Microvirga soli 100 Microvirga lotononidis 100 100 Microvirga pakistanensis 68 Microvirga makkahensis Microvirga subterranea 70 Microvirga aerophila 60 Microvirga flavescens Microvirga massiliensis

28 Salinarimonas rosea Boseaceae 100 Bosea lathyri 100 Bosea massiliensis 78 Bosea eneae 75 28 Bosea vestrisii 100 Bosea thiooxidans Bosea minatitlanensis

Chelatococcaceae 73 63 Chelatococcus daeguensis Chelatococcus composti 100 Camelimonas fluminis 75 Chelatococcus reniformis Pseudochelatococcus lubricantis 25 indica subsp. lacticogenes 100 20 subsp. indica 70 Beijerinckia derxii subsp. venezuelae 88 Beijerinckia mobilis 100 Beijerinckia doebereinerae 57 silvestris 38 stellata 80 Lichenihabitans psoromatis 63 Rhodoblastus acidophilus 57 Methylocystis heyeri 100 Methylocystis parvus 83 Methylosinus trichosporium

Nitrobacteraceae 60 oligotrophicum 40 Bradyrhizobium denitrificans Bradyrhizobium niftali Bradyrhizobium frederickii 100 Bradyrhizobium centrosematis 70 Bradyrhizobium cosmicum Bradyrhizobium betae Bradyrhizobium rifense 18 13 Bradyrhizobium liaoningense 10 Bradyrhizobium americanum 25 15 Bradyrhizobium cajani Bradyrhizobium shewense 100 Bradyrhizobium japonicum Bradyrhizobium canariense 25 Bradyrhizobium lupini 35 pseudopalustris 25 18 Tardiphaga robiniae 30 Rhodopseudomonas rhenobacensis 15 Rhodopseudomonas palustris 98 winogradskyi Nitrobacter vulgaris 78 13 Nitrobacter hamburgensis 88 carboxidovorans 100 28 63 48 Bradyrhizobium archetypum 53 Bradyrhizobium murdochi 100 Bradyrhizobium australiense 10 50 Bradyrhizobium namibiense 100100 Bradyrhizobium pachyrhizi Bradyrhizobium ripae 40 Bradyrhizobium embrapense Bradyrhizobium mercantei 53 Bradyrhizobium viridifuturi Pseudolabrys taiwanensis 100 Rhodoplanes tepidicaeni 53 Rhodoplanes tepidamans Rhodoplanes azumiensis 80 Rhodoplanes serenus

Xanthobacteraceae 100 Ancylobacter rudongensis 100 8 novella 75 Ancylobacter oerskovii 100 caulinodans Azorhizobium doebereinerae 18 78 Aquabacter spiritensis 100 Aquabacter cavernae Labrys portucalensis 25 90 Labrys wisconsinensis viridis Methylocystaceae 100 Hansschlegelia zhihuaiae 30 Hansschlegelia quercus 3 100 Methylopila oligotropha Albibacter methylovorans 100 100 Chenggangzhangella methanolivorans Agaricicola taiwanensis Kaistiaceae 100 Kaistia defluvii 78 Kaistia granuli 88 Kaistia dalseonensis 23 Kaistia geumhonensis 100 Pseudoxanthobacter liyangensis 57 Segnochrobactrum spirostomi 5 Amorphaceae 100 Amorphus coralli Amorphus suaedae 65 Acuticoccus sediminis 100 Acuticoccus kandeliae 5 Hyphomicrobiales~5 100 Pleomorphomonas carboxyditropha Pleomorphomonas oryzae 10 Phreatobacter cathodiphilus 100 Prosthecomicrobium hirschii

5 Neomegalonema perideroedes 13 Rhabdaerophilum calidifontis Hyphomicrobiaceae 75 Hyphomicrobium denitrificans 75 Pedomicrobium americanum 100 Pedomicrobium australicum 38 Hyphomicrobium zavarzinii Rhodomicrobium vannielii 100 38 Rhodomicrobium lacus Aestuariivirga litoralis 100 Hyphomicrobiaceae~1 100 Methyloceanibacter methanicus 55 Methyloceanibacter stevinii 90 Methyloceanibacter superfactus 78 Methyloceanibacter marginalis 60 Methyloligella solikamskensis 18 Dichotomicrobium thermohalophilum Rhodopseudomonas julia 100 Tepidamorphaceae Butyratibacter algicola 100 Lutibaculum baratangense

Hyphomicrobiales~4 45 etli 45 Rhizobium lentis Rhizobium bangladeshense Rhizobium binae Rhizobium aegyptiacum Rhizobium aethiopicum Rhizobium phaseoli 30 Rhizobium pisi Rhizobium anhuiense Rhizobium leguminosarum Rhizobium laguerreae 20 100 Rhizobium ruizarguesonis 100 Rhizobium freirei 100 Rhizobium dioscoreae 60 Rhizobium rhizogenes 18 43 Rhizobium lusitanum Rhizobium paranaense 30 Rhizobium cauense 100 Rhizobium metallidurans 100 Rhizobium favelukesii Rhizobium gallicum Rhizobium mongolense subsp. mongolense 100 Rhizobium azibense 43 100 Rhizobium cellulosilyticum 50 Rhizobium zeae 35 Rhizobium yantingense 100 Neorhizobium huautlense 18 Neorhizobium tomejilense Rhizobium soli 100 Rhizobium marinum subsp. marinum 48 90 Rhizobium marinum subsp. pelagicum 100 Rhizobium petrolearium 100 Rhizobium oryzicola 25 Rhizobium rhizoryzae 25 Rhizobium capsici 25 Allorhizobium pseudoryzae 57 Rhizobium straminoryzae 45 Allorhizobium oryzae Rhizobium paknamense

Aurantimonadaceae 100 Aureimonas flava Aureimonas jatrophae 100 100 55 Aureimonas rubiginis 45 Aureimonas endophytica 20 Aureimonas ferruginea 20 Mangrovicella endophytica 100 endophytica 25 68 Aurantimonas aggregata 40 Aureimonas glaciistagni 70 endophytica 100 Fulvimarina manganoxydans 28 15 Jiella aquimaris 50 Jiella endophytica Consotaella salsifontis

33 Rhizobiaceae~1 60 Martelella mediterranea 100 Martelella limonii Martelella endophytica 100 Martelella suaedae

Rhizobiaceae~2 Pararhizobium haloflavum 100 100 Georhizobium profundi

Rhizobiaceae~3 57 rosae 38 Agrobacterium cavarae 45 Agrobacterium salinitolerans 100 Agrobacterium radiobacter Agrobacterium arsenijevicii 23 Agrobacterium fabacearum 100 Rhizobium daejeonense Rhizobium selenitireducens 100 Rhizobium naphthalenivorans 18 23 Allorhizobium vitis 100 Allorhizobium oryziradicis 70 Allorhizobium terrae 23 Rhizobium halophytocola

Rhizobiaceae~4 43 Ensifer americanus 25 Ensifer fredii Ensifer saheli 30 Ensifer meliloti 100 Ensifer numidicus 28 Ensifer medicae 15 Ensifer arboris 73 Ensifer alkalisoli 43 Ensifer garamanticus 13 Ensifer mexicanus 57 57 Ensifer terangae Ensifer kostiensis Ensifer adhaerens 18 100 Pararhizobium giardinii Pararhizobium antarcticum 28 Ciceribacter thiooxidans

Rhizobiaceae~5 60 Shinella yambaruensis 45 Shinella granuli 53 Shinella zoogloeoides 78 Shinella fusca 40 Shinella pollutisoli Mycoplana dimorpha

Brucellaceae ceti 35 5 18 68 Brucella ciceri 48 57 50 Brucella cytisi Brucella lupini 25 43 Brucella grignonensis 33 Ochrobactrum teleogrylli 100 asaccharolyticum 38 Falsochrobactrum ovis 100 53 Paenochrobactrum glaciei 13 Brucella gallinifaecis 55 Brucella oryzae Daeguia caeni 5 Brucella endophytica Bartonellaceae 30 kosoyi 100 13 100 Bartonella krasnovii 13 13 100 Bartonella birtlesii Bartonella vinsonii subsp. vinsonii 15 33 25 100 Bartonella schoenbuchensis 23 Bartonella bovis 10085 Bartonella capreoli 8 57 73 Bartonella ancashensis Bartonella apis

Phyllobacteriaceae 100 loti 100 15 Phyllobacterium trifolii Phyllobacterium endophyticum 38 Phyllobacterium leguminum 73 Phyllobacterium salinisoli Tianweitania sediminis Rhizobiaceae~6 Hoeflea alexandrii 13 80 Hoeflea phototrophica 100 Hoeflea marina

Phyllobacteriaceae~1 88 Ahrensia kielensis 100 Ahrensia marina 38 Roseitalea porphyridii Oricola cellulosilytica 100 20 Pseudohoeflea suaedae Aquamicrobium defluvii 100 Aquamicrobium terrae

Phyllobacteriaceae~2 Mesorhizobium opportunistum 100 Mesorhizobium erdmanii Mesorhizobium jarvisii 10010020 Mesorhizobium plurifarium 100 Mesorhizobium atlanticum 100 Mesorhizobium shonense 53 Mesorhizobium abyssinicae Mesorhizobium amorphae 100 Mesorhizobium tianshanense Mesorhizobium delmotii 100 Mesorhizobium prunaredense 100 Mesorhizobium wenxiniae 25100 Mesorhizobium muleiense Mesorhizobium mediterraneum 25 Mesorhizobium tamadayense 35 Mesorhizobium norvegicum 100 13 Mesorhizobium loti Mesorhizobium australicum 100 aganoensis 83 Aminobacter niigataensis 10 98 2843 Aminobacter anthyllidis Mesorhizobium chacoense Mesorhizobium alhagi Mesorhizobium oceanicum 63 8 Mesorhizobium carbonis 15 Phyllobacteriaceae~3 35 Mesorhizobium composti Nitratireductor indicus 45 Mesorhizobium sediminum 13 Nitratireductor aquibiodomus 10 13 Salaquimonas pukyongi

Notacmeibacteraceae 30 Notoacmeibacter ruber 100 Zhengella mangrovi 15 Nitratireductor alexandrii Chelativorans intermedius Limoniibacter endophyticus Devosiaceae 43 Devosia epidermidihirudinis 30 Devosia limi 28 Devosia neptuniae 20 Devosia psychrophila Devosia glacialis 100100 23 Devosia submarina 48 Devosia soli 100 Devosia marina 25 Devosia chinhatensis 43 Devosia enhydra 100 Devosia mishustinii 40 Devosia honganensis 35 Devosia geojensis 57 Devosia pacifica Pelagibacterium lacus 100 Pelagibacterium lentulum 53 55 Pelagibacterium montanilacus Maritalea mobilis 57 Cucumibacter marinus

Tewmperatibacteraceae_Kordiimonadales 95 Kordiimonas gwangyangensis 100 Kordiimonas lipolytica Kordiimonas pumila 43 Emcibacteraceae_Emcibacterales 53 Emcibacter nanhaiensis Luteithermobacter gelatinilyticus 23 100 Paremcibacter congregatus Kiloniella majae 48 Magnetovibrio blakemorei 48 subsp. conorii 57 Rickettsia conorii subsp. indica 100 Rickettsia conorii subsp. israelensis 65 90 100 Rickettsia heilongjiangensis 53 Rickettsia montanensis 100

80 57 50 Ehrlichia muris subsp. muris 100 Ehrlichia ruminantium bovis 78 risticii 100 100 Neorickettsia findlayensis

Sneathiellaceae_Sneathiellales 57 Sneathiella glossodoripedis Sneathiella limimaris 100 Sneathiella aquimaris

Rhodospirillales~3+Sneathiellales~1 Acetobacteraceae 100 Acetobacter orleanensis 35 Acetobacter cerevisiae Acetobacter malorum 33 Acetobacter musti 70 Acetobacter sacchari 100 Acetobacter sicerae 60 Acetobacter aceti Acetobacter estunensis 68 100 Acetobacter oryzifermentans 100 Acetobacter oryzoeni Acetobacter pomorum 100 Acetobacter lovaniensis 90 Acetobacter fabarum 100 Acetobacter ghanensis 85 Acetobacter lambici 60 Gluconobacter cerevisiae 100 100 Gluconobacter oxydans Gluconobacter frateurii 100 100 Gluconobacter thailandicus 100 Saccharibacter floricola Commensalibacter intestini Asaia platycodi 8 73 Neoasaia chiangmaiensis 100 Komagataeibacter medellinensis 23 Komagataeibacter oboediens 63 Komagataeibacter intermedius 40 48 Komagataeibacter kakiaceti Komagataeibacter nataicola Komagataeibacter europaeus Komagataeibacter swingsii 73 Komagataeibacter saccharivorans Komagataeibacter sucrofermentans 38 100 Komagataeibacter xylinus 100 Komagataeibacter cocois Gluconacetobacter entanii 45 73 100 Komagataeibacter hansenii Gluconacetobacter diazotrophicus 100 Gluconacetobacter liquefaciens 100 Granulibacter bethesdensis Lichenicoccus roseus 100 88 Acidiphilium multivorum Acidiphilium iwatense 100 Acidocella aluminiidurans Rhodovastum atsumiense 100 Roseomonas suffusca 100 Roseomonas cervicalis 38 Teichococcus ludipueritiae 100 78 Roseomonas wenyumeiae Roseomonas vastitatis Roseomonas globiformis 100 75 Roseomonas gilardii subsp. rosea 83 Roseomonas gilardii subsp. gilardii Roseomonas mucosa 25 73 Roseomonas elaeocarpi 60 Roseomonas aeriglobus Roseomonas harenae 70 75 18 Roseomonas radiodurans 100 Roseomonas frigidaquae 60 Roseomonas selenitidurans 83 Roseomonas stagni Roseomonas algicola 78 3 Roseomonas terricola 100 Roseomonas bella 100 Roseomonas oryzicola 60 Roseomonas soli 90 Roseomonas eburnea 60 100 23 Roseomonas alkaliterrae Roseomonas arctica 20 Caldovatus sediminis 100 Crenalkalicoccus roseus 100 Belnapia moabensis 28 Belnapia rosea 75 100 Paracraurococcus ruber 78 Siccirubricoccus deserti 33 Rubritepida flocculans Rhodovarius crocodyli 13 13 Humitalea rosea Elioraea tepidiphila 100 Elioraea thermophila

Sneathiellaceae~1_Sneathiellales~1 100 Ferrovibrio soli 70 Ferrovibrio xuzhouensis Marinibaculum pumilum 100 23 Geminicoccaceae Geminicoccus roseus 8 85 Arboricoccus pini 8 Reyranella massiliensis

18 Rhodospirillaceae~1 Hypericibacter adhaerens 98 Hypericibacter terrae

Thalassobaculaceae 90 Oceanibaculum indicum 100 Oceanibaculum nanhaiense Oceanibaculum pacificum 100 Tagaea marina 8 Azospirillaceae 43 zeae 40 Azospirillum agricola 60 Azospirillum thermophilum 53 Azospirillum lipoferum 57 Azospirillum griseum 100 Azospirillum canadense Azospirillum fermentarium 38 33 Niveispirillum cyanobacteriorum 100 Niveispirillum lacus 100 Niveispirillum fermenti 100 Oleisolibacter albus 5 Skermanella pratensis 23 Nitrospirillum iridis 23 Rhodospirillaceae~2 Dongia mobilis 18 Aliidongia dinghuensis

38 Rhodospirillaceae~3 65 Magnetospirillum kuznetsovii 100 Magnetospirillum gryphiswaldense 65 Magnetospirillum moscoviense 3 53 Magnetospirillum molischianum Oleiliquidispirillum nitrogeniifigens

30 Geminicoccaceae~1 Tistrella bauzanensis 100 Tistrella mobilis

100 Algihabitans albus Fodinicurvata sediminis 55 Ferruginivarius sediminum 80 Rhodovibrio sodomensis

Rhodospirillales Rhodospirillaceae 100 Rhodospirillum rubrum 45 Pararhodospirillum photometricum 15 Caenispirillum bisanense Marispirillum indicum 30 Roseospirillum parvum

20 Thalassospiraceae Thalassospira profundimaris 90 Thalassospira povalilytica 33 Thalassospira australica 53 Thalassospira xianhensis 25 100 Thalassospira lohafexi Thalassospira marina Marivibrio halodurans Magnetococcus marinus

Deferribacteraceae_Deferribacterales_Deferribacteres 83 Calditerrivibrio nitroreducens Geovibrio ferrireducens 100 93 Deferribacter desulfuricans Deferribacter thermophilus 100 Deferribacter abyssi 45 80 Deferribacter autotrophicus Desulfurispirillum indicum +Nautiliales~1 Campylobacteraceae 45 Campylobacter novaezeelandiae 45 Campylobacter armoricus 70 Campylobacter peloridis 30 Campylobacter volucris 28 Campylobacter ornithocola 43 Campylobacter subantarcticus Campylobacter lari subsp. concheus 100 Campylobacter hepaticus 100 53 Campylobacter insulaenigrae 57 subsp. jejuni 100 Campylobacter coli Campylobacter lanienae 60 Campylobacter iguaniorum 100 Campylobacter fetus subsp. testudinum 40 Campylobacter fetus subsp. venerealis Campylobacter curvus 100 40 Campylobacter pinnipediorum subsp. pinnipediorum 100 Campylobacter pinnipediorum subsp. caledonicus 88 Campylobacter blaseri 100 Campylobacter geochelonis Sulfurospirillum halorespirans 100 73 Sulfurospirillum deleyianum Arcobacteraceae 100 Poseidonibacter antarcticus Arcobacter nitrofigilis 100 60 Arcobacter canalis

Helicobacteraceae~1 100 Sulfurimonas autotrophica Sulfurimonas gotlandica

Helicobacteraceae_2+Nautiliaceae~1 Sulfurovum lithotrophicum 78 Nitratifractor salsuginis

Helicobacteraceae 100 Helicobacter mehlei 48 Helicobacter vulpis 50 Helicobacter ailurogastricus 100 Helicobacter baculiformis 88 30 90 Helicobacter labacensis 98 Helicobacter suis 100 100 Helicobacter cetorum 3053 Helicobacter fennelliae 73 Helicobacter himalayensis Helicobacter macacae 53 Helicobacter marmotae 3520 28 53 Helicobacter equorum 50 Helicobacter typhlonius 53 70 Helicobacter japonicus 65 90 55 100 45 Helicobacter pametensis 3528 Helicobacter brantae 35 Helicobacter anseris 73 Helicobacter mustelae 100 53 Helicobacter enhydrae Wolinella succinogenes 48 Nautiliaceae_Nautiliales 88 Caminibacter mediatlanticus Caminibacter profundus 100 Nautilia profundicola 50 Lebetimonas natsushimae 48 Cetia pacifica

Desulfurellaceae_Desulfurellales_Deltaproteobacteria~1 Desulfurella multipotens 90 Hippea maritima

Desulfovibrionales_Deltaproteobacteria~2 Desulfovibrionaceae 100 Desulfovibrio simplex 83 Desulfovibrio oxamicus 50 Desulfovibrio alaskensis Desulfovibrio paquesii 80 Desulfovibrio indonesiensis 100 Desulfovibrio hydrothermalis 23 100 Desulfovibrio ferrireducens Desulfovibrio salexigens 100 100 Pseudodesulfovibrio piezophilus 100 13 15 Pseudodesulfovibrio profundus Pseudodesulfovibrio aespoeensis 43 68 23 Desulfovibrio halophilus Desulfovibrio idahonensis Desulfohalovibrio reitneri 40 Desulfohalovibrio alkalitolerans 100 Desulfovibrio bizertensis Desulfovibrio senezii 50 Desulfocurvus thunnarius 53 100 Desulfocurvus vexinensis 83 Desulfovibrio carbinoliphilus 100 Desulfovibrio fructosivorans 73 Desulfovibrio marrakechensis 83 Desulfovibrio magneticus 55 50 Desulfovibrio putealis Desulfocurvibacter africanus subsp. uniflagellum

Desulfonatronaceae 100 Desulfonatronum parangueonense 65 Desulfonatronum thiosulfatophilum 100 Desulfonatronum zhilinae

Desulfomicrobiaceae 100 Desulfomicrobium macestii 100 Desulfomicrobium norvegicum 83 Desulfomicrobium baculatum 100 Desulfomicrobium orale

Desulfohalobiaceae Desulfohalobium retbaense 68 Desulfonauticus autotrophicus 100 Desulfonauticus submarinus

Deltaproteobacteria+Oligoflexia Desulfobacteraceae_Desulfobacterales 100 Desulfobacter hydrogenophilus 78 Desulfobacter postgatei Desulfotignum balticum 100 35 Desulfotignum phosphitoxidans Desulfotignum toluenicum 90 Desulfobacula toluolica Desulfobacterium autotrophicum 60 100 Desulfobacterium vacuolatum 100 100 Desulfobacterium niacini Desulfobotulus sapovorans 33 Desulfofrigus oceanense 100 20 Desulfoluna spongiiphila Desulfatiferula olefinivorans 5 100 Desulforegula conservatrix 48 Desulfococcus multivorans Desulfosarcina alkanivorans 55 50 Desulfatirhabdium butyrativorans

Sytrophaceae~1_Syntrophobacterales~1 Syntrophus gentianae 100 Syntrophus aciditrophicus

43 Desulfobulbaceae_Desulfobacterales~1 100 Desulfotalea psychrophila 40 Desulfotalea arctica 100 Desulfobacterium catecholicum 50 Desulfopila inferna 80 Desulfurivibrio alkaliphilus 23 Desulfobulbus propionicus

78 Syntrophobacteraceae_Syntrophobacterales Syntrophobacter fumaroxidans 100 Syntrophobacter sulfatireducens Silvanigrella aquatica 25 Halobacteriovorax marinus Desulfuromonadales 15 Geobacteraceae 100 Pelobacter propionicus 88 Geobacter lovleyi Geomonas bemidjiensis 90 65 Geobacter uraniireducens Geobacter soli 68 Geobacter grbiciae 100 Geobacter metallireducens

85 Desulfuromonadaceae+Geobacteraceae~1 68 Desulfuromonas michiganensis 57 Pelobacter acetylenicus 38 Pelobacter carbinolicus Desulfuromonas acetoxidans 100 Pelobacter massiliensis 90 Geopsychrobacter electrodiphilus

Myxococcales Archangiaceae+Myxococcaceae 100 Corallococcus terminator Corallococcus coralloides 53 95 Corallococcus exiguus Corallococcus macrosporus 65 Myxococcus stipitatus 10 85 48 Archangium disciforme 65 Archangium minus Archangium gephyra 50 43 Cystobacter badius 100 100 Cystobacter fuscus Cystobacter ferrugineus 100 80 Melittangium boletus 98 Aggregicoccus edonensis Simulacricoccus ruber 100 Stigmatella erecta 95 Stigmatella aurantiaca Anaeromyxobacter dehalogenans Polyangiaceae+Phaselicystidaceae 68 75 Racemicystis crocea 60 Phaselicystis flava 100 Polyangium fumosum 100 33 Sorangium cellulosum Chondromyces pediculatus 60 Haliangium ochraceum Lujinxingia sediminis Thermodesulfobacteriaceae_Thermodesulfobacteriales 5 100 Thermodesulfobacterium hveragerdense 98 Thermodesulfobacterium thermophilum Thermosulfurimonas dismutans 95 78 Thermosulfurimonas marina Thermodesulfatator indicus 83 100 Thermodesulfatator autotrophicus Thermosulfuriphilus ammonigenes

Firmicutes+Tenericutes Lactobacillales Lactobacillaceae+Leuconostocaceae 100 Levilactobacillus paucivorans 70 "Levilactobacillus suantsaiihabitans" 100 Levilactobacillus hammesii Levilactobacillus spicheri 45 8 Lactiplantibacillus pentosus 57 Lactiplantibacillus plantarum subsp. plantarum Lactiplantibacillus paraplantarum 40 100 Lactiplantibacillus fabifermentans 88 Secundilactobacillus paracollinoides Secundilactobacillus kimchicus 100 Secundilactobacillus malefermentans 100 Lactobacillus bombintestini 45 88 Apilactobacillus micheneri Fructilactobacillus fructivorans 33 Lentilactobacillus kefiri Lentilactobacillus otakiensis 63 Lentilactobacillus sunkii 90 Lentilactobacillus parabuchneri 65 53 Lentilactobacillus buchneri 57 90 Lentilactobacillus parakefiri 38 40 Lentilactobacillus kisonensis Lentilactobacillus rapi 88 Lentilactobacillus diolivorans Lentilactobacillus farraginis 80100 Lentilactobacillus hilgardii Lentilactobacillus curieae 100 Pediococcus pentosaceus 78 Pediococcus acidilactici 33 Pediococcus claussenii 95 Pediococcus damnosus 100 Pediococcus inopinatus 80 Limosilactobacillus reuteri Limosilactobacillus antri 90 48 Limosilactobacillus frumenti 57 Limosilactobacillus pontis Limosilactobacillus gastricus 25 55 Limosilactobacillus mucosae 100 100 Paucilactobacillus suebicus 68 Paucilactobacillus vaccinostercus Paucilactobacillus wasatchensis 50 Paucilactobacillus oligofermentans 100 Lacticaseibacillus casei 98 Lacticaseibacillus chiayiensis 50 Lacticaseibacillus rhamnosus 88 Lacticaseibacillus saniviri Lacticaseibacillus manihotivorans 57 Lactobacillus helveticus 30 Lactobacillus gallinarum 28 Lactobacillus acidophilus 20 Lactobacillus crispatus 40 Lactobacillus amylovorus 55 Lactobacillus ultunensis Lactobacillus kefiranofaciens subsp. kefiranofacie 90 80 Lactobacillus kefiranofaciens subsp. kefirgranum 8 100 Lactobacillus amylolyticus 38 Lactobacillus xujianguonis 100 Lactobacillus kalixensis 100 Lactobacillus delbrueckii subsp. delbrueckii 60 63 Lactobacillus delbrueckii subsp. bulgaricus Lactobacillus bombicola Lactobacillus mulieris 78 68 Lactobacillus gasseri 100 Lactobacillus johnsonii 25 70 Lactobacillus taiwanensis 100 Lactobacillus hominis Lactobacillus iners Amylolactobacillus amylophilus 98 Amylolactobacillus amylotrophicus 60 Companilactobacillus kimchii 18 48 "Companilactobacillus suantsaicola" 100 Companilactobacillus halodurans 50 Companilactobacillus farciminis 50 100 Companilactobacillus futsaii 100 Companilactobacillus musae 50 Companilactobacillus heilongjiangensis Companilactobacillus nantensis 30 55 Companilactobacillus nuruki 65 Companilactobacillus allii 20 Companilactobacillus nodensis 33 Companilactobacillus insicii 83 Companilactobacillus tucceti 45 Companilactobacillus versmoldensis 80 Companilactobacillus salsicarnum Companilactobacillus metriopterae Latilactobacillus sakei subsp. sakei 100 Latilactobacillus graminis 23 30 Leuconostoc mesenteroides subsp. cremoris 55 Leuconostoc litchii Leuconostoc inhae 63 50 Leuconostoc kimchii 100 Leuconostoc gelidum subsp. aenigmaticum 80 Leuconostoc gelidum subsp. gasicomitatum 50 Leuconostoc palmae Leuconostoc mesenteroides subsp. jonggajibkimchii 40 100 Leuconostoc mesenteroides subsp. dextranicum 100 Leuconostoc mesenteroides subsp. mesenteroides 63 Fructobacillus fructosus 57 68 Convivina intestini Leuconostoc fallax 100 Oenococcus oeni 100 70 Oenococcus kitaharae 100 Weissella koreensis 100 Weissella soli Weissella hellenica 90 100 75 Weissella bombi Weissella muntiaci 88 Weissella fabaria Weissella ghanensis 100 Weissella fabalis Ligilactobacillus salivarius 100 50 Ligilactobacillus apodemi Ligilactobacillus faecis 35 Ligilactobacillus animalis Liquorilactobacillus capillatus 100 88 30 Liquorilactobacillus aquaticus 65 Liquorilactobacillus uvarum Liquorilactobacillus mali 38 Liquorilactobacillus satsumensis 78 Liquorilactobacillus oeni

Streptococcaceae 100 Streptococcus porcinus 55 Streptococcus pseudoporcinus 23 Streptococcus bovimastitidis 53 Streptococcus penaeicida 30 Streptococcus parauberis 100 Streptococcus agalactiae 15 Streptococcus dysgalactiae subsp. dysgalactiae 18 100 Streptococcus iniae Streptococcus uberis 13 Streptococcus ictaluri 18 Streptococcus urinalis Streptococcus henryi 88 Streptococcus macacae 100 Streptococcus dentapri Streptococcus ferus 100 53 Streptococcus criceti 57 Streptococcus oriloxodontae 10 33 Streptococcus orisuis 13 40 Streptococcus sobrinus Streptococcus dentasini 90 Streptococcus ratti 20 Streptococcus ursoris 25 Streptococcus orisasini 30 Streptococcus mutans 100 Streptococcus troglodytae Streptococcus dentiloxodontae 5 48 Streptococcus halotolerans Streptococcus thoraltensis 30 Streptococcus ovis 100 Streptococcus minor 30 Streptococcus pneumoniae 18 Streptococcus oralis oralis subsp. oralis 23 Streptococcus mitis 18 Streptococcus oralis subsp. tigurinus 18 55 Streptococcus oralis subsp. dentisani 60 48 Streptococcus downii Streptococcus infantis 100 Streptococcus peroris 100 Streptococcus cristatus 20 Streptococcus sinensis 25 Streptococcus gordonii 15 Streptococcus australis 2520 Streptococcus parasanguinis Streptococcus sanguinis 18 Streptococcus himalayensis 100 Streptococcus respiraculi Streptococcus marmotae 78 23 Streptococcus azizii 13 10 13 Streptococcus suis 65 Streptococcus intermedius Streptococcus constellatus subsp. constellatus 100 Streptococcus constellatus subsp. pharyngis 63 18 Streptococcus anginosus subsp. anginosus 43 Streptococcus massiliensis 30 Streptococcus moroccensis Streptococcus merionis 100 Streptococcus ruminantium 63 Streptococcus infantarius subsp. infantarius 100 Streptococcus equinus 55 Streptococcus gallolyticus subsp. macedonicus Streptococcus vestibularis 18 100 Streptococcus salivarius subsp. salivarius Streptococcus salivarius subsp. thermophilus 33 Streptococcus loxodontisalivarius 63 Streptococcus saliviloxodontae 100 Lactococcus garvieae subsp. garvieae Lactococcus petauri 100 40 50 Lactococcus lactis subsp. lactis 83 Lactococcus lactis subsp. hordniae 78 Lactococcus lactis subsp. tructae 100 Lactococcus allomyrinae 78 Lactococcus nasutitermitis 100 Lactococcus reticulitermitis 100 Lactococcus carnosus 93 Lactococcus paracarnosus Floricoccus penangensis

Enterococcaceae~1 Enterococcus dispar 823 Enterococcus asini

Enterococcaceae_2 53 Enterococcus sulfureus 30 Enterococcus italicus 3 100 Enterococcus saccharolyticus subsp. saccharolyticu Enterococcus saccharolyticus subsp. taiwanensis 40 3 Enterococcus eurekensis Enterococcus cecorum 100 Enterococcus columbae 18 10 Tetragenococcus halophilus subsp. halophilus Enterococcaceae~4 55 Enterococcus pallens 100 Enterococcus florum 100 Enterococcus avium Enterococcus gilvus Enterococcus pseudoavium 13 23 100 Enterococcus viikkiensis Enterococcus gallinarum

Enterococcaceae~5 Enterococcus hirae 23 Enterococcus villorum 50 Enterococcus mundtii Enterococcus ratti 10018 Enterococcus xinjiangensis Enterococcus durans

25 Enterococcus phoeniculicola Enterococcaceae Enterococcus moraviensis 20 Enterococcus silesiacus 45 Enterococcus rotai 100 Enterococcus ureilyticus 23 83 Enterococcus termitis Enterococcus wangshanyuanii

70 Enterococcaceae~6 100 Vagococcus teuberi 100 40 Vagococcus penaei Vagococcus elongatus 100 Vagococcus xieshaowenii Catellicoccus marimammalium Carnobacteriaceae 25 Carnobacterium inhibens subsp. inhibens 30 Carnobacterium iners Carnobacterium gallinarum 25 100 Alloiococcus otitis 48 Dolosigranulum pigrum 100 Alkalibacterium subtropicum 23 100 Alkalibacterium psychrotolerans Marinilactibacillus piezotolerans Desemzia incerta

Aerococcaceae 100 Facklamia hominis 100 25 Facklamia languida Facklamia ignava 60 100 Aerococcus viridans Aerococcus urinaehominis 53 28 100 Aerococcus christensenii Aerococcus urinae 90 Aerococcus sanguinicola Granulicatella adiacens 45 Carnobacteriaceae~1 Jeotgalibaca ciconiae 100 Trichococcus pasteurii 65 Trichococcus collinsii 100 Trichococcus palustris

Listeriaceae_Caryophanales~1 75 Listeria seeligeri 100 Listeria welshimeri 100 Listeria rocourtiae Listeria weihenstephanensis 95 Listeria booriae 45 100 Listeria goaensis Listeria valentina 85 75 Listeria thailandensis Listeria costaricensis

Caryophanales~2 Staphylococcaceae 100 Staphylococcus pseudintermedius 55 Staphylococcus intermedius 100 Staphylococcus ursi 100 Staphylococcus hyicus Staphylococcus microti 65 Staphylococcus muscae 100 73 Staphylococcus carnosus subsp. carnosus Staphylococcus condimenti 43 100 Staphylococcus piscifermentans Staphylococcus debuckii 40 30 Staphylococcus edaphicus 45 Staphylococcus saprophyticus subsp. saprophyticus 65 Staphylococcus succinus subsp. succinus 75 100 Staphylococcus casei Staphylococcus equorum subsp. linens Staphylococcus kloosii 6840 Staphylococcus pettenkoferi Staphylococcus aureus subsp. aureus 100 Staphylococcus argenteus 70 Staphylococcus simiae 78 100 Staphylococcus saccharolyticus Staphylococcus devriesei 5040 Staphylococcus petrasii subsp. croceilyticus 88 Staphylococcus petrasii subsp. petrasii 53 Staphylococcus hominis subsp. hominis Mammaliicoccus sciuri Mammaliicoccus stepanovicii Macrococcus goetzii 57 60 Macrococcus epidermidis 70 Macrococcus bohemicus 48 Macrococcus caseolyticus subsp. caseolyticus Macrococcus caseolyticus subsp. hominis 43 Macrococcus canis 43 Macrococcus bovicus 75 80 60 Macrococcus lamae 43 Macrococcus brunensis Macrococcus carouselicus 6340 Macrococcus equipercicus Macrococcus hajekii 85 Salinicoccus roseus Salinicoccus carnicancri 100 10 Jeotgalicoccus huakuii

43 Exiguobacterium sibiricum 30 Exiguobacterium undae 23 Exiguobacterium oxidotolerans 75 Exiguobacterium antarcticum Exiguobacterium acetylicum 23 Gemella haemolysans 100 Gemella morbillorum

Caryophanaceae+Bacillaceae_Caryophanales Lysinibacillus sphaericus 15 83 Solibacillus isronensis Solibacillus cecembensis 38 45 Lysinibacillus odysseyi 100 Ureibacillus manganicus 30 Lysinibacillus antri 100 Ureibacillus chungkukjangi 100 ndiopicus 18 Lysinibacillus composti 33 Ureibacillus composti 100 Ureibacillus thermosphaericus 100 Psychrobacillus lasiicapitis 100 Psychrobacillus vulpis 38 Chryseomicrobium excrementi 100 Chryseomicrobium palamuruense 100 Sporosarcina saromensis Sporosarcina siberiensis 100 33 Paenisporosarcina indica 100 Planococcus halotolerans 28 Planococcus halocryophilus 33 50 Planococcus versutus 55 Planococcus rifietoensis Planococcus salinus 18 Bhargavaea cecembensis 80 Bhargavaea ginsengi 100 15 Siminovitchia fortis Siminovitchia acidinfaciens 35 Neobacillus notoginsengisoli 5 Bacillus marinisedimentorum 50 Pradoshia eiseniae Pueribacillus theae 23 Weizmannia coagulans 100 Peribacillus simplex 100 Brevibacterium frigoritolerans 100 Peribacillus psychrosaccharolyticus Bacillus alkalitolerans 15 75 Peribacillus acanthi 35 Neobacillus jeddahensis Neobacillus niacini 100 Neobacillus pocheonensis 100 Mesobacillus rigiliprofundi 100 Mesobacillus fermenti 70 100 Mesobacillus maritimus 100 40 Mesobacillus foraminis Mesobacillus subterraneus 70 Robertmurraya beringensis 100 Robertmurraya kyonggiensis 43 Niallia nealsonii 50 Niallia taxi Niallia oryzisoli 100 50 Cytobacillus ciccensis 80 Cytobacillus eiseniae 100 Cytobacillus formosensis 13 5 Cytobacillus gottheilii Lederbergia lentus 40 Falsibacillus albus 100 20 Bacillus salitolerans 8 Priestia aryabhattai 80 Priestia flexa 100 Gottfriedia solisilvae 100 Sutcliffiella horikoshii 100 Bacillus tianshenii Bacillus methanolicus 100 48 Geobacillus thermocatenulatus Geobacillus proteiniphilus 100 Geobacillus stearothermophilus Geobacillus thermoleovorans 70 75 Geobacillus vulcani 50 Geobacillus thermodenitrificans subsp. thermodenit 100 Geobacillus subterraneus subsp. aromaticivorans 48 Geobacillus subterraneus 100 Parageobacillus thermoglucosidasius 55 Parageobacillus thermantarcticus debilis Anoxybacillus flavithermus subsp. flavithermus 100 Anoxybacillus gonensis 100 43 Flavobacterium thermophilum 100 Anoxybacillus kamchatkensis 33 Anoxybacillus vitaminiphilus 23 Anoxybacillus geothermalis 15 Anoxybacillus caldiproteolyticus 2553 Anoxybacillus contaminans 53 Anoxybacillus amylolyticus Anoxybacillus sediminis 100 Bacillus songklensis 100 Jeotgalibacillus alimentarius 5 70 Jeotgalibacillus malaysiensis Jeotgalibacillus marinus 83 100 Jeotgalibacillus soli Rossellomorea aquimaris 100 Bacillus coahuilensis Bacillus toyonensis Bacillus proteolyticus 3 Bacillus mycoides 10038 Bacillus wiedmannii Bacillus fungorum 45 Bacillus mobilis 33 Bacillus pacificus Bacillus paranthracis 20 Bacillus cereus Bacillus albus Bacillus luti 75 Bacillus nitratireducens Bacillus tropicus 78 Bacillus paramycoides Bacillus pseudomycoides 30 Bacillus cytotoxicus 100 Ectobacillus panaciterrae Ectobacillus antri 70 Ectobacillus funiculus 100 3 100 Metabacillus litoralis 100 Metabacillus crassostreae Metabacillus malikii 15 Metabacillus indicus Bacillus mojavensis 10010 Bacillus subtilis subsp. subtilis 10 Bacillus inaquosorum 8 Bacillus cabrialesii 100 100 Bacillus nakamurai Bacillus vallismortis 28 Bacillus amyloliquefaciens subsp. amyloliquefacien 18 Bacillus stercoris 55 Bacillus atrophaeus 48 Bacillus licheniformis Bacillus haynesii 5 100 63 Bacillus glycinifermentans 48 Bacillus swezeyi Bacillus australimaris 30 Bacillus pumilus Bacillus zhangzhouensis 70 Bacillus aerophilus 75 Bacillus xiamenensis 18 Bacillus stratosphericus 10 Bacillus altitudinis 5 Bacillus capparidis 8 Bacillus carboniphilus Heyndrickxia oleronia 20 Margalitia camelliae 38 Bacillus acidicola Bacillus salinus 33 Bacillus isabeliae Bacillus wudalianchiensis Turicibacter sanguinis Bacillaceae~1_Caryophanales~2 100 Pseudogracilibacillus marinus 18 Oceanobacillus zhaokaii 100 Oceanobacillus chungangensis 18 Oceanobacillus picturae 90 Oceanobacillus oncorhynchi subsp. incaldanensis 100 Oceanobacillus sojae 100 Oceanobacillus iheyensis 100 Oceanobacillus rekensis 53 Oceanobacillus polygoni 5 Ornithinibacillus contaminans Ornithinibacillus salinisoli 100 Virgibacillus marismortui 100 Virgibacillus salarius 15 Virgibacillus soli Virgibacillus kekensis 15100 Virgibacillus sediminis 38 Lentibacillus amyloliquefaciens 100 Virgibacillus natechei Lentibacillus juripiscarius 25100 Virgibacillus necropolis Virgibacillus flavescens 38 43 Virgibacillus byunsanensis Amphibacillus xylanus 40 65 Alkalilactibacillus ikkensis Paraliobacillus sediminis 100 Paraliobacillus quinghaiensis Halolactibacillus halophilus 100 Halolactibacillus miurensis 57 88 Gracilibacillus thailandensis 30 Gracilibacillus salitolerans Gracilibacillus massiliensis 100 60 Gracilibacillus halotolerans 63 Halobacillus halophilus Halobacillus campisalis Salimicrobium halophilum Halobacillus trueperi 100 Halobacillus karajensis 100 80 Halobacillus profundi Halobacillus locisalis 100 Thalassobacillus hwangdonensis Halalkalibacillus sediminis

Caryophanales~3 Paenibacillus polymyxa 50 100 Paenibacillus shenyangensis 73 Paenibacillus wulumuqiensis Paenibacillus hunanensis 55 Paenibacillus nicotianae 15 Paenibacillus xylanivorans 8 15 Paenibacillus xylanilyticus 35 Paenibacillus taichungensis 100 Paenibacillus pabuli 18 Paenibacillus xylanexedens 10 100 Paenibacillus tundrae Paenibacillus medicaginis 18 100 Paenibacillus terreus Paenibacillus shunpengii Paenibacillus glucanolyticus 55 Paenibacillus ihbetae 83 Paenibacillus sonchi 60 Paenibacillus helianthi 100 Paenibacillus typhae 100 100 Paenibacillus forsythiae 70 Paenibacillus zanthoxyli Paenibacillus rhizophilus 55 83 Paenibacillus stellifer 100 100 Paenibacillus tritici 100 Paenibacillus wynnii 33 100 Paenibacillus borealis 3 Paenibacillus antarcticus 8 Paenibacillus selenii Chengkuizengella marina 28 Paenibacillus lentus 100 Paenibacillus ihumii 100 5 Paenibacillus favisporus 53 Paenibacillus rhizosphaerae Paenibacillus azoreducens 68 Paenibacillus relictisesami 100 Paenibacillus alvei 8 Paenibacillus apiarius Paenibacillus turicensis 1030 Paenibacillus aceti Paenibacillus yonginensis 53 Paenibacillus pocheonensis 3 100 Paenibacillus ferrarius 57 Paenibacillus aceris Paenibacillus thalictri 45 100 Paenibacillus esterisolvens 83 Paenibacillus yunnanensis 100 Paenibacillus piri 53 43 Paenibacillus xerothermodurans Paenibacillus mucilaginosus 10020 Paenibacillus chitinolyticus Paenibacillus guangzhouensis 100 Paenibacillus swuensis 18 100 Cohnella endophytica Cohnella ginsengisoli 100 Cohnella kolymensis 30 Paenibacillus larvae subsp. larvae Xylanibacillus composti 8 Paenibacillus antri 50 Paenibacillus solisilvae 5 53 Paenibacillus rhizoryzae 100 Paenibacillus montanisoli 53 Paenibacillus taihuensis 100 Paenibacillus phyllosphaerae 73 Paenibacillus aurantiacus 33 Paenibacillus sepulcri 48 Paenibacillus mendelii Paenibacillus curdlanolyticus 23 100 100 Paenibacillus cellulosilyticus 100 Paenibacillus catalpae Paenibacillus castaneae 100 100 Paenibacillus algorifonticola 38 100 Paenibacillus paeoniae 100 15 Paenibacillus agaridevorans Paenibacillus protaetiae 28 Paenibacillus quercus 20 Paenibacillus mesophilus Saccharibacillus kuerlensis 100 100 Saccharibacillus qingshengii Desulfuribacillus stibiiarsenatis Caldalkalibacillus mannanilyticus Bacillaceae~2 5 100 Alkalicoccus urumqiensis 73 Salisediminibacterium selenitireducens 55 Evansella cellulosilyticus Bacillus tamaricis 100 Evansella polygoni 100 100 Salibacterium lacus 100 Salibacterium salarium 33 Aliibacillus thermotolerans 68 Geomicrobium sediminis Thalassorhabdus alkalitolerans

15 Bacillaceae~3 53 Anaerobacillus isosaccharinicus Alkalihalobacillus miscanthi 100 30 Alkalihalobacillus clausii 18 Alkalihalobacillus pseudalcaliphilus Fermentibacillus polygoni 1003560 Alkalihalobacillus wakoensis Alkalihalobacillus hemicellulosilyticus 50 48 Bacillus oceani Alkalihalobacillus lindianensis 23 Alkalihalobacillus halodurans 10 5 Sporolactobacillaceae Sporolactobacillus nakayamae subsp. nakayamae 85 Pullulanibacillus pueri 100 Pullulanibacillus camelliae

Paenibacillaceae~2 30 Brevibacillus nitrificans 100 Brevibacillus porteri 45 Brevibacillus fortis 68 Brevibacillus schisleri 100 Brevibacillus migulae 50 Brevibacillus sediminis Aneurinibacillus migulanus

Bacillaceae~4_Caryophanales~4 Fictibacillus macauensis 48 Fictibacillus aquaticus

Thermoactinomycetaceae_Caryophanales~5 100 Risungbinella massiliensis 57 Geothermomicrobium terrae 100 100 Thermoflavimicrobium daqui Laceyella sacchari 100 100 Laceyella putida 75 Laceyella thermophila Thermoactinomyces vulgaris 100 100 Thermoactinomyces khenchelensis 100 Kroppenstedtia eburnea 45 Kroppenstedtia sanguinis Marinithermofilum abyssi 73 68 Planifilum fulgidum 100 Planifilum yunnanense Novibacillus thermophilus

Alicyclobacillaceae_Caryophanales~6 100 Alicyclobacillus acidocaldarius subsp. acidocaldar Alicyclobacillus acidocaldarius subsp. rittmannii 98 63 Alicyclobacillus acidoterrestris Alicyclobacillus acidiphilus 70 Alicyclobacillus hesperidum 100 100 Alicyclobacillus sacchari 50 Alicyclobacillus ferrooxydans 50 Alicyclobacillus contaminans 100 50 Alicyclobacillus pomorum 53 Alicyclobacillus aeris Alicyclobacillus cycloheptanicus 68 Kyrpidia spormannii Tumebacillus avium

Mollicutes_Tenericutes Mycoplasmataceae~1_Mycoplasmatales~1 Mycoplasma gallopavonis 60 90 Mycoplasma anatis 35 Mycoplasma anserisalpingitidis Mycoplasma pullorum 43 Mycoplasma crocodyli 100 90 Mycoplasma alligatoris 100 Mycoplasma agalactiae 50 Mycoplasma bovis 35 Mycoplasma fermentans 100 Mycoplasma bovigenitalium Mycoplasma iners 68 Mycoplasma marinum 100 Mycoplasma todarodis 100 Mycoplasma hyorhinis Mycoplasma procyoni 45 100 Mycoplasma moatsii 65 Mycoplasma auris 65 Mycoplasma neophronis Mycoplasma hominis 25 Mycoplasma anseris 98 Mycoplasma cloacale 100 100 Mycoplasma orale 100 Mycoplasma hyosynoviae Mycoplasma salivarium 57 Mycoplasma subdolum

Entomoplasmataceae+Mycoplasmataceae_Entomoplasmatales+Mycoplasmatales Mycoplasma leachii 48 Mycoplasma capricolum subsp. capripneumoniae 55 Mycoplasma capricolum subsp. capricolum 70 Mycoplasma mycoides subsp. mycoides Mycoplasma cottewii 28 100 Mycoplasma putrefaciens Entomoplasma freundtii 5050 Williamsoniiplasma lucivorax 98 Williamsoniiplasma luminosum Mesoplasma photuris 93 Mesoplasma seiffertii 95 15 70 Mesoplasma syrphidae Mesoplasma grammopterae 100 Mesoplasma florum 75 Mesoplasma entomophilum 80 Mesoplasma coleopterae Mesoplasma chauliocola 78 100 Entomoplasma ellychniae 90 Mesoplasma corruscae

Spiroplasmataceae~1+Entomoplasmataceae~1_Spiroplasmatales~1+Entomoplasmatales~1 100 Spiroplasma lineolae 93 Spiroplasma tabanidicola 23 Spiroplasma helicoides 55 Spiroplasma corruscae 100 Spiroplasma turonicum 20 98 Spiroplasma litorale 65 Spiroplasma chinense Spiroplasma velocicrescens 38 23 Spiroplasma culicicola 100 Mesoplasma melaleucae Spiroplasma diabroticae Spiroplasma diminutum 28 78 88 Spiroplasma cantharicola Spiroplasma monobiae 5557 Spiroplasma taiwanense 93 28 Spiroplasma montanense Spiroplasma clarkii Spiroplasma lampyridicola 57 28 Spiroplasma leptinotarsae Spiroplasma sabaudiense 57 Spiroplasmataceae_Spiroplasmatales 90 Spiroplasma melliferum 100 Spiroplasma phoeniceum 88 Spiroplasma insolitum Spiroplasma syrphidicola 48 100 100 Spiroplasma chrysopicola Spiroplasma atrichopogonis 95 Spiroplasma eriocheiris

Mycoplasmataceae~2_Mycoplasmatales~2 100 Ureaplasma urealyticum Ureaplasma miroungigenitalium 60 100 Ureaplasma zalophigenitalium Mycoplasma iowae 100 Mycoplasma penetrans 100 100 Mycoplasma amphoriforme Mycoplasma tullyi 100 Mycoplasma genitalium

100 100 Acholeplasma palmae Acholeplasma axanthum Erysipelotrichiaceae_Erysipelotrichales_Erysipelotrichia_Firmicutes~1 100 Allobaculum stercoricanis 40 90 Dubosiella newyorkensis Amedibacillus dolichus Erysipelothrix rhusiopathiae 30 95 Erysipelothrix piscisicarius 75 Erysipelothrix tonsillarum Erysipelothrix larvae 100 53 Solobacterium moorei Anaerorhabdus furcosa 78 Holdemania massiliensis

Firmicutes~2 Coprobacillaceae_Erysipelotrichales~1_Erysipelotrichia~1 90 Eggerthia catenaformis Catenibacterium mitsuokai

35 100 Clostridium~1_Clostridiaceae~1_Eubacteriales~1_Clostridia~1 75 Clostridium cocleatum Clostridium spiroforme 100 Clostridium ramosum

Fusobacteriales_Fusobacteriia_Fusobacteria Fusobacteriaceae 73 Fusobacterium nucleatum subsp. animalis 55 Fusobacterium simiae 68 Fusobacterium periodonticum 100 Fusobacterium varium 90 Fusobacterium necrophorum subsp. funduliforme Cetobacterium somerae 100 93 Cetobacterium ceti 100 Ilyobacter polytropus Ilyobacter tartaricus 100 Ilyobacter insuetus

Leptotrichiaceae 95 Streptobacillus moniliformis 100 100 Streptobacillus notomytis 100 Streptobacillus canis Oceanivirga salmonicida 53 100 Sneathia sanguinegens Sebaldella termitidis 40 100 Pseudoleptotrichia goodfellowii Leptotrichia buccalis 88 Leptotrichia wadei 98 Leptotrichia shahii 60 Leptotrichia hofstadii

Firmicutes~3 Eubacteriales~2_Clostridia~2 Lachnospiraceae 100 "Mediterraneibacter torques" 25 "Mediterraneibacter lactaris" Coprococcus comes 10035 Mediterraneibacter glycyrrhizinilyticus 55 Faecalicatena fissicatena 20 Faecalicatena contorta 100 Faecalicatena orotica 100 63 Clostridium scindens Clostridium hylemonae 100 Dorea formicigenerans 15 Faecalimonas umbilicata 100 Blautia hansenii 50 25 Blautia glucerasea Blautia hydrogenotrophica 100 Blautia faecicola Robinsoniella peoriensis 40 Lacrimispora saccharolytica 23 83 Lacrimispora celerecrescens 100 Clostridium methoxybenzovorans Lacrimispora amygdalina 100 93 Clostridium indicum Lachnoanaerobaculum umeaense 100 Butyrivibrio crossotus 100100 100 Butyrivibrio proteoclasticus Marvinbryantia formatexigens 3 57 Enterocloster bolteae 100 23 Enterocloster asparagiformis 100 Roseburia hominis Agathobacter rectalis 100 Shuttleworthia satelles 30 Lachnospira eligens 100 Bacteroides pectinophilus 100 Clostridium phytofermentans Anaerobium acetethylicum 90 57 Acetivibrio ethanolgignens 33 75 Anaerostipes hadrus Anaerostipes butyraticus 100 Anaerostipes caccae Anaerobutyricum soehngenii 100 Lachnospiraceae~1 100 Cellulosilyticum lentocellum Cellulosilyticum ruminicola

65 Vallitaleaceae 100 Abyssivirga alkaniphila Petrocella atlantisensis 60 Vallitalea okinawensis

Clostridiaceae~1 68 Intestinibacter bartlettii 100 Terrisporobacter mayombei Romboutsia hominis 60 Peptostreptococcaceae 70 Peptostreptococcus russellii Clostridioides mangenotii 100 100 Clostridioides difficile 35 Clostridiceae~2 18 Paraclostridium benzoelyticum 100 Paraclostridium bifermentans 4333 Eubacterium tenue Paeniclostridium ghonii 57 Paeniclostridium sordellii 100 Sporacetigenium mesophilum

57 Clostridiaceae~3 Clostridium paradoxum 98 Clostridium thermoalcaliphilum Peptoclostridium acidaminophilum Clostridiaceae~4 100 100 Alkaliphilus oremlandii Alkaliphilus peptidifermentans 38 88 Alkaliphilus hydrothermalis 100 Clostridium formicaceticum 100 Anaerovirgula multivorans 35 Anoxynatronum buryatiense 100 Isachenkonia alkalipeptolytica 78 Geosporobacter subterraneus

Eubacteriaceae~1 73 Mogibacterium pumilum 100 Eubacterium saphenum 30 Aminipila butyrica 78 Fusibacter tunisiensis

Peptoniphiliaceae_Eubacteriales~3_Clostridia~3 100 Anaerococcus prevotii 100 Anaerococcus tetradius 33 Anaerococcus hydrogenalis Anaerococcus vaginalis 100 Anaerococcus rubeinfantis

Tissierellaceae_Tissierellales_Tissierelia 70 Tissierella praeacuta Tissierella creatinini 3878 Soehngenia saccharolytica 70 Gudongella oleilytica

Clostridiaceae~4_Eubacteriales~3_Clostridia~4 100 53 Keratinibaculum paraultunense 57 Tepidimicrobium xylanilyticum

15 Eubacteriales~5_Clostridia~5 Anaerosalibacter bizertensis 70 Sporanaerobacter acetigenes Gottschalkia acidurici 100 Dethiosulfatibacter aminovorans 28 Clostridiaceae~5_Eubacteriales~6_Clostridia~6 38 Caldisalinibacter kiritimatiensis 53 Thermohalobacter berrensis Caloranaerobacter ferrireducens 100 Sporosalibacterium tautonense

Eubacteriaceae_Eubacteriales_Clostridia~7 90 Acetobacterium woodii 60 Eubacterium limosum Alkalibaculum sporogenes 80 Anaerofustis stercorihominis

Clostridia Clostridiaceae_Eubacteriales~7 Clostridium beijerinckii 48 Clostridium saccharoperbutylacetonicum 100 Clostridium chromiireducens Clostridium butyricum 33 33 Clostridium baratii 100 Clostridium moniliforme Clostridium sardiniense 40 100 Clostridium paraputrificum 35 100 Clostridium chauvoei 50 Clostridium septicum 70 Clostridium tertium 100 80 Clostridium isatidis Clostridium gasigenes 20 Clostridium disporicum 85 100 Clostridium saudiense Clostridium perfringens 43 Clostridium tarantellae 30 Clostridium amylolyticum 60 Clostridium putrefaciens 100 100 Clostridium algidicarnis Clostridium cellulovorans 100 Youngiibacter multivorans Proteiniclasticum ruminis 3 63 Clostridium cadaveris 50 Clostridium ljungdahlii 100 Clostridium tyrobutyricum Clostridium kluyveri 35 Clostridium carboxidivorans 100 83 Clostridium thiosulfatireducens 100 Clostridium sulfidigenes 57 Clostridium subterminale 20 53 Clostridium frigoris 100 Clostridium bowmanii 100 Clostridium pascui 13 83 Clostridium acetobutylicum Clostridium felsineum 100 Clostridium neuense 30 88 Clostridium guangxiense Clostridium cochlearium 100 Clostridium novyi 93 Clostridium haemolyticum 57 Clostridium bovifaecis 90 73 Ilyobacter delafieldii Clostridium grantii 100 Clostridium sporogenes 100 Clostridium tepidum 100 Hathewaya limosa 73 Hathewaya histolytica 88 Oceanirhabdus sediminicola 100 Thermobrachium celere Caloramator australicus 100 100 Caloramator fervidus 20 Fonticella tunisiensis

Thermoanaerobacteraceae~1_Thermoanaerobacterales~1 23 Thermoanaerobacterium xylanolyticum 8 Thermohydrogenium kirishiense 48 75 Thermoanaerobacterium thermosaccharolyticum Caldanaerobius polysaccharolyticus Mahella australiensis

33 Caldicoprobacteraceae_Eubacteriales~8 Caldicoprobacter faecalis 100 Caldicoprobacter guelmensis

Oscillospiraceae_Eubacteriales~9 100 Ruminococcus albus 50 Ruminococcus champanellensis 85 Ruminococcus flavefaciens 35 Hydrogenoanaerobacterium saccharovorans 100 15 Massiliimalia massiliensis Massiliimalia timonensis 100 100 Paludicola psychrotolerans 100 Hydrogeniiclostridium mannosilyticum 100 Caproicibacter fermentans 70 55 Acutalibacter muris 40 Ethanoligenens harbinense 100 Clostridium methylpentosum Eubacterium siraeum 100 Flavonifractor plautii Intestinimonas massiliensis 3 100 Oscillibacter valericigenes 85 Ruminiclostridium cellulolyticum 100 Ruminiclostridium papyrosolvens 10 95 Ruminiclostridium cellobioparum subsp. cellobiopar 63 100 100 Ruminiclostridium cellobioparum subsp. termitidis Ruminiclostridium hungatei 95 Clostridium thermosuccinogenes 50 Pseudobacteroides cellulosolvens 78 Acetivibrio cellulolyticus 100 Acetivibrio alkalicellulosi 100 Acetivibrio thermocellus 100 Saccharofermentans acetigenes Thermoclostridium stercorarium subsp. thermolactic

Proteinivoraceae_Eubacteriales~10 Proteinivorax hydrogeniformans 100 Proteinivorax tanatarense

Eubacteriales~11_Clostridia~8_Firmicutes~4 Peptococcaceae~1 100 Desulfosporosinus youngiae Desulfosporosinus lacus 73 28 Desulfosporosinus hippei 60 Desulfosporosinus auripigmenti 90 Desulfitobacterium hafniense 100 Desulfitobacterium metallireducens 43 Syntrophobotulus glycolicus 90 Dehalobacter restrictus 18 Heliobacterium modesticaldum Peptococcus niger Peptococcaceae~2 35 100 Desulfotomaculum reducens 100 Desulfotomaculum ferrireducens 100 Desulfotomaculum ruminis Desulfotomaculum hydrothermale 65 Desulfofarcimen acetoxidans 50 Desulfohalotomaculum peckii 100 Desulfohalotomaculum halophilum

Firmicutes~5 Negativicutes Veillonellaceae_Veillonellales 100 Megasphaera elsdenii Megasphaera paucivorans 57 70 Megasphaera hexanoica Dialister invisus 100 85 Dialister micraerophilus 48 Veillonella parvula 100 Veillonella atypica Veillonella dispar 100 Veillonella ratti 100 100 Veillonella criceti

Selenomonadaceae_Selenomonadales 57 Selenomonas sputigena 60 Mitsuokella multacida 100 Mitsuokella jalaludinii 73 Megamonas funiformis 60 Propionispira paucivorans

100 Thermosinus carboxydivorans Sporomusaceae_Selenomonadales 53 Sporomusa paucivorans 53 Sporomusa malonica 100 Sporomusa aerivorans Sporomusa acidovorans 90 53 100 Pelosinus propionicus Pelosinus fermentans 100 Acetonema longum

Acidaminococcaceae_Acidaminococcales 100 Acidaminococcus fermentans 85 Succinispira mobilis 100

Desulfofundulus solfataricus 18 Thermolithobacter carboxydivorans

Verrucomicrobia Verrucomicrobiales_Verrucomicrobiae Verrucomicrobiaceae+Rubritaleaceae 100 Haloferula rosea 75 Haloferula phyci Rubritalea tangerina 65 35 Akkermansia muciniphila Prosthecobacter vanneervenii 83 53 Verrucomicrobium spinosum Coraliomargarita akajimensis

100 Opitutaceae_Opitutales 55 Geminisphaera colitermitum 10 Nibricoccus aquaticus

50 33 Pontiella sulfatireligans Pontiella desulfatans 100 Tichowtungia aerotolerans Lentisphaera araneosa Chlamydiales_Chlamydiia_Chlamydiae Chlamydiaceae 53 88 Chlamydia psittaci 100 Chlamydia abortus Chlamydia avium 83 Chlamydia trachomatis 98 Chlamydia suis 90 Chlamydia muridarum 63 Chlamydia pecorum Chlamydia pneumoniae 100 63 Parachlamydia acanthamoebae Simkania negevensis 93 Waddlia chondrophila

Planctomycetia_Planctomycetes 38 Pirellulales Pirellulaceae 100 Rhodopirellula baltica 100 Rhodopirellula lusitana Blastopirellula marina 60 Lacipirellulaceae Lacipirellula parvula 98 Posidoniimonas corsicana 55 Planctomycetaceae_Planctomycetales 43 Gimesia maris 75 Fuerstia marisgermanicae Thalassoglobus neptunius 100 45 95 Rubinisphaera brasiliensis Planctopirus limnophila Ramlibacter aquaticus

78 Isosphaeraceae_Isosphaerales Paludisphaera borealis 100 Isosphaera pallida

Acidobacteria Acidobacteriaceae_Acidobacteriales_Acidobacteriia 68 Granulicella arctica 60 Granulicella sapmiensis 100 Granulicella pectinivorans 78 Granulicella tundricola 40 Granulicella sibirica 18 Edaphobacter lichenicola 38 3 Granulicella mallensis 78 Edaphobacter dinghuensis Edaphobacter modestus 93 33 Edaphobacter bradus 60 Terriglobus saanensis Terriglobus aquaticus 10075 Terriglobus tenax 40 Terriglobus albidus 50 Acidipila rosea 98 Acidipila dinghuensis 50 Silvibacterium bohemicum 100 Acidicapsa acidisoli 100 Acidicapsa dinghuensis 48 Occallatibacter riparius Terracidiphilus gabretensis 78 100 Occallatibacter savannae

Blastocatellaceae_Blastocatellales_Balstocatellia 63 33 Aridibacter nitratireducens Tellurimicrobium multivorans 48 Stenotrophobacter roseus

Geothrix fermentans

10 Halanaerobales_Clostridia~9_Firmicutes~6 Halobacteroidaceae 100 Orenia marismortui 90 Natroniella acetigena Acetohalobium arabaticum

Halanaerobiaceae 100 100 Halanaerobium praevalens 3 100 Halanaerobium sehlinense 100 Halanaerobium saccharolyticum subsp. saccharolytic 100 Halanaerobium acetethylicum Halothermothrix orenii

Thermodesulfovibrio hydrogeniphilus 10 Endomicrobium proavitum 23 Thermodesulfobium acidiphilum Actinobacteria Mycobacteriaceae 18 arosiense Mycobacterium paraffinicum 30 Mycobacterium paraseoulense 90 Mycobacterium seoulense 100 Mycobacterium basiliense 100 80 Mycobacterium pseudoshottsii 100 Mycobacterium shottsii 15 Mycobacterium 80 Mycobacterium decipiens Mycobacterium haemophilum Mycobacterium malmoense 8 Mycobacterium nebraskense Mycobacterium bohemicum Mycobacterium innocens 40 30 Mycobacterium persicum 100 Mycobacterium pseudokansasii Mycobacterium attenuatum Mycobacterium angelicum Mycobacterium paragordonae 100 Mycobacterium alsense 80 Mycobacterium florentinum 45 28 Mycobacterium stomatepiae 100 Mycobacterium montefiorense 53 Mycobacterium triplex 18 Mycobacterium shigaense 20 Mycobacterium sherrisii Mycobacterium palustre 68 Mycobacterium kubicae Mycobacterium parascrofulaceum 25 33 35 Mycobacterium europaeum Mycobacterium saskatchewanense 100 Mycobacterium paraense 68 Mycobacterium arupense 100 Mycobacterium minnesotense 40 23 Mycobacterium virginiense 60 Mycobacterium senuense Mycobacterium algericum 25 3 20 Mycobacterium longobardum Mycobacterium botniense 100 Mycobacterium heckeshornense Mycobacterium talmoniae Mycobacterium holsaticum subsp. abscessus Mycobacterium abscessus subsp. bolletii 60 Mycobacterium abscessus subsp. massiliense 100 Mycobacterium stephanolepidis subsp. chelonae 85 100 Mycobacterium chelonae subsp. bovis Mycobacterium chelonae 15 Mycobacterium immunogenum 40 Mycobacterium austroafricanum Mycobacterium neglectum 100 Mycobacterium pyrenivorans 80 Mycobacterium brisbanense 30 Mycobacterium aquaticum 18 Mycobacterium cosmeticum 35 Mycobacterium neoaurum 50 Mycobacterium frederiksbergense Mycobacterium fluoranthenivorans 100 553 45 Mycobacterium diernhoferi 70 Mycobacterium arabiense Mycobacterium sediminis 65 Mycobacterium hodleri Mycobacterium aubagnense 28 Mycobacterium mucogenicum 73 Mycobacterium phocaicum Mycobacterium peregrinum 100 Mycobacterium arcueilense 65 Mycobacterium alvei 40 Mycobacterium montmartrense Mycobacterium septicum 18 33 Mycobacterium neworleansense 35 Mycobacterium boenickei 23 Mycobacterium porcinum 15 8 Mycobacterium conceptionense Mycobacterium syngnathidarum Mycobacterium lutetiense 28 subsp. fortuitum Mycobacterium fortuitum subsp. acetamidolyticum Mycobacterium houstonense Mycobacterium senegalense 453 Mycobacterium farcinogenes Mycobacterium kyogaense 100 Mycobacterium parafortuitum 100 Mycobacterium duvalii Mycobacterium rutilum 3 Mycobacterium rhodesiae 100 8 Mycobacterium sphagni Mycobacterium phlei 28 Mycobacterium insubricum 43 Mycobacterium madagascariense 10018 Mycolicibacterium stellerae 8 Mycobacterium grossiae Mycobacterium palauense 5 Mycobacterium pulveris 53 20 Mycobacterium confluentis 73 Mycobacterium neumannii 23 Mycobacterium lehmannii 35 Mycobacterium gadium 100 Mycobacterium thermoresistibile Mycobacterium moriokaense 100 100 Mycobacterium mageritense 53 Mycobacterium wolinskyi Mycobacterium hassiacum

Nocardiaceae~1 35 Hoyosella subflava Hoyosella altamirensis 100 Hoyosella rhizosphaerae 30 Tsukamurellaceae 20 Tsukamurella pseudospumae Tsukamurella hominis Tsukamurella ocularis 100 Tsukamurella pulmonis 25 Tsukamurella tyrosinosolvens 33 Tsukamurella spumae Tsukamurella paurometabola 10038 Tsukamurella strandjordii Tsukamurella inchonensis

Corynebacteriaceae coyleae 2315 Corynebacterium thomssenii Corynebacterium gottingense 18 Corynebacterium tuscaniense 10028 Corynebacterium aquatimens 60 Corynebacterium capitovis 38 Corynebacterium timonense Corynebacterium mycetoides 23 5568 Corynebacterium sanguinis Corynebacterium lipophiloflavum 30 Corynebacterium liangguodongii 78 Corynebacterium accolens 35 55 Corynebacterium macginleyi Corynebacterium tuberculostearicum 35 Corynebacterium pseudodiphtheriticum 28 Corynebacterium ammoniagenes Corynebacterium phocae 23 38 Corynebacterium aurimucosum 23 50 Corynebacterium diphtheriae subsp. lausannense 100 Corynebacterium belfantii 53 Corynebacterium rouxii 100 Corynebacterium matruchotii 15 Corynebacterium mustelae 5 40 Corynebacterium silvaticum Corynebacterium aquilae 10053 Corynebacterium argentoratense Corynebacterium epidermidicanis 23 20 Corynebacterium pyruviciproducens Corynebacterium uterequi 100 Corynebacterium yudongzhengii 100 Corynebacterium frankenforstense Corynebacterium otitidis 10023 Corynebacterium halotolerans 100 Corynebacterium suranareeae 63 Corynebacterium glutamicum 63 Corynebacterium crudilactis 45 Corynebacterium callunae 45 100 Corynebacterium faecale Corynebacterium efficiens 63 Corynebacterium terpenotabidum 30 Corynebacterium glyciniphilum Corynebacterium kroppenstedtii 90 100 2073 Corynebacterium urealyticum Corynebacterium resistens 57100 Corynebacterium auriscanis Corynebacterium bovis Corynebacterium amycolatum 70 80 Corynebacterium sphenisci

Dietziaceae 100 Dietzia psychralcaliphila Dietzia lutea 100 Dietzia maris 100 Dietzia kunjamensis subsp. schimae

Nocardiaceae Nocardia seriolae 78 80 Nocardia concava Nocardia heshunensis 2068 Nocardia yunnanensis 45 Nocardia otitidiscaviarum 35 Nocardia uniformis 28 Nocardia stercoris Nocardia yamanashiensis 23 25 Nocardia niigatensis 80 Nocardia tengchongensis 8 Nocardia crassostreae 40 13 Nocardia acidivorans Nocardia nova 100 Nocardia macrotermitis 23 Nocardia zhihengii Nocardia jiangxiensis 13 18 Nocardia rayongensis 43 Nocardia vinacea 13 Nocardia pseudovaccinii 68 18 Nocardia anaemiae Nocardia aurantia Nocardia pseudobrasiliensis 3 48 Nocardia mexicana 38 Nocardia thraciensis 23 Nocardia artemisiae 100 Nocardia lijiangensis Nocardia exalbida 57 Nocardia rhamnosiphila 100 60 Nocardia carnea 88 Nocardia testacea 70 Nocardia sienata 25 Nocardia flavorosea 28 Nocardia paucivorans 85 Nocardia brevicatena 100 Nocardia cyriacigeorgica 100 Nocardia thailandica 13 Nocardia abscessus 8 48 Nocardia salmonicida subsp. cummidelens 35 Nocardia salmonicida subsp. salmonicida 30 Nocardia fluminea 48 Nocardia ignorata 45 Nocardia lasii 70 Nocardia mangyaensis 100 Nocardia camponoti 48 Nocardia halotolerans 33 18 Nocardia colli 15 Nocardia cavernae Nocardia goodfellowii 63 5 Nocardia sungurluensis 13 43 Nocardia tenerifensis 100 Nocardia aurea Nocardia transvalensis 1025 Nocardia jiangsuensis Nocardia kroppenstedtii 100 Nocardia higoensis 40 Nocardia shimofusensis 18 Nocardia asiatica 35 Nocardia veterana 100 Nocardia aobensis 25 Nocardia casuarinae Nocardia africana 5710025 Nocardia elegans Nocardia vaccinii 20 Nocardia araoensis Streptomyces gardneri 15 Nocardia arthritidis 28 Nocardia amamiensis 3848 Nocardia pneumoniae Nocardia bhagyanarayanae 100 100 Rhodococcus soli Rhodococcus subtropicus 40 Smaragdicoccus niigatensis

Gordoniaceae 53 Gordonia alkanivorans 45 Gordonia westfalica 20 Gordonia namibiensis 20 Gordonia rubripertincta 28 Gordonia amicalis Gordonia desulfuricans 40 18 Gordonia paraffinivorans Gordonia hongkongensis 15 Gordonia lacunae 100 Gordonia terrae 25 Gordonia insulae 38 100 Gordonia sihwensis 48 Gordonia phthalatica 48 Gordonia hirsuta Gordonia malaquae 232550 Gordonia spumicola Gordonia amarae 65 Gordonia araii 65 Gordonia crocea Gordonia defluvii 2518 Gordonia effusa 43 Gordonia sputi 80 Gordonia aichiensis 100 25 Gordonia otitidis Gordonia jinhuaensis 25 Gordonia mangrovi 100 45 Gordonia bronchialis Gordonia polyisoprenivorans 48 Gordonia oryzae Gordonia soli 57 70 Williamsia limnetica 45 Williamsia muralis 18 Williamsia maris Williamsia spongiae 3348 Williamsia herbipolensis Williamsia sterculiae

Nocardiaceae~2_Mycobacteriales~1 Rhodococcus oryzae 53 Nocardia coeliaca 100 Rhodococcus erythropolis 100 Rhodococcus qingshengii 70 33 Nocardia globerula 23 Rhodococcus marinonascens Tsukamurella wratislaviensis 25 Rhodococcus olei 38 Rhodococcus canchipurensis 100 Rhodococcus pedocola 10 Rhodococcus rhodnii 23 Rhodococcus triatomae 13 Nocardia corynebacterioides 50 Antrihabitans stalactiti Millisia brevis 8 65 Rhodococcus biphenylivorans 100 Rhodococcus artemisiae Rhodococcus rhodochrous 57 Rhodococcus ruber 25 Rhodococcus phenolicus 38 Rhodococcus zopfii

Mycobacteriales+Pseudonocardiales+Actinopolysporales ~1_Pseudonocardiales~1 45 Amycolatopsis balhimycina 23 Amycolatopsis kentuckyensis 100 Amycolatopsis eburnea 43 Amycolatopsis rifamycinica 100 Amycolatopsis vancoresmycina 100 Amycolatopsis silviterrae Amycolatopsis benzoatilytica 100100 Amycolatopsis halotolerans 65 Amycolatopsis sulphurea Amycolatopsis jejuensis 25 Amycolatopsis nivea 57 50 Amycolatopsis alba 100 Amycolatopsis umgeniensis 100 Amycolatopsis keratiniphila Amycolatopsis decaplanina 23 Amycolatopsis azurea 7835 Amycolatopsis lurida Amycolatopsis oliviviridis 15 48 Amycolatopsis nigrescens Amycolatopsis minnesotensis 30 13 Amycolatopsis anabasis Amycolatopsis magusensis 100 Amycolatopsis marina 33 Amycolatopsis suaedae 33 Amycolatopsis dongchuanensis 20 Amycolatopsis acidiphila Amycolatopsis acidicola 3035 Haloechinothrix halophila 83 Amycolatopsis tucumanensis 100 Amycolatopsis methanolica Amycolatopsis ruanii 100 Amycolatopsis taiwanensis 55 90 Amycolatopsis alkalitolerans 100 Amycolatopsis pithecellobii 35 25 Saccharomonospora cyanea 48 Saccharomonospora xinjiangensis 48 Saccharomonospora piscinae 100 Saccharomonospora azurea 100 Saccharomonospora viridis 100 Saccharomonospora glauca 45 Saccharomonospora saliphila Saccharomonospora halophila 88 Saccharomonospora iraqiensis 25 100 Prauserella rugosa 43 Prauserella endophytica 80 Prauserella coralliicola 78 48 Prauserella flavalba 43 Prauserella marina 28 Prauserella oleivorans Prauserella soli 80 Thermocrispum agreste Thermocrispum municipale 100 Sciscionella marina 43 Pseudonocardiaceae_2+Actinopolysporaceae_Pseudonocardiales~2+Actinopolysporales 43 Actinopolyspora halophila 100 Actinopolyspora mortivallis Actinopolyspora salinaria 80 75 Actinopolyspora mzabensis 100 Salinifilum ghardaiensis 100 Salinifilum proteinilyticum Saccharopolyspora coralli 100 Saccharopolyspora maritima 28 Saccharopolyspora hordei 68100 48 Saccharopolyspora hirsuta 38 Saccharopolyspora hattusasensis 65 Saccharopolyspora spinosa Saccharopolyspora spongiae 3560 Saccharopolyspora halophila Saccharopolyspora cebuensis 38 Pseudonocardiaceae~3_Pseudonocardiales~3 100 Actinophytocola corallina Actinophytocola glycyrrhizae 48 93 Actinophytocola sediminis Actinophytocola xinjiangensis 100 Actinophytocola xanthii Herbihabitans rhizosphaerae Pseudonocardiaceae_Pseudonocardiales 40 Pseudonocardia asaccharolytica 100 Pseudonocardia acidicola 25 Pseudonocardia saturnea 15 Pseudonocardia xinjiangensis Pseudonocardia petroleophila 5 63 Pseudonocardia alaniniphila 43 Pseudonocardia yunnanensis 13 Pseudonocardia salamisensis Pseudonocardia aurantiaca 333 Pseudonocardia spinosispora 80 Pseudonocardia spinosa 100 Pseudonocardia cypriaca 100 40 Pseudonocardia hierapolitana 20 Pseudonocardia rhizophila 25 60 Pseudonocardia mongoliensis Pseudonocardia sediminis 38 Pseudonocardia profundimaris 68 Pseudonocardia dioxanivorans Pseudonocardia benzenivorans 100 Pseudonocardia hydrocarbonoxydans 43 25 Pseudonocardia sulfidoxydans 70 Pseudonocardia lutea 35 Pseudonocardia yuanmonensis 23 Pseudonocardia mangrovi 43 Pseudonocardia kujensis 53 Pseudonocardia halophobica 100 Pseudonocardia ailaonensis 100 Pseudonocardia xishanensis 40 Pseudonocardia kongjuensis 100 Pseudonocardia soli 100 Pseudonocardia autotrophica 20 100 Pseudonocardia carboxydivorans Pseudonocardia alni 75 Actinomycetospora chibensis Actinomycetospora rhizophila 90 45 Actinomycetospora atypica 78 Actinomycetospora chiangmaiensis 40 Kibdelosporangium aridum subsp. aridum 48 Kibdelosporangium phytohabitans Kibdelosporangium metalli 45 73 Kibdelosporangium philippinense Kibdelosporangium lantanae 100 Actinocrispum wychmicini

Pseudonocardiaceae~4_Pseudonocardiales~4 50 Actinokineospora diospyrosa Actinokineospora enzanensis 5583 Actinokineospora riparia 100 Actinokineospora spheciospongiae 60 Actinokineospora pegani 35 Actinokineospora acnipugnans Actinokineospora iranica

Pseudonocardiaceae~5_Pseudonocardiales~5 50 Lentzea soli 8 45 Lentzea terrae Lentzea guizhouensis 48 43 Lentzea jiangxiensis 30 Lentzea albidocapillata subsp. albidocapillata 100 Lentzea albidocapillata subsp. violacea 100 Lentzea waywayandensis 33 Lentzea pudingi 25 Lentzea cavernae 100 Lentzea aerocolonigenes 38 Lentzea rhizosphaerae 28 Lentzea flava 100 Lentzea nigeriaca Actinosynnema pretiosum subsp. auranticum 33 Actinosynnema mirum 100 Saccharothrix espanaensis 100 Saccharothrix variisporea 553 100 Saccharothrix violaceirubra Saccharothrix coeruleofusca 10063 Saccharothrix syringae Saccharothrix texasensis 38 Saccharothrix saharensis 23 Saccharothrix carnea Saccharothrix lopnurensis 10065 Saccharothrix deserti Saccharothrix ecbatanensis 25 53 Saccharothrix hoggarensis Actinorectispora metalli 10 Umezawaea endophytica

Pseudonocardiaceae~6_Pseudonocardiales~6 55 Allokutzneria albata 90 Allokutzneria multivorans Allokutzneria oryzae 43 Crossiella equi

100 Pseudonocardiaceae~7_Pseudonocardiales~7 93 Actinoalloteichus cyanogriseus 73 Actinoalloteichus spitiensis Actinoalloteichus hymeniacidonis 100 Goodfellowiella coeruleoviolacea

Pseudonocardiaceae~8_Pseudonocardiales~8 Kutzneria chonburiensis 80 Kutzneria albida

Micromonosporales+Glycomycetales Micromonosporaceae_Micromonosporales 8 Micromonospora soli 10 Micromonospora pallida 23 Micromonospora viridifaciens 100 Micromonospora costi Micromonospora rosaria 8 48 Micromonospora coriariae 100 Micromonospora endolithica Micromonospora chersina 13 100 Micromonospora citrea Micromonospora auratinigra Micromonospora narathiwatensis 13 Micromonospora yangpuensis 100 Plantactinospora endophytica 65 Plantactinospora sonchi 100 Plantactinospora veratri 10 Plantactinospora soyae 18 88 Plantactinospora solaniradicis Micromonospora zhanjiangensis Micromonospora avicenniae 53 Micromonospora azadirachtae 8 38 Micromonospora olivasterospora 25 Micromonospora pelagivivens 10 Micromonospora craterilacus 15 Micromonospora craniellae Micromonospora endophytica 100 13 Micromonospora radicis Verrucosispora sonchi 100 Micromonospora phaseoli 100 Salinispora pacifica 78 Salinispora goodfellowii Salinispora tropica 100 88 Salinispora arenicola Micromonospora deserti 100 Micromonospora parathelypteridis Micromonospora vulcania 35 Micromonospora arida 43 Micromonospora profundi 100 Micromonospora saelicesensis 45 Micromonospora chokoriensis 33 Micromonospora violae 3 20 Micromonospora inaquosa Micromonospora orduensis Micromonospora fulva 50 Micromonospora aurantiaca Micromonospora maritima 100 100 Micromonospora sediminis 33 Micromonospora globispora Micromonospora purpureochromogenes 100 Micromonospora palomenae Micromonospora coxensis 8 15 Micromonospora humi 20 Micromonospora carbonacea 10 Micromonospora krabiensis Micromonospora mangrovi 57 Micromonospora oryzae 100 Micromonospora harpali 45 13 Micromonospora haikouensis Micromonospora wenchangensis 100 Micromonospora matsumotoense Micromonospora schwarzwaldensis Actinoplanes rectilineatus 10 100 Actinoplanes lobatus Actinoplanes capillaceus 1045 Actinoplanes utahensis 57 Actinoplanes cyaneus 35 Actinoplanes regularis 13 Actinoplanes palleronii 100 20 Actinoplanes missouriensis Actinoplanes lutulentus 50 Actinoplanes octamycinicus 100 Actinoplanes teichomyceticus 100 88 Actinoplanes consettensis 10 Actinoplanes humidus 100 Actinoplanes friuliensis 100 Actinoplanes sediminis 100 Actinoplanes deccanensis 100 Actinoplanes abujensis Actinoplanes cibodasensis 100 13 Actinoplanes durhamensis 23 Actinoplanes rhizophilus 38 Actinoplanes deserti 33 Actinoplanes rishiriensis Mangrovihabitans endophyticus 18 Pseudosporangium ferrugineum 100 Krasilnikovia cinnamomea 5 25 Asanoa endophytica 30 Asanoa iriomotensis 100 Asanoa siamensis Asanoa ferruginea 848 Asanoa ishikariensis 25 25 Phytohabitans flavus Phytohabitans kaempferiae 18 Phytohabitans rumicis 848 Phytohabitans suffuscus 100 Catenuloplanes niger 3 Catenuloplanes castaneus 100 Catenuloplanes nepalensis 100 Dactylosporangium fulvum 100 Dactylosporangium roseum 45 Dactylosporangium solaniradicis 65 Dactylosporangium matsuzakiense Dactylosporangium vinaceum 80 70 Dactylosporangium salmoneum 30 Dactylosporangium maewongense 100 Dactylosporangium cerinum 33 Dactylosporangium aurantiacum Virgisporangium myanmarense 5 Catellatospora citrea subsp. citrea 13 Catellatospora paridis 15 Catellatospora vulcania 13 Catellatospora coxensis 45 25 Catellatospora citrea subsp. methionotrophica 40 Catellatospora chokoriensis 100 Catellatospora sichuanensis 48 Catellatospora bangladeshensis 23 Catellatospora tagetis 83 Catelliglobosispora koreensis 80 Allorhizocola rhizosphaerae 55 Hamadaea tsunoensis 100 Hamadaea flava Luedemannella flava 80 68 Luedemannella helvata 10015 Micromonospora pattaloongensis 100 Micromonospora ovatispora Micromonospora polyrhachis 88 20 Micromonospora sonneratiae Pilimelia anulata 100 Pilimelia columellifera subsp. columellifera 100 Micromonospora sediminimaris Micromonospora trujilloniae 100 Micromonospora gifhornensis Longispora urticae 78 Longispora albida

Glycomycetaceae_Glycomycetales 100 Glycomyces dulcitolivorans 68 Glycomyces artemisiae 53 Glycomyces albidus 57 Glycomyces paridis 100 78 Glycomyces lechevalierae 100 Glycomyces rutgersensis 100 Glycomyces algeriensis 85 78 Glycomyces rhizosphaerae Glycomyces harbinensis Glycomyces anabasis 100 57 Glycomyces arizonensis 63 Glycomyces tenuis 100 Glycomyces sediminimaris 55 Salininema proteolyticum 100 Salilacibacter albus 93 Stackebrandtia nassauensis 88 Stackebrandtia cavernae 23 85 Stackebrandtia albiflava 100 Stackebrandtia endophytica

30 Phytomonospora cypria 100 Phytomonospora endophytica Actinocatenispora sera

Jiangelliaceae_Jiangellales 53 Jiangella asiatica 100 Jiangella alba 68 Jiangella endophytica 60 Jiangella anatolica 60 Jiangella rhizosphaerae Jiangella aurantiaca 48 Jiangella ureilytica 80 88 Jiangella mangrovi 100 Phytoactinopolyspora endophytica 53 Phytoactinopolyspora halotolerans Phytoactinopolyspora alkaliphila 88 Phytoactinopolyspora mesophila

Propionibacteriales 53 Nocardioides simplex 48 Nocardioides aromaticivorans Nocardioides nitrophenolicus 100 Nocardioides kongjuensis 100 Nocardioides caeni Nocardioides vastitatis 100 Nocardioides albus 20 100 Nocardioides panzhihuensis 13 Nocardioides luteus Nocardioides agrisoli 43 23 Nocardioides ginkgobilobae 18 Nocardioides panacihumi 73 Nocardioides terrae 78 Nocardioides eburneiflavus 100 Nocardioides alpinus Nocardioides zhouii 18 33 Nocardioides flavus 100 Nocardioides cavernae Nocardioides seonyuensis 100 55 Nocardioides kandeliae Nocardioides rotundus 100 Nocardioides euryhalodurans Nocardioides allogilvus 40 Nocardioides gansuensis 10 Nocardioides panaciterrulae 20 Nocardioides intraradicalis Nocardioides soli 100 Nocardioides aquiterrae 80 Nocardioides pyridinolyticus 48 100 Nocardioides plantarum 100 Nocardioides dongxiaopingii 13 Nocardioides antarcticus 38 100 Nocardioides deserti 40 Nocardioides nanhaiensis 20 Nocardioides lianchengensis 23 Nocardioides kribbensis Nocardioides flavescens 100 Nocardioides daejeonensis 30 Nocardioides dubius 28 Nocardioides houyundeii 20 Nocardioides yefusunii 100 Nocardioides jishulii 35 Nocardioides jensenii 63 Nocardioides daedukensis Nocardioides massiliensis 18 35 Marmoricola pocheonensis 100 Marmoricola solisilvae 15 70 88 Marmoricola ginsengisoli 53 Marmoricola aurantiacus Nocardioides echinoideorum Nocardioides guangzhouensis 48 Nocardioides pakistanensis 38 Nocardioides speluncae 70 fastidiosum 25 Aeromicrobium endophyticum 63 Aeromicrobium chenweiae 100 60 Aeromicrobium yanjiei 45 Aeromicrobium ginsengisoli 100 Aeromicrobium panaciterrae 53 78 Aeromicrobium marinum 53 Aeromicrobium choanae Aeromicrobium camelliae Aeromicrobium massiliense 90 Mumia flava 100 Mumia zhuanghuii

Propionibacteriaceae 50 Acidipropionibacterium microaerophilum 100 Acidipropionibacterium virtanenii Cutibacterium granulosum 90 100 subsp. acnes 100 Cutibacterium acnes subsp. defendens 48 Cutibacterium modestum 65 Cutibacterium avidum 50 Propionibacterium acidifaciens 48 85 Propionibacterium cyclohexanicum 45 Propionimicrobium lymphophilum 33 78 Vaginimicrobium propionicum Arachnia rubra Tessaracoccus antarcticus 100 100 Tessaracoccus aquimaris 40 Tessaracoccus flavus 48 Tessaracoccus defluvii 80 Tessaracoccus flavescens 35 Tessaracoccus rhinocerotis 55 88 Tessaracoccus terricola Aestuariimicrobium soli 45 Auraticoccus cholistanensis 100 Auraticoccus monumenti 100 Mariniluteicoccus flavus 15 Mariniluteicoccus endophyticus 83 Desertihabitans aurantiacus 90 Desertihabitans brevis Propionicimonas paludicola 80 Naumannella cuiyingiana 45 Enemella evansiae Microlunatus speluncae 100 23 83 Microlunatus aurantiacus 18 Microlunatus phosphovorus 43 100 Microlunatus ginsengisoli Microlunatus soli 65 Microlunatus endophyticus 20 100 Microlunatus sagamiharensis Microlunatus antarcticus 45 100 Microlunatus spumicola Friedmanniella luteola

Kribbellaceae 18 Kribbella solani 18 Kribbella podocarpi 100 Kribbella speibonae Kribbella jejuensis 45 Kribbella jiaozuonensis 100 Kribbella soli 20 Kribbella mirabilis 25 Kribbella turkmenica 100 Kribbella capetownensis 48 10 Kribbella monticola 100 Kribbella catacumbae Kribbella qitaiheensis 13 Kribbella koreensis 60 Kribbella ginsengisoli 4833 Kribbella albertanoniae Kribbella antibiotica 4023 Kribbella yunnanensis 100 Kribbella sandramycini Kribbella italica 78 Kribbella flavida Kribbella deserti

Actinopolymorphaceae Actinopolymorpha singaporensis 100 Tenggerimyces flavus

Streptosporangiales Nonomuraea rhodomycinica 100 38 Nonomuraea bangladeshensis 100 Nonomuraea wenchangensis 23 Nonomuraea fuscirosea Nonomuraea jabiensis 53 Nonomuraea deserti 15 33 Nonomuraea diastatica 80 Nonomuraea longispora 8 Nonomuraea mesophila 80 Nonomuraea phyllanthi Nonomuraea nitratireducens 28 100 Nonomuraea maritima Nonomuraea jiangxiensis 35 Nonomuraea kuesteri 35 Nonomuraea harbinensis 33 Nonomuraea glycinis Nonomuraea guangzhouensis 100100 Nonomuraea cavernae Nonomuraea muscovyensis 100 28 Nonomuraea lactucae 33 Nonomuraea typhae 78 Nonomuraea endophytica 53 Nonomuraea soli 65 Nonomuraea thailandensis 23 Nonomuraea solani 43 Nonomuraea purpurea 63 Nonomuraea insulae Nonomuraea rhizophila Nonomuraea stahlianthi 63 Nonomuraea mangrovi 57 Microbispora camponoti 23 Microbispora bryophytorum 25 Microbispora fusca 45 100 Microbispora soli Microbispora hainanensis 60 48 Microbispora triticiradicis 35 55 Microbispora catharanthi 100 Sphaerimonospora thailandensis Planotetraspora thailandica Planotetraspora phitsanulokensis 60 57 Herbidospora galbida 100 Herbidospora yilanensis 60 Herbidospora daliensis 13 Herbidospora sakaeratensis 5057 Herbidospora soli Acrocarpospora corrugata 28 100 Sphaerisporangium rubeum 40 Sphaerisporangium aureirubrum 38 Sphaerisporangium rufum Sphaerisporangium dianthi 100100 Sphaerisporangium rhizosphaerae Sphaerisporangium melleum Thermostaphylospora chromogena 2023 Thermocatellispora tengchongensis 80 Thermocatellispora soli Streptosporangium canum 33 50 Streptosporangium fenghuangense Streptosporangium corydalis 68 Streptosporangium lutulentum 100 23 Streptosporangium amethystogenes subsp. fukuiense 100 18 Streptosporangium jiaoheense 100 Streptosporangium taraxaci 100 Streptosporangium nanhuense Streptosporangium shengliense 80 Streptosporangium anatoliense Streptosporangium algeriense 100 Streptosporangium terrae Sinosporangium album 100 Sinosporangium siamense

Thermomonosporaceae 100 Thermomonospora curvata Thermomonospora amylolytica 38 68 Thermomonospora cellulosilytica 30 Actinomadura sputi 70 Actinomadura adrarensis 100 Actinomadura livida Actinomadura jiaoheensis 100100 Actinomadura sporangiiformans 100 Actinomadura rubteroloni 5 100 Actinomadura geliboluensis 45 Actinomadura syzygii 5 Actinomadura glauciflava 68 Actinomadura lepetitiana 100 100 Actinomadura deserti Actinomadura rifamycini 33 25 Actinomadura roseirufa Actinomadura physcomitrii Actinomadura barringtoniae 50 Actinomadura montaniterrae 100 33 Actinomadura gamaensis 100 Actinomadura logoneensis 100 Actinomadura harenae 38 Actinomadura keratinilytica Actinomadura miaoliensis 100 70 35 Actinomadura viridilutea Actinomadura hibisca 50 Actinomadura macrotermitis Actinocorallia populi 100 Actinocorallia glomerata 100 Actinocorallia longicatena 33 75 Actinocorallia lasiicapitis 55 Actinoallomurus bryophytorum 35 Actinoallomurus yoronensis 33 Actinoallomurus radicium 100 Actinoallomurus amamiensis Actinoallomurus caesius 78 Actinoallomurus spadix 100 Actinoallomurus acanthiterrae

Nocardiopsaceae 30 100 Nocardiopsis valliformis 100 Nocardiopsis metallicus 63 Nocardiopsis ganjiahuensis 83 Nocardiopsis oceani 48 Nocardiopsis nanhaiensis 100 Nocardiopsis terrae 18 Nocardiopsis alba 100 Nocardiopsis sinuspersici 35 Nocardiopsis arvandica 18 Nocardiopsis algeriensis Nocardiopsis aegyptia 13 Nocardiopsis synnemataformans 10035 Nocardiopsis dassonvillei Nocardiopsis deserti 43 Nocardiopsis halotolerans 90 Nocardiopsis lucentensis 100 Nocardiopsis kunsanensis 50 Nocardiopsis xinjiangensis 73 Nocardiopsis rhizosphaerae 75 57 Nocardiopsis nikkonensis 50 Actinorugispora endophytica 35 Marinactinospora endophytica 45 Nocardiopsis ansamitocini 43 Nocardiopsis potens Nocardiopsis rosea 60 Nocardiopsis sediminis 100 Streptomonospora flavalba 100 Streptomonospora amylolytica 60 Streptomonospora salina 48 73 Streptomonospora algeriensis Streptomonospora sediminis 95 100 Streptomonospora tuzyakensis Streptomonospora nanhaiensis 43 100 Streptomonospora halotolerans Salinactinospora qingdaonensis Thermobifida cellulosilytica Thermobispora bispora 28 Trebonia kvetii

Streptomycetaceae_Streptomycetales 100 Streptomyces microflavus 100 Streptomyces fulvorobeus 8 Streptomyces chrysomallus subsp. chrysomallus Streptomyces anulatus Streptomyces globisporus subsp. globisporus Streptomyces parvus Streptomyces rubiginosohelvolus Streptomyces badius 100100 Streptomyces atroolivaceus 80 Streptomyces clavifer 10 Streptomyces finlayi Streptomyces candidus 18 10 Streptomyces fukangensis 1005 Kitasatospora albolonga 30 Streptomyces cavourensis subsp. cavourensis Streptomyces bacillaris 318 Streptomyces sundarbansensis Streptomyces nitrosporeus 38 Streptomyces lunaelactis Streptomyces spiroverticillatus Streptomyces gulbargensis Streptomyces showdoensis 2333 Streptomyces viridobrunneus 100100 Streptomyces laurentii 100 Streptomyces roseicoloratus 15 Streptomyces bikiniensis 100 Streptomyces cinereoruber subsp. cinereoruber 100 Streptomyces tritici 50 Streptomyces clavuligerus Streptomyces tsukubensis 1368 Streptomyces oryziradicis Streptomyces polygonati 18 3 Streptomyces sanyensis Streptomyces wedmorensis Streptomyces exfoliatus Streptomyces zaomyceticus 100 Streptomyces litmocidini Streptomyces venezuelae 65 Kitasatospora griseola Kitasatospora paracochleata 40 Kitasatospora setae 43 Kitasatospora cystarginea Kitasatospora mediocidica 55 Kitasatospora atroaurantiaca 38 75 Kitasatospora psammotica 23 Kitasatospora aureofaciens Kitasatospora putterlickiae 40 100 Kitasatospora herbaricolor 100 Kitasatospora indigofera 100 "Kitasatospora fumigata" Streptomyces purpureus 18 Streptomyces lactacystinicus 23 Kitasatospora azatica 48 Kitasatospora kifunensis 100 Streptacidiphilus neutrinimicus 30 70 Streptacidiphilus albus Streptacidiphilus carbonis 100 13 Streptacidiphilus monticola 100 Streptacidiphilus bronchialis Streptomyces paludis Streptomyces lushanensis 3 40 Streptomyces netropsis 18 Streptomyces stramineus 13 Streptomyces olivoverticillatus 100 15 Streptomyces eurocidicus 23 Streptomyces werraensis 8 Streptomyces gobitricini 35 Streptomyces zhihengii 10 Streptomyces formicae Streptomyces amakusaensis 60 Streptomyces inusitatus 100 Streptomyces atratus 53 Streptomyces sanglieri 50 Streptomyces gelaticus 13 Streptomyces pulveraceus Streptomyces peucetius 55 100 Streptomyces kurssanovii 68 Streptomyces michiganensis 30 Streptomyces xanthochromogenes Streptomyces mauvecolor 30 Streptomyces noboritoensis 55 Streptomyces helvaticus 100 Streptomyces chryseus Streptomyces altiplanensis 100 Streptomyces crystallinus 100 25 Streptomyces bottropensis 25 Streptomyces phaeochromogenes Streptomyces tauricus 57 Streptomyces rectiviolaceus 30 Streptomyces durmitorensis 5 28 Streptomyces kanamyceticus Streptomyces huasconensis 13 100 Streptomyces krungchingensis 28 Streptomyces siamensis 100 Streptomyces dengpaensis 20 10 Streptomyces arcticus Streptomyces seoulensis 63 Streptomyces similanensis Streptomyces phaeofaciens 13 Streptomyces cacaoi subsp. asoensis Streptomyces humidus Streptomyces capitiformicae Streptomyces ipomoeae 10 45 Streptomyces hygroscopicus subsp. ossamyceticus 28 Streptomyces torulosus 100 30 Streptomyces neyagawaensis 30 Streptomyces tailanensis 28 Streptomyces heilongjiangensis 18 Streptomyces diastatochromogenes 60 Streptomyces scabiei 5100 Streptomyces europaeiscabiei 28 Streptomyces deccanensis Streptomyces polymachus 10 100 Streptomyces lacrimifluminis Streptomyces turgidiscabies 25 Streptomyces geranii Streptomyces mirabilis 57 Streptomyces niveoruber 15 Streptomyces dangxiongensis 10 Streptomyces griseochromogenes 33 Streptomyces griseorubiginosus 3 Streptomyces cinnabarigriseus 28 Streptomyces canus 3 Streptomyces prunicolor 75 Streptomyces hokutonensis 100 Streptomyces adustus Streptomyces cavernae 3 Streptomyces flavovariabilis 100 100 Streptomyces blastmyceticus 30 Streptomyces cinnamoneus subsp. albosporus 8 Streptomyces orinoci 3 Streptomyces gamaensis 100 Streptomyces cinnamoneus subsp. cinnamoneus 100 Streptoverticillium cinnamoneum subsp. sparsum 3 Streptomyces mobaraensis Streptomyces rubrus 338 Streptomyces roseifaciens 50 Streptomyces morookaense 33 3 Streptomyces thioluteus Streptomyces luteireticuli 25 100 Streptomyces mashuensis Streptomyces varsoviensis Streptomyces cyaneus 3 Streptomyces acidiscabies 25 Streptomyces spongiae 100 Streptomyces smyrnaeus 15 Streptomyces cacaoi subsp. cacaoi 13 Streptomyces reniochalinae 20 Streptomyces qinglanensis Streptomyces diacarni 100 Streptomyces abyssalis 48 100 100 Streptomyces xishensis 100 Streptomyces glycovorans 28 Streptomyces karpasiensis 65 Streptomyces daqingensis 10025 Streptomyces haliclonae Streptomyces panacagri 13 Streptomyces armeniacus Streptomyces albiaxialis 68 Streptomyces iconiensis Streptomyces rubrisoli 100 Streptomyces lycii 100 8 Streptomyces tateyamensis 75 Streptomyces flaveus 38 Streptomyces vastus Streptomyces montanus 80 Streptomyces sporangiiformans 10020 Streptomyces resistomycificus Streptomyces alboniger 100 Streptomyces chartreusis 20 Streptomyces humiferus Streptomyces violaceolatus 100 Streptomyces coelescens Streptomyces violaceoruber 100 Streptomyces lienomycini 100 Streptomyces marokkonensis 100 Streptomyces ardesiacus Streptomyces tendae 13 Streptomyces tritolerans 55 Streptomyces fragilis 5 Streptomyces chilikensis 15 Streptomyces eurythermus 100 Streptomyces ambofaciens 100 Streptomyces paradoxus 15 Streptomyces misionensis 3 Streptomyces variabilis Streptomyces griseoloalbus Streptomyces scopiformis 50 Streptomyces fradiae 43 Streptomyces somaliensis 23 Streptomyces griseosporeus 5 Streptomyces glomeratus 50 Streptomyces harenosi 100 5 Streptomyces leeuwenhoekii 25 5 Streptomyces speibonae 5 Streptomyces lannensis Streptomyces chiangmaiensis 100 Streptomyces caeni Streptomyces thermovulgaris 5 8 Streptomyces bullii 33 Streptomyces thermocarboxydovorans Streptomyces bluensis 100 3 13 Streptomyces pluripotens Streptomyces chromofuscus 10 Streptomyces cinereospinus 543 Streptomyces coeruleofuscus Streptomyces rutgersensis 70 Streptomyces gougerotii 60 Streptomyces diastaticus subsp. diastaticus Streptomyces intermedius 60 Streptomyces alfalfae 10 Streptomyces silaceus 43 Streptomyces aureoverticillatus 100 Streptomyces lasiicapitis 33 Streptomyces variegatus 100 8 Streptomyces fulvissimus 30 15 Streptomyces flavofungini Streptomyces spectabilis 100 Streptomyces griseoaurantiacus Streptomyces xylanilyticus 45 Streptomyces coacervatus Streptomyces phyllanthi Streptomyces lincolnensis 18 Streptomyces antibioticus Streptomyces cyaneochromogenes 100 Streptomyces lasalocidi 555 Streptomyces galbus Streptomyces capoamus 4848 Streptomyces regensis Streptomyces cyslabdanicus 15 Streptomyces lydicus 13 Streptomyces inhibens 8 Streptomyces nigrescens Streptomyces sioyaensis Streptomyces hygroscopicus subsp. glebosus 100 Streptomyces libani subsp. rufus Streptomyces platensis 10015 Streptomyces kronopolitis 35 Streptomyces albulus 100 5 Streptomyces noursei 18 Streptomyces griseocarneus 38 Streptomyces catenulae Streptomyces misakiensis 30 Streptomyces ramulosus 5 10 Streptomyces niger 57 Streptomyces olivaceiscleroticus 73 Streptomyces ochraceiscleroticus 50 Streptomyces purpurogeneiscleroticus Streptomyces monomycini 13 Streptomyces rimosus Streptomyces sclerotialus 40 35 Streptomyces chrestomyceticus Streptomyces paromomycinus 50 Streptomyces albofaciens 5 Streptomyces hygroscopicus subsp. hygroscopicus 28 Streptomyces demainii Streptomyces samsunensis 65 Streptomyces solisilvae 30 Streptomyces yogyakartensis 100 Streptomyces violaceusniger 38 Streptomyces iranensis 100 Streptomyces melanosporofaciens Streptomyces geldanamycininus 100 Streptomyces asiaticus 28 10 Streptomyces rhizosphaericus Streptomyces cangkringensis 100 Streptomyces griseiniger Streptomyces amphotericinicus 45 Streptomyces violaceus 10 Streptomyces janthinus 8 Streptomyces jeddahensis Streptomyces cinerochromogenes 155 Streptomyces fabae Streptomyces violarus Streptomyces geysiriensis 15 25 Streptomyces andamanensis 8 Streptomyces aurantiogriseus 15 Streptomyces anandii Streptomyces brasiliensis 5 1540 Streptomyces thermodiastaticus 75 Streptomyces asterosporus Streptomyces aureorectus Streptomyces virens 55 Streptomyces calvus 100 Streptomyces graminearus 25 Streptomyces griseomycini 13 Streptomyces thermospinosisporus 15 Streptomyces prasinosporus 5 Streptomyces triticisoli 23 Streptomyces cellulosae 10 Streptomyces pseudogriseolus 30 Streptomyces afghaniensis 100 Streptomyces africanus 40 Streptomyces levis Streptomyces caelestis 28 100 Streptomyces fumanus Streptomyces atrovirens 10 Streptomyces koyangensis Streptomyces poonensis 100 Streptomyces fumigatiscleroticus 3 13 Streptomyces griseoviridis Streptomyces naganishii 10 Streptomyces spiralis 5 5 Streptomyces hebeiensis 30 Streptomyces triticagri Streptomyces kalpinensis 13 Streptomyces tacrolimicus 25 Streptomyces rhizophilus Streptomyces graminisoli 13 100 Streptomyces shenzhenensis 33 Streptomyces lanatus 18 Streptomyces cerasinus 18 Streptomyces niveiscabiei 100 Streptomyces panaciradicis 10 Streptomyces costaricanus 25 Streptomyces griseofuscus 100 Streptomyces murinus Streptomyces jiujiangensis 50 Streptomyces durhamensis Streptomyces filipinensis 100 Streptomyces puniciscabiei 5 5 Streptomyces subrutilus Streptomyces vinaceus 10048 Streptomyces cirratus 38 Streptomyces sporoverrucosus 68 Streptomyces goshikiensis Streptomyces virginiae Streptomyces amritsarensis 45 55 Streptomyces yangpuensis 100 50 Streptomyces flavotricini Streptomyces globosus 70 60 Streptomyces toxytricini Streptomyces katrae Streptomyces polychromogenes Streptomyces racemochromogenes 88 Streptomyces endophyticus Streptomyces fractus 100 Streptomyces cahuitamycinicus Streptomyces salilacus 60 88 Streptomyces capparidis 93 Streptomyces vitaminophilus 30 Streptomyces tyrosinilyticus 75 100 Streptomyces thermolineatus Streptomyces xinghaiensis 100 Streptomyces durbertensis 35 63 Streptomyces niveus Streptomyces camponoticapitis 15 100 Streptomyces fuscigenes 65 Streptomyces tremellae 18 Streptomyces avermitilis Streptomyces atriruber 10060 Streptomyces indicus 100 Streptomyces caldifontis 18 Streptomyces apocyni 100 Streptomyces yeochonensis 100 Streptomyces bryophytorum Streptomyces celluloflavus 100 68 Streptomyces kasugaensis 100 Streptomyces tirandamycinicus 100 Streptomyces youssoufiensis 28 Streptomyces zagrosensis 65 Streptomyces prasinus 100 Streptomyces boninensis Streptomyces coryli 68 Streptomyces smaragdinus 80 Streptomyces bohaiensis 90 Streptomyces lonarensis 38 Streptomyces otsuchiensis 100 Streptomyces lopnurensis Streptomyces alkaliphilus 73 10020 Streptomyces calidiresistens Streptomyces sodiiphilus 83 Streptomyces triticirhizae 30 Streptomyces zhaozhouensis 78 Streptomyces sediminis 100 Streptomyces hoynatensis 48 78 Streptomyces klenkii Streptomyces specialis 100 100 Streptomyces avicenniae Streptomyces harbinensis Yinghuangia aomiensis

Catenulisporaceae_Catenulisporales 100 Catenulispora acidiphila Catenulispora subtropica 100 Catenulispora fulva

Micrococcales+Bifidobacteriales 100 Microbacterium saccharophilum 18 Microbacterium awajiense 18 Microbacterium thalassium 28 Microbacterium kitamiense Microbacterium chocolatum 23 100 Microbacterium neimengense 25 Microbacterium telephonicum 10 Microbacterium hominis 100 Microbacterium yannicii 28 100 Microbacterium aureliae Microbacterium xylanilyticum 3 Microbacterium testaceum 8 Microbacterium oleivorans 38 Microbacterium invictum Microbacterium sediminis 13 100 Microbacterium wangchenii 68 Microbacterium foliorum Microbacterium phyllosphaerae 100 Microbacterium hydrocarbonoxydans Microbacterium profundi 100 33 Microbacterium keratanolyticum Microbacterium paraoxydans 100 35 Microbacterium deserti 65 Microbacterium lacusdiani 100 Microbacterium album 100 Microbacterium marinilacus 40 Microbacterium sediminicola 38 Microbacterium arborescens 80 Microbacterium imperiale 100 Microbacterium ulmi 65 Microbacterium mangrovi 100 Microbacterium faecale 100 Microbacterium suaedae 18 Microbacterium halotolerans 50 45 Microbacterium halophytorum Microbacterium agarici 53 43 Microbacterium protaetiae 100 Microbacterium pseudoresistens 60 Microbacterium bovistercoris 20 Microbacterium soli 25 Microbacterium esteraromaticum Mycetocola zhujimingii 50 Okibacterium fritillariae 50 Okibacterium endophyticum Agrococcus carbonis 100 Agrococcus jejuensis 60 Agrococcus terreus 38 Agromyces flavus 100 Agromyces marinus 40 Agromyces mediolanus 100 Agromyces protaetiae 100 57 Agromyces ulmi 20 Agromyces kandeliae Agromyces bauzanensis 25 Agromyces iriomotensis 23 100 Agromyces cerinus subsp. cerinus 28 Agromyces badenianii 23 100 Agromyces subbeticus Agromyces tardus 100 Agromyces humi Agromyces aureus Humibacter albus 8 50 Leifsonia naganoensis 10 73 20 Leifsonia lichenia Leifsonia poae 25 Schumannella luteola 100 Leifsonia rubra Salinibacterium hongtaonis 45 57 Agreia bicolorata 80 Agreia pratensis 8 Subtercola boreus 40 Leifsonia antarctica 10 Microterricola pindariensis 25 Leifsonia kafniensis Glaciibacter superstes 100 70 Herbiconiux flava 100 Herbiconiux solani Herbiconiux ginsengi 13 Lysinimonas yzui 100 Protaetiibacter intestinalis 100 Frondihabitans sucicola 100 Frigoribacterium faeni 65 Frigoribacterium endophyticum 8 Lacisediminihabitans profunda 100 Glaciihabitans tibetensis Glaciihabitans arcticus 3 Marisediminicola antarctica Clavibacter michiganensis subsp. phaseoli 100 100 Clavibacter tessellarius 40 Clavibacter michiganensis subsp. michiganensis 90 Clavibacter nebraskensis 100 33 Clavibacter sepedonicus 10 Clavibacter capsici 100 Planctomonas psychrotolerans Planctomonas deserti 30 Alpinimonas psychrophila Aurantimicrobium minutum 48 Klugiella xanthotipulae Cryobacterium flavum 100 100 Cryobacterium aureum Cryobacterium levicorallinum 100 Cryobacterium luteum 15 Cryobacterium psychrophilum 35 Cryobacterium melibiosiphilum Cryobacterium soli 90 Cryobacterium zongtaii 100 100 Amnibacterium kyonggiense 5 53 Amnibacterium endophyticum 55 Amnibacterium flavum 55 Labedella endophytica Labedella populi 20 73 100 Labedella phragmitis Cryobacterium tepidiphilum 73 38 Microcella alkaliphila 3 Microcella putealis 100 Yonghaparkia alkaliphila Pontimonas salivibrio 35 Huakuichenia soli Gulosibacter macacae Rathayibacter iranicus 100 Rathayibacter caricis 100 30 Rathayibacter tritici 43 Rathayibacter oskolensis 30 Rathayibacter toxicus Gryllotalpicola reticulitermitis 100 Gryllotalpicola protaetiae 25 Curtobacterium citreum Curtobacterium pusillum 100 Curtobacterium herbarum 100 Curtobacterium flaccumfaciens 70 Leucobacter chironomi 100 Leucobacter muris 100 Leucobacter zeae 50 Leucobacter weissii 15 Leucobacter komagatae 100 Leucobacter aridicollis Leucobacter iarius 100 Leucobacter exalbidus 25 Leucobacter luti 48 Leucobacter chromiireducens subsp. solipictus 68 Leucobacter chromiireducens subsp. chromiireducens

Bifidobacteriaceae_Bifidobacteriales 90 Bifidobacterium longum subsp. suillum Bifidobacterium longum subsp. infantis 25 20 Bifidobacterium imperatoris Bifidobacterium scaligerum 38 33 Bifidobacterium felsineum 40 43 Bifidobacterium cebidarum Bifidobacterium breve 23 Bifidobacterium samirii 75 Bifidobacterium pullorum subsp. gallinarum 13 Bifidobacterium pullorum subsp. saeculare 100 Bifidobacterium pullorum subsp. pullorum 10 Bifidobacterium tibiigranuli 100 Bifidobacterium subtile 100 Bifidobacterium animalis subsp. animalis 90 Bifidobacterium animalis subsp. lactis Bifidobacterium canis 8 63 83 Bifidobacterium anseris Bifidobacterium italicum 90 90 Bifidobacterium choerinum 83 100 Bifidobacterium castoris Bifidobacterium criceti Bifidobacterium globosum 98 Bifidobacterium pseudolongum subsp. pseudolongum 100 75 93 Bifidobacterium gallicum 33 Bifidobacterium dolichotidis Bifidobacterium cuniculi 48 Bifidobacterium magnum 70 Bifidobacterium indicum 48 Bifidobacterium asteroides 100 Bifidobacterium actinocoloniiforme Bifidobacterium minimum 10 98 Bifidobacterium porcinum Bifidobacterium thermacidophilum 100 Bifidobacterium boum 38 Bifidobacterium adolescentis 100 28 Bifidobacterium dentium Bifidobacterium catenulatum subsp. kashiwanohense 4890 Bifidobacterium angulatum 48 Bifidobacterium merycicum Bifidobacterium callitrichos 90 8 Bifidobacterium catenulatum subsp. catenulatum 78 Bifidobacterium pseudocatenulatum 10 100 Bifidobacterium leontopitheci 23 18 Bifidobacterium scardovii Bifidobacterium tsurumiense 38 33 Bifidobacterium parmae Bifidobacterium bifidum 18 100 Bifidobacterium goeldii 53 Gardnerella swidsinskii 100 Gardnerella leopoldii Gardnerella piotii 20 Bifidobacterium commune 73 Bifidobacterium bombi 100 100 Bifidobacterium callimiconis 43 Bifidobacterium vansinderenii 25 Bifidobacterium primatium Bifidobacterium catulorum 55 Bifidobacterium margollesii 50 Bifidobacterium tissieri Alloscardovia criceti 100 Parascardovia denticolens

Brevibacteriaceae 100 Brevibacterium antiquum 55 Brevibacterium sandarakinum Brevibacterium sanguinis 100 100 Brevibacterium oceani 35 Brevibacterium siliguriense 78 Brevibacterium sediminis 100 Brevibacterium profundi 100 Brevibacterium mcbrellneri 38 Brevibacterium otitidis Brevibacterium senegalense 73 100 Brevibacterium album Sediminivirga luteola

Micrococcaceae+Yaniellaceae 53 Pseudarthrobacter phenanthrenivorans Pseudarthrobacter oxydans 18 100 Pseudarthrobacter polychromogenes Pseudarthrobacter chlorophenolicus 100 Pseudarthrobacter equi 100 35 glacialis 88 Arthrobacter alpinus Arthrobacter stackebrandtii 70 43 Arthrobacter cryoconiti 8 Acaricomes phytoseiuli 100 Psychromicrobium lacuslunae 23 Paenarthrobacter ilicis Paenarthrobacter aurescens 5 Paenarthrobacter nitroguajacolicus 25 43 Arthrobacter cupressi Arthrobacter celericrescens 75 Arthrobacter silvisoli Arthrobacter globiformis 45 Arthrobacter pascens 3 Glutamicibacter arilaitensis 100 Glutamicibacter halophytocola 35 Glutamicibacter mysorens 40 Glutamicibacter endophyticus 73 Glutamicibacter ardleyensis 5 38 Glutamicibacter protophormiae Paeniglutamicibacter antarcticus 10 100 Paeniglutamicibacter psychrophenolicus Galactobacter valiniphilus 3 100 Arthrobacter nanjingensis 68 Arthrobacter woluwensis 100 Micrococcus terreus Citricoccus alkalitolerans 3 100 Citricoccus nitrophenolicus 8 Zhihengliuella halotolerans 80 Zhihengliuella flava 100 Arthrobacter agilis Arthrobacter zhaoguopingii 810 Arthrobacter ginkgonis 53 Arthrobacter paludis 100 Arthrobacter castelli 48 Arthrobacter monumenti 43 Arthrobacter yangruifuii 15 Arthrobacter luteolus 100 Arthrobacter crystallopoietes Arthrobacter roseus 68 Kocuria rhizophila 100 Kocuria varians Kocuria carniphila 70 63 Kocuria atrinae 45 Kocuria coralli 85 Kocuria subflava 38 Kocuria palustris 100 Rothia dentocariosa Rothia endophytica 85 Rothia nasimurium 68 Rothia koreensis 7357 Rothia halotolerans 75 Kocuria polaris 13 100 Kocuria rosea Kocuria dechangensis 38 Kocuria flava 80 Nesterenkonia pannonica 60 Nesterenkonia populi 83 Nesterenkonia alba Nesterenkonia alkaliphila 100 88 Nesterenkonia muleiensis 68 Nesterenkonia massiliensis 43 90 Nesterenkonia rhizosphaerae 73 Nesterenkonia sphaerica 93 Nesterenkonia salmonea Nesterenkonia halotolerans 70 100 Nesterenkonia lutea Yaniella halotolerans 100 Sinomonas humi 57 Sinomonas atrocyanea 90 Sinomonas notoginsengisoli 25 Sinomonas mesophila Arthrobacter mobilis 30 Dermabacteraceae 100 Brachybacterium vulturis 43 Brachybacterium avium 70 30 Brachybacterium faecium 100 Brachybacterium conglomeratum 10 100 Brachybacterium saurashtrense 43 Brachybacterium alimentarium 85 Brachybacterium tyrofermentans 100 Brachybacterium hainanense Brachybacterium rhamnosum 100 23 Brachybacterium nesterenkovii 33 Brachybacterium huguangmaarense 5 90 Brachybacterium endophyticum Devriesea agamarum

Demequinaceae 70 Demequina globuliformis 55 Demequina flava 53 Demequina sediminicola 100 Demequina salsinemoris Demequina aurantiaca 100 Demequina oxidasica 85 Demequina mangrovi 45 Demequina rhizosphaerae 43 88 Demequina soli 28 Demequina silvatica 100 45 Demequina iriomotensis 55 Demequina gelatinilytica Demequina subtropica 7530 Demequina maris Demequina phytophila

Intrasporangiaceae 100 Terrabacter carboxydivorans 38 Terrabacter lapilli 33 Terrabacter terrae 100 Terrabacter terrigena 43 Terrabacter tumescens 33 Intrasporangium flavum Pedococcus dokdonensis 13 100 Phycicoccus elongatus Phycicoccus duodecadis 55 33 Phycicoccus endophyticus 100 Oryzobacter terrae 68 Ornithinicoccus halotolerans 40 Ornithinicoccus hortensis Segeticoccus rhizosphaerae 40 90 Ornithinicoccus soli 100 Oryzihumus leptocrescens 33 Janibacter limosus 33 Janibacter indicus 15 100 Janibacter corallicola Janibacter anophelis 35 28 Janibacter hoylei Knoellia sinensis Kribbia dieselivorans

Dermacoccaceae 100 Barrientosiimonas humi 35 Demetria terragena 48 Flexivirga endophytica 100 Flexivirga alba 60 Calidifontibacter terrae 33 Dermacoccus profundi 100 Dermacoccus barathri 38 Dermatophilaceae 53 Arsenicicoccus bolidensis Austwickia chelonae 10045 Kineosphaera limosa Piscicoccus intestinalis 55 Mobilicoccus pelagius 80 Mobilicoccus caccae 18 Ornithinimicrobiaceae 100 Ornithinimicrobium humiphilum 43 Ornithinimicrobium cerasi 70 Ornithinimicrobium flavum Serinicoccus chungangensis 100 Serinicoccus profundi 40 Kytococcaceae Kytococcus sedentarius 98 Kytococcus schroeteri

Cellulomonadaceae 60 Cellulomonas telluris 100 Cellulomonas shaoxiangyii 5 30 Cellulomonas terrae Cellulomonas persica 100 33 Cellulomonas composti 33 Cellulomonas massiliensis 78 Cellulomonas fimi 30 Cellulomonas biazotea 100 Cellulomonas algicola 100 55 Cellulomonas endophytica Cellulomonas citrea 30 Cellulomonas aerilata Cellulomonas rhizosphaerae

20 Promicromonosporaceae Oerskovia paurometabola 60 Oerskovia turbata 48 Oerskovia jenensis Sediminihabitans luteus 57 73 Paraoerskovia marina Paraoerskovia sediminicola 23 Tropicihabitans flavus 5 Jonesiaceae 100 Sanguibacter keddieii 73 Sanguibacter inulinus 13 Flavimobilis marinus 100 Jonesia denitrificans Jonesia quinghaiensis 68 28 Timonella senegalensis Rarobacter faecitabidus Cellulomonadaceae~1 100 Cellulomonas bogoriensis 5 Actinotalea ferrariae 100 Pseudactinotalea suaedae

Actinomycetaceae_Actinomycetales 75 wuliandei 100 Actinomyces qiguomingii 98 65 55 90 Actinomyces massiliensis 13 Actinomyces johnsonii 100 Actinomyces naeslundii 33 68 75 Actinomyces oris Actinomyces urogenitalis 100 Actinomyces radicidentis Actinomyces vulturis 53 100 Schaalia odontolytica 100 Schaalia suimastitidis 65 Schaalia vaccimaxillae 100 Varibaculum cambriense 75 98 Mobiluncus holmesii Mobiluncus curtisii 100 Mobiluncus mulieris Actinomyces liubingyangii 80 85 haemolyticum 83 Arcanobacterium phocae 18 45 Arcanobacterium bovis 80 Actinotignum urinale 100 65 Arcanobacterium hippocoleae Fudania jinshanensis

Ruaniaceae_Micrococcales~1 Haloactinobacterium album 35 43 Ruania albidiflava

Beutenbergiaceae_Micrococcales~2 Serinibacter salmoneus 80 Beutenbergia cavernae

Promicromonosporaceae_Micrococcales~3 78 Promicromonospora kermanensis 100 Promicromonospora alba 100 Promicromonospora soli 100 Promicromonospora iranensis 35 Myceligenerans crystallogenes 100 Isoptericola variabilis 78 Isoptericola chiayiensis 1853 Isoptericola dokdonensis 85 Isoptericola jiangsuensis Isoptericola halalbus 1825 Xylanimonas cellulosilytica 80 Xylanimonas allomyrinae 100 Xylanimonas ulmi 13 Cellulosimicrobium marinum 20 Luteimicrobium album 40 33 Luteimicrobium xylanilyticum Luteimicrobium subarcticum

Bogoriellacae_Micrococcales~4 70 Georgenia soli 43 Georgenia muralis 45 Georgenia subflava Georgenia ruanii 6053 Georgenia yuyongxinii 60 Georgenia sediminis Aquipuribacter nitratireducens Kineosporiaceae_Kineosporiales 100 Kineosporia aurantiaca 100 Kineosporia mikuniensis 40 Kineosporia rhizophila Pseudokineococcus galaxeicola 78 Quadrisphaera oryzae 55 Kineococcus radiotolerans 30 43 65 Kineococcus mangrovi 75 Kineococcus gynurae 85 Kineococcus aureolus Kineococcus terrestris 75 28 45 Kineococcus gypseus Kineococcus glutinatus 15 Nakamuraceae_Nakamurales 55 Nakamurella flavida 53 Nakamurella flava Nakamurella multipartita 100 8 Nakamurella intestinalis Sporichthya polymorpha Cryptosporangiaceae_Cryptosporangiales Cryptosporangium aurantiacum Cryptosporangium eucalypti 100 Cryptosporangium phraense

Geodermatophilaceae_Geodermatophilales 63 Geodermatophilus nigrescens Geodermatophilus arenarius 18 100 Geodermatophilus saharensis 30 100 Geodermatophilus daqingensis Geodermatophilus tzadiensis 75 Geodermatophilus africanus Klenkia brasiliensis 100 Klenkia marina 88 65 Blastococcus saxobsidens Blastococcus deserti 60 Blastococcus aggregatus 43 Modestobacter marinus 28 28 Modestobacter roseus 35 Modestobacter italicus 100 Modestobacter altitudinis Modestobacter caceresii 23 Modestobacter lacusdianchii Cumulibacter manganitolerans

Frankiaceae_Frankiales 63 Frankia irregularis Frankia asymbiotica 55 85 Frankia inefficax 50 Frankia canadensis 65 Frankia casuarinae 50 Frankia alni 35 Frankia coriariae 28 Acidothermus cellulolyticus 23 Jatrophihabitantaceae_Jatrophihabitantales Jatrophihabitans endophyticus 100 Jatrophihabitans huperziae 65 Jatrophihabitans soli

Acidimicrobiales_Acidimicrobiia 100 Ilumatobacter coccineus 63 Ilumatobacter nonamiensis Acidimicrobium ferrooxidans 48 Egicoccus halophilus Coriobacteriia Eggerthellaceae+Coriobacteriaceae_Eggertellales+Coriobacteriales 35 Adlercreutzia equolifaciens subsp. equolifaciens Senegalimassilia faecalis 1848 Ellagibacter isourolithinifaciens 23 Slackia heliotrinireducens 60 35 Slackia piriformis Cryptobacterium curtum Eggerthella lenta

48 100 Coriobacteriaceae~1_Coriobacteriales~1 100 Collinsella aerofaciens 100 Collinsella intestinalis 100 Collinsella stercoris 100 Collinsella tanakaei Coriobacterium glomerans 85 Atopobiaceae_Coriobacteriales~2 100 Lancefieldella parvula 70 Lancefieldella rimae Fannyhessea vaginae 60 100 Parolsenella massiliensis 13 Parolsenella catena 100 Olsenella uli

Solirubribacterales Patulibacteeraceae 100 Patulibacter americanus 100 Patulibacter minatonensis Patulibacter medicamentivorans 100 Conexibacter woesei Rubrobacter xylanophilus Symbiobacterium thermophilum 100 Firmicutes~7 Clostridia~10 Syntrophomonadaceae_Eubacteriales~12 100 Syntrophomonas cellicola 100 Syntrophomonas wolfei subsp. saponavida 60 Syntrophomonas wolfei subsp. wolfei 100 Syntrophomonas erecta 45 Syntrophothermus lipocalidus

13 Moorella thermoacetica Thermoanaerobacteraceae~2_Thermoanaerobacterales~2 Carboxydothermus hydrogenoformans 78 Thermacetogenium phaeum 10 Sulfobacillus acidophilus Eubacteriales~13_Clostridia~11 55 65 Thermaerobacter nagasakiensis 73 Thermaerobacter subterraneus Thermaerobacter litoralis 100 Thermaerobacter marianensis

Chloroflexi 90 Pelolinea submarina 53 Caldilinea aerophila 100 Dehalogenimonas formicexedens Dehalogenimonas lykanthroporepellens 80 Tepidiforma bonchosmolovskayae Chloroflexia Chloroflexaceae_Cloroflexales 100 Chloroflexus aggregans Chloroflexus aurantiacus 33 100 Herpetosiphonaceae_Herpetosiphonales 100 Herpetosiphon aurantiacus Herpetosiphon gulosus 100 100 Herpetosiphon llansteffanensis

100 Thermomicrobia Thermomicrobium roseum 48 100 Sphaerobacter thermophilus

Ktedonobacteria Ktedonosporobacter rubrisoli 100 Ktedonobacter racemifer 5 Cyanophyceae_Cyanobacteria Nostocales 13 Aliinostoc morphoplasticum 38 Kryptousia microlepis 73 Fortiea necridiiformans 23 Nostoc neudorfense 60 Desmonostoc salinum Ancylothrix terrestris 18 Synechococcales Synechococcaceae 100 Prochlorococcus marinus subsp. pastoris Prochlorococcus marinus subsp. marinus 15 45 Prochlorothrix hollandica Loriellopsis cavernicola

Deinococci_Deinococcus−Thermus Deinococcaceae_Deinococcales 75 Deinococcus soli 100 Deinococcus saudiensis Deinococcus actinosclerus 53 80 Deinococcus arenae Deinococcus grandis 4343 Deinococcus radiotolerans 68 Deinococcus knuensis 100 Deinococcus seoulensis Deinococcus aquaticus 20 100 100 Deinococcus caeni 65 Deinococcus deserti 35 100 Deinococcus malanensis Deinococcus navajonensis 100 Deinococcus hohokamensis Deinococcus arcticus 100 90 Deinococcus multiflagellatus 100 Deinococcus gobiensis 23 Deinococcus petrolearius 25 Deinococcus puniceus 50 23 Deinococcus metalli Deinococcus saxicola 40 100 Deinococcus koreensis Deinococcus wulumuqiensis 100 Deinococcus geothermalis 45 57 Deinococcus aetherius Deinococcus carri 43 Deinococcus terrestris 100 Deinococcus maricopensis 53 Deinococcus radiomollis 88 Deinococcus proteolyticus 93 Deinococcus radiophilus Truepera radiovictrix Thermaceae_Thermales 100 Thermus amyloliquefaciens 55 Thermus caldifontis 68 Thermus caliditerrae 100 Thermus tengchongensis 43 Thermus thermamylovorans 100 100 Thermus islandicus 60 48 Thermus arciformis 55 Thermus aquaticus Thermus thermophilus 98 Thermus filiformis 40 Thermus oshimai 100 Marinithermus hydrothermalis Oceanithermus profundus 48 Meiothermus ruber 50 100 Meiothermus luteus 100 Meiothermus rufus 85 Meiothermus granaticius 100 Calidithermus timidus Meiothermus silvanus

Bacteroidetes Flavobacteriales_Flavobacteriia Flavobacteriaceae 40 Maribacter dokdonensis Maribacter arcticus 23 57 Maribacter aurantiacus 50 Maribacter algicola 38 Maribacter cobaltidurans 35 Maribacter thermophilus 70 Maribacter algarum 78 Maribacter polysiphoniae 40 Maribacter luteus 70 25 Maribacter maritimus Pricia antarctica Muriicola marianensis 100 Robiginitalea biformata 100 Muricauda hadalis 43 Muricauda amoyensis Muricauda alvinocaridis 100 63 88 Muricauda aquimarina 75 Muricauda ruestringensis 45 43 Muricauda marina Muricauda nanhaiensis 100 98 Croceitalea eckloniae 100 Croceitalea marina Flagellimonas algicola 100 100 Flagellimonas pacifica Pelagihabitans pacificus 30 Arenibacter aquaticus 65 Arenibacter antarcticus 53 Arenibacter nanhaiticus 55 100 Cellulophaga algicola Cellulophaga baltica 95 Cellulophaga tyrosinoxydans Cellulophaga lytica 90 Cellulophaga fucicola 100 Tenacibaculum discolor 100 Tenacibaculum gallaicum 98 Tenacibaculum aestuarii 100 Tenacibaculum ovolyticum Tenacibaculum todarodis 85 Polaribacter staleyi 18 100 100 Polaribacter irgensii 18 Polaribacter vadi Polaribacter marinaquae 40 18 Polaribacter dokdonensis 100 Polaribacter septentrionalilitoris 50 80 Polaribacter aquimarinus Tenacibaculum maritimum 15 Polaribacter huanghezhanensis 68 Polaribacter pacificus 28 100 Lutibacter citreus Lutibacter profundi 33 Urechidicola croceus 100 Wenyingzhuangia fucanilytica Flavicella sediminum 75 Winogradskyella psychrotolerans 100 Winogradskyella sediminis 43 Winogradskyella rapida 100 Winogradskyella crassostreae 28 Winogradskyella maritima 75 Winogradskyella exilis 43 Arcticiflavibacter luteus 40 Ichthyenterobacterium magnum 100 Hanstruepera crassostreae 73 Hanstruepera neustonica Bizionia argentinensis 48 Formosa maritima 55 Antarcticimonas flava 3 Mangrovimonas yunxiaonensis 100 100 10 Mangrovimonas spongiae 100 Gelidibacter sediminis Subsaxibacter arcticus 15 100 28 Subsaxibacter sediminis Xanthomarina gelatinilytica Formosa agariphila 5 100 Formosa algae 68 Formosa sediminum Bizionia berychis 25 Confluentibacter citreus Algibacter alginicilyticus 5 100 25 Algibacter pacificus Gelatiniphilus marinus 8 80 Oceanihabitans sediminis 50 Aestuariibaculum suncheonense Aquibacter zeaxanthinifaciens 15 Gaetbulibacter marinus 100 38 Wocania ichthyoenteri 100 Changchengzhania lutea 13 Algibacter psychrophilus Sabulilitoribacter arenilitoris 8 100 10038 Hyunsoonleella flava Marinivirga aestuarii 3 100 Arenitalea lutea 75 Lacinutrix cladophorae Lacinutrix iliipiscaria 28 Lacinutrix salivirga 38 13 Olleya algicola 100 Pontimicrobium aquaticum Flavivirga eckloniae Flavivirga rizhaonensis 48 Psychroserpens mesophilus Seonamhaeicola maritimus 100 18 Pseudofulvibacter marinus 100 Aquimarina atlantica 28 Aquimarina algiphila 48 Aquimarina aggregata 100 Aquimarina latercula 45 Aquimarina intermedia 48 Aquimarina hainanensis 100 Aquimarina penaei 38 Aquimarina agarilytica Dokdonia donghaensis 100 83 Dokdonia pacifica Kordia algicida 100 Kordia zhangzhouensis Patiriisocius marinistellae 100 Ulvibacter antarcticus Gramella salexigens 25 60 Gramella oceani Gramella flava 10 100 63 100 Gramella bathymodioli Gramella aestuarii 43 Gramella antarctica 40 Salegentibacter salarius 25 Haloflavibacter putidus 53 Salegentibacter chungangensis Zunongwangia profunda 100 35 Zunongwangia atlantica 100 Antarcticibacterium arcticum 35 Antarcticibacterium flavum 100 Salinimicrobium oceani 33 Salinimicrobium soli 20 88 Salinimicrobium catena Psychroflexus gondwanensis 15 30 Paramesonia marina 53 Leeuwenhoekiella aestuarii 100 Leeuwenhoekiella nanhaiensis Leeuwenhoekiella blandensis 33 28 Croceibacter atlanticus 100 Nonlabens dokdonensis 53 Nonlabens xylanidelens Nonlabens sediminis 80 38 Nonlabens spongiae Nonlabens halophilus 10 Nonlabens marinus 35 63 Aequorivita aquimaris 100 Aequorivita lutea 80 Aequorivita echinoideorum 83 Aequorivita soesokkakensis 55 Aequorivita sinensis Planktosalinus lacus 73 Capnocytophaga ochracea 65 35 Capnocytophaga haemolytica 100 Capnocytophaga granulosa 57 Coenonia anatina 43 Joostella marina Galbibacter marinus 68 100 Robertkochia solimangrovi Sinomicrobium soli 100 Sinomicrobium pectinilyticum Paucihalobacter ruber 45 Flavobacterium ustbae Flavobacterium zhairuonense 100 Flavobacterium sharifuzzamanii 10 Flavobacterium phragmitis 53 Flavobacterium tistrianum 15 Flavobacterium artemisiae 100 Flavobacterium johnsoniae subsp. johnsoniae 65 Flavobacterium notoginsengisoli Flavobacterium banpakuense 100 33 Flavobacterium chungbukense 23 Flavobacterium limi Flavobacterium pallidum 100 10 Flavobacterium magnum Flavobacterium flevense 33 Flavobacterium gilvum Flavobacterium commune 100 80 Flavobacterium palustre 3 Flavobacterium maotaiense 100 Flavobacterium ureilyticum Flavobacterium terriphilum 350 Flavobacterium ranwuense 100 Flavobacterium rhamnosiphilum 100 Flavobacterium laiguense 30 Flavobacterium succinicans 3 45 Flavobacterium fluviale Flavobacterium plurextorum 100 Flavobacterium tructae 100 Flavobacterium aquidurense Flavobacterium pectinovorum 5 Flavobacterium piscis 5 Flavobacterium hercynium 5 Flavobacterium cupreum 30 Flavobacterium circumlabens 73 Flavobacterium ovatum 3 100 Flavobacterium faecale 40 Flavobacterium frigidarium 30 8 Flavobacterium bomense 88 100 Flavobacterium caseinilyticum Flavobacterium limicola Flavobacterium reichenbachii 13 33 Flavobacterium olei Flavobacterium swingsii 100 33 Flavobacterium restrictum Flavobacterium fluvii 33100 Flavobacterium nackdongense Flavobacterium psychrotolerans 20 Flavobacterium antarcticum 100 Flavobacterium phocarum 13 Flavobacterium buctense 53 Flavobacterium aquatile Flavobacterium kingsejongi 100 100 Flavobacterium macacae 15 Flavobacterium ardleyense 5 28 Flavobacterium qiangtangense Flavobacterium supellecticarium Flavobacterium aurantiibacter Flavobacterium indicum 35 63 Flavobacterium aquimarinum 43 Flavobacterium jumunjinense Flavobacterium maris 8 1365 Flavobacterium luticocti 65 Flavobacterium tibetense 63 Flavobacterium enshiense 10 Flavobacterium humicola 48 Flavobacterium ichthyis 75 Flavobacterium lacus 100 Flavobacterium piscinae 28 Flavobacterium orientale 20 Flavobacterium stagni 23 28 Flavobacterium yanchengense Flavobacterium lutivivi 73 Flavobacterium subsaxonicum 40 Flavobacterium zepuense 20 Flavobacterium rivuli 100 Flavobacterium cerinum Flavobacterium hauense 3 13 Flavobacterium suzhouense 90 45 Flavobacterium beibuense Flavobacterium rakeshii 80 Flavobacterium alkalisoli 18 98 Flavobacterium salilacus subsp. salilacus 57 Flavobacterium salilacus subsp. altitudinum Flavobacterium arcticum 33 Flavobacterium suaedae 40 100 Flavobacterium naphthae 53 Myroides cloacae Myroides aquimaris 100 Flavobacterium tangerinum 63 60 Myroides odoratimimus subsp. odoratimimus Myroides profundi 100 Myroides odoratus

Weeksellaceae 100 Chryseobacterium takakiae 100 Chryseobacterium nepalense Chryseobacterium hispalense 20 100 Chryseobacterium shandongense 10 Chryseobacterium wanjuense 25 10 Chryseobacterium daeguense Chryseobacterium formosense 10 Chryseobacterium populi Chryseobacterium aquaticum subsp. greenlandense Chryseobacterium piperi 35100 Chryseobacterium glaciei 50 Chryseobacterium polytrichastri 100 Chryseobacterium lineare Chryseobacterium endophyticum 25 Chryseobacterium echinoideorum 38 28 Chryseobacterium taihuense 35 Chryseobacterium gleum 48 Chryseobacterium gallinarum Chryseobacterium oleae 38 75 Chryseobacterium kwangjuense Chryseobacterium culicis 57 Chryseobacterium aureum 13 70 23 Chryseobacterium ureilyticum Chryseobacterium aurantiacum 40 Chryseobacterium joostei 50 78 Epilithonimonas vandammei 100 Chryseobacterium hominis 35 Chryseobacterium bovis 813 Chryseobacterium pallidum Chryseobacterium caeni 85 Riemerella anatipestifer 48 Riemerella columbina 30 Cloacibacterium normanense 20 Amniculibacterium aquaticum Chryseobacterium lacus 100 80 Chryseobacterium salivictor 3 40 Kaistella daneshvariae 90 Chryseobacterium treverense Chryseobacterium montanum 23 100 Chryseobacterium marinum 100 Chryseobacterium humi 57 Chryseobacterium tenax Chryseobacterium halperniae 100 43 100 Chryseobacterium xixisoli Elizabethkingia anophelis subsp. anophelis 100 Faecalibacter macacae 93 Algoriella xinjiangensis 100 Weeksella virosa 100 Weeksella massiliensis Apibacter raozihei

Crocinitomicaceae 100 Fluviicola taffensis 75 Wandonia haliotis 100 Brumimicrobium mesophilum 100 Brumimicrobium salinarum Putridiphycobacter roseus 83 Vicingus serpentipes Cryomorphaceae Phaeocystidibacter luteus 100 Phaeocystidibacter marisrubri

Bacteroidales_Bacteroidia Bacteroidaceae+Prevotellaceae Prevotellaceae 45 Prevotella dentalis 38 Prevotella baroniae 83 Prevotella buccae 35 Prevotella bergensis 33 Prevotella multisaccharivorax 20 Prevotella oris 5 Prevotella albensis 25 Prevotella paludivivens Prevotella oulorum 23 Prevotella copri 5 43 Prevotella vespertina 38 Prevotella histicola 40 Prevotella jejuni 38 Prevotella scopos 100 Prevotella fusca 25 Prevotella multiformis 65 Prevotella nigrescens 65 Prevotella pallens 93 Prevotella disiens Prevotella brunnea 98 35 Prevotella corporis Prevotella bivia 100 75 Prevotella amnii 100 Prevotella loescheii 48 Prevotella shahii 70 Prevotella saccharolytica 48 Prevotella marshii 100 65 Prevotella oralis 75 Prevotella buccalis 90 Prevotella timonensis 65 Prevotella nanceiensis 70 Prevotella micans Paraprevotella xylaniphila

53 Bacteroidaceae~1 Phocaeicola salanitronis 100 Bacteroides gallinaceum

45 Bacteroides helcogenes Bacteroidaceae~2 100 Phocaeicola vulgatus 73 Phocaeicola sartorii 38 Phocaeicola paurosaccharolyticus 100 Phocaeicola coprocola 100 Phocaeicola plebeius 50 Bacteroides zoogleoformans Bacteroidaceae~3 45 Bacteroides rodentium 50 Bacteroides uniformis 55 100 Bacteroides fluxus Bacteroidaceae~4 Bacteroides stercoris 43 50 Bacteroides eggerthii

Bacteroidaceae~5 53 Bacteroides intestinalis Bacteroides cellulosilyticus 18 90 Bacteroides oleiciplenus 57 Bacteroides stercorirosoris

Bacteroidaceae~6 35 Bacteroides pyogenes 35 Bacteroides faecis 25 Bacteroides caecimuris 50 Bacteroides acidifaciens 35 40 Bacteroides caccae Bacteroides faecichinchillae Bacteroidaceae 48 Bacteroides fragilis 40 Bacteroides salyersiae 100 70 Bacteroides nordii Bacteroides graminisolvens Bacteroides coprosuis

18 Dysgonomonadaceae 50 Dysgonomonas gadei 85 Dysgonomonas hofstadii 98 Dysgonomonas mossii Dysgonomonas capnocytophagoides 30 Paludibacter propionicigenes Porphyromonadaceae 100 Porphyromonas circumdentaria 90 Porphyromonas gingivicanis 20 35 Porphyromonas asaccharolytica 100 Porphyromonas uenonis 40 Porphyromonas macacae 80 Porphyromonas bennonis Porphyromonas levii 100 100 100 Porphyromonas somerae Porphyromonas cangingivalis 63 Porphyromonas crevioricanis 80 Porphyromonas gulae Tannerella forsythia 53 Tannerellaceae 20 98 Parabacteroides distasonis Parabacteroides johnsonii 50100 Parabacteroides merdae Parabacteroides goldsteinii 100 98 Parabacteroides chongii Macellibacteroides fermentans Muribaculaceae 85 Duncaniella dubosii 100 Duncaniella freteri Muribaculum gordoncarteri 28 100 Barnesiella viscericola Odoribacter splanchnicus 38 Marinilabiliaceae 83 Alkaliflexus imshenetskii Alkalitalea saponilacus 60 23 Anaerophaga thermohalophila

Marinilabiliaceae~1 Carboxylicivirga sediminis 70 Labilibacter sediminis

100 Prolixibacteraceae 45 88 Puteibacter caeruleilacunae Maribellus luteus 100 Draconibacterium sediminis 100 100 Draconibacterium orientale 57 Marinifilaceae Ancylomarina longa 100 Marinifilum breve

Rikenellaceae 55 Alistipes onderdonkii subsp. onderdonkii 100 Alistipes finegoldii 83 Alistipes shahii 100 Alistipes putredinis 48 Alistipes communis 93 Alistipes inops 60 Alistipes indistinctus 100 Alistipes ihumii 100 Mucinivorans hirudinis Rikenella microfusus

Sphingobacteriaceae_Sphingobacteriales_Sphingobacteriia 45 Pedobacter polaris 78 Pedobacter cryotolerans 100 Pedobacter frigiditerrae 100 Pedobacter nanyangensis 100 Pedobacter chitinilyticus 100 Pedobacter xixiisoli 100 Pedobacter rhizosphaerae 100 Pedobacter changchengzhani 100 Pedobacter frigidisoli 30 Pedobacter agri Pedobacter soli 43 Pedobacter zeae 40 Pedobacter lusitanus 57 Pedobacter cryoconitis 100 100 Pedobacter hartonius 53 43 Pedobacter westerhofensis Pedobacter antarcticus 57 Pedobacter duraquae 100 68 Pedobacter steynii 100 Pedobacter metabolipauper Pedobacter heparinus 100100 Pedobacter africanus Pedobacter frigoris Pedobacter yulinensis 100 Mucilaginibacter pineti 53 Mucilaginibacter pocheonensis Mucilaginibacter gynuensis 13100 Mucilaginibacter mallensis 23 100 Mucilaginibacter pedocola 38 Mucilaginibacter terrenus 23 Mucilaginibacter xinganensis 28 Mucilaginibacter terrigena 100 Mucilaginibacter ginsengisoli 100 Mucilaginibacter paludis 100 Mucilaginibacter oryzae 100 28 Mucilaginibacter jinjuensis 100 Mucilaginibacter polytrichastri Pararcticibacter amylolyticus 23 100 73 Daejeonella rubra Daejeonella oryzae 57 Pedobacter mongoliensis 100 63 Sphingobacterium detergens 35 Sphingobacterium tabacisoli 100 Sphingobacterium spiritivorum Sphingobacterium cavernae 43 100 Sphingobacterium psychroaquaticum 100 Sphingobacterium cellulitidis 50 Sphingobacterium mizutaii Sphingobacterium griseoflavum 88 25 Sphingobacterium alkalisoli 100 Sphingobacterium olei 100 55 Parapedobacter defluvii 55 Parapedobacter lycopersici 100 Sphingobacterium chuzhouense 100 Sphingobacterium terrae Albibacterium bauzanense 25 100 Pedobacter indicus 100 Pedobacter alpinus Pedobacter cryophilus 100 Pedobacter psychrophilus Solitalea longa

Chitinophagaceae_Chitinophagales_Chitinophagia 100 Terrimonas soli 10 Terrimonas ferruginea 10 Parasegetibacter terrae 18 Niastella caeni Paraflavitalea soli 100 100 Sediminibacterium roseum 38 Hydrotalea sandarakina Agriterribacter humi 13 88 Filimonas lacunae 13 Filimonas effusa 100 Arvibacter aurantiibacter 75 Deminuibacter soli 40 18 Flavisolibacter tropicus 23 Paracnuella aquatica Niveitalea solisilvae 20 100 Ferruginibacter alkalilentus Segetibacter koreensis Niabella aurantiaca 80 Niabella ginsenosidivorans 78 Chitinophaga pinensis 40 Chitinophaga ginsengisoli 70 Chitinophaga silvisoli 55 Chitinophaga tropicalis 30 48 Chitinophaga parva 100 Chitinophaga alhagiae 23 Chitinophaga lutea 60 Chitinophaga rhizosphaerae 33 100 Chitinophaga deserti 90 Chitinophaga sedimenti Chitinophaga caeni 68 100 Chitinophaga eiseniae 100 Chitinophaga flava 100 Chitinophaga dinghuensis 65 Chitinophaga ginsengisegetis Haoranjiania flava 100 Taibaiella chishuiensis Taibaiella helva 60 88 Flavipsychrobacter stenotrophus

Lewinellaceae_Saprospirales_Saprospiria Lewinella lacunae 100 Phaeodactylibacter luteus 100 Phaeodactylibacter xiamenensis 85 Haliscomenobacter hydrossis

Cytophagales_Cytophagia Spirosomaceae 38 Spirosoma radiotolerans 50 Spirosoma pollinicola 100 Spirosoma fluviale 83 Spirosoma linguale 100 Spirosoma aerophilum 43 Spirosoma litoris 63 Spirosoma arboris 38 Spirosoma telluris 53 Spirosoma luteum 100 Spirosoma spitsbergense 35 100 Spirosoma panaciterrae 100 48 Spirosoma aerolatum Spirosoma koreense 100 Spirosoma luteolum 100 Spirosoma carri 100 Spirosoma lacussanchae 100 Rudanella lutea 95 Arsenicibacter rosenii Larkinella harenae 63 65 Dyadobacter psychrophilus 100 Dyadobacter sediminis Dyadobacter jiangsuensis 55 100 100 Dyadobacter bucti Runella aurantiaca 100 Runella slithyformis Emticicia oligotrophica 100 100 Jiulongibacter sediminis 90 Lacihabitans lacunae Flectobacillus major

100 Cytophagaceae 43 Aquirufa rosea 100 Sandaracinomonas limnophila

Fulvivirgaceae 40 100 Chryseolinea flava Chryseolinea serpens 100 Chryseotalea sanaruensis 25 Cesiribacter andamanensis 38 Roseivirga seohaensis subsp. aquiponti 18 Reichenbachiella versicolor 13 Nafulsella turpanensis Marivirga tractuosa 20 Reichenbachiellaceae Marinoscillum furvescens 100 Marinoscillum pacificum

Cyclobacteriaceae Algoriphagus locisalis 70 Algoriphagus antarcticus 100 Algoriphagus aquimarinus 100 20 Algoriphagus resistens 100 Algoriphagus marinus 100 Algoriphagus litoralis 100 Algoriphagus aquatilis 50 Algoriphagus sanaruensis 63 Algoriphagus lacus 100 Algoriphagus taiwanensis 100 Algoriphagus formosus Algoriphagus marincola 40 Algoriphagus kandeliae 100 Cyclobacterium lianum 85 Cyclobacterium plantarum 40 Cyclobacterium qasimii 73 100 Cyclobacterium marinum 100 35 Echinicola rosea 100 Belliella aquatica Belliella marina 100 43 Nitritalea halalkaliphila 85 Cecembia rubra 83 Cecembia calidifontis 100 100 Fontibacter ferrireducens 45 98 Cecembia lonarensis Mongoliibacter ruber Lunatimonas lonarensis 48 Aquiflexum aquatile Flexithrix dorotheae Hymenobacteraceae 83 Hymenobacter latericoloratus 43 Hymenobacter luteus 30 Hymenobacter sediminis 100 Hymenobacter aquatilis 30 Hymenobacter pallidus Hymenobacter seoulensis 100 90 Hymenobacter fodinae 48 Hymenobacter gelipurpurascens Hymenobacter mucosus 38 60 Hymenobacter perfusus 100 Hymenobacter humicola 90 Hymenobacter psychrophilus Hymenobacter amundsenii 35 55 Hymenobacter rutilus 93 63 Hymenobacter defluvii 98 Hymenobacter profundi 73 Hymenobacter aquaticus Hymenobacter chitinivorans 55 Hymenobacter metallicola 100 Hymenobacter roseosalivarius 53 Hymenobacter cavernae 90 98 Hymenobacter daeguensis 100 Hymenobacter soli 100 Hymenobacter monticola Hymenobacter glacialis 57 100 Hymenobacter lapidarius 85 Hymenobacter sedentarius 100 Hymenobacter humi 70 100 Hymenobacter coccineus 78 Hymenobacter polaris 90 100 Hymenobacter flocculans 93 Hymenobacter setariae 100 Hymenobacter ginkgonis Hymenobacter bucti Adhaeribacter terrae 43 57 83 Adhaeribacter terreus Pontibacter roseus 95 Edaphorhabdus rosea 53 100 Pontibacter chitinilyticus 35 Pontibacter silvestris 100 18 Pontibacter arcticus Pontibacter terrae 93 Pontibacter aydingkolensis 57 80 Pontibacter brevis Rufibacter latericius 90 Rufibacter ruber 98 Rufibacter roseus Adhaeribacter aerolatus 93 Adhaeribacter rhizoryzae 68

Balneolaceae_Balneolales_Balneolia_Balneolaeota 100 Gracilimonas tropica 75 Gracilimonas amylolytica Balneola vulgaris 100 Rhodohalobacter barkolensis

Rhodothermales_Rhodothermia_Rhodothermaeota Salinibacteraceae 90 Longimonas haloalkaliphila 100 Salisaeta longa 100 Salinibacter ruber 30 Roseithermus sacchariphilus 98 Rhodobthermaceae Rhodothermus marinus 98 Rhodothermus profundi

Chlorobiaceae_Chlorobiales_Chlorobia_Chlorobi 100 Chlorobium phaeobacteroides Chlorobium limicola 100 Chlorobaculum tepidum Gemmatimonas phototrophica 28 Fibrobacter succinogenes subsp. succinogenes Clostridia~12_Firmicutes~8 Thermoanaerobacteraceae~1_Thermoanaerobacterales~3 45 Thermoanaerobacter wiegelii 73 Thermoanaerobacter siderophilus Thermoanaerobacter ethanolicus 75 60 Thermoanaerobacter acetoethylicus 100 Thermoanaerobacter brockii subsp. finnii 63 Thermoanaerobacter pseudethanolicus 57 90 Thermoanaerobacter kivui Thermoanaerobacter sulfurigignens 100 Thermoanaerobacter italicus 100 Thermoanaerobacter mathranii subsp. mathranii Caldanaerobacter subterraneus subsp. pacificus 53 Caldanaerobacter subterraneus subsp. tengcongensis 30 Thermosediminibacteraceae_Thermosediminibacterales 100 Thermosediminibacter oceani Fervidicola ferrireducens

20 Thermoanaerobacteraceae_Thermoanaerobacterales Ammonifex degensii 100 Desulfothermobacter acidiphilus

100 Thermoanaerobacterales~4_Clostridia~13_Firmicutes~9 100 Caldicellulosiruptor kristjanssonii 33 Caldicellulosiruptor lactoaceticus 33 Caldicellulosiruptor owensensis 75 Caldicellulosiruptor kronotskyensis 100 Caldicellulosiruptor hydrothermalis Caldicellulosiruptor saccharolyticus

38 Dictyoglomaceae_Dictyoglomales_Dictyoglomia_Dictyoglomi Dictyoglomus thermophilum 100 Dictyoglomus turgidum

Spirochaetia_Spirochaetes Spirochaetales Borreliaceae Borrelia burgdorferi Borrelia sinica 35 Borrelia lusitaniae 100 Borrelia maritima 53 Borrelia afzelii 100 Borrelia spielmanii 100 100 Borrelia valaisiana Borrelia mayonii 38 Borrelia coriaceae 88 Borrelia turcica 100 Spirochaeta aurantia subsp. aurantia Spirochaetaceae Oceanispirochaeta litoralis 100 Spirochaeta isovalerica 40 Sphaerochaeta halotolerans 60 Spirochaetaceae~1 Sediminispirochaeta bajacaliforniensis 100 38 Sediminispirochaeta smaragdinae Spirochaeta thermophila 85 Treponemataceae 100 Treponema socranskii subsp. paredis 60 Treponema succinifaciens Treponema brennaborense 48 70 Treponema maltophilum 98 Treponema denticola 57 Treponema phagedenis 65 Treponema medium 100 55 Treponema zuelzerae Treponema stenostreptum

Brachyspiraceae_Brachyspirales 100 Brachyspira murdochii 100 Brachyspira hyodysenteriae Brachyspira intermedia 100 Brachyspira pilosicoli

Leptospiraceae_Leptospirales 100 Leptospira interrogans 33 Leptospira kirschneri 45 Leptospira noguchii Leptospira santarosai 35 Leptospira tipperaryensis 10063 Leptospira stimsonii 100 Leptospira adleri 100 Leptospira gomenensis Leptospira barantonii 83 50 Leptospira dzianensis Leptospira yasudae 20 Leptospira ellisii Leptospira langatensis 78 Leptospira sarikeiensis Leptospira semungkisensis 100 Leptospira haakeii Leptospira selangorensis Leptospira neocaledonica 100 Leptospira saintgironsiae 100 Leptospira koniambonensis Leptospira hartskeerlii 100 Leptospira andrefontaineae Leptospira venezuelensis 78 Leptospira dzoumogneensis Leptospira fainei 100 70 Leptospira fletcheri Leptospira perolatii Leptospira bandrabouensis 100 45 Leptospira bouyouniensis 100 Leptospira kemamanensis 100 Leptospira harrisiae Leptospira montravelensis Leptospira jelokensis Leptospira mtsangambouensis Leptospira congkakensis 30 Leptospira noumeaensis 60 Leptospira bourretii 100 Leptospira brenneri 60 Leptospira perdikensis Leptospira biflexa Leptospira ognonensis 100 Leptospira ilyithenensis 90 Leptospira kobayashii

Thermotogae Thermotogales Fervidobacteraceae 100 Fervidobacterium riparium Fervidobacterium pennivorans

Thermotogaceae 85 98 Thermotoga maritima 55 Thermotoga neapolitana 90 Thermotoga petrophila Thermotoga naphthophila Pseudothermotoga subterranea 88 100 Pseudothermotoga lettingae 100 100 Pseudothermotoga elfii Thermotoga profunda 100 Thermotoga caldifontis 57 Pseudothermotoga thermarum

38 Petrotoga mobilis

70 Kosmotogaceae_Kosmotogales Kosmotoga pacifica 100 Kosmotoga olearia

Coprothermobacter proteolyticus 20 Synergistaceae_Synergistales_Synergistia_Synergistetes 50 Dethiosulfovibrio peptidovorans 78 Aminobacterium colombiense 80 Thermanaerovibrio velox 100 Thermanaerovibrio acidaminovorans 48 Thermovirga lienii 20 Acetomicrobium flavidum exile Aquificales_Aquificea Aquificaceae 90 Thermocrinis albus 48 Thermocrinis ruber 48 Hydrogenobacter subterraneus 100 Thermocrinis minervae Hydrogenobacter thermophilus 100 Hydrogenothermaceae 100 Sulfurihydrogenibium kristjanssonii Sulfurihydrogenibium yellowstonense 100 68 Persephonella hydrogeniphila Desulfobacteriaceae Thermovibrio ammonificans 100 Desulfurobacterium thermolithotrophum

Archaea Euryarchaeota Halobacteria Haloferacales Halorubraceae 50 Halorubrum trapanicum 48 Halorubrum xinjiangense Halorubrum coriense Halorubrum ezzemoulense 68 Halorubrum californiense 45 Halorubrum sodomense 75 Halorubrum tebenquichense 40 53 Halorubrum ejinorense Halorubrum distributum Halorubrum pallidum Halorubrum saccharovorum 25 Halorubrum amylolyticum Halorubrum lipolyticum 2325 Halorubrum halophilum 23 Halorubrum aidingense 60 Halorubrum kocurii 30 Halorubrum lacusprofundi 43 Halorubrum salsamenti Halorubrum orientale 28 80 Halorubrum trueperi 60 Halorubrum rubrum 100 Halorubrum aethiopicum 28 Halorubrum cibi 7350 Halorubrum glutamatedens 48 Halorubrum aquaticum 80 Halorubrum vacuolatum Halorubrum luteum 100 Halorubrum gandharaense Haloparvum alkalitolerans

25 Haloferaceae~1 30 Haloplanus natans 38 Haloplanus rubicundus 100 Haloplanus vescus Haloplanus aerogenes 100 100 Haloplanus rallus Haloplanus salinarum 68 43 Haloplanus litoreus

Haloferacaceae~2 100 Halogranum rubrum 100 Halogranum amylolyticum 18 Halogranum gelatinilyticum Haloprofundus halophilus 33 28 Halegenticoccus soli Halobium salinum Haloferacaceae Haloferax volcanii 28 Haloferax prahovense 33 Haloferax gibbonsii 100 Haloferax lucentense 33 43 Haloferax denitrificans 70 Haloferax sulfurifontis 100 Haloferax mediterranei 73 Haloferax mucosum Haloferax elongans 100 Haloferax larsenii 78 Halobellus litoreus 65 Halobellus rufus 60 90 Halobellus captivus 90 Halobellus ramosii Halobellus clavatus 63 55 Halobellus limi 80 Halogeometricum borinquense 83 Halogeometricum rufum 40 Halogeometricum pallidum 93 55 Halogeometricum limi 25 57 Halopelagius fulvigenes Halopelagius longus 100 Halopelagius inordinatus 53 Halolamina rubra 73 Halolamina salina 95 Halolamina sediminis 100 Halolamina pelagica 23 Halolamina salifodinae 100 Halonotius pteroides 100 Halohasta litorea

Halorubraceae Halobaculum gomorrense 100 Halobaculum roseum

Salinirubrum litoreum Natrialbaceae_Natrialbales 33 Haloterrigena jeotgali 100 Haloterrigena thermotolerans Haloterrigena mahii 100 25 Haloterrigena saccharevitans 70 Natrinema pallidum 90 Natrinema altunense 25 Natrinema gari 48 Natrinema versiforme 18 Haloterrigena turkmenica 70 Haloterrigena salina 80 Haloterrigena salifodinae Haloterrigena limicola 68 Haloterrigena hispanica 90 Haloterrigena longa 43 Natrinema ejinorense 63 Natrinema salaciae Natrinema soli 40 78 Halostagnicola larsenii Halostagnicola kamekurae 100 Halostagnicola alkaliphila 0.10 83 Natrialba magadii 100 65 23 Natrialba hulunbeirensis 40 Natrialba chahannaoensis Natronorubrum tibetense 10 70 Natrialba aegyptia 45 Natrialba taiwanensis Natrialba asiatica 18 10 Natrialba swarupiae 60 Natronorubrum sulfidifaciens 33 Natronorubrum halophilum 33 Natronorubrum sediminis 48 8 Natronococcus roseus 33 100 Haloterrigena daqingensis Natronorubrum bangense Natrarchaeobius halalkaliphilus 100 Halopiger aswanensis 60 Halopiger thermotolerans 100 Halopiger djelfimassiliensis 45 Halopiger salifodinae 10 Natronolimnohabitans innermongolicus 65 Natrarchaeobaculum sulfurireducens 78 Natrarchaeobaculum aegyptiacum 100 Natronococcus jeotgali 40 Natronococcus occultus 33 Halovivax asiaticus 100 Halovivax ruber 10 100 Halobiforma lacisalsi 90 Halobiforma haloterrestris Halobiforma nitratireducens 28 Natronobacterium gregoryi 38 85 Natronobacterium texcoconense Saliphagus infecundisoli Halobacteriaceae~1_Halobacteriales~1 40 Natronoarchaeum persicum 100 Natronoarchaeum rubrum 40 Natronoarchaeum mannanilyticum 78 Salinarchaeum chitinilyticum Halobacteriaceae~2_Halobacteriales~2 45 Haloarchaeobius litoreus 85 Haloarchaeobius iranensis Haloarchaeobius salinus 100 Haloarchaeobius amylolyticus 68 Haloarchaeobius baliensis

Halobacteriales~3 Halococcaceae 50 Halococcus morrhuae 40 68 Halococcus dombrowskii 63 Halococcus qingdaonensis 100 Halococcus thailandensis 50 Halococcus sediminicola 30 Halococcus hamelinensis 100 100 Halococcus salsus 100 Halococcus saccharolyticus Halococcus agarilyticus 100 Halococcus salifodinae 85 Halobacteriaceae~3 70 Halalkalicoccus jeotgali 80 Halalkalicoccus subterraneus Halalkalicoccus paucihalophilus 33 100 Halalkalicoccus tibetensis

Halobacteriaceae~4 98 Halostella salina Halostella pelagica 90 Halostella limicola

35 Halobacteriaceae~5 100 Haladaptatus paucihalophilus 33 Haladaptatus litoreus 100 Haladaptatus cibarius 48 Halorussus halophilus 45 Halomicrococcus hydrotolerans 73 Halorussus amylolyticus Halorussus litoreus

70 Halobacteriaceae_Halobacteriales 83 Halobacterium salinarum 93 Halobacterium rubrum 100 Halobacterium jilantaiense Halobacterium noricense 90 50 Halarchaeum acidiphilum 43 Halarchaeum salinum 100 Halarchaeum rubridurum Halarchaeum nitratireducens 10043 100 Halarchaeum solikamskense Halocalculus aciditolerans Salarchaeum japonicum

Haloarculaceae_Halobacteriales~4 Haloarcula argentinensis 23 Haloarcula quadrata 40 Haloarcula vallismortis 38 Haloarcula marismortui 45 Haloarcula hispanica 50 Haloarcula amylolytica 40 Haloarcula japonica 65 Haloarcula salaria 100 45 Halomicroarcula amylolytica 48 60 Halomicroarcula salina Haloarcula tradensis Halomicrobium mukohataei 100 Halovenus rubra 40 Halovenus aranensis 35 Salinirussus salinus Salinibaculum litoreum 53 33 100 Halorhabdus tiamatea Halorhabdus utahensis 38 100 Halococcoides cellulosivorans 100 Halorientalis regularis Halorientalis pallida 80 33 Halorientalis brevis 98 Halosimplex rubrum Halosimplex carlsbadense 95 Halosimplex litoreum

Halobacteriaceae~6+Haloarculaceae~1_Halobacteriales~5 100 Natronomonas moolapensis 100 Natronomonas pharaonis 38 Natronomonas halophila Halocatena pleomorpha 93 Halomarina oriensis 57 100 Halomarina rubra Halomarina salina 28 Salinirubellus salinus

80 Methanomicrobia Methanomicrobiales Methanocorpusculaceae 38 Methanocorpusculum bavaricum 100 Methanocorpusculum sinense 40 Methanocalculus alkaliphilus 43 Methanofollis liminatans 100 Methanospirillum hungatei Methanoregula boonei 50 Methanosphaerula palustris

100 Methanomicrobiaceae Methanoculleus marisnigri 75 Methanoculleus chikugoensis 100 Methanoculleus horonobensis Methanoculleus hydrogenitrophicus 88 Methanolacinia petrolearia 48 Methanoplanus endosymbiosus 100 Methanoplanus limicola 100 80 Methanogenium frigidum Methanogenium marinum 100 Methanogenium cariaci

Methanocella arvoryzae 28 Methanosarcinales Methanosarcinaceae 100 40 Methanosarcina vacuolata 100 Methanosarcina siciliae 70 Methanosarcina semesiae 40 Methanolobus zinderi 95 Methanococcoides burtonii Methanococcoides methylutens 10068 Methanohalophilus halophilus 100 Methanohalophilus mahii Methanosalsum zhilinae 33 Methanohalobium evestigatum 100 Methanosaetaceae Methanothrix soehngenii 100 Methanothrix thermoacetophila

Methanobacteriales_Methanobacteria Methanobacteriaceae 100 Methanobrevibacter smithii 100 Methanobrevibacter ruminantium 60 Methanosphaera stadtmanae 100 Methanobacterium oryzae Methanothermobacter marburgensis 100 100 Methanothermobacter thermautotrophicus Methanothermus sociabilis

Thermococcaceae_Thermococcales_Thermococci Thermococcus celer Thermococcus barossii 35 Thermococcus hydrothermalis 100 Thermococcus thioreducens 83 33 Thermococcus coalescens 18 Thermococcus piezophilus 50 Thermococcus siculi 15 Thermococcus celericrescens 28 Thermococcus cleftensis 5 Thermococcus stetteri 35 Thermococcus kodakarensis Thermococcus peptonophilus 48 Thermococcus gammatolerans Thermococcus eurythermalis 53 Thermococcus guaymasensis 43 Thermococcus pacificus 23 Thermococcus waiotapuensis 10 100 Thermococcus zilligii 20 Thermococcus fumicolans 35 Thermococcus gorgonarius Thermococcus acidaminovorans 57 Thermococcus paralvinellae Pyrococcus kukulkanii 50 Pyrococcus furiosus 40 100 Pyrococcus woesei 83 Pyrococcus horikoshii 100 Thermococcus sibiricus Thermococcus litoralis 100 38 Thermococcus aegaeus Archaeoglobaceae_Archaeoglobales_Archaeoglobi Archaeoglobus fulgidus 100 85 Archaeoglobus profundus Ferroglobus placidus 100 57 Archaeoglobus veneficus Archaeoglobus sulfaticallidus

Methanococcales_Methanococci Methanococcaceae 23 60 Methanococcus vannielii 100 Methanococcus aeolicus 85 Methanothermococcus okinawensis 75 Methanothermococcus thermolithotrophicus Methanofervidicoccus abyssi 98 Methanocaldococcaceae~1 Methanotorris igneus 93 Methanotorris formicicus

95 Methanocaldococcaceae 60 Methanocaldococcus fervens 73 Methanocaldococcus bathoardescens Methanocaldococcus jannaschii 85 Methanocaldococcus infernus

Thermoprotei_Crenarchaeota Sulfolobaceae_Sulfolobales 100 Sulfurisphaera tokodaii 40 Sulfurisphaera javensis 100 Saccharolobus caldissimus Metallosphaera sedula

Desulfurococcales Desulfurococcaceae 100 100 Desulfurococcus amylolyticus 93 Desulfurococcus mucosus 35 Thermosphaera aggregans 100 Staphylothermus hellenicus 100 Staphylothermus marinus Thermogladius calderae 45 Pyrodictium delaneyi

Thermoproteales 100 Thermoproteaceae 23 Pyrobaculum arsenaticum 55 Pyrobaculum igneiluti 18 Pyrobaculum organotrophum 53 Pyrobaculum ferrireducens 28 100 Pyrobaculum neutrophilum 100 Pyrobaculum aerophilum 100 Pyrobaculum calidifontis Thermoproteus tenax Vulcanisaeta distributa 68 Thermofilum adornatum