12. Tree of Life, 2550 taxa

One-per-species tree of life, made from the completed and draft genomes available on 1 April, 2013, in phyloxml format.

_images/fig_tree.png

In order to provide correspondence to NCBI’s taxonomy and the reference genomes, this chapter presents the list of reference genomes linked to NCBI on the basis of genus and species names. The complete directory name from the NCBI ftp site also appears below, and the combination allows the current release of each genome to be located.

Sequedex was developed with a signature list and phylogenetic classification based on a bacterial one-per-genus tree of 403 taxa. Since that time, we have increased both the breadth and resolution of this tree to include bacteria, archaea, and eukaryotes at the one-per-species resolution. The tree was based on an amino acid alignment of the concatenated RNA polymerase beta and beta prime subunits (for bacteria) or the analogous subunits of RNA pol II (for eukaryotes).

Phylogenetic information can be visualized in a variety of ways, and this chapter attempts to start the user with phylum-level, family-level, and species-level identifications of what is present in a sample. Although labeled as phylum and family, we took liberties in using the pair of classifications that best suited the density of reference genomes in each region of the phylogeny, to obtain a labeling scheme that is parsimonious, spanning, and non-overlapping. By clicking on the taxon names, the user can easily compare to all levels of the taxonomy assigned by NCBI.

As described in the Introduction, Sequedex captures the uncertainty inherent in classifying fragments of DNA by making phylogenetic assignments to the nodes of a binary phylogenetic tree, and not to individual taxa. Consequently, some node numbers are indicative of phyla, some nodes are indicative of families, and some are specific to a pair of taxa. In the table below, we provide all three types of information. Because of the way the nodes on the trees were numbered, through a depth-first traversal, node numbers intermediate between these two extremes are intermediate nodes between the group name (family or phylum) and the leaves. PDF files are available with page-sized chunks of the tree throughout the tree, and are indicated at the beginning of each section, Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

There are undoubtably minor mistakes in this classification. The nature of the signature peptide method, however, is such that these mistakes serve to bluzrr out phylogenetic signals, not result in spurious assignments to specific nodes.

12.1. Bacteroidetes, et al.

This group contains Chlamydia, Verrucomicrobia, Planctomycetes, Spirochaetes, Fusobacteria, Elusimicrobia, Gemmatimonads, Salinibacter, Chlorobia, Cytophaga, Pedobacteria,Flavobacteria, and bacteroidetes. Annotated pdfs with node numbers and family names are available for:

Phylum Family Organism
Elusimicrobia Elusimicrobiales uncultured Termite group 1 bacterium phylotype Rs D17 uid59059
(node 6) (node 6) Elusimicrobium minutum Pei191 uid58949
Fusobacteriales Fusobacteriaceae Ilyobacter polytropus DSM 2926 uid59769
(nodes 8-24) (nodes 9-20) Fusobacterium mortiferum ATCC 9817 uid55571
.   Fusobacterium varium ATCC 27725 uid55573
.   Fusobacterium 12 1B uid81787
.   Fusobacterium ulcerans ATCC 49185 uid55615
.   Fusobacterium gonidiaformans ATCC 25563 uid55569
.   Fusobacterium D12 uid55613
.   Fusobacterium necrophorum funduliforme 1 1 36S uid81603
.   Fusobacterium oral taxon 370 F0437 uid78149
.   Fusobacterium periodonticum ATCC 33693 uid55335
.   Fusobacterium D11 uid55627
.   Fusobacterium nucleatum ATCC 25586 uid57885
.   Fusobacterium 4 1 13 uid55609
. Leptotrichiaceae Sebaldella termitidis ATCC 33386 uid41865
. (nodes 21-24) Streptobacillus moniliformis DSM 12112 uid41863
.   Leptotrichia goodfellowii F0264 uid41359
.   Leptotrichia buccalis C 1013 b uid59211
.   Leptotrichia hofstadii F0254 uid55767
Spirochaetes Leptospiraceae Turneriella parva DSM 21527 uid168321
(nodes 25-74) (nodes 26-40) Leptonema illini DSM 21528 uid82715
.   Leptospira biflexa serovar Patoc Patoc 1 Ames uid58511
.   Leptospira meyeri serovar Hardjo Went 5 uid177325
.   Leptospira alexanderi serovar Manhao 3 L 60 uid171099
.   Leptospira kirschneri 200802841 uid180750
.   Leptospira noguchii 2006001870 uid78701
.   Leptospira kmetyi serovar Malaysia Bejo Iso9 uid171098
.   Leptospira interrogans serovar Copenhageni Fiocruz L1 130 uid58065
.   Leptospira borgpetersenii serovar Hardjo bovis JB197 uid58509
.   Leptospira weilii 2006001853 uid179809
.   Leptospira Fiocruz LV3954 uid178558
.   Leptospira santarosai 2000030832 uid78697
.   Leptospira licerasiae MMD4847 uid180102
.   Leptospira broomii 5399 uid171097
.   Leptospira inadai serovar Lyme 10 uid171096
. Brachyspiraceae Brachyspira pilosicoli 95 1000 uid50609
. (nodes 42-46) Brachyspira intermedia PWS A uid158369
.   Brachyspira hyodysenteriae WA1 uid59291
.   Brachyspira 30446 uid183377
.   Brachyspira hampsonii 30599 uid188379
.   Brachyspira murdochii DSM 12563 uid48819
. Spirochaetacea Borrelia valaisiana VS116 uid54823
. (nodes 47-74) Borrelia spielmanii A14S uid55069
.   Borrelia afzelii HLJ01 uid177930
.   Borrelia garinii BgVir uid162165
.   Borrelia bissettii DN127 uid71231
.   Borrelia burgdorferi JD1 uid161197
.   Borrelia SV1 uid55065
.   Borrelia crocidurae Achema uid162335
.   Borrelia recurrentis A1 uid58793
.   Borrelia duttonii Ly uid58791
.   Borrelia hermsii DAH uid59225
.   Borrelia turicatae 91E135 uid58311
.   Spirochaeta coccoides DSM 17374 uid66331
.   Sphaerochaeta pleomorpha Grapes uid82365
.   Spirochaeta Buddy uid63633
.   Spirochaeta thermophila DSM 6192 uid53037
.   Spirochaeta africana DSM 8902 uid81779
.   Spirochaeta caldaria DSM 7334 uid68753
.   Treponema azotonutricium ZAS 9 uid67365
.   Treponema primitia ZAS 2 uid67367
.   Treponema denticola ATCC 35405 uid57583
.   Treponema vincentii ATCC 35580 uid55865
.   Treponema phagedenis F0421 uid62291
.   Treponema pallidum Chicago uid159543
.   Treponema paraluiscuniculi Cuniculi A uid68447
.   Treponema brennaborense DSM 12168 uid66607
.   Treponema succinifaciens DSM 2489 uid65781
.   Treponema saccharophilum DSM 2985 uid156761
.   Treponema JC4 uid158669
Chlamydiae Chlamydiaceae Chlamydophila abortus S26 3 uid57963
(nodes 77-88) (nodes 79-86) Chlamydia psittaci 01DC12 uid179070
.   Chlamydophila psittaci 01DC11 uid159527
.   Chlamydophila caviae GPIC uid57783
.   Chlamydophila felis Fe C 56 uid57971
.   Chlamydia muridarum Nigg uid57785
.   Chlamydia trachomatis 434 Bu uid61633
.   Chlamydophila pneumoniae AR39 uid57809
.   Chlamydophila pecorum E58 uid66295
. Waddliaceae Waddlia chondrophila WSU 86 1044 uid49531
. Parachlamydiaceae Candidatus Protochlamydia amoebophila UWE25 uid58079
. (node 88) Parachlamydia acanthamoebae UV7 uid68335
.   Simkania negevensis Z uid68451
Verrucomicrobia Lentisphaeraceae Lentisphaera araneosa HTCC2155 uid54167
(nodes 90-98) Methylacidiphilaceae Methylacidiphilum fumariolicum uid159999
. (node 92) Methylacidiphilum infernorum V4 uid59161
. Spartobacteria Chthoniobacter flavus Ellin428 uid55037
. Verrucomicrobia Verrucomicrobium spinosum DSM 4136 uid54121
. (node 94) Akkermansia muciniphila ATCC BAA 835 uid58985
.   bacterium Ellin514 uid54925
. Optitae Coraliomargarita akajimensis DSM 45221 uid47079
. (nodes 96-98) Verrucomicrobiae bacterium DG1235 uid54739
.   Opitutaceae bacterium TAV1 uid82717
.   Opitutus terrae PB90 1 uid58965
Planctomycetes   planctomycete KSU 1 uid163683
(nodes 99-110)   Phycisphaera mikurensis NBRC 102666 uid157331
.   Gemmata obscuriglobus UQM 2246 uid54931
.   Isosphaera pallida ATCC 43644 uid62207
.   Singulisphaera acidiphila DSM 18658 uid81777
.   Planctomyces brasiliensis DSM 5305 uid60583
.   Planctomyces maris DSM 8797 uid54323
.   Planctomyces limnophilus DSM 3776 uid48643
.   Schlesneria paludicola DSM 18645 uid175442
.   Blastopirellula marina DSM 3645 uid54189
.   Pirellula staleyi DSM 6068 uid43209
.   Rhodopirellula baltica SH 1 uid61589
.   Rhodopirellula europaea 6C uid189169
Gemmatimonadetes Gemmatimonadlaes Gemmatimonas aurantiaca T 27 uid58813
WWE1 WWE1 Candidatus Cloacamonas acidaminovorans Evry uid62959
Fibrobacteres Fibrobacterales Fibrobacter succinogenes S85 uid161919
Chlorobi Chlorobiales Chloroherpeton thalassium ATCC 35110 uid59187
(nodes 115-124) (nodes 115-124) Chlorobium phaeobacteroides BS1 uid58131
.   Prosthecochloris aestuarii DSM 271 uid58151
.   Chlorobaculum parvum NCIB 8327 uid59185
.   Chlorobium tepidum TLS uid57897
.   Chlorobium limicola DSM 245 uid58127
.   Chlorobium luteolum DSM 273 uid58175
.   Chlorobium phaeovibrioides DSM 265 uid58129
.   Chlorobium chlorochromatii CaD3 uid58375
.   Chlorobium ferrooxidans DSM 13031 uid54401
.   Pelodictyon phaeoclathratiforme BU 1 uid58173
Ignavibacteria Ignavibacteriales Ignavibacterium album JCM 16511 uid162097
(node 126) (node 126) Melioribacter roseus P3M uid170941
Bacteroidetes Order_II Rhodothermus marinus DSM 4252 uid41729
(nodes 127-299) (node 128) Salinibacter ruber DSM 13855 uid58513
. unclassified Cardinium endosymbiont cEper1 of Encarsia pergandiella uid175524
. unclassified Candidatus Amoebophilus asiaticus 5a2 uid58963
. Cytophagia Emticicia oligotrophica DSM 17448 uid177079
. (nodes 132-150) Leadbetterella byssophila DSM 17132 uid60161
.   Fibrella aestuarina uid178352
.   Fibrisoma limi uid169430
.   Spirosoma linguale DSM 74 uid43413
.   Runella slithyformis DSM 19594 uid68317
.   Dyadobacter fermentans DSM 18053 uid59049
.   Cytophaga hutchinsonii ATCC 33406 uid57651
.   Flexibacter litoralis DSM 6794 uid168257
.   Microscilla marina ATCC 23134 uid54163
.   Marivirga tractuosa DSM 4126 uid60837
.   Fulvivirga imtechensis AK7 uid186536
.   Mariniradius saccharolyticus AK6 uid185795
.   Cecembia lonarensis LW9 uid175678
.   Marinilabilia AK2 uid176937
.   Indibacter alkaliphilus LW1 uid175140
.   Algoriphagus PR1 uid54611
.   Belliella baltica DSM 15883 uid168182
.   Cyclobacterium marinum DSM 745 uid71485
.   Echinicola vietnamensis DSM 17526 uid184076
. Sphingobacteriia Chitinophaga pinensis DSM 2588 uid59113
. (nodes 152-162) Niabella soli DSM 19437 uid82551
.   Niastella koreensis GR20 10 uid83125
.   Haliscomenobacter hydrossis DSM 1100 uid66777
.   Saprospira grandis Lewin uid89375
.   Solitalea canadensis DSM 3403 uid81783
.   Pedobacter saltans DSM 12145 uid61349
.   Pedobacter BAL39 uid54703
.   Pedobacter heparinus DSM 2366 uid59111
.   Mucilaginibacter paludis DSM 18603 uid60581
.   Sphingobacterium 21 uid64755
.   Sphingobacterium spiritivorum ATCC 33300 uid55527
. Flavobacteriia Cellulophaga lytica DSM 7489 uid63401
. (nodes 164-218) Cellulophaga algicola DSM 14237 uid62159
.   Flavobacteriales bacterium HTCC2170 uid51877
.   Zobellia galactanivorans uid70621
.   Robiginitalea biformata HTCC2501 uid58285
.   Mesoflavibacter zeaxanthinifaciens S86 uid81109
.   Muricauda ruestringensis DSM 13258 uid72479
.   Galbibacter ck I2 15 uid176601
.   Joostella marina DSM 19592 uid163687
.   Imtechella halotolerans K1 uid158663
.   Capnocytophaga CM59 uid174242
.   Capnocytophaga gingivalis ATCC 33624 uid55451
.   Capnocytophaga canimorsus Cc5 uid70727
.   Capnocytophaga sputigena ATCC 33612 uid55407
.   Capnocytophaga ochracea DSM 7271 uid59197
.   Capnocytophaga oral taxon 324 F0483 uid183775
.   Kordia algicida OT 1 uid54687
.   Bizionia argentinensis JUB59 uid72961
.   Lacinutrix 5H 3 7 4 uid68067
.   Psychroflexus torquis ATCC 700755 uid54205
.   Gillisia limnaea DSM 15749 uid82719
.   Gramella forsetii KT0803 uid58881
.   Zunongwangia profunda SM A87 uid48073
.   Krokinobacter 4H 3 7 5 uid66593
.   Leeuwenhoekiella blandensis MED217 uid54243
.   Croceibacter atlanticus HTCC2559 uid49661
.   Aquimarina agarilytica ZC1 uid173055
.   Persicivirga dokdonensis DSW 6 uid186842
.   Aequorivita sublithincola DSM 14238 uid168181
.   unidentified eubacterium SCB49 uid54737
.   Myroides odoratus DSM 2801 uid82721
.   Myroides injenensis M09 0166 uid171989
.   Myroides odoratimimus CCUG 10230 uid81601
.   Flavobacterium columnare ATCC 49512 uid80731
.   Flavobacterium indicum GPTSA100 9 uid157999
.   Flavobacteria bacterium BAL38 uid54617
.   Flavobacterium psychrophilum JIP02 86 uid61627
.   Flavobacterium branchiophilum FL 15 uid73421
.   Flavobacterium frigoris PS1 uid156765
.   Flavobacterium CF136 uid171678
.   Flavobacterium F52 uid170864
.   Flavobacterium johnsoniae UW101 uid58493
.   Polaribacter irgensii 23 P uid54179
.   Polaribacter MED152 uid54207
.   Riemerella anatipestifer ATCC 11845 DSM 15868 uid159857
.   Elizabethkingia anophelis Ag1 uid80705
.   Bergeyella zoohelcum ATCC 43767 uid181642
.   Flavobacteriaceae bacterium 3519 10 uid59413
.   Chryseobacterium CF314 uid171677
.   Chryseobacterium gleum ATCC 35910 uid55393
.   Ornithobacterium rhinotracheale DSM 15997 uid168256
.   Weeksella virosa DSM 16922 uid63627
.   Candidatus Uzinura diaspidicola ASNER uid186740
.   Candidatus Sulcia muelleri CARI uid52535
.   Owenweeksia hongkongensis DSM 17368 uid82951
.   Fluviicola taffensis DSM 16823 uid65271
. Rikenellaceae Alistipes indistinctus YIT 12060 uid75115
. (nodes 220-222) Alistipes putredinis DSM 17216 uid54803
.   Alistipes finegoldii DSM 17242 uid168180
.   Alistipes JC136 uid174622
. Porphyromonadaceae Odoribacter laneus YIT 12061 uid82557
. (node 225) Odoribacter splanchnicus DSM 20712 uid63397
. Marinilabiliaceae Anaerophaga HS1 uid80885
. (node 226-227) Marinilabilia salmonicolor JCM 21150 uid177805
.   Anaerophaga thermohalophila DSM 12881 uid72977
. Porphyromonadacea Porphyromonas endodontalis ATCC 35406 uid55449
. (nodes 229-244) Porphyromonas asaccharolytica DSM 20707 uid66603
.   Porphyromonas uenonis 60 3 uid55869
.   Porphyromonas catoniae F0037 uid183770
.   Porphyromonas oral taxon 279 F0450 uid174237
.   Porphyromonas gingivalis ATCC 33277 uid58879
.   Tannerella forsythia ATCC 43037 uid83157
.   Parabacteroides distasonis ATCC 8503 uid58301
.   Parabacteroides goldsteinii CL02T12C30 uid178274
.   Parabacteroides johnsonii CL02T12C29 uid181649
.   Parabacteroides merdae ATCC 43184 uid54545
.   Candidatus Azobacteroides pseudotrichonymphae genomovar CFP2 uid59163
.   Dysgonomonas gadei ATCC BAA 286 uid67099
.   Dysgonomonas mossii DSM 22836 uid67097
.   Barnesiella intestinihominis YIT 11860 uid175259
.   Tannerella 6 1 58FAA CT1 uid80413
.   Paludibacter propionicigenes WB4 uid
. Bacteroidaceae Bacteroides vulgatus ATCC 8482 uid58253
. (nodes246-267) Bacteroides plebeius DSM 17135 uid54991
.   Bacteroides coprophilus DSM 18228 uid55301
.   Bacteroides salanitronis DSM 18170 uid63269
.   Bacteroides coprocola DSM 17136 uid54879
.   Bacteroides coprosuis DSM 18011 uid66921
.   Bacteroides oleiciplenus YIT 12058 uid182882
.   Bacteroides cellulosilyticus CL02T12C19 uid181624
.   Bacteroides intestinalis DSM 17393 uid54881
.   Bacteroides helcogenes P 36 108 uid62135
.   Bacteroides fluxus YIT 12057 uid66157
.   Bacteroides D20 uid42369
.   Bacteroides clarus YIT 12056 uid66155
.   Bacteroides eggerthii 1 2 48FAA uid61869
.   Bacteroides stercoris ATCC 43183 uid54825
.   Bacteroides fragilis 638R uid84217
.   Bacteroides nordii CL02T12C05 uid170043
.   Bacteroides salyersiae CL02T12C01 uid170041
.   Bacteroides finegoldii CL09T03C10 uid181638
.   Bacteroides caccae ATCC 43185 uid54521
.   Bacteroides faecis MAJ27 uid86875
.   Bacteroides ovatus 3 8 47FAA uid68195
.   Bacteroides xylanisolvens CL03T12C04 uid181622
. Prevotellaceae Paraprevotella clara YIT 11840 uid76949
. (nodes 268-299) Paraprevotella xylaniphila YIT 11841 uid66381
.   Prevotella tannerae ATCC 51259 uid55769
.   Prevotella ruminicola 23 uid47507
.   Prevotella marshii DSM 16973 uid51709
.   Prevotella stercorea DSM 18206 uid78321
.   Prevotella saccharolytica F0055 uid183769
.   Prevotella buccae ATCC 33574 uid61457
.   Prevotella copri DSM 18205 uid55277
.   Prevotella bryantii B14 uid50549
.   Prevotella oralis ATCC 33269 uid61459
.   Prevotella buccalis ATCC 35310 uid42969
.   Prevotella timonensis CRIS 5C B1 uid42971
.   Prevotella oulorum F0390 uid72969
.   Prevotella maculosa OT 289 uid81767
.   Prevotella oris C735 uid49959
.   Prevotella salivae DSM 15606 uid61887
.   Prevotella multisaccharivorax DSM 17128 uid68187
.   Prevotella bergensis DSM 17361 uid55893
.   Prevotella dentalis DSM 3688 uid184818
.   Prevotella amnii CRIS 21A A uid52821
.   Prevotella bivia DSM 20514 uid182041
.   Prevotella histicola F0411 uid76947
.   Prevotella veroralis F0319 uid55991
.   Prevotella C561 uid72971
.   Prevotella melaninogenica ATCC 25845 uid51377
.   Prevotella denticola F0289 uid65091
.   Prevotella multiformis DSM 16608 uid63431
.   Prevotella micans F0438 uid81791
.   Prevotella nigrescens ATCC 33563 uid70557
.   Prevotella pallens ATCC 700821 uid70559
.   Prevotella disiens FB035 09AN uid51531
.   Prevotella intermedia 17 uid163151

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.2. Alpha proteobacteria, et al.

This group contains Helicobacter, Campylobacter, Acidobacteriales, Aquificae, Deferribacteria, Desulfovibriales, Desulfotaleales, Myxococcus, Gebacteriales, Rhizobia, Caulobacteriales, Rhodobacteria, Sphingomonads, Rickettesia, Rhodospirilliae. PDFs are available for:

Phylum Family Organism
Epsilon_proteobacteria Campylobacteraceae Sulfurospirillum barnesii SES 3 uid168117
(nodes 302-340) (nodes 306-319) Sulfurospirillum deleyianum DSM 6946 uid41861
.   Campylobacter lari RM2100 uid58115
.   Campylobacter upsaliensis JV21 uid61485
.   Campylobacter coli 1091 uid180315
.   Campylobacter jejuni 81116 uid58771
.   Campylobacter gracilis RM3268 uid55421
.   Campylobacter fetus 82 40 uid58545
.   Campylobacter rectus RM3267 uid55417
.   Campylobacter FOBRC14 uid173871
.   Campylobacter 10 1 50 uid80421
.   Campylobacter concisus 13826 uid58667
.   Arcobacter nitrofigilis DSM 7299 uid49001
.   Arcobacter butzleri ED 1 uid158699
.   Arcobacter L uid158135
. Helicobacteraceae Wolinella succinogenes DSM 1740 uid61591
. (nodes 320-337) Helicobacter winghamensis ATCC BAA 430 uid55619
.   Helicobacter canadensis MIT 98 5491 uid55289
.   Helicobacter pullorum MIT 98 5489 uid55293
.   Helicobacter cinaedi PAGU611 uid162219
.   Helicobacter hepaticus ATCC 51449 uid57737
.   Helicobacter bilis ATCC 43879 uid55617
.   Helicobacter mustelae 12198 uid46647
.   Helicobacter cetorum MIT 00 7128 uid162217
.   Helicobacter acinonychis Sheeba uid58685
.   Helicobacter pylori 2017 uid161151
.   Helicobacter suis HS1 uid62531
.   Helicobacter bizzozeronii CIII 1 uid68141
.   Helicobacter felis ATCC 49179 uid61409
.   Thiovulum ES uid170493
.   Sulfuricurvum kujiense DSM 16994 uid60789
.   Sulfurimonas autotrophica DSM 16294 uid53043
.   Sulfurimonas denitrificans DSM 1251 uid58185
.   Sulfurimonas GD1 uid81843
.   Nitratifractor salsuginis DSM 16511 uid62183
. unclassified Sulfurovum AR uid162597
. unclassified Sulfurovum NBC37 1 uid58863
. unclassified Nitratiruptor SB155 2 uid58861
. Nautiliales Caminibacter mediatlanticus TB 2 uid54669
. (node 340) Nautilia profundicola AmH uid59345
Aquificae Desulfurellaceae Desulfurobacterium thermolithotrophum DSM 11699 uid63405
(nodes 342-352) (node 343) Thermovibrio ammonificans HB 1 uid62095
. Hydrogenthermaceae Persephonella marina EX H1 uid58119
. (nodes 345-347) Sulfurihydrogenibium azorense Az Fu1 uid58121
.   Sulfurihydrogenibium yellowstonense SS 5 uid54637
.   Sulfurihydrogenibium YO3AOP1 uid58855
. Aquificaceae Aquifex aeolicus VF5 uid57765
. (nodes 348-352) Hydrogenivirga 128 5 R1 1 uid54685
.   Hydrogenobacter thermophilus TK 6 uid159875
.   Thermocrinis albus DSM 14484 uid46231
.   Hydrogenobaculum HO uid190882
.   Hydrogenobaculum Y04AAS1 uid58857
Acidobacteria Holophagae Holophaga foetida DSM 6591 uid81781
(nodes 355-362) unclassified Candidatus Chloracidobacterium thermophilum B uid73587
. Solibacteres Candidatus Solibacter usitatus Ellin6076 uid58139
. unclassified Candidatus Koribacter versatilis Ellin345 uid58479
. Acidobacteriaceae Acidobacterium capsulatum ATCC 51196 uid59127
. (nodes 359-362) Acidobacterium MP5ACTX9 uid50551
.   Granulicella mallensis MP5ACTX8 uid49957
.   Terriglobus roseus DSM 18391 uid168183
.   Terriglobus saanensis SP1PR4 uid53251
Chrysiogenetes Chrysiogenetes Desulfurispirillum indicum S5 uid45897
Deferribacteres Deferribacterales Deferribacter desulfuricans SSM1 uid46653
(nodes 364-366) (nodes 364-366) Denitrovibrio acetiphilus DSM 12809 uid46657
.   Calditerrivibrio nitroreducens DSM 19672 uid60821
.   Flexistipes sinusarabici DSM 4947 uid68147
Delta_proteobacteria Desulfovibrionales Desulfovibrio fructosovorans JJ uid51537
(nodes 368-426) (nodes 374-391) Desulfovibrio magneticus RS 1 uid59309
.   Desulfovibrio FW1012B uid43335
.   Desulfovibrio U5L uid162937
.   Desulfovibrio aespoeensis Aspo 2 uid42613
.   Desulfovibrio hydrothermalis AM13 DSM 14728 uid184831
.   Desulfovibrio salexigens DSM 2638 uid59223
.   Desulfovibrio alaskensis G20 uid57941
.   Desulfovibrio A2 uid73581
.   Desulfovibrio vulgaris DP4 uid58679
.   Desulfovibrio piger ATCC 29098 uid54519
.   Desulfovibrio 6 1 46AFAA uid72975
.   Desulfovibrio desulfuricans ATCC 27774 uid59213
.   Bilophila wadsworthia 3 1 6 uid61875
.   Lawsonia intracellularis N343 uid186598
.   Desulfovibrio africanus Walvis Bay uid66847
.   Desulfohalobium retbaense DSM 5692 uid59183
.   Desulfonatronospira thiodismutans ASO3 1 uid55423
.   Desulfomicrobium baculatum DSM 4028 uid59217
. Desulfobulbaceae delta proteobacterium MLMS 1 uid54339
. (nodes 392-395) Desulfurivibrio alkaliphilus AHT2 uid49487
.   Desulfobulbus propionicus DSM 2032 uid62265
.   Desulfocapsa sulfexigens DSM 10523 uid189952
.   Desulfotalea psychrophila LSv54 uid58153
. Desulfobacteraceae Desulfatibacillum alkenivorans AK 01 uid58913
. (nodes 397-400) Desulfococcus oleovorans Hxd3 uid58777
.   Desulfobacterium autotrophicum HRM2 uid59061
.   Desulfobacter postgatei 2ac9 uid76943
.   Desulfobacula toluolica Tol2 uid175777
. Syntrophobaceae Desulfobacca acetoxidans DSM 11109 uid65785
. Desulfarculales Desulfarculus baarsii DSM 2075 uid51371
. Syntrophobaceae Syntrophobacter fumaroxidans MPOB uid58177
. Syntrophobaceae Syntrophus aciditrophicus SB uid58539
. (node 403) Desulfomonile tiedjei DSM 6799 uid168320
. Desulfuromonadales Geobacter metallireducens GS 15 uid57731
. (nodes 405-414) Geobacter sulfurreducens KN400 uid161977
.   Geobacter M18 uid55771
.   Geobacter bemidjiensis Bem uid58749
.   Geobacter M21 uid59037
.   Geobacter FRC 32 uid58543
.   Geobacter uraniireducens Rf4 uid58475
.   Geobacter lovleyi SZ uid58713
.   Pelobacter propionicus DSM 2379 uid58255
.   Desulfuromonas acetoxidans DSM 684 uid54145
.   Pelobacter carbinolicus DSM 2380 uid58241
. Myxococcales Stigmatella aurantiaca DW4 3 1 uid158509
. (nodes 416-425) Cystobacter fuscus DSM 2262 uid188352
.   Corallococcus coralloides DSM 2259 uid157997
.   Myxococcus stipitatus DSM 14675 uid186549
.   Chondromyces apiculatus DSM 436 uid175317
.   Myxococcus fulvus HW 1 uid68443
.   Anaeromyxobacter dehalogenans 2CP 1 uid58989
.   Anaeromyxobacter Fw109 5 uid58755
.   Sorangium cellulosum So ce 56 uid61629
.   Haliangium ochraceum DSM 14365 uid41425
.   Plesiocystis pacifica SIR 1 uid54707
. Bdelovibrionales Bacteriovorax marinus SJ uid82341
. (node 426) Bdellovibrio bacteriovorus HD100 uid61595
. unclassified SAR324 cluster bacterium JCVI SC AAA005 uid86871
. Desulfurellales Hippea maritima DSM 10411 uid65267
Zeta_proteobacteria Mariprofundales Mariprofundus ferrooxydans PV 1 uid54269
Alpha_proteobacteria Magnetococcales Magnetococcus MC 1 uid57833
(nodes 428-690 Rickettsiales Neorickettsia risticii Illinois uid58889
. (nodes 430-464) Neorickettsia sennetsu Miyayama uid57965
.   Wolbachia wRi uid59371
.   Wolbachia endosymbiont of Culex quinquefasciatus Pel uid61645
.   Wolbachia pipientis wAlbB uid81759
.   Ehrlichia ruminantium Gardel uid58245
.   Ehrlichia canis Jake uid58071
.   Ehrlichia chaffeensis Arkansas uid57933
.   Anaplasma phagocytophilum HZ uid57951
.   Anaplasma centrale Israel uid42155
.   Anaplasma marginale Florida uid58577
.   Candidatus Midichloria mitochondrii IricVA uid68687
.   Orientia tsutsugamushi Boryong uid61621
.   Rickettsia bellii OSU 85 389 uid58681
.   Rickettsia helvetica C9P9 uid173054
.   Rickettsia heilongjiangensis 054 uid70839
.   Rickettsia japonica YH uid73963
.   Rickettsia slovaca 13 B uid82369
.   Rickettsia sibirica 246 uid54113
.   Rickettsia africae ESF 5 uid58799
.   Rickettsia conorii Malish 7 uid57633
.   Rickettsia parkeri Portsmouth uid158045
.   Rickettsia peacockii Rustic uid59301
.   Rickettsia philipii 364D uid89383
.   Rickettsia rickettsii Arizona uid86655
.   Candidatus Rickettsia amblyommii GAT 30V uid156845
.   Rickettsia montanensis OSU 85 930 uid158043
.   Rickettsia massiliae AZT80 uid86751
.   Rickettsia rhipicephali 3 7 female6 CWPP uid156977
.   Rickettsia akari Hartford uid58161
.   Rickettsia australis Cutlack uid158039
.   Rickettsia felis URRWXCal2 uid58331
.   Rickettsia endosymbiont of Ixodes scapularis uid55851
.   Rickettsia canadensis CA410 uid88063
.   Rickettsia prowazekii BuV67 CWPP uid158063
.   Rickettsia typhi B9991CWPP uid158357
. SAR_11 Candidatus Pelagibacter ubique HTCC1062 uid58401
. (nodes 466-468) Candidatus Pelagibacter IMCC9063 uid66305
.   alpha proteobacterium HIMB59 uid175778
. unclassified Candidatus Hodgkinia cicadicola Dsem uid59311
. Rhodospirillales Tistrella mobilis KA081020 065 uid167486
. Rickettsiales Candidatus Odyssella thessalonicensis L13 uid72365
. Rhodospirillales Azospirillum brasilense Sp245 uid162161
. (nodes 472-507) Azospirillum B510 uid46085
.   Azospirillum lipoferum 4B uid82343
.   Azospirillum amazonense Y2 uid73583
.   Rhodospirillum centenum SW uid58805
.   Oceanibaculum indicum P24 uid176351
.   Thalassobaculum L2 uid182483
.   SAR 116 cluster alpha proteobacterium HIMB100 uid78325
.   Candidatus Puniceispirillum marinum IMCC1322 uid47081
.   Thalassospira profundimaris WP0211 uid176349
.   Thalassospira xiamenensis M 5 DSM 17429 uid176348
.   Magnetospirillum magneticum AMB 1 uid58527
.   Phaeospirillum molischianum uid156755
.   Caenispirillum salinarum AK4 uid182892
.   Rhodospirillum photometricum uid159003
.   Rhodospirillum rubrum ATCC 11170 uid57655
.   Micavibrio aeruginosavorus ARL 13 uid73585
.   Acetobacteraceae bacterium AT 5844 uid80697
.   Roseomonas cervicalis ATCC 49957 uid49155
.   Acidiphilium cryptum JF 5 uid58447
.   Acidiphilium multivorum AIU301 uid63345
.   Granulibacter bethesdensis CGDNIH1 uid58661
.   Commensalibacter intestini A911 uid75109
.   Gluconacetobacter diazotrophicus PAl 5 uid59075
.   Gluconacetobacter hansenii ATCC 23769 uid48811
.   Gluconacetobacter europaeus LMG 18494 uid73763
.   Gluconacetobacter oboediens 174Bp2 uid73765
.   Gluconacetobacter SXCC 1 uid66379
.   Gluconacetobacter xylinus NBRC 3288 uid46523
.   Gluconobacter frateurii NBRC 101659 uid178735
.   Gluconobacter thailandicus NBRC 3255 uid191942
.   Gluconobacter morbifer G707 uid76941
.   Gluconobacter oxydans 621H uid58239
.   Acetobacter aceti NBRC 14818 uid70715
.   Acetobacter tropicalis NBRC 101654 uid68643
.   Acetobacter pasteurianus IFO 3283 01 42C uid158377
.   Acetobacter pomorum DM001 uid65823
. Sphingomonadales Sphingopyxis alaskensis RB2256 uid58351
. (nodes 509-534) Sphingobium SYK 6 uid73353
.   Sphingomonas SKA58 uid54251
.   Sphingobium chlorophenolicum L 1 uid52597
.   Sphingobium indicum B90A uid167985
.   Sphingobium japonicum UT26S uid47077
.   Sphingobium AP49 uid171561
.   Sphingobium yanoikuyae ATCC 51230 uid182888
.   Zymomonas mobilis ATCC 10988 uid55403
.   Sphingomonas wittichii RW1 uid58691
.   Sphingomonas KC8 uid77733
.   Sphingomonas elodea ATCC 31461 uid157063
.   Sphingomonas echinoides ATCC 14820 uid169543
.   Sphingomonas PAMC 26605 uid169544
.   Sphingomonas S17 uid66923
.   Novosphingobium aromaticivorans DSM 12444 uid57747
.   Novosphingobium nitrogenifigens DSM 19370 uid64475
.   Novosphingobium pentaromativorans US6 1 uid78315
.   Novosphingobium PP1Y uid67383
.   Sphingomonas LH128 uid174245
.   Novosphingobium AP12 uid171681
.   Novosphingobium Rr 2 17 uid170038
.   Erythrobacter NAP1 uid54197
.   Erythrobacter litoralis HTCC2594 uid58299
.   Erythrobacter SD 21 uid54677
.   Citromicrobium bathyomarinum JL354 uid48817
.   Citromicrobium JLT1363 uid70837
. Rhodobacteraceae Rhodobacter sphaeroides 2 4 1 uid57653
. (nodes 536-576) Rhodobacter SW2 uid40865
.   Rhodobacter capsulatus SB 1003 uid47509
.   Paracoccus denitrificans PD1222 uid58187
.   Paracoccus TRP uid70151
.   Ketogulonicigenium vulgare Y25 uid59581
.   Ketogulonigenium vulgarum WSH 001 uid161161
.   Oceaniovalibus guishaninsula JLT2003 uid176356
.   Oceanicola granulosus HTCC2516 uid54177
.   Thalassiobium R2A62 uid55955
.   Octadecabacter antarcticus 238 uid54699
.   Loktanella vestfoldensis SKA53 uid54169
.   Roseobacter CCS2 uid54627
.   Celeribacter baekdonensis B30 uid176352
.   Maritimibacter alkaliphilus HTCC2654 uid53325
.   Dinoroseobacter shibae DFL 12 uid58707
.   Jannaschia CCS1 uid58147
.   Rhodobacterales bacterium HTCC2083 uid54195
.   Roseobacter denitrificans OCh 114 uid58597
.   Roseobacter litoralis Och 149 uid54719
.   Oceanibulbus indolifex HEL 45 uid54697
.   Roseobacter GAI101 uid55361
.   Sulfitobacter EE 36 uid54191
.   Oceanicola S124 uid81119
.   Sagittula stellata E 37 uid54621
.   Pelagibaca bermudensis HTCC2601 uid53327
.   Citreicella SE45 uid55957
.   Citreicella 357 uid160001
.   Ruegeria TM1040 uid58193
.   Silicibacter TrichCH4B uid55971
.   Phaeobacter gallaeciensis 2 10 uid54715
.   Ruegeria R11 uid54725
.   Roseobacter MED193 uid54257
.   Roseobacter SK209 2 6 uid54629
.   Ruegeria pomeroyi DSS 3 uid57863
.   Silicibacter lacuscaerulensis ITI 1157 uid55959
.   Rhodobacteraceae bacterium KLH11 uid55441
.   Ruegeria TW15 uid73135
.   Roseovarius nubinhibens ISM uid54183
.   Roseovarius TM1035 uid54723
.   Roseobacter AzwK 3b uid54721
.   Oceanicola batsensis HTCC2597 uid54175
. Parvularculales Parvularcula bermudensis HTCC2503 uid51641
. Caulobacterales Phenylobacterium zucineum HLK1 uid58959
. (nodes 580-588) Caulobacter AP07 uid171682
.   Caulobacter K31 uid58551
.   Caulobacter crescentus CB15 uid57891
.   Caulobacter segnis ATCC 21756 uid41709
.   Brevundimonas diminuta 470 4 uid183780
.   Brevundimonas subvibrioides ATCC 15264 uid42117
.   Brevundimonas BAL3 uid54665
.   Asticcacaulis biprosthecum C19 uid66137
.   Asticcacaulis excentricus CB 48 uid55641
. Hyphomonadaceae Hirschia baltica ATCC 49814 uid59365
. (nodes 589-591) Hyphomonas neptunium ATCC 15444 uid58433
.   Maricaulis maris MCS10 uid58689
.   Oceanicaulis alexandrii HTCC2633 uid54173
. Phyllobacteriaceae Parvibaculum lavamentivorans DS 1 uid58739
. Hyphomicrobiaceae Rhodomicrobium vannielii ATCC 17100 uid43247
. (nodes 594-595) Hyphomicrobium denitrificans ATCC 51888 uid50325
.   Hyphomicrobium MC1 uid68453
. Methylobacteriaceae Microvirga WSM3557 uid167863
. (nodes 599-604) Methylobacterium 4 46 uid58843
.   Methylobacterium nodulans ORS 2060 uid59023
.   Methylobacterium extorquens AM1 uid57605
.   Methylobacterium populi BJ001 uid58937
.   Methylobacterium GXF4 uid170037
.   Methylobacterium radiotolerans JCM 2831 uid58845
. Beijerinckiaceae Beijerinckia indica ATCC 9039 uid59057
. (node 606) Methylocella silvestris BL2 uid59433
. Methylocystaceae Methylosinus trichosporium OB3b uid49119
. (node 607-608) Methylocystis ATCC 49242 uid62743
.   Methylocystis SC2 uid174072
. Xanthobacteraceae Starkeya novella DSM 506 uid48815
. (nodes 610-611) Azorhizobium caulinodans ORS 571 uid58905
.   Xanthobacter autotrophicus Py2 uid58453
. Rhodobacteraceae Rhodovulum PH10 uid174236
. Bradyrhizobiaceae Bradyrhizobiaceae bacterium SG 6C uid68635
. (Nodes 613-625) Afipia 1NLS2 uid49955
.   Oligotropha carboxidovorans OM4 uid162135
.   Rhodopseudomonas palustris BisA53 uid58445
.   Nitrobacter hamburgensis X14 uid58293
.   Nitrobacter winogradskyi Nb 255 uid58295
.   Nitrobacter Nb 311A uid54203
.   Bradyrhizobium WSM471 uid82711
.   Bradyrhizobium japonicum USDA 110 uid57599
.   Bradyrhizobium S23321 uid158167
.   Bradyrhizobium YR681 uid171652
.   Bradyrhizobium STM 3843 uid80711
.   Bradyrhizobium BTAi1 uid58505
.   Bradyrhizobium uid80709
. Hyphomicrobiaceae Pelagibacterium halotolerans B2 uid74393
. Rhodobacteraceae Pseudovibrio JE062 uid54711
. (nodes 628-631) Polymorphum gilvum SL003B 26A1 uid65447
.   Roseibium TrichSKD4 uid53349
.   Labrenzia aggregata IAM 12614 uid54575
.   Labrenzia alexandrii DFL 11 uid54727
.   Ahrensia R2A130 uid51717
. Aurantimonadaceae Aurantimonas manganoxydans SI85 9A1 uid54267
. (node 634) Fulvimarina pelagi HTCC2506 uid54193
. Phyllobacteriaceae Hoeflea phototrophica DFL 43 uid54683
. Rhizobiaceae Sinorhizobium medicae WSM419 uid58549
. (nodes 637-654) Sinorhizobium meliloti 1021 uid57603
.   Sinorhizobium fredii HH103 uid86865
.   Candidatus Liberibacter asiaticus psy62 uid59227
.   bacterium BT 1 uid184079
.   Rhizobium CF122 uid171679
.   Rhizobium mesoamericanum STM3625 uid178067
.   Rhizobium CF142 uid175318
.   Rhizobium etli CFN 42 uid58377
.   Rhizobium CCGE 510 uid173872
.   Rhizobium leguminosarum bv trifolii WSM1325 uid58991
.   Rhizobium AP16 uid171562
.   Rhizobium tropici CIAT 899 uid185179
.   Agrobacterium H13 3 uid63403
.   Agrobacterium tumefaciens C58 uid57865
.   Rhizobium CF080 uid180531
.   Agrobacterium vitis S4 uid58249
.   Agrobacterium albertimagni AOL15 uid176603
.   Rhizobium PDO1 076 uid180152
. Phyllobacteriaceae Mesorhizobium alhagi CCNWXJ12 2 uid78825
. (nodes 656-664) Mesorhizobium loti MAFF303099 uid57601
.   Mesorhizobium amorphae CCNWGS0123 uid76939
.   Mesorhizobium opportunistum WSM2075 uid40861
.   Mesorhizobium ciceri biovar biserrulae WSM1271 uid62101
.   Mesorhizobium australicum WSM2073 uid75101
.   Chelativorans BNC1 uid58069
.   Nitratireductor indicus C115 uid176490
.   Nitratireductor aquibiodomus RA22 uid168057
.   Nitratireductor pacificus pht 3B uid176350
. Bartonellaceae Bartonella tamiae Th239 uid170859
. (nodes 666-680) Bartonella bacilliformis KC583 uid58533
.   Bartonella melophagi K 2C uid170858
.   Bartonella clarridgeiae 73 uid62131
.   Bartonella doshiae NCTC 12862 uid170852
.   Bartonella alsatica IBS 382 uid170862
.   Bartonella DB5 6 uid170850
.   Bartonella taylorii 8TBB uid170861
.   Bartonella elizabethae F9251 uid181718
.   Bartonella tribocorum CIP 105476 uid59129
.   Bartonella grahamii as4aup uid59405
.   Bartonella rattimassiliensis 15908 uid170856
.   Bartonella birtlesii LL WM9 uid170860
.   Bartonella washoensis 085 0475 uid170851
.   Bartonella quintana RM 11 uid174512
.   Bartonella henselae Houston 1 uid57745
. Phyllobacteriaceae Phyllobacterium YR531 uid171653
. Brucellaceae Ochrobactrum anthropi ATCC 49188 uid58921
. (nodes 682-690) Brucella melitensis ATCC 23457 uid59241
.   Brucella pinnipedialis B2 94 uid71131
.   Brucella ovis ATCC 25840 uid58113
.   Brucella ceti B1 94 uid55807
.   Brucella microti CCM 4915 uid59319
.   Brucella neotomae 5K33 uid55801
.   Brucella abortus A13334 uid83615
.   Brucella canis ATCC 23365 uid59009
.   Brucella suis 1330 uid159871

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.3. Beta and Gamma Proteobacteria

This group contains Enteric, Haemophilus, Vibrio, Shewanella, Pseudomonads, Coxiella, Thiomicrospira, Nitrosococcus, Xanthomonads, Methylobacteria, Acidothiobacillus, Francisella, Neisseria, Burkholderiales, Azoarcus, Thiobacillus.

Phylum Family Organism
Gamma_proteobacteria Enterobacteriales Serratia marcescens FGI94 uid185180
(nodes 692-1082) (nodes 705-792) Serratia symbiotica Cinara cedri uid82363
.   Serratia odorifera 4Rx13 uid42253
.   Serratia plymuthica AS9 uid67313
.   Serratia proteamaculans 568 uid58725
.   Rahnella aquatilis CIP 78 65 ATCC 33071 uid86855
.   Serratia M24T3 uid158323
.   Candidatus Hamiltonella defensa 5AT Acyrthosiphon pisum uid59289
.   Candidatus Regiella insecticola LSR1 uid51727
.   Yersinia frederiksenii ATCC 33641 uid54347
.   Yersinia enterocolitica 8081 uid57741
.   Yersinia aldovae ATCC 35236 uid55243
.   Yersinia intermedia ATCC 29909 uid54349
.   Yersinia bercovieri ATCC 43970 uid54343
.   Yersinia mollaretii ATCC 43969 uid54345
.   Yersinia ruckeri ATCC 29473 uid55249
.   Yersinia rohdei ATCC 43380 uid55247
.   Yersinia kristensenii ATCC 33638 uid55245
.   Yersinia pestis KIM 10 uid57875
.   Yersinia pseudotuberculosis IP 31758 uid58487
.   Brenneria EniD312 uid75111
.   Pectobacterium carotovorum PC1 uid59295
.   Pectobacterium atrosepticum SCRI1043 uid57957
.   Pectobacterium wasabiae WPP163 uid41297
.   Hafnia alvei ATCC 51873 uid80687
.   Edwardsiella ictaluri 93 146 uid59403
.   Edwardsiella tarda EIB202 uid41819
.   Photorhabdus asymbiotica uid59243
.   Photorhabdus luminescens laumondii TTO1 uid61593
.   Xenorhabdus bovienii SS 2004 uid46345
.   Xenorhabdus nematophila ATCC 19061 uid49133
.   Proteus mirabilis HI4320 uid61599
.   Morganella morganii KT uid180867
.   Providencia stuartii MRSN 2154 uid162193
.   Providencia burhodogranariea DSM 19968 uid181280
.   Providencia rettgeri DSM 1131 uid55121
.   Providencia rustigianii DSM 4541 uid55071
.   Providencia alcalifaciens Dmel2 uid181281
.   Erwinia billingiae Eb661 uid50547
.   Erwinia tasmaniensis Et1 99 uid59029
.   Erwinia amylovora ATCC 49946 uid46943
.   Erwinia pyrifoliae DSM 12163 uid159693
.   Pantoea At 9b uid55845
.   Pantoea GM01 uid171648
.   Pantoea stewartii DC283 uid86627
.   Pantoea ananatis AJ13355 uid162073
.   Pantoea Sc1 uid157059
.   Pantoea agglomerans 299R uid185797
.   Pantoea vagans C9 1 uid49871
.   Cronobacter sakazakii ATCC BAA 894 uid58145
.   Cronobacter turicensis z3032 uid40821
.   Enterobacter Ag1 uid170516
.   Escherichia hermannii NBRC 105704 uid84453
.   Enterobacter cloacae ATCC 13047 uid48363
.   Enterobacter hormaechei ATCC 49162 uid67395
.   Enterobacter cancerogenus ATCC 35316 uid55079
.   Enterobacter mori LMG 25706 uid75365
.   Enterobacter 638 uid58727
.   Enterobacter asburiae LF7a uid72793
.   Yokenella regensburgei ATCC 43003 uid80693
.   Citrobacter freundii 4 7 47CFAA uid80411
.   Citrobacter youngae ATCC 29220 uid55081
.   Enterobacteriaceae bacterium FGI 57 uid185181
.   Klebsiella oxytoca E718 uid170256
.   Enterobacter aerogenes EA1509E uid187411
.   Klebsiella pneumoniae 1084 uid174151
.   Klebsiella variicola At 22 uid42113
.   Citrobacter koseri ATCC BAA 895 uid58143
.   Citrobacter rodentium ICC168 uid43089
.   Salmonella bongori NCTC 12419 uid70155
.   Salmonella enterica arizonae serovar 62 z4 z23 uid58191
.   Escherichia blattae DSM 4481 uid165043
.   Escherichia coli K 12 substr MG1655 uid57779
.   Shigella flexneri 2002017 uid159233
.   Shigella sonnei 53G uid84383
.   Shigella boydii CDC 3083 94 uid58415
.   Shigella dysenteriae Sd197 uid58213
.   Escherichia fergusonii ATCC 35469 uid59375
.   Escherichia albertii TW07627 uid55089
.   Dickeya dadantii 3937 uid52537
.   Dickeya zeae Ech1591 uid59297
.   Sodalis glossinidius morsitans uid58553
.   Candidatus Moranella endobia PCIT uid68739
.   secondary endosymbiont of Ctenarytaina eucalypti uid172737
.   Baumannia cicadellinicola Hc Homalodisca coagulata uid58111
.   Buchnera aphidicola 5A Acyrthosiphon pisum uid59285
.   Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis uid57853
.   Candidatus Blochmannia chromaiodes 640 uid185308
.   Candidatus Riesia pediculicola USDA uid46841
. Pasteurellales Gallibacterium anatis UMN179 uid66567
. (nodes 793-817) Haemophilus parasuis SH0165 uid59273
.   Mannheimia haemolytica PHL213 uid54093
.   Actinobacillus suis H91 0380 uid176363
.   Actinobacillus ureae ATCC 25976 uid62663
.   Haemophilus ducreyi 35000HP uid57625
.   Actinobacillus pleuropneumoniae serovar 3 JL03 uid58891
.   Actinobacillus minor 202 uid55633
.   Haemophilus sputorum HK 2154 uid173855
.   Haemophilus parahaemolyticus HK385 uid165733
.   Haemophilus paraphrohaemolyticus HK411 uid162935
.   Pasteurella dagmatis ATCC 43325 uid41077
.   Pasteurella multocida 3480 uid161955
.   Haemophilus somnus 129PT uid57929
.   Actinobacillus succinogenes 130Z uid58247
.   Mannheimia succiniciproducens MBEL55E uid58197
.   Pasteurella bettyae CCUG 2042 uid165735
.   Haemophilus haemolyticus HK386 uid180431
.   Haemophilus oral taxon 851 F0397 uid81771
.   Haemophilus aegyptius ATCC 11116 uid65831
.   Haemophilus influenzae 10810 uid86647
.   Haemophilus parainfluenzae T3T1 uid72801
.   Haemophilus pittmaniae HK 85 uid72189
.   Aggregatibacter actinomycetemcomitans ANH9381 uid80743
.   Aggregatibacter segnis ATCC 33393 uid61481
.   Aggregatibacter aphrophilus NJ8700 uid59407
. Vibrionales Vibrio parahaemolyticus BB22OP uid184822
. (nodes 818-851) Vibrio EJY3 uid83161
.   Vibrio alginolyticus 12G01 uid54241
.   Vibrio ichthyoenteri ATCC 700023 uid72183
.   Vibrio scophthalmi LMG 19158 uid72185
.   Vibrio rotiferianus DAT722 uid73893
.   Vibrio AND4 uid54233
.   Vibrio campbellii CAIM 519 uid188135
.   Vibrio harveyi ATCC BAA 1116 uid58957
.   Vibrio sinaloensis DSM 21326 uid63103
.   Vibrio brasiliensis LMG 20546 uid63101
.   Vibrio orientalis CIP 102891 ATCC 33934 uid179869
.   Vibrio coralliilyticus ATCC BAA 450 uid41031
.   Vibrio tubiashii ATCC 19109 uid72181
.   Vibrio caribbenthicus ATCC BAA 2122 uid60579
.   Vibrio nigripulchritudo ATCC 27043 uid72179
.   Vibrio shilonii AK1 uid54743
.   Vibrionales bacterium SWAT 3 uid54745
.   Vibrio cyclitrophicus ZF14 uid175805
.   Vibrio splendidus LGP32 uid59353
.   Vibrio anguillarum 775 uid68057
.   Vibrio ordalii ATCC 33509 uid80489
.   Vibrio vulnificus CMCP6 uid62909
.   Vibrio furnissii NCTC 11218 uid82347
.   Vibrio cholerae IEC224 uid89389
.   Vibrio RC586 uid41619
.   Aliivibrio salmonicida LFI1238 uid59251
.   Vibrio fischeri ES114 uid58163
.   Enterovibrio AK16 uid188104
.   Grimontia hollisae CIP 101886 uid41501
.   Photobacterium profundum SS9 uid62923
.   Photobacterium AK15 uid186537
.   Photobacterium damselae CIP 102761 uid41873
.   Photobacterium leiognathi mandapamensis svers 1 1 uid66161
.   Photobacterium angustum S14 uid54237
. Aeromonadales Oceanimonas GK1 uid81627
. (nodes 852-859) Aeromonas veronii B565 uid66323
.   Aeromonas salmonicida A449 uid58631
.   Aeromonas media WS uid180868
.   Aeromonas caviae Ae398 uid67585
.   Aeromonas hydrophila ATCC 7966 uid58617
.   Aeromonas aquariorum AAK1 uid178353
.   Tolumonas auensis DSM 9187 uid59395
.   Succinatimonas hippei YIT 12066 uid62747
. Alteromonadales_1 Moritella PE36 uid54201
. (nodes 960-878) Psychromonas CNPT3 uid54249
.   Psychromonas ingrahamii 37 uid58521
.   Ferrimonas balearica DSM 9799 uid53371
.   Shewanella amazonensis SB2B uid58257
.   Shewanella MR 4 uid58345
.   Shewanella oneidensis MR 1 uid57949
.   Shewanella baltica BA175 uid52601
.   Shewanella HN 41 uid68137
.   Shewanella putrefaciens 200 uid161927
.   Shewanella denitrificans OS217 uid58263
.   Shewanella frigidimarina NCIMB 400 uid58265
.   Shewanella loihica PV 4 uid58349
.   Shewanella piezotolerans WP3 uid58745
.   Shewanella halifaxensis HAW EB4 uid59007
.   Shewanella pealeana ATCC 700345 uid58705
.   Shewanella woodyi ATCC 51908 uid58721
.   Shewanella sediminis HAW EB3 uid58835
.   Shewanella benthica KT99 uid54155
.   Shewanella violacea DSS12 uid47085
. unclassified Gallaecimonas xiamenensis 3 C 1 uid176353
. Alteromonadales_2 Glaciecola HTCC2999 uid54867
. (nodes 881-891) Glaciecola lipolytica E3 uid178730
.   Glaciecola arctica BSs20135 uid178729
.   Glaciecola psychrophila 170 uid178725
.   Glaciecola chathamensis S18K6 uid178731
.   Glaciecola polaris LMG 21857 uid178726
.   Glaciecola mesophila KMM 241 uid178728
.   Alteromonas macleodii AltDE1 uid179068
.   Alteromonas SN2 uid67349
.   Glaciecola punicea DSM 14233 ACAM 611 uid157053
.   Glaciecola nitratireducens FR1064 uid73759
.   Glaciecola pallidula DSM 14239 ACAM 615 uid178727
. Chromatiales Rheinheimera A13L uid68139
. (nodes 893-894) Alishewanella aestuarii B11 uid171146
.   Alishewanella agri BL06 uid170036
. Pseudoalteromonadaceae Pseudoalteromonas tunicata D2 uid54181
. (nodes 895-907) Pseudoalteromonas spongiae UST010723 006 uid168330
.   Pseudoalteromonas luteoviolacea B ATCC 29581 uid186644
.   Pseudoalteromonas rubra ATCC 29570 uid168329
.   Pseudoalteromonas flavipulchra JG1 uid177806
.   Pseudoalteromonas piscicida JCM 20779 uid168328
.   Pseudoalteromonas citrea NCIMB 1889 uid168326
.   Pseudoalteromonas SM9913 uid61247
.   Pseudoalteromonas undina NCIMB 2128 uid168331
.   Pseudoalteromonas marina mano4 uid168327
.   Pseudoalteromonas haloplanktis TAC125 uid58431
.   Pseudoalteromonas arctica A 37 1 2 uid168325
.   Pseudoalteromonas Bsw20308 uid179221
.   Pseudoalteromonas BSi20652 uid78645
. Alteromonadales Colwellia psychrerythraea 34H uid57855
. Idiomarinaceae Idiomarina A28L uid68223
. (nodes 909-911) Idiomarina xiamenensis 10 D 4 uid176354
.   Idiomarina baltica OS145 uid54159
.   Idiomarina loihiensis L2TR uid58087
. Oceanospirillales Kangiella koreensis DSM 16069 uid59209
. Pseudomonadales Pseudomonas GM18 uid171673
. (nodes 915-944) Pseudomonas mandelii JR 1 uid175806
.   Pseudomonas GM41 2012 uid171667
.   Pseudomonas chlororaphis aureofaciens 30 84 uid181709
.   Pseudomonas GM80 uid171657
.   Pseudomonas GM30 uid171669
.   Pseudomonas GM55 uid171663
.   Pseudomonas fragi A22 uid173061
.   Pseudomonas viridiflava UASWS0038 uid178273
.   Pseudomonas avellanae BPIC 631 uid177065
.   Pseudomonas syringae B728a uid57931
.   Pseudomonas brassicacearum NFM421 uid66303
.   Pseudomonas PAMC 25886 uid170201
.   Pseudomonas fluorescens A506 uid165185
.   Pseudomonas synxantha BG33R uid167316
.   Pseudomonas extremaustralis 14 3 substr 14 3b uid170171
.   Pseudomonas poae RE 1 1 14 uid188480
.   Pseudomonas fuscovaginae UPB0736 uid174621
.   Pseudomonas M47T1 uid167375
.   Pseudomonas HYS uid177807
.   Pseudomonas entomophila L48 uid58639
.   Pseudomonas GM84 uid171656
.   Pseudomonas putida BIRD 1 uid162055
.   Pseudomonas fulva 12 X uid67351
.   Pseudomonas pseudoalcaligenes CECT 5344 uid171984
.   Pseudomonas mendocina NK 01 uid66299
.   Pseudomonas Chol1 uid178064
.   Pseudomonas stutzeri A1501 uid58641
.   Azotobacter vinelandii DJ uid57597
.   Pseudomonas psychrotolerans L19 uid78819
.   Pseudomonas aeruginosa DK2 uid168996
. OMG_group Congregibacter litoralis KT71 uid54253
. (node 946) marine gamma proteobacterium HTCC2080 uid54583
. Alteromonadales_3 Alteromonas S89 uid81111
. (nodes 947-951) Saccharophagus degradans 2 40 uid57921
.   Teredinibacter turnerae T7901 uid59267
.   Simiduia agarivorans SA1 uid177713
.   Cellvibrio BR uid167161
.   Cellvibrio japonicus Ueda107 uid59139
. Oceanospirillales Hahella chejuensis KCTC 2396 uid58483
. Alteromonadales_4 Marinobacter aquaeolei VT8 uid59419
. (nodes 956-959) Marinobacter adhaerens HP15 uid162009
.   Marinobacter algicola DG893 uid54691
.   Marinobacter BSs20148 uid171995
.   Marinobacter ELB17 uid54619
. Oceanospirillales_1 Marinomonas MED121 uid54255
. (nodes 960-966) Marinomonas mediterranea MMB 1 uid64753
.   Marinomonas MWYL1 uid58715
.   Marinomonas posidonica IVIA Po 181 uid67323
.   Marinobacterium stanieri S30 uid81115
.   Neptuniibacter caesariensis uid54227
.   Bermanella marisrubri uid54229
.   Reinekea blandensis MED297 uid54199
. unclassified SAR86 cluster bacterium SAR86C uid173062
. Oceanospirillales_2 Candidatus Portiera aleyrodidarum BT B uid173859
. (nodes 967-974) Chromohalobacter salexigens DSM 3043 uid62921
.   Halomonas elongata DSM 2581 uid52781
.   Halomonas KM 1 uid171986
.   Halomonas boliviensis LC1 uid78313
.   Halomonas titanicae BH1 uid188651
.   Halomonas GFAJ 1 uid78821
.   Halomonas TD01 uid68639
. Oceanospirillales_3 gamma proteobacterium HdN1 uid51635
. (nodes 975-979) Alcanivorax W11 5 uid176219
.   Alcanivorax dieselolei B5 uid176364
.   Alcanivorax hongdengensis A 11 3 uid176602
.   Alcanivorax borkumensis SK2 uid58169
.   Alcanivorax DG881 uid54659
. Moraxellaceae Enhydrobacter aerosaccus SK60 uid55439
. (nodes 980-1004) Moraxella macacae 0408225 uid183957
.   Moraxella catarrhalis BBH18 uid48809
.   Psychrobacter PAMC 21119 uid172255
.   Psychrobacter arcticus 273 4 uid58021
.   Psychrobacter cryohalolentis K5 uid58373
.   Psychrobacter 1501 2011 uid67091
.   Psychrobacter PRwf 1 uid58459
.   Acinetobacter radioresistens DSM 6976 NBRC 102413 uid180968
.   Acinetobacter ADP1 uid61597
.   Acinetobacter ursingii DSM 16037 CIP 107286 uid173056
.   Acinetobacter bereziniae LMG 1003 uid173060
.   Acinetobacter P8 3 8 uid77731
.   Acinetobacter johnsonii SH046 uid41583
.   Acinetobacter lwoffii SH145 uid41587
.   Acinetobacter HA uid167861
.   Acinetobacter RUH2624 uid40849
.   Acinetobacter nosocomialis Ab22222 uid181746
.   Acinetobacter baumannii 1656 2 uid158677
.   Acinetobacter calcoaceticus PHEA 2 uid83123
.   Acinetobacter oleivorans DR1 uid50119
.   Acinetobacter NBRC 100985 uid78547
.   Acinetobacter parvus DSM 16617 CIP 108168 uid173057
.   Acinetobacter junii SH205 uid41585
.   Acinetobacter ATCC 27244 uid55389
.   Acinetobacter haemolyticus ATCC 19194 uid47361
. Legionellales Legionella pneumophila 2300 99 Alcoy uid48801
. (nodes 1005-1010) Legionella drancourtii LLAP12 uid56003
.   Legionella longbeachae NSW150 uid46099
.   Fluoribacter dumoffii Tex KL uid167163
.   Coxiella burnetii CbuG Q212 uid58893
.   Diplorickettsia massiliensis 20B uid176383
.   Rickettsiella grylli uid54407
. Thiotrichales Beggiatoa alba B18LD uid163695
. (nodes 1012-1015) Methylophaga aminisulfidivorans MP uid67817
.   Methylophaga thiooxidans DMS010 uid54693
.   Methylophaga JAM1 uid162947
.   Methylophaga JAM7 uid162949
. Chromatiales Nitrosococcus halophilus Nc4 uid46803
. (nodes 1018-1028) Nitrosococcus oceani ATCC 19707 uid58403
.   Nitrosococcus watsonii C 113 uid50331
.   Thiothrix nivea DSM 5205 uid163685
.   Thioalkalivibrio K90mix uid46181
.   Thioalkalivibrio nitratireducens DSM 14787 uid184011
.   Thioalkalivibrio thiocyanoxidans ARh 4 uid74027
.   Thiorhodospira sibirica ATCC 700588 uid74023
.   Ectothiorhodospira PHS 1 uid82731
.   Nitrococcus mobilis Nb 231 uid54185
.   Alkalilimnicola ehrlichii MLHE 1 uid58467
.   Halorhodospira halophila SL1 uid58473
. Xanthomonadales Hydrocarboniphaga effusa AP103 uid169224
. (nodes 1029-1050) Salinisphaera shabanensis E1L3A uid67923
.   Frateuria aurantia DSM 6220 uid81775
.   Rhodanobacter fulvus Jip2 uid167858
.   Rhodanobacter spathiphylli B39 uid167859
.   Rhodanobacter 2APBS1 uid74431
.   Rhodanobacter thiooxydans LCS2 uid167856
.   Pseudoxanthomonas suwonensis 11 1 uid62105
.   Xylella fastidiosa 9a5c uid57849
.   Xanthomonas campestris 8004 uid57595
.   Xanthomonas oryzae KACC 10331 uid58155
.   Xanthomonas perforans 91 118 uid63619
.   Xanthomonas fuscans aurantifolii ICPB 10535 uid47495
.   Xanthomonas axonopodis citri 306 uid57889
.   Xanthomonas gardneri ATCC 19865 uid63615
.   Xanthomonas vesicatoria ATCC 35937 uid63613
.   Stenotrophomonas maltophilia D457 uid162199
.   Pseudomonas geniculata N1 uid176938
.   Stenotrophomonas SKA14 uid54729
.   Pseudoxanthomonas spadix BD a59 uid75113
.   Xanthomonas translucens DAR61454 uid185791
.   Xanthomonas albilineans GPE PC73 uid43163
.   Xanthomonas sacchari NCPPB 4393 uid86877
. Chromatiales Thiorhodovibrio 970 uid74037
. (nodes 1052-1057) Thioflavicoccus mobilis 8321 uid184343
.   Thiocapsa marina 5811 uid72573
.   Marichromatium purpuratum 984 uid72575
.   Allochromatium vinosum DSM 180 uid46083
.   Thiorhodococcus drewsii AZ1 uid72963
.   Thiocystis violascens DSM 198 uid74025
. Thiotrichales Cycloclasticus P1 uid176368
. Methylococcales Methylococcus capsulatus Bath uid57607
. (nodes 1059-1062) Methylomonas methanica MC09 uid67363
.   Methylomicrobium alcaliphilum uid77119
.   Methylobacter tundripaludum SV96 uid53253
.   Methylomicrobium album BG8 uid67385
. Cardiobacteriales Dichelobacter nodosus VCS1703A uid57643
. (nodes 1064-1065) Cardiobacterium hominis ATCC 15826 uid55949
.   Cardiobacterium valvarum F0432 uid80727
. Xanthanomonadales Wohlfahrtiimonas chitiniclastica SH04 uid188353
. Chromatiales Halothiobacillus neapolitanus c2 uid41317
. sulfur-oxid_symb Candidatus Ruthia magnifica Cm Calyptogena magnifica uid58645
. (node 1069) Candidatus Vesicomyosocius okutanii HA uid59427
. Piscirickettsiaceae Thiomicrospira crunogena XCL 2 uid58183
. (nodes 1070-1071) Thioalkalimicrobium aerophilum AL3 uid74029
.   Thioalkalimicrobium cyclicum ALM1 uid67391
. unclassified Candidatus Tremblaya princeps PCIT uid68741
. Burkholderiales Candidatus Zinderia insecticola CARI uid52459
. unclassified Candidatus Carsonella ruddii CE isolate Thao2000 uid172732
. Francisellaceae Francisella cf novicida 3523 uid162107
. (nodes 1075-1079) Francisella novicida U112 uid58499
.   Francisella tularensis FSC198 uid58693
.   Francisella noatunensis orientalis Toba 04 uid164779
.   Francisella philomiragia ATCC 25017 uid59105
.   Francisella TX077308 uid68321
. Acidithiobacillales Acidithiobacillus caldus SM 1 uid70791
. (nodes 1080-1082) Acidithiobacillus thiooxidans ATCC 19377 uid157459
.   Acidithiobacillus ferrivorans SS3 uid67387
.   Acidithiobacillus ferrooxidans ATCC 23270 uid57649
Beta_proteobacteria Burkholderiaceae Candidatus Burkholderia kirkii UZHbot1 uid74017
(nodes 1083-1218) (nodes 1088-1133) Burkholderia SJ98 uid160003
.   Burkholderia YI23 uid81081
.   Burkholderia CCGE1002 uid42523
.   Burkholderia H160 uid55101
.   Burkholderia phytofirmans PsJN uid58729
.   Burkholderia xenovorans LB400 uid57823
.   Burkholderia CCGE1001 uid42975
.   Burkholderia phenoliruptrix BR3459a uid176370
.   Burkholderia phymatum STM815 uid58699
.   Burkholderia terrae BS001 uid168186
.   Burkholderia gladioli BSR3 uid66301
.   Burkholderia glumae BGR1 uid59397
.   Burkholderia oklahomensis C6786 uid54789
.   Burkholderia thailandensis E264 uid58081
.   Burkholderia mallei NCTC 10247 uid58385
.   Burkholderia pseudomallei K96243 uid57733
.   Burkholderia multivorans ATCC 17616 uid58697
.   Burkholderia 383 uid58073
.   Burkholderia ubonensis Bu uid54793
.   Burkholderia ambifaria AMMD uid58303
.   Burkholderia TJI49 uid179699
.   Burkholderia cepacia GG4 uid173858
.   Burkholderia vietnamiensis G4 uid58075
.   Burkholderia cenocepacia AU 1054 uid58371
.   Burkholderia rhizoxinica HKI 454 uid60487
.   Candidatus Glomeribacter gigasporarum uid73781
.   Polynucleobacter necessarius asymbioticus QLW P1DMWA 1 uid58611
.   Ralstonia PBA uid170039
.   Ralstonia pickettii 12D uid58859
.   Ralstonia solanacearum CFBP2957 uid50545
.   Cupriavidus metallidurans CH34 uid57815
.   Cupriavidus taiwanensis LMG 19424 uid61615
.   Cupriavidus necator N 1 uid68689
.   Ralstonia eutropha H16 uid62925
.   Oxalobacter formigenes HOxBLS uid55623
.   Herbaspirillum CF444 uid171676
.   Herbaspirillum YR522 uid171654
.   Herbaspirillum frisingense GSF30 uid179598
.   Herbaspirillum seropedicae SmR1 uid50427
.   Collimonas fungivorans Ter331 uid70793
.   Herminiimonas arsenicoxydans uid58291
.   Janthinobacterium Marseille uid58603
.   Massilia timonae CCUG 45783 uid182886
.   Janthinobacterium HH01 uid188444
.   Lautropia mirabilis ATCC 51599 uid62167
.   Limnobacter MED105 uid54689
. unclassified_Burk Thiomonas 3As uid178369
. (node 1135) Thiomonas intermedia K12 uid48825
. Sutterellaceae Parasutterella excrementihominis YIT 11859 uid66383
. (nodes 1137-1138) Sutterella parvirubra YIT 11816 uid86919
.   Sutterella wadsworthensis 2 1 59BFAA uid181408
. unclassified_Burk Leptothrix cholodnii SP 6 uid58971
. (nodes 1140-1142) Methylibium petroleiphilum PM1 uid58085
.   Rubrivivax benzoatilyticus JA2 uid66743
.   Rubrivivax gelatinosus IL144 uid158163
. Comamonadaceae Hydrogenophaga PBC uid167376
. (nodes 1143-1164) Hylemonella gracilis ATCC 19624 uid66745
.   Rhodoferax ferrireducens T118 uid58353
.   Polaromonas naphthalenivorans CJ2 uid58273
.   Polaromonas CF318 uid171649
.   Polaromonas JS666 uid58207
.   Ramlibacter tataouinensis TTB310 uid68279
.   Variovorax CF313 uid171650
.   Variovorax paradoxus EPS uid62107
.   Acidovorax KKS102 uid176500
.   Acidovorax NO 1 uid80409
.   Acidovorax delafieldii 2AN uid55645
.   Acidovorax radicis N35 uid74319
.   Acidovorax CF316 uid170384
.   Verminephrobacter At4 uid73529
.   Verminephrobacter eiseniae EF01 2 uid58675
.   Acidovorax avenae ATCC 19860 uid42497
.   Acidovorax citrulli AAC00 1 uid58429
.   Alicycliphilus denitrificans BC uid49953
.   Acidovorax ebreus TPSY uid59233
.   Comamonas testosteroni CNB 2 uid62961
.   Delftia acidovorans SPH 1 uid58703
.   Delftia Cs1 4 uid67319
. Alcaligenaceae Bordetella parapertussis 12822 uid57615
. (nodes 1165-1176) Bordetella pertussis CS uid158859
.   Bordetella bronchiseptica 253 uid178913
.   Bordetella avium 197N uid61563
.   Achromobacter SY8 uid78829
.   Achromobacter xylosoxidans A8 uid59899
.   Achromobacter piechaudii ATCC 43553 uid47029
.   Bordetella petrii DSM 12804 uid61631
.   Alcaligenes faecalis NCIB 8687 uid170035
.   Pusillimonas T7 7 uid66391
.   Taylorella asinigenitalis MCE3 uid73771
.   Taylorella equigenitalis ATCC 35865 uid170255
.   Candidatus Kinetoplastibacterium blastocrithidii ex Strigomonas culicis uid183629
. Rhodocyclaceae Candidatus Accumulibacter phosphatis clade IIA UW 1 uid59207
. (nodes 1177-1182) Dechloromonas aromatica RCB uid58025
.   Dechlorosoma suillum PS uid81439
.   Methyloversatilis universalis FAM5 uid67399
.   Aromatoleum aromaticum EbN1 uid58231
.   Azoarcus BH72 uid61603
.   Thauera MZ1T uid58987
. Hydrogenophilales Thiobacillus denitrificans ATCC 25259 uid58189
. Hydrogenophilales Sulfuricella denitrificans skB26 uid170240
. Methylophilales Methylobacillus flagellatus KT uid58049
. (nodes 1186-1190) Methylovorus glucosetrophus SIP3 4 uid59367
.   Methylovorus MP688 uid60723
.   Methylophilales bacterium HTCC2181 uid54577
.   Methylotenera 301 uid49469
.   Methylotenera mobilis JLW8 uid59373
. Nitrosomonadales Nitrosospira multiformis ATCC 25196 uid58361
. (nodes 1192-1195) Nitrosomonas europaea ATCC 19718 uid57647
.   Nitrosomonas eutropha C91 uid58363
.   Nitrosomonas AL212 uid55727
.   Nitrosomonas Is79A3 uid68745
. Gallionellales Gallionella capsiferriformans ES 2 uid51505
. (node 1196) Sideroxydans lithotrophicus ES 1 uid46801
. Neisseriaceae Neisseria oral taxon 014 F0314 uid49701
. (nodes 1197-1218) Neisseria sicca ATCC 29256 uid55323
.   Neisseria macacae ATCC 33926 uid70617
.   Neisseria mucosa ATCC 25996 uid55321
.   Neisseria lactamica 020 06 uid60851
.   Neisseria gonorrhoeae FA 1090 uid57611
.   Neisseria meningitidis 053442 uid58587
.   Neisseria cinerea ATCC 14685 uid55315
.   Neisseria flavescens NRL30031 H210 uid55317
.   Neisseria subflava NJ9703 uid55325
.   Neisseria weaveri ATCC 51223 uid179870
.   Neisseria wadsworthii 9715 uid74035
.   Eikenella corrodens ATCC 23834 uid55333
.   Neisseria shayeganii 871 uid73821
.   Neisseria bacilliformis ATCC BAA 1200 uid65827
.   Kingella denitrificans ATCC 33394 uid63429
.   Kingella oralis ATCC 51147 uid55763
.   Simonsiella muelleri ATCC 29453 uid47807
.   Kingella kingae ATCC 23330 uid67095
.   Laribacter hongkongensis HLHK9 uid59265
.   Chromobacterium violaceum ATCC 12472 uid58001
.   Lutiella nitroferrum 2002 uid55377
.   Pseudogulbenkiania NH8B uid73423

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.4. Actinobacteria

This group contains Rubrobacteria, Slackia, Acidothermus, Streptomyces, and Nocardia

Phylum Family Organism
Actinobacteria Coriobacteriales Atopobium parvulum DSM 20469 uid59195
(nodes 1221-1510) (nodes 1224-1238) Atopobium rimae ATCC 49626 uid55409
.   Atopobium vaginae DSM 15829 uid53885
.   Olsenella oral taxon 809 F0356 uid76573
.   Olsenella uli DSM 7084 uid51367
.   Coriobacterium glomerans PW2 uid65787
.   Collinsella tanakaei YIT 12063 uid73035
.   Collinsella aerofaciens ATCC 25986 uid54525
.   Collinsella intestinalis DSM 13280 uid55125
.   Collinsella stercoris DSM 13279 uid54813
.   Cryptobacterium curtum DSM 15641 uid59041
.   Eggerthella lenta DSM 2243 uid59079
.   Eggerthella YY7918 uid68707
.   Slackia piriformis YIT 12062 uid175495
.   Slackia heliotrinireducens DSM 20476 uid59051
.   Slackia exigua ATCC 700122 uid55993
. Rubrobacteridae Rubrobacter xylanophilus DSM 9941 uid58057
. (nodes 1239-1240) Conexibacter woesei DSM 14684 uid43467
.   Patulibacter I11 uid80835
. Acidimicrobiales Acidimicrobium ferrooxidans DSM 10331 uid59215
. Bifidobacteriales Bifidobacterium angulatum DSM 20098 uid55113
. (nodes 1249-1263) Bifidobacterium breve ACS 071 V Sch8b uid158863
.   Bifidobacterium 12 1 47BFAA uid61873
.   Bifidobacterium longum BBMN68 uid60163
.   Bifidobacterium bifidum BGN4 uid167988
.   Bifidobacterium dentium Bd1 uid43091
.   Bifidobacterium adolescentis ATCC 15703 uid58559
.   Bifidobacterium catenulatum DSM 16992 uid55369
.   Bifidobacterium pseudocatenulatum DSM 20438 uid55303
.   Gardnerella vaginalis 409 05 uid43211
.   Bifidobacterium animalis ATCC 25527 uid162513
.   Bifidobacterium gallicum DSM 20093 uid55371
.   Bifidobacterium asteroides PRL2011 uid176921
.   Scardovia wiggsiae F0424 uid181651
.   Parascardovia denticolens DSM 10105 uid61281
.   Scardovia inopinata F0304 uid47829
. Microbacteriaceae Candidatus Aquiluna IMCC13023 uid158317
. (nodes 1264-1271) Tropheryma whipplei TW08 27 uid57961
.   Leucobacter chromiiresistens JG 31 uid162357
.   Microbacterium laevaniformans OR221 uid157055
.   Microbacterium testaceum StLB037 uid62789
.   Leifsonia xyli CTCB07 uid57759
.   Clavibacter michiganensis NCPPB 382 uid61625
.   marine actinobacterium PHSC20C1 uid54153
.   Salinibacterium PAMC 21357 uid172846
. Actinomycetaceae Actinobaculum massiliae ACS 171 V Col2 uid182883
. (nodes 1272-1287) Arcanobacterium haemolyticum DSM 20595 uid49489
.   Actinomyces graevenitzii C83 uid80681
.   Actinomyces oral taxon 170 F0386 uid66153
.   Actinomyces oris K20 uid63275
.   Actinomyces viscosus C505 uid51663
.   Actinomyces urogenitalis DSM 15434 uid55459
.   Actinomyces massiliensis F0489 uid180496
.   Mobiluncus curtisii ATCC 43063 uid49695
.   Mobiluncus mulieris 28 1 uid42169
.   Actinomyces coleocanis DSM 15436 uid55457
.   Actinomyces turicensis ACS 279 V Col4 uid175493
.   Actinomyces georgiae F0490 uid180495
.   Actinomyces ICM39 uid171968
.   Actinomyces odontolyticus ATCC 17982 uid54529
.   Actinomyces ICM47 uid170984
.   Atopobium ICM58 uid171969
. Brevibacteriaceae Brevibacterium linens BL2 uid54109
. (node 1291) Brevibacterium mcbrellneri ATCC 49030 uid48125
. Micrococcaceae_1 Rothia mucilaginosa uid43093
. (nodes 1292-1306) Rothia aeria F0474 uid158319
.   Rothia dentocariosa ATCC 17931 uid49331
.   Kocuria palustris TAGA27 uid182893
.   Kocuria rhizophila DC2201 uid59099
.   Arthrobacter crystallopoietes BAB 32 uid184765
.   Renibacterium salmoninarum ATCC 33209 uid58899
.   Arthrobacter aurescens TC1 uid58109
.   Arthrobacter FB24 uid58141
.   Arthrobacter globiformis NBRC 12137 uid78817
.   Arthrobacter chlorophenolicus A6 uid58969
.   Arthrobacter phenanthrenivorans Sphe3 uid63629
.   Arthrobacter arilaitensis Re117 uid53509
.   Nesterenkonia F uid81597
.   Citricoccus CH26A uid85573
.   Micrococcus luteus NCTC 2665 uid59033
. Dermabacteraceae Brachybacterium squillarum M 6 3 uid86873
. (nodes 1307-1308) Brachybacterium faecium DSM 4810 uid58649
.   Brachybacterium paraconglomeratum LC44 uid162599
. Microccineae Beutenbergia cavernae DSM 12333 uid59047
. Celluomonadaceae Cellulomonas fimi ATCC 484 uid66779
. (node 1311) Cellulomonas flavigena DSM 20109 uid48821
. Promicromonosporaceae Isoptericola variabilis 225 uid67501
. (node 1313) Xylanimonas cellulosilytica DSM 15894 uid41935
. Micrococcineae_2 Jonesia denitrificans DSM 20603 uid59053
. (node 1314) Sanguibacter keddieii DSM 10542 uid40845
. Kineosporiaceae Kineococcus radiotolerans SRS30216 uid58067
. Intrasporangiaceae Intrasporangium calvum DSM 43043 uid61729
. (nodes 1317-1318) Janibacter HTCC2649 uid54213
.   Janibacter hoylei PVAS 1 uid175562
. Dermacoccaceae Dermacoccus Ellin185 uid59483
. Dermatophilaceae Austwickia chelonae NBRC 105200 uid174617
. (nodes 1320-1322) Kineosphaera limosa NBRC 100340 uid174615
.   Mobilicoccus pelagius NBRC 104925 uid84451
. Dermatophilaceae Kytococcus sedentarius DSM 20547 uid59071
. Intrasporangiaceae Serinicoccus profundi MCCC 1A05965 uid86869
. Propionibacterineae Propionibacterium avidum ATCC 25577 uid74033
. (nodes 1324-1333) Propionibacterium acnes 266 uid162059
.   Propionibacterium humerusii P08 uid170491
.   Propionibacterium acidipropionici ATCC 4875 uid179069
.   Propionibacterium freudenreichii shermanii CIRM BIA1 uid49535
.   Propionibacterium propionicum F0230a uid170533
.   Microlunatus phosphovorus NM 1 uid68055
.   Kribbella flavida DSM 17836 uid43465
.   Aeromicrobium marinum DSM 15272 uid55873
.   Nocardioidaceae bacterium Broad 1 uid64407
.   Nocardioides JS614 uid58149
. unclassified actinobacterium SCGC AAA027 L06 uid174471
. Catenulisporineae Catenulispora acidiphila DSM 44928 uid59077
. Streptomyceniaea Kitasatospora setae KM 6054 uid77027
. (nodes 1336-1373) Streptomyces cattleya NRRL 8057 DSM 46488 uid162187
.   Streptomyces auratus AGR0001 uid171646
.   Streptomyces rimosus ATCC 10970 uid185996
.   Streptomyces bingchenggensis BCW 1 uid82931
.   Streptomyces violaceusniger Tu 4113 uid52609
.   Streptomyces somaliensis DSM 40738 uid176939
.   Streptomyces clavuligerus ATCC 27064 uid47867
.   Streptomyces tsukubaensis NRRL18488 uid162933
.   Streptomyces pristinaespiralis ATCC 25486 uid59511
.   Streptomyces W007 uid80699
.   Streptomyces griseus NBRC 13350 uid58983
.   Streptomyces roseosporus NRRL 11379 uid55565
.   Streptomyces globisporus C 1027 uid178734
.   Streptomyces flavogriseus ATCC 33331 uid40839
.   Streptomyces SirexAA E uid72627
.   Streptomyces venezuelae ATCC 10712 uid177080
.   Streptomyces C uid55823
.   Streptomyces Mg1 uid55043
.   Streptomyces albus J1074 uid55547
.   Streptomyces S4 uid78151
.   Streptomyces SPB74 uid48415
.   Streptomyces Tu6071 uid66919
.   Streptomyces turgidiscabies Car8 uid185785
.   Streptomyces avermitilis MA 4680 uid57739
.   Streptomyces griseoaurantiacus M045 uid66149
.   Streptomyces hygroscopicus jinggangensis 5008 uid89409
.   Streptomyces e14 uid47353
.   Streptomyces chartreusis NRRL 12338 uid156769
.   Streptomyces ghanaensis ATCC 14672 uid55543
.   Streptomyces sviceus ATCC 29083 uid59513
.   Streptomyces acidiscabies 84 104 uid170242
.   Streptomyces scabiei 87 22 uid46531
.   Streptomyces viridochromogenes DSM 40736 uid55829
.   Streptomyces zinciresistens K42 uid72955
.   Streptomyces griseoflavus Tu4000 uid55831
.   Streptomyces coelicoflavus ZG0656 uid180030
.   Streptomyces coelicolor A3 2 uid57801
.   Streptomyces lividans TK24 uid55825
. Acidothermaceae Acidothermus cellulolyticus 11B uid58501
. Streptosporangineae Nocardiopsis alba ATCC BAA 2165 uid174334
. (nodes 1377-1379) Thermobifida fusca YX uid57703
.   Thermomonospora curvata DSM 43183 uid41885
.   Streptosporangium roseum DSM 43021 uid42521
.   Thermobispora bispora DSM 43833 uid48999
. Frankiaea Frankia CN3 uid78145
. (nodes 1381-1386) Frankia EuI1c uid42615
.   Frankia symbiont of Datisca glomerata uid46257
.   Frankia EAN1pec uid58367
.   Frankia EUN1f uid46069
.   Frankia CcI3 uid58397
.   Frankia alni ACN14a uid58695
.   Frankia QA3 uid169226
. Glycomycetaceae Stackebrandtia nassauensis DSM 44728 uid46663
. Micromonosporineae Actinoplanes missouriensis 431 uid158169
. (nodes 1390-1395) Actinoplanes SE50 110 uid162333
.   Micromonospora lupini Lupac 08 uid163145
.   Verrucosispora maris AB 18 032 uid66297
.   Salinispora arenicola CNS 205 uid58659
.   Salinispora tropica CNB 440 uid58565
.   Micromonospora ATCC 39149 uid55817
.   Micromonospora aurantiaca ATCC 27029 uid42501
. Geodermatophilaceae Modestobacter marinus uid167487
. (nodes 1397-1398) Geodermatophilus obscurus DSM 43160 uid43725
.   Blastococcus saxobsidens DD2 uid89391
. Nakamurellaceae Nakamurella multipartita DSM 44233 uid59221
. Pseudonocardiaceae Pseudonocardia dioxanivorans CB1190 uid65087
. (node 1401-1417) Pseudonocardia P1 uid63251
.   Saccharopolyspora erythraea NRRL 2338 uid62947
.   Saccharopolyspora spinosa NRRL 18395 uid73653
.   Actinosynnema mirum DSM 43827 uid58951
.   Saccharothrix espanaensis DSM 44229 uid184826
.   Amycolatopsis azurea DSM 43854 uid189461
.   Amycolatopsis decaplanina DSM 44594 uid191935
.   Amycolatopsis mediterranei S699 uid158689
.   Streptomyces AA4 uid55821
.   Amycolatopsis ATCC 39116 uid159503
.   Saccharomonospora marina XMU15 uid83009
.   Saccharomonospora paurometabolica YIM 90007 uid75123
.   Saccharomonospora viridis DSM 43017 uid59055
.   Saccharomonospora glauca K62 uid82727
.   Saccharomonospora cyanea NA 134 uid83011
.   Saccharomonospora azurea NA 128 uid75103
.   Saccharomonospora xinjiangensis XJ 54 uid158329
. Nocardiaceae Nocardia cyriacigeorgica GUH 2 uid89395
. (nodes 1421-1429) Nocardia farcinica IFM 10152 uid58203
.   Nocardia brasiliensis ATCC 700358 uid86913
.   Rhodococcus P14 uid175804
.   Rhodococcus pyridinivorans AK37 uid79055
.   Rhodococcus equi 103S uid60171
.   Rhodococcus opacus B4 uid13791
.   Rhodococcus imtechensis RKJ300 uid158667
.   Rhodococcus jostii RHA1 uid58325
.   Rhodococcus erythropolis PR4 uid59019
.   Rhodococcus AW25M09 uid187352
. Segniliparaceae Segniliparus rotundus DSM 44985 uid49049
. (node 1432) Segniliparus rugosus ATCC BAA 974 uid61889
. Tsukamurellaceae Tsukamurella paurometabola DSM 20162 uid48829
. Gordoniaceae Gordonia soli NBRC 108243 uid188136
. (nodes 1434-1453) Gordonia rhizosphera NBRC 16068 uid174616
.   Gordonia bronchialis DSM 43247 uid41403
.   Gordonia KTR9 uid174812
.   Gordonia terrae NBRC 100016 uid84449
.   Gordonia amarae NBRC 15530 uid78545
.   Gordonia polyisoprenivorans VH2 uid86651
.   Gordonia otitidis NBRC 100426 uid84445
.   Gordonia aichiensis NBRC 108223 uid186538
.   Gordonia sputi NBRC 100414 uid84447
.   Gordonia paraffinivorans NBRC 108238 uid191944
.   Gordonia alkanivorans NBRC 16433 uid72353
.   Gordonia amicalis NBRC 100051 uid186539
.   Gordonia namibiensis NBRC 108229 uid174798
.   Gordonia rubripertincta NBRC 101908 uid186606
.   Gordonia effusa NBRC 100432 uid78815
.   Gordonia araii NBRC 100433 uid78543
.   Gordonia hirsuta DSM 44140 NBRC 16056 uid186540
.   Gordonia malaquae NBRC 108250 uid191943
.   Gordonia neofelifaecis NRRL B 59395 uid64473
.   Gordonia sihwensis NBRC 108236 uid186541
. Mycobacteriaceae Mycobacterium abscessus uid61613
. (nodes 1454-1483) Mycobacterium massiliense GO 06 uid170732
.   Mycobacterium fortuitum DSM 46621 uid175127
.   Mycobacterium JLS uid58489
.   Mycobacterium KMS uid58491
.   Mycobacterium phlei RIVM601174 uid158325
.   Mycobacterium hassiacum DSM 44199 uid176492
.   Mycobacterium thermoresistibile ATCC 19527 uid76937
.   Mycobacterium chubuense NBB4 uid168322
.   Mycobacterium vanbaalenii PYR 1 uid58463
.   Mycobacterium gilvum PYR GCK uid59421
.   Mycobacterium vaccae ATCC 25954 uid175128
.   Mycobacterium smegmatis JS623 uid184820
.   Mycobacterium rhodesiae NBB3 uid75107
.   Mycobacterium tusciae JS617 uid82725
.   Mycobacterium JDM601 uid67369
.   Mycobacterium xenopi RIVM700367 uid158327
.   Mycobacterium africanum GM041182 uid68839
.   Mycobacterium tuberculosis CCDC5079 uid161943
.   Mycobacterium bovis AF2122 97 uid57695
.   Mycobacterium canettii CIPT 140010059 uid70731
.   Mycobacterium leprae Br4923 uid59293
.   Mycobacterium ulcerans Agy99 uid62939
.   Mycobacterium marinum M uid59423
.   Mycobacterium liflandii 128FXT uid59005
.   Mycobacterium parascrofulaceum ATCC BAA 614 uid48977
.   Mycobacterium avium 104 uid57693
.   Mycobacterium colombiense CECT 3035 uid71463
.   Mycobacterium MOTT36Y uid164001
.   Mycobacterium indicus pranii MTCC 9506 uid175523
.   Mycobacterium intracellulare ATCC 13950 uid167994
. Corynebacteriaceae Amycolicicoccus subflavus DQS3 9A1 uid67253
. (nodes 1484-1510) Dietzia alimentaria 72 uid177888
.   Dietzia cinnamea P4 uid62173
.   Corynebacterium amycolatum SK46 uid55411
.   Corynebacterium kroppenstedtii DSM 44385 uid59411
.   Corynebacterium urealyticum DSM 7109 uid61639
.   Corynebacterium jeikeium K411 uid58399
.   Corynebacterium resistens DSM 45100 uid50555
.   Corynebacterium bovis DSM 20582 uid67345
.   Corynebacterium nuruki S6 4 uid77677
.   Corynebacterium variabile DSM 44702 uid62003
.   Corynebacterium glucuronolyticum ATCC 51866 uid55539
.   Corynebacterium matruchotii ATCC 14266 uid51885
.   Corynebacterium diphtheriae 241 uid83607
.   Corynebacterium pseudotuberculosis 1002 uid159677
.   Corynebacterium ulcerans 0102 uid169879
.   Corynebacterium durum F0235 uid183766
.   Corynebacterium efficiens YS 314 uid62905
.   Corynebacterium glutamicum ATCC 13032 uid57905
.   Corynebacterium ammoniagenes DSM 20306 uid48813
.   Corynebacterium casei uid78139
.   Corynebacterium accolens ATCC 49725 uid55467
.   Corynebacterium pseudogenitalium ATCC 33035 uid55395
.   Corynebacterium tuberculostearicum SK141 uid55413
.   Corynebacterium aurimucosum ATCC 700975 uid59409
.   Corynebacterium striatum ATCC 6940 uid55471
.   Corynebacterium genitalium ATCC 33030 uid52785
.   Corynebacterium lipophiloflavum DSM 44291 uid55469

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.5. Firmicutes, et al.

This group contains Thermotogae, Dictyoglomus, Thermoanaerovibrio, Deinococcus/Thermus, Chloroflexi, Syntrophomonads, Selenomonads, Bacilli, Lactobacilli, Mycoplasmas, and Clostridia. Annotated pdfs with node numbers are available for:

Family names and links to Genbank are below.

Phylum Family Organism
.   Candidatus Methylomirabilis oxyfera uid161981
Nitrospirae Nitrospirales Leptospirillum ferriphilum ML 04 uid175904
(nodes 1517-1520) (node 1517) Leptospirillum ferrooxidans C2 3 uid158171
. Nitrospiraceae Candidatus Nitrospira defluvii uid51175
. (nodes 1519-1520) Candidatus Poribacteria WGA A3 uid43489
.   Thermodesulfovibrio yellowstonii DSM 11347 uid59257
Thermodesulfobacteria Thermodesulfobacteria Thermodesulfatator indicus DSM 15286 uid68285
.   Thermodesulfobacterium OPB45 uid68283
.   Plautia stali symbiont uid65033
.   Candidatus Cloacamonas acidaminovorans Evry uid62959
.   Caldithrix abyssi DSM 13497 uid81765
Deinococcus-Thermus Thermales Thermus aquaticus Y51MC23 uid55053
(nodes 1524-1540) (nodes 1525-1533) Thermus CCB US3 UF1 uid81197
.   Thermus thermophilus HB27 uid58033
.   Thermus scotoductus SA 01 uid62273
.   Thermus RLM uid156767
.   Thermus oshimai JL 2 uid178948
.   Meiothermus ruber DSM 1279 uid46661
.   Meiothermus silvanus DSM 9946 uid49485
.   Marinithermus hydrothermalis DSM 14884 uid65783
.   Oceanithermus profundus DSM 14977 uid60855
. Deinococcus Truepera radiovictrix DSM 17093 uid49533
. (nodes 1534-1540) Deinococcus peraridilitoris DSM 19664 uid183485
.   Deinococcus maricopensis DSM 21211 uid62225
.   Deinococcus proteolyticus MRP uid63399
.   Deinococcus geothermalis DSM 11300 uid58275
.   Deinococcus gobiensis I 0 uid162509
.   Deinococcus deserti VCD115 uid58615
.   Deinococcus radiodurans R1 uid57665
Dictyoglomi Dictyoglomi Dictyoglomus thermophilum H 6 12 uid59439
(node 1544) (node 1544) Dictyoglomus turgidum DSM 6724 uid59177
.   Thermodesulfobium narugense DSM 14796 uid66601
.   Coprothermobacter proteolyticus DSM 5265 uid59253
.   Caldisericum exile AZM16c01 uid158173
Thermotogae Thermotogae Kosmotoga olearia TBF 19 5 1 uid59205
(nodes 1547-1561) (nodes 1547-1561) Mesotoga prima MesG1 Ag 4 2 uid52599
.   Marinitoga piezophila KA3 uid81629
.   Petrotoga mobilis SJ95 uid58747
.   Thermotoga lettingae TMO uid58419
.   Thermotoga thermarum DSM 5069 uid68449
.   Thermosipho africanus TCF52B uid59095
.   Thermosipho melanesiensis BI429 uid58683
.   Fervidobacterium nodosum Rt17 B1 uid58625
.   Fervidobacterium pennivorans DSM 9078 uid78143
.   Thermotoga petrophila RKU 1 uid58655
.   Thermotoga maritima MSB8 uid57723
.   Thermotoga naphthophila RKU 10 uid42777
.   Thermotoga neapolitana DSM 4359 uid59065
.   Thermotoga RQ2 uid58935
.   Thermotoga EMP uid174473
Synergistetes Synergistetes Anaerobaculum hydrogeniformans ATCC BAA 1850 uid55759
(nodes 1562-1571) (nodes 1562-1571) Anaerobaculum mobile DSM 13181 uid168323
.   Thermovirga lienii DSM 17291 uid77129
.   Synergistes 3 1 syn1 uid80429
.   Aminomonas paucivorans DSM 12260 uid60577
.   Thermanaerovibrio acidaminovorans DSM 6589 uid41925
.   Thermanaerovibrio velox DSM 12556 uid80703
.   Aminobacterium colombiense DSM 12261 uid47083
.   Dethiosulfovibrio peptidovorans DSM 11002 uid54917
.   Jonquetella anthropi DSM 22815 uid182031
.   Pyramidobacter piscolens W5455 uid42959
Chloroflexi Chloroflexi Herpetosiphon aurantiacus DSM 785 uid58599
(nodes 1572-1589) Chloroflexales Roseiflexus castenholzii DSM 13941 uid58287
. (nodes 1575-1578 Roseiflexus RS 1 uid58523
.   Oscillochloris trichoides DG6 uid59465
.   Chloroflexus aggregans DSM 9485 uid58621
.   Chloroflexus aurantiacus J 10 fl uid57657
.   Thermobaculum terrenum ATCC BAA 798 uid42011
.   Thermomicrobium roseum DSM 5159 uid59341
. Sphaerobacterales Nitrolancetus hollandicus Lb uid168185
. (node 1581) Sphaerobacter thermophilus DSM 20745 uid41997
.   Ktedonobacter racemifer DSM 44963 uid49671
. Dehalococcoidetes Dehalogenimonas lykanthroporepellens BL DC 9 uid48131
. (nodes 1584-1588) Dehalococcoides VS uid42393
.   Dehalococcoides mccartyi BTF08 uid190183
.   Dehalococcoides CBDB1 uid58413
.   Dehalococcoides BAV1 uid58477
.   Dehalococcoides ethenogenes 195 uid57763
.   Anaerolinea thermophila UNI 1 uid62245
.   Caldilinea aerophila DSM 14535 NBRC 104270 uid158165
Clostridia Clostridiaceae Clostridium nexile DSM 1787 uid55077
(nodes 1591-1819) (nodes 1602-1649) Clostridium hylemonae DSM 15053 uid55299
.   Clostridium scindens ATCC 35704 uid54533
.   Dorea formicigenerans 4 6 53AFAA uid73033
.   Dorea longicatena DSM 13814 uid54515
.   Clostridium D5 uid63427
.   Ruminococcus gnavus ATCC 29149 uid54537
.   Ruminococcus torques ATCC 27756 uid54511
.   Ruminococcus lactaris ATCC 29176 uid54903
.   Bryantella formatexigens DSM 14469 uid54943
.   Blautia hansenii DSM 20583 uid55275
.   Blautia hydrogenotrophica DSM 10507 uid54939
.   Ruminococcus 5 1 39BFAA uid55629
.   Ruminococcus obeum ATCC 29174 uid54509
.   Roseburia hominis A2 183 uid73419
.   Roseburia intestinalis L1 82 uid55267
.   Shuttleworthia satelles DSM 14600 uid55775
.   Eubacterium rectale ATCC 33656 uid59169
.   Clostridium SY8519 uid68705
.   Butyrivibrio proteoclasticus B316 uid51489
.   Eubacterium cellulosolvens 6 uid61055
.   Eubacterium eligens ATCC 27750 uid59171
.   Butyrivibrio crossotus DSM 2876 uid55091
.   Bacteroides pectinophilus ATCC 43243 uid54987
.   Johnsonella ignava ATCC 51276 uid77897
.   Eubacterium saburreum DSM 3986 uid61491
.   Lachnospiraceae oral taxon 107 F0167 uid66385
.   Clostridium M62 1 uid54557
.   Clostridium symbiosum WAL 14163 uid63097
.   Clostridium bolteae ATCC BAA 613 uid54523
.   Clostridium clostridioforme 2 1 49FAA uid76955
.   Clostridium citroniae WAL 17108 uid76581
.   Clostridiales bacterium 1 7 47FAA uid55287
.   Clostridium hathewayi DSM 13479 uid55373
.   Clostridium saccharolyticum WM1 uid51419
.   Oribacterium oral taxon 078 F0262 uid55773
.   Oribacterium sinus F0268 uid55891
.   Oribacterium ACB7 uid79229
.   Oribacterium ACB1 uid79231
.   Oribacterium ACB8 uid170518
.   Eubacterium ventriosum ATCC 27560 uid54517
.   Clostridium phytofermentans ISDg uid58519
.   Clostridium L2 50 uid54559
.   Coprococcus eutactus ATCC 27759 uid54541
.   Eubacterium hallii DSM 3353 uid54535
.   Anaerostipes 3 2 56FAA uid61867
.   Anaerostipes caccae DSM 14662 uid54561
.   Clostridium SS2 1 uid54553
.   Eubacterium hadrum DSM 3319 uid183778
.   Clostridium lentocellum DSM 5427 uid49117
.   Oscillibacter valericigenes uid73895
.   Ruminococcaceae bacterium D16 uid52825
.   Bacteroides capillosus ATCC 29799 uid54531
.   Flavonifractor plautii ATCC 29863 uid80691
. Ruminococcaceae Clostridium methylpentosum DSM 5476 uid55281
. (nodes 1654-1664) Eubacterium siraeum DSM 15702 uid54603
.   Ruminococcus albus 7 uid51721
.   Ruminococcus flavefaciens FD 1 uid55965
.   Clostridium leptum DSM 753 uid54605
.   Clostridium MSTE9 uid180497
.   Anaerotruncus colihominis DSM 17241 uid54807
.   Ethanoligenens harbinense YUAN 3 uid46255
.   Subdoligranulum 4 3 54A2FAA uid80415
.   Subdoligranulum variabile DSM 15176 uid54539
.   Faecalibacterium cf prausnitzii KLE1255 uid60645
.   Faecalibacterium prausnitzii A2 165 uid54551
.   Clostridiales genomosp BVAB3 UPII9 5 uid46219
. Clostridiaceae Clostridium stercorarium DSM 8532 uid186819
. (nodes 1665-1670 Clostridium cellulolyticum H10 uid58709
.   Clostridium BNL1100 uid84307
.   Clostridium papyrosolvens DSM 2782 uid55815
.   Clostridium thermocellum ATCC 27405 uid57917
.   Acetivibrio cellulolyticus CD2 uid51533
.   Clostridium clariflavum DSM 19732 uid82345
. Family III Caldicellulosiruptor saccharolyticus DSM 8903 uid58289
. (nodes 1672-1677) Caldicellulosiruptor bescii DSM 6725 uid59201
.   Caldicellulosiruptor kronotskyensis 2002 uid60491
.   Caldicellulosiruptor hydrothermalis 108 uid60157
.   Caldicellulosiruptor kristjanssonii 177R1B uid60393
.   Caldicellulosiruptor lactoaceticus 6A uid60575
.   Caldicellulosiruptor owensensis OL uid60165
.   Caldicellulosiruptor obsidiansis OB47 uid51501
.   Mahella australiensis 50 1 BON uid66917
.   Thermoanaerobacterium thermosaccharolyticum DSM 571 uid51639
.   Thermoanaerobacterium xylanolyticum LX 11 uid63163
.   Thermoanaerobacterium saccharolyticum JW SL YS485 uid167781
. Thermoanaerobacteraceae Thermoanaerobacter tengcongensis MB4 uid57813
. (nodes 1683-1690) Thermoanaerobacter pseudethanolicus ATCC 33223 uid58339
.   Thermoanaerobacter wiegelii Rt8 B1 uid52581
.   Thermoanaerobacter X514 uid58589
.   Thermoanaerobacter X561 uid55835
.   Thermoanaerobacter siderophilus SR4 uid169227
.   Thermoanaerobacter brockii finnii Ako 1 uid55639
.   Thermoanaerobacter italicus Ab9 uid46241
.   Thermoanaerobacter ethanolicus CCSD1 uid55837
. Clostridiaceae Caloramator australicus RC3 uid171387
. (nodes 1691-1710) Candidatus Arthromitus SFB mouse Japan uid71379
.   Clostridium perfringens 13 uid57681
.   Clostridium butyricum 5521 uid54843
.   Clostridium DL VIII uid78327
.   Clostridium beijerinckii NCIMB 8052 uid58137
.   Clostridium Maddingley MBC34 26 uid178945
.   Clostridium 7 2 43FAA uid55597
.   Clostridium celatum DSM 1785 uid183779
.   Clostridium JC122 uid174326
.   Clostridium tetani E88 uid57683
.   Clostridium botulinum A2 Kyoto uid59229
.   Clostridium sporogenes ATCC 15579 uid54895
.   Clostridium carboxidivorans P7 uid48985
.   Clostridium kluyveri DSM 555 uid58885
.   Clostridium ljungdahlii DSM 13528 uid50583
.   Clostridium novyi NT uid58643
.   Clostridium cellulovorans 743B uid51503
.   Clostridium acetobutylicum ATCC 824 uid57677
.   Clostridium arbusti SL206 uid171987
.   Clostridium pasteurianum DSM 525 uid185802
.   Anaerofustis stercorihominis DSM 17244 uid54805
.   Acetobacterium woodii DSM 1030 uid88073
.   Pseudoramibacter alactolyticus ATCC 23263 uid61507
.   Eubacterium limosum KIST612 uid59777
.   Eubacterium saphenum ATCC 49989 uid55765
. Family XIII Eubacterium infirmum F0142 uid81785
. (node 1718) Mogibacterium CM50 uid174240
. Family XI Peptoniphilus oral taxon 375 F0436 uid71189
. (nodes 1719-1732) Peptoniphilus duerdenii ATCC BAA 1640 uid51739
.   Peptoniphilus indolicus ATCC 29427 uid74031
.   Peptoniphilus lacrimalis 315 B uid42973
.   Peptoniphilus harei ACS 146 V Sch2b uid61041
.   Peptoniphilus rhinitidis 1 13 uid171988
.   Parvimonas micra ATCC 33270 uid54527
.   Parvimonas oral taxon 110 F0139 uid67821
.   Finegoldia magna ATCC 29328 uid58867
.   Helcococcus kunzii ATCC 51366 uid83005
.   Anaerococcus hydrogenalis ACS 025 V Sch4 uid63589
.   Anaerococcus vaginalis ATCC 51170 uid56001
.   Anaerococcus lactolyticus ATCC 51172 uid55391
.   Anaerococcus prevotii DSM 20548 uid59219
.   Anaerococcus tetradius ATCC 35098 uid55461
.   Clostridium acidurici 9a uid176126
. Peptostreptococcaceae Peptostreptococcus anaerobius 653 L uid46195
. (nodes 1736-1739) Peptostreptococcus stomatis DSM 17678 uid52563
.   Clostridium hiranonis DSM 13275 uid55075
.   Clostridium bartlettii DSM 16795 uid54809
.   Clostridium difficile 630 uid57679
.   Filifactor alocis ATCC 35896 uid46625
. Eubacteriaceae Eubacteriaceae bacterium ACC19a uid79227
. (nodes 1741-1742) Eubacterium AS15 uid173856
.   Eubacterium yurii margaretiae ATCC 43715 uid52347
.   Alkaliphilus metalliredigens QYMF uid58171
.   Alkaliphilus oremlandii OhILAs uid58495
. Thermoanaerobacterales Thermosediminibacter oceani DSM 16646 uid51421
. (node 1744-1745) Tepidanaerobacter acetatoxydans Re1 uid184827
.   Tepidanaerobacter Re1 uid66873
. Family XVII Thermaerobacter marianensis DSM 12885 uid61727
. (node 1747) Thermaerobacter subterraneus DSM 13965 uid61053
. Syntrophomonadaceae Syntrophomonas wolfei Goettingen uid58179
. (node 1748) Syntrophothermus lipocalidus DSM 12680 uid49527
. Halanaerobales Halothermothrix orenii H 168 uid58585
. (nodes 1749-1752) Halanaerobium hydrogeniformans uid60191
.   Halanaerobium praevalens DSM 2228 uid161959
.   Acetohalobium arabaticum DSM 5501 uid51423
.   Halobacteroides halobius DSM 5150 uid184862
.   Dethiobacter alkaliphilus AHT 1 uid55401
.   Natranaerobius thermophilus JW NM WN LF uid59001
.   Sulfobacillus acidophilus DSM 10332 uid88061
.   Symbiobacterium thermophilum IAM 14863 uid58165
. Thermoanaerobacterales Moorella thermoacetica ATCC 39073 uid58051
. (node 1759) Thermacetogenium phaeum DSM 12270 uid177811
. Peptococcaceae Thermincola potens JR uid48823
. (nodes 1760-1783) Desulfotomaculum kuznetsovii DSM 6115 uid67357
.   Desulfotomaculum gibsoniae DSM 7213 uid76945
.   Pelotomaculum thermopropionicum SI uid58877
.   Desulfotomaculum acetoxidans DSM 771 uid59109
.   Desulfotomaculum carboxydivorans CO 1 SRB uid67317
.   Desulfotomaculum nigrificans DSM 574 uid63161
.   Desulfotomaculum ruminis DSM 2154 uid67507
.   Desulfotomaculum hydrothermale Lam5 DSM 18033 uid179385
.   Desulfotomaculum reducens MI 1 uid58277
.   Candidatus Desulforudis audaxviator MP104C uid59067
.   Ammonifex degensii KC4 uid41053
.   Carboxydothermus hydrogenoformans Z 2901 uid57821
.   Heliobacterium modesticaldum Ice1 uid58279
.   Dehalobacter 11DCA uid177715
.   Syntrophobotulus glycolicus DSM 8271 uid63343
.   Desulfosporosinus acidiphilus SJ4 uid156759
.   Desulfosporosinus OT uid72957
.   Desulfosporosinus orientis DSM 765 uid82939
.   Desulfosporosinus meridiei DSM 13257 uid75097
.   Desulfosporosinus youngiae DSM 17734 uid82713
.   Desulfitobacterium metallireducens DSM 15288 uid75095
.   Desulfitobacterium dichloroeliminans LMG P 21439 uid82555
.   Desulfitobacterium dehalogenans ATCC 51507 uid82553
.   Desulfitobacterium hafniense DCB 2 uid57749
. Negativicutes Veillonella dispar ATCC 17748 uid55331
. (nodes 1784-1819) Veillonella oral taxon 158 F0412 uid61047
.   Veillonella parvula DSM 2008 uid41927
.   Veillonella 3 1 44 uid47845
.   Veillonella 6 1 27 uid47835
.   Veillonella ACP1 uid172974
.   Veillonella atypica ACS 049 V Sch6 uid51525
.   Veillonella ratti ACS 216 V Col6b uid182889
.   Anaeroglobus geminatus F0357 uid80689
.   Megasphaera micronuciformis F0359 uid60585
.   Megasphaera elsdenii DSM 20460 uid71135
.   Megasphaera genomosp type 1 28L uid46567
.   Megasphaera UPII 135 E uid71191
.   Dialister invisus DSM 15470 uid55761
.   Dialister succinatiphilus YIT 11850 uid81763
.   Dialister micraerophilus DSM 19965 uid65829
.   Dialister microaerophilus UPII 345 E uid61045
.   Phascolarctobacterium YIT 12067 uid62745
.   Acidaminococcus fermentans DSM 20731 uid43471
.   Acidaminococcus D21 uid55871
.   Acidaminococcus intestini RyC MR95 uid74445
.   Megamonas funiformis YIT 11815 uid82999
.   Selenomonas CM52 uid174241
.   Selenomonas sputigena ATCC 35185 uid55329
.   Selenomonas infelix ATCC 43532 uid76957
.   Selenomonas flueggei ATCC 43531 uid55953
.   Selenomonas F0473 uid182887
.   Selenomonas FOBRC9 uid173853
.   Selenomonas artemidis F0399 uid62283
.   Selenomonas oral taxon 137 F0430 uid61049
.   Selenomonas noxia ATCC 43541 uid55895
.   Centipeda periodontii DSM 2778 uid67397
.   Mitsuokella multacida DSM 20544 uid55073
.   Selenomonas ruminantium lactilytica TAM6421 uid157247
.   Pelosinus fermentans A11 uid180746
.   Thermosinus carboxydivorans Nor1 uid54463
.   Acetonema longum DSM 6540 uid68557
Lactobacillales Streptococcaceae Streptococcus SK643 uid161589
(nodes 1822-1956) (nodes 1826-1874) Streptococcus mitis B6 uid46097
.   Streptococcus pneumoniae 670 6B uid52533
.   Streptococcus pseudopneumoniae IS7493 uid71153
.   Streptococcus GMD4S uid180425
.   Streptococcus C300 uid62527
.   Streptococcus oralis Uo5 uid65449
.   Streptococcus BS35b uid172972
.   Streptococcus M143 uid42367
.   Streptococcus SK140 uid161587
.   Streptococcus peroris ATCC 700780 uid62543
.   Streptococcus infantis ATCC 700779 uid180433
.   Streptococcus cristatus ATCC 51100 uid179856
.   Streptococcus sanguinis SK36 uid58381
.   Streptococcus AS14 uid172973
.   Streptococcus gordonii Challis substr CH1 uid57667
.   Streptococcus 2 1 36FAA uid41507
.   Streptococcus australis ATCC 700641 uid179855
.   Streptococcus parasanguinis ATCC 15912 uid49313
.   Streptococcus intermedius JTH08 uid168614
.   Streptococcus anginosus 1 2 62CV uid62163
.   Streptococcus constellatus pharyngis SK1060 uid72195
.   Streptococcus suis 05ZYH33 uid58663
.   Streptococcus macacae NCTC 11558 uid71359
.   Streptococcus mutans GS 5 uid169223
.   Streptococcus ratti FA 1 uid172632
.   Streptococcus criceti uid71271
.   Streptococcus downei F0415 uid60561
.   Streptococcus thermophilus CNRZ1066 uid58221
.   Streptococcus salivarius 57 I uid162151
.   Streptococcus vestibularis ATCC 49124 uid62665
.   Streptococcus C150 uid62525
.   Streptococcus equinus ATCC 9812 uid62297
.   Streptococcus infantarius CJ18 uid87033
.   Streptococcus bovis ATCC 700338 uid52359
.   Streptococcus macedonicus ACA DC 198 uid81631
.   Streptococcus agalactiae 2603V R uid57943
.   Streptococcus urinalis 2285 97 uid71277
.   Streptococcus ictaluri 707 05 uid71275
.   Streptococcus equi 4047 uid59259
.   Streptococcus canis FSL Z3 227 uid168663
.   Streptococcus pyogenes A20 uid178106
.   Streptococcus dysgalactiae equisimilis AC 2713 uid178644
.   Streptococcus iniae 9117 uid175677
.   Streptococcus parauberis KCTC 11537 uid67355
.   Streptococcus uberis 0140J uid57959
.   Streptococcus porcinus Jelinkova 176 uid66741
.   Streptococcus pseudoporcinus LQ 940 04 uid179694
.   Lactococcus garvieae ATCC 49156 uid73413
.   Lactococcus lactis cremoris A76 uid160937
. Leuconostocaceae Leuconostoc mesenteroides ATCC 8293 uid57919
. (nodes 1878-1893) Leuconostoc pseudomesenteroides 4882 uid171985
.   Leuconostoc argentinum KCTC 3773 uid64589
.   Leuconostoc citreum KM20 uid58481
.   Leuconostoc kimchii IMSNU 11154 uid48589
.   Leuconostoc gasicomitatum LMG 18811 uid50385
.   Leuconostoc gelidum JB7 uid175682
.   Leuconostoc carnosum JB16 uid176371
.   Fructobacillus fructosus KCTC 3544 uid68703
.   Leuconostoc fallax KCTC 3537 uid66211
.   Oenococcus kitaharae DSM 17330 uid81361
.   Oenococcus oeni PSU 1 uid59417
.   Weissella koreensis KACC 15510 uid68837
.   Weissella ceti NC36 uid184763
.   Weissella paramesenteroides ATCC 33313 uid55901
.   Weissella cibaria KACC 11862 uid66733
.   Weissella confusa LBAE C39 2 uid168254
. Lactobacillaceae_3 Lactobacillus pentosus KCA1 uid169225
. (nodes 1894-1914) Lactobacillus plantarum JDM1 uid59361
.   Pediococcus claussenii ATCC BAA 344 uid81103
.   Pediococcus acidilactici 7 4 uid42365
.   Pediococcus pentosaceus ATCC 25745 uid57981
.   Lactobacillus suebicus KCTC 3549 uid80667
.   Lactobacillus vaginalis ATCC 49540 uid55515
.   Lactobacillus reuteri DSM 20016 uid58471
.   Lactobacillus antri DSM 16041 uid55491
.   Lactobacillus oris F0423 uid179841
.   Lactobacillus mucosae LM1 uid86029
.   Lactobacillus coleohominis 101 4 CHN uid55977
.   Lactobacillus gastricus PS3 uid84443
.   Lactobacillus fermentum CECT 5716 uid162003
.   Lactobacillus brevis ATCC 367 uid57989
.   Lactobacillus malefermentans KCTC 3548 uid80665
.   Lactobacillus hilgardii ATCC 8290 uid55501
.   Lactobacillus buchneri NRRL B 30929 uid66205
.   Lactobacillus kisonensis F0435 uid81769
.   Lactobacillus fructivorans KCTC 3543 uid68677
.   Lactobacillus florum 2F uid177324
.   Lactobacillus sanfranciscensis TMW 1 1304 uid72937
. Lactobacillaceae_2 Lactobacillus mali KCTC 3596 DSM 20444 uid180535
. (nodes 1915-1919) Lactobacillus vini DSM 20605 uid175441
.   Lactobacillus animalis KCTC 3501 uid67869
.   Lactobacillus ruminis ATCC 27782 uid73417
.   Lactobacillus acidipiscis KCTC 13900 uid80675
.   Lactobacillus salivarius CECT 5713 uid162005
. Lactobacillaceae_1 Lactobacillus coryniformis CECT 5711 uid180492
. (nodes 1921-1940) Lactobacillus curvatus CRL 705 uid76157
.   Lactobacillus sakei 23K uid58281
.   Lactobacillus rhamnosus ATCC 8530 uid162169
.   Lactobacillus paracasei 8700 2 uid55295
.   Lactobacillus zeae KCTC 3804 uid80671
.   Lactobacillus versmoldensis KCTC 3814 uid80673
.   Lactobacillus iners AB 1 uid51205
.   Lactobacillus hominis CRBIP 24 179 uid170497
.   Lactobacillus gasseri ATCC 33323 uid57687
.   Lactobacillus johnsonii DPC 6026 uid162057
.   Lactobacillus jensenii 115 3 CHN uid40897
.   Lactobacillus delbrueckii bulgaricus 2038 uid161929
.   Lactobacillus equicursoris CIP 110162 uid177398
.   Lactobacillus amylolyticus DSM 11664 uid48293
.   Lactobacillus ultunensis DSM 16047 uid55513
.   Lactobacillus acidophilus 30SC uid63605
.   Lactobacillus helveticus DPC 4571 uid58761
.   Lactobacillus kefiranofaciens ZW3 uid67985
.   Lactobacillus crispatus ST1 uid48359
.   Lactobacillus gigeriorum CRBIP 24 85 uid170495
.   Lactobacillus pasteurii CRBIP 24 76 uid170496
. Enterococcaceae Melissococcus plutonius ATCC 35311 uid66803
. (nodes 1941-1946) Enterococcus faecalis 62 uid159663
.   Enterococcus faecium Aus0004 uid87025
.   Enterococcus casseliflavus ATCC 12755 uid63559
.   Enterococcus saccharolyticus 30 1 uid76953
.   Tetragenococcus halophilus uid74441
.   Enterococcus italicus DSM 15952 uid61487
. Carnobacteriaceae Carnobacterium 17 4 uid65789
. (nodes 1947-1951) Carnobacterium AT7 uid54673
.   Granulicatella adiacens ATCC 49175 uid55951
.   Granulicatella elegans ATCC 700633 uid40873
.   Alloiococcus otitis ATCC 51267 uid182884
.   Dolosigranulum pigrum ATCC 51524 uid83001
. Aerococcaceae Facklamia hominis CCUG 36813 uid175684
. (nodes 1952-1956) Facklamia languida
.   Eremococcus coleocola ACS 139 V Col8 uid61037
.   Facklamia ignava CCUG 37419 uid175683
.   Aerococcus urinae ACS 120 V Col10a uid64757
.   Aerococcus viridans ATCC 11563 uid48397
Bacillales Family XI Gemella sanguinis M325 uid66133
(nodes 1957-2064) (nodes 1961-1962) Gemella haemolysans ATCC 10379 uid55327
. Staphylococcaceae Gemella moribillum M424 uid61881
. (nodes 1963-1975) Macrococcus caseolyticus JCSC5402 uid59003
.   Staphylococcus carnosus TM300 uid59401
.   Staphylococcus pseudintermedius ED99 uid162109
.   Staphylococcus lugdunensis HKU09 01 uid46233
.   Staphylococcus hominis C80 uid61127
.   Staphylococcus haemolyticus JCSC1435 uid62919
.   Staphylococcus caprae C87 uid61125
.   Staphylococcus epidermidis ATCC 12228 uid57861
.   Staphylococcus warneri SG1 uid187059
.   Staphylococcus aureus 04 02981 uid161969
.   Staphylococcus pettenkoferi VCU012 uid179999
.   Staphylococcus arlettae CVD059 uid175126
.   Staphylococcus equorum Mu2 uid169178
.   Staphylococcus saprophyticus ATCC 15305 uid58411
. Planococcaceae Sporosarcina newyorkensis uid70561
. (nodes 1976-1982) Planococcus antarcticus DSM 14505 uid167855
.   Planococcus donghaensis MPA1U2 uid63099
.   Solibacillus silvestris StLB046 uid168516
.   Bacillus B14905 uid54613
.   Lysinibacillus sphaericus C3 41 uid58945
.   Kurthia JC30 uid174325
.   Kurthia JC8E uid174327
. Listeria Listeria grayi DSM 20601 uid55523
. (nodes 1983-1986) Listeria ivanovii PAM 55 uid73473
.   Listeria seeligeri serovar 1 2b SLCC3954 uid46215
.   Listeria monocytogenes 07PF0776 uid162185
.   Listeria welshimeri serovar 6b SLCC5334 uid61605
. Bacillaceae Anoxybacillus flavithermus WK1 uid59135
. (nodes 1988-2039) Geobacillus thermoleovorans CCB US3 UF5 uid82949
.   Geobacillus G11MC16 uid55035
.   Geobacillus thermodenitrificans NG80 2 uid58829
.   Geobacillus thermoglucosidans TNO 09 020 uid181720
.   Geobacillus WCH70 uid59045
.   Bacillus methanolicus MGA3 uid179596
.   Bacillus 2 A 57 CT2 uid62059
.   Bacillus NRRL B 14911 uid54211
.   Bacillus 1NLA3E uid81841
.   Bacillus bataviensis LMG 21833 uid178560
.   Bacillus coahuilensis m4 4 uid54797
.   Bacillus SG 1 uid54663
.   Bacillus m3 13 uid59767
.   Bacillus 10403023 uid174324
.   Bacillus megaterium DSM319 uid48371
.   Bacillus pseudomycoides DSM 12442 uid55213
.   Bacillus mycoides DSM 2048 uid55207
.   Bacillus weihenstephanensis KBAB4 uid58315
.   Bacillus 7 6 55CFAA CT2 uid80427
.   Bacillus cereus 03BB102 uid59299
.   Bacillus anthracis A0248 uid59385
.   Bacillus thuringiensis Al Hakam uid58795
.   Bacillus licheniformis ATCC 14580 uid58097
.   Bacillus HYC 10 uid176491
.   Bacillus pumilus SAFR 032 uid59017
.   Bacillus 5B6 uid161591
.   Bacillus amyloliquefaciens DSM 7 uid53535
.   Bacillus atrophaeus 1942 uid59887
.   Bacillus mojavensis RO H 1 uid171173
.   Bacillus subtilis 168 uid57675
.   Bacillus coagulans 2 6 uid68053
.   Bacillus smithii 7 3 47FAA uid80423
.   Bacillus azotoformans LMG 9581 uid178561
.   Ornithinibacillus TW25 uid72367
.   Lentibacillus Grbi uid86863
.   Oceanobacillus iheyensis HTE831 uid57867
.   Oceanobacillus Ndiop uid174322
.   Salimicrobium MJ3 uid176218
.   Halobacillus BAB 2008 uid184766
.   Halobacillus halophilus DSM 2266 uid162033
.   Amphibacillus xylanus NBRC 15112 uid176453
.   Exiguobacterium AT1b uid59093
.   Exiguobacterium antarcticum B7 uid176125
.   Exiguobacterium sibiricum 255 15 uid58053
.   Bacillus macauensis ZFHKF 1 uid169222
.   Bacillus halodurans C 125 uid57791
.   Bacillus clausii KSM K16 uid58237
.   Bacillus alcalophilus ATCC 27647 uid173850
.   Bacillus pseudofirmus OF4 uid45847
.   Bacillus selenitireducens MLS10 uid49513
.   Bacillus cellulosilyticus DSM 2522 uid43329
.   Caldalkalibacillus thermarum TA2 A1 uid67815
. Sporolactobacillus Sporolactobacillus inulinus CASD uid82635
. (node 2041) Sporolactobacillus vineae DSM 21990 SL153 uid171990
. Paenibacillaceae Brevibacillus laterosporus GI 9 uid180972
. (node 2043-2062 Brevibacillus agri BAB 2500 uid184804
.   Brevibacillus brevis NBRC 100599 uid59175
.   Desmospora 8437 uid67093
.   Paenibacillus alvei DSM 29 uid174248
.   Paenibacillus dendritiformis C454 uid82723
.   Paenibacillus popilliae ATCC 14706 uid180969
.   Paenibacillus oral taxon 786 D14 uid55903
.   Paenibacillus peoriae KCTC 3763 uid167853
.   Paenibacillus terrae HPL 003 uid82371
.   Paenibacillus polymyxa E681 uid53477
.   Paenibacillus lactis 154 uid75105
.   Paenibacillus vortex V453 uid61489
.   Paenibacillus Y412MC10 uid41127
.   Thermobacillus composti KWC4 uid74021
.   Paenibacillus curdlanolyticus YK9 uid51723
.   Paenibacillus JDR 2 uid59021
.   Paenibacillus JC66 uid174323
.   Paenibacillus HGF7 uid67401
.   Paenibacillus elgii B69 uid76799
.   Paenibacillus mucilaginosus 3016 uid89377
. Alicylobacillaceae Kyrpidia tusciae DSM 2912 uid48361
. (node 2063-2064) Alicyclobacillus acidocaldarius DSM 446 uid59199
.   Alicyclobacillus hesperidum URH17 3 68 uid174618
Erysipelotrichi Erysipelotrichi Clostridium spiroforme DSM 1552 uid54607
(nodes 2066-2080) (nodes 2066-2080) Clostridium ramosum DSM 1402 uid54811
.   Coprobacillus 3 3 56FAA uid80685
.   Catenibacterium mitsuokai DSM 15897 uid54829
.   Coprobacillus 29 1 uid62161
.   Erysipelothrix rhusiopathiae Fujisawa uid68021
.   Eubacterium biforme DSM 3989 uid55117
.   Eubacterium 3 1 31 uid81761
.   Eubacterium dolichum DSM 3991 uid54609
.   Clostridium HGF2 uid61051
.   Erysipelotrichaceae bacterium 21 3 uid81609
.   Holdemania filiformis DSM 12042 uid55297
.   Bulleidia extructa W1219 uid43197
.   Solobacterium moorei F0204 uid62281
.   Haloplasma contractile SSD 17B uid67925
.   Turicibacter PC909 uid46977
Mollicutes Acholeplasmataceae Acholeplasma laidlawii PG 8A uid58901
(nodes 2081-2119) (nodes 2082-2084) Candidatus Phytoplasma australiense uid61641
.   Aster yellows witches broom phytoplasma AYWB uid58297
.   Onion yellows phytoplasma OY M uid58015
. Micoplasmataceae Spiroplasma melliferum IPMB4A uid185130
. (nodes 2085-2119) Mesoplasma florum L1 uid58055
.   Mycoplasma putrefaciens KS1 uid72481
.   Mycoplasma G5847 uid184764
.   Mycoplasma mycoides capri LC 95010 uid66189
.   Mycoplasma leachii 99 014 6 uid162031
.   Mycoplasma capricolum ATCC 27343 uid58525
.   Ureaplasma parvum serovar 3 ATCC 27815 uid58887
.   Ureaplasma urealyticum serovar 10 ATCC 33699 uid59011
.   Mycoplasma iowae 695 uid74019
.   Mycoplasma penetrans HF 2 uid57729
.   Mycoplasma gallisepticum CA06 2006 052 5 2P uid172630
.   Mycoplasma genitalium G37 uid57707
.   Mycoplasma pneumoniae 309 uid85495
.   Mycoplasma suis Illinois uid61897
.   Candidatus Mycoplasma haemolamae Purdue uid171259
.   Mycoplasma wenyonii Massachusetts uid170731
.   Mycoplasma haemocanis Illinois uid82367
.   Mycoplasma haemofelis Langford 1 uid62461
.   Mycoplasma arthritidis 158L3 1 uid58005
.   Mycoplasma hominis ATCC 23114 uid41875
.   Mycoplasma hyorhinis GDL 1 uid87003
.   Mycoplasma conjunctivae uid59325
.   Mycoplasma hyopneumoniae 168 uid162053
.   Mycoplasma ovipneumoniae SC01 uid79051
.   Mycoplasma mobile 163K uid58077
.   Mycoplasma pulmonis UAB CTIP uid61569
.   Mycoplasma columbinum SF7 uid72177
.   Mycoplasma fermentans JER uid53543
.   Mycoplasma agalactiae PG2 uid61619
.   Mycoplasma bovis HB0801 uid168665
.   Mycoplasma alligatoris A21JP2 uid46947
.   Mycoplasma anatis 1340 uid71183
.   Mycoplasma synoviae 53 uid58061
.   Mycoplasma canis PG 14 uid180388
.   Mycoplasma cynos C142 uid184824

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.6. Cyanobacteria

This group contains Cyanobacteria. An annotated pdf with node numbers is available for

For a recent discussion of the cyanobacterial phylogeny, please see Shih, et al., Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.
Phylum Family Organism
Cyanobacteria Prochlorales Synechococcus RCC307 uid61609
(nodes 2120-2212) (nodes 2121-2145) Cyanobium gracile PCC 6307 uid182931
.   Cyanobium PCC 7001 uid54675
.   Synechococcus WH 5701 uid54219
.   Synechococcus CB0205 uid61893
.   Prochlorococcus marinus MIT 9303 uid58305
.   Prochlorococcus marinus MIT 9313 uid57773
.   Synechococcus WH 8102 uid61581
.   Synechococcus BL107 uid54225
.   Synechococcus CC9605 uid58319
.   Synechococcus RS9917 uid54221
.   Synechococcus RS9916 uid54223
.   Synechococcus WH 7803 uid61607
.   Synechococcus WH 7805 uid54217
.   Synechococcus CC9311 uid58123
.   Synechococcus WH 8016 uid74433
.   Prochlorococcus marinus NATL1A uid58423
.   Prochlorococcus marinus CCMP1375 uid57995
.   Prochlorococcus marinus MIT 9211 uid58309
.   Prochlorococcus marinus MIT 9515 uid58313
.   Prochlorococcus marinus pastoris CCMP1986 uid57761
.   Prochlorococcus marinus MIT 9312 uid58357
.   Prochlorococcus marinus AS9601 uid58307
.   Prochlorococcus marinus MIT 9301 uid58437
.   Prochlorococcus marinus MIT 9202 uid54709
.   Prochlorococcus marinus MIT 9215 uid58819
. Gloeobacteriales Synechococcus elongatus PCC 6301 uid58235
. (nodes 2147,2149-2157) Synechococcus elongatus PCC 7942 uid58045
.   Acaryochloris marina MBIC11017 uid58167
.   Cyanothece PCC 7425 uid59435
.   Synechococcus PCC 6312 uid182934
.   Thermosynechococcus elongatus BP 1 uid57907
.   Synechococcus PCC 7502 uid183008
.   Pseudanabaena biceps PCC 7429 uid187056
.   Pseudanabaena PCC 7367 uid183004
.   Gloeobacter violaceus PCC 7421 uid58011
.   Synechococcus JA 2 3B a 2 13 uid58537
.   Synechococcus JA 3 3Ab uid58535
. Oscillatoriales Leptolyngbya PCC 6406 uid186936
. (nodes 2159/62, 2164/70) Synechococcus PCC 7335 uid54731
.   Leptolyngbya PCC 7375 uid182890
.   Geitlerinema PCC 7407 uid183007
.   Oscillatoriales cyanobacterium JSC 12 uid179140
.   Oscillatoria acuminata PCC 6304 uid183003
.   Oscillatoria PCC 6506 uid50611
.   Microcoleus vaginatus FGP 2 uid67389
.   Oscillatoria PCC 7112 uid183110
.   Trichodesmium erythraeum IMS101 uid57925
.   Lyngbya PCC 8106 uid54161
.   Arthrospira platensis C1 uid181584
.   Arthrospira platensis Paraca uid55907
. Nostocales Cylindrospermopsis raciborskii CS 505 uid42983
. (nodes 2172-2189) Raphidiopsis brookii D9 uid42981
.   Anabaena cylindrica PCC 7122 uid183339
.   Nostoc azollae 0708 uid49725
.   Anabaena 90 uid179383
.   Nodularia spumigena CCY9414 uid54171
.   Nostoc punctiforme PCC 73102 uid57767
.   Cylindrospermum stagnale PCC 7417 uid183111
.   Calothrix PCC 7507 uid182930
.   Nostoc PCC 7107 uid182932
.   Nostoc PCC 7524 uid182933
.   Anabaena variabilis ATCC 29413 uid58043
.   Nostoc PCC 7120 uid57803
.   Calothrix PCC 6303 uid183109
.   Rivularia PCC 7116 uid182929
.   Fischerella JSC 11 uid75099
.   Chroococcidiopsis thermalis PCC 7203 uid183002
.   Gloeocapsa PCC 7428 uid183112
.   Synechocystis PCC 7509 uid186935
. Croococcales Chamaesiphon PCC 6605 uid183005
. (nodes 2190-2212) Crinalium epipsammum PCC 9333 uid183113
.   Microcoleus chthonoplastes PCC 7420 uid54695
.   Lyngbya majuscula 3L uid66849
.   Dactylococcopsis salina PCC 8305 uid183341
.   Halothece PCC 7418 uid183338
.   Leptolyngbya PCC 7376 uid182928
.   Synechococcus PCC 7002 uid59137
.   Stanieria cyanosphaera PCC 7437 uid183115
.   Xenococcus PCC 7305 uid186938
.   Gloeocapsa PCC 73106 uid186937
.   Cyanobacterium PCC 10605 uid183340
.   Cyanobacterium stanieri PCC 7202 uid183337
.   Pleurocapsa PCC 7327 uid183006
.   Synechocystis PCC 6803 substr GT I uid158059
.   Cyanothece PCC 8801 uid59027
.   Cyanothece PCC 8802 uid59143
.   cyanobacterium UCYN A uid43697
.   Crocosphaera watsonii WH 0003 uid179643
.   Cyanothece ATCC 51142 uid59013
.   Cyanothece PCC 7424 uid59025
.   Cyanothece PCC 7822 uid52547
.   Microcystis aeruginosa NIES 843 uid59101
.   Microcystis aeruginosa TAIHU98 uid185796

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.7. Archaea

This group contains the Archaea. Annotated pdfs with node numbers and family names are available for

Phylum Family Organism
Nanoarchaeota   Nanoarchaeum equitans Kin4 M uid58009
Euryarachaeota   Methanopyrus kandleri AV19 uid57883
Korarchaeota   Candidatus Korarchaeum cryptofilum OPF8 uid58601
Crenarchaeota   Sulfolobus acidocaldarius DSM 639 uid58379
(nodes 2219-2252)   Sulfolobus tokodaii 7 uid57807
.   Sulfolobus islandicus HVE10 4 uid162067
.   Sulfolobus solfataricus 98 2 uid167998
.   Acidianus hospitalis W1 uid66875
.   Metallosphaera yellowstonensis MK1 uid82737
.   Metallosphaera cuprina Ar 4 uid66329
.   Metallosphaera sedula DSM 5348 uid58717
.   Staphylothermus hellenicus DSM 12710 uid45893
.   Thermogladius 1633 uid167488
.   Thermosphaera aggregans DSM 11486 uid48993
.   Desulfurococcus mucosus DSM 2162 uid62227
.   Desulfurococcus fermentans DSM 16532 uid75119
.   Desulfurococcus kamchatkensis 1221n uid59133
.   Hyperthermus butylicus DSM 5456 uid57755
.   Pyrolobus fumarii 1A uid73415
.   Aeropyrum pernix K1 uid57757
.   Acidilobus saccharovorans 345 15 uid51395
.   Caldisphaera lagunensis DSM 15908 uid183486
.   Ignicoccus hospitalis KIN4 I uid58365
.   Fervidicoccus fontis Kam940 uid162201
.   Ignisphaera aggregans DSM 17230 uid51875
.   Thermofilum pendens Hrk 5 uid58563
.   Pyrobaculum calidifontis JCM 11548 uid58787
.   Pyrobaculum islandicum DSM 4184 uid58635
.   Pyrobaculum neutrophilum V24Sta uid58421
.   Pyrobaculum arsenaticum DSM 13514 uid58409
.   Pyrobaculum oguniense TE7 uid84411
.   Pyrobaculum 1860 uid82379
.   Pyrobaculum aerophilum IM2 uid57727
.   Thermoproteus tenax Kra 1 uid74443
.   Thermoproteus uzoniensis 768 20 uid65089
.   Caldivirga maquilingensis IC 167 uid58711
.   Vulcanisaeta distributa DSM 14429 uid52827
.   Vulcanisaeta moutnovskia 768 28 uid63631
Thaumarchaeota   Candidatus Nitrososphaera gargensis Ga9 2 uid176707
(nodes 2253-2258)   Cenarchaeum symbiosum A uid61411
.   Nitrosopumilus maritimus SCM1 uid58903
.   marine archaeal group 1 BD31 uid81845
.   Candidatus Nitrosopumilus AR2 uid176130
.   Candidatus Nitrosoarchaeum limnia BG20 uid169874
.   Nitrosopumilus MY1 uid70553
Euryarchaeota Thermococcales Pyrococcus yayanosii CH1 uid68281
(nodes 2259-2400) (nodes 2260-2274) Pyrococcus furiosus COM1 uid169620
.   Pyrococcus ST04 uid167261
.   Pyrococcus abyssi GE5 uid62903
.   Pyrococcus NA2 uid66551
.   Pyrococcus horikoshii OT3 uid57753
.   Thermococcus barophilus MP uid54733
.   Thermococcus litoralis DSM 5473 uid82997
.   Thermococcus sibiricus MM 739 uid59399
.   Thermococcus onnurineus NA1 uid59043
.   Thermococcus 4557 uid70841
.   Thermococcus CL1 uid168259
.   Thermococcus kodakarensis KOD1 uid58225
.   Thermococcus zilligii AN1 uid176935
.   Thermococcus AM4 uid54735
.   Thermococcus gammatolerans EJ3 uid59389
. Methanococci Methanocaldococcus infernus ME uid48803
. (nodes 2277-2287) Methanocaldococcus vulcanius M7 uid41131
.   Methanocaldococcus jannaschii DSM 2661 uid57713
.   Methanocaldococcus fervens AG86 uid59347
.   Methanocaldococcus FS406 22 uid42499
.   Methanococcus voltae A3 uid49529
.   Methanococcus maripaludis C5 uid58741
.   Methanococcus vannielii SB uid58767
.   Methanococcus aeolicus Nankai 3 uid58823
.   Methanothermococcus okinawensis IH1 uid51535
.   Methanotorris formicicus Mc S 70 uid82739
.   Methanotorris igneus Kol 5 uid67321
.   Methanothermus fervidus DSM 2088 uid60167
.   Methanosphaera stadtmanae DSM 3091 uid58407
.   Methanobacterium formicicum DSM 3637 uid176604
.   Methanobacterium Maddingley MBC34 uid178946
.   Methanobacterium AL 21 uid63623
.   Methanobacterium SWAN 1 uid67359
.   Methanobrevibacter ruminantium M1 uid45857
.   Methanobrevibacter smithii ATCC 35061 uid58827
.   Methanothermobacter marburgensis Marburg uid51637
.   Methanothermobacter thermautotrophicus Delta H uid57877
.   Aciduliprofundum boonei T469 uid43333
.   Aciduliprofundum MAR08 339 uid184407
.   Thermoplasma acidophilum DSM 1728 uid61573
.   Thermoplasma volcanium GSS1 uid57751
.   Ferroplasma acidarmanus fer1 uid54095
.   Picrophilus torridus DSM 9790 uid58041
.   Ferroglobus placidus DSM 10642 uid40863
.   Archaeoglobus veneficus SNP6 uid65269
.   Archaeoglobus profundus DSM 5631 uid43493
.   Archaeoglobus fulgidus DSM 4304 uid57717
.   Methanocella arvoryzae MRE50 uid61623
.   Methanocella conradii HZ254 uid157911
.   Methanocella paludicola SANAE uid42887
.   Methanosaeta thermophila PT uid58469
.   Methanosaeta harundinacea 6Ac uid81199
.   Methanosaeta concilii GP6 uid66207
.   Methanosarcina barkeri Fusaro uid57715
.   Methanosarcina acetivorans C2A uid57879
.   Methanosarcina mazei Go1 uid57893
.   Methanohalobium evestigatum Z 7303 uid49857
.   Methanosalsum zhilinae DSM 4017 uid68249
.   Methanohalophilus mahii DSM 5219 uid47313
.   Methanococcoides burtonii DSM 6242 uid58023
.   Methanomethylovorans hollandica DSM 15978 uid184864
.   Methanolobus psychrophilus R15 uid177925
.   Methanofollis liminatans DSM 4140 uid170729
.   Methanoplanus limicola DSM 2279 uid82735
.   Methanoplanus petrolearius DSM 11571 uid52695
.   Methanospirillum hungatei JF 1 uid58181
.   Methanocorpusculum labreanum Z uid58785
.   Methanoculleus bourgensis MS2 uid171377
.   Methanoculleus marisnigri JR1 uid58561
.   Methanosphaerula palustris E1 9c uid59193
.   Methanolinea tarda NOBI 1 uid76575
.   Methanoregula boonei 6A8 uid58815
.   Methanoregula formicicum SMSP uid184406
.   Halorubrum hochstenium ATCC 700873 uid188622
.   Halorubrum tebenquichense DSM 14210 uid188611
.   Halorubrum coriense DSM 10284 uid188619
.   Halorubrum californiensis DSM 19288 uid188618
.   Halorubrum distributum JCM 10118 uid188621
.   Halorubrum terrestre JCM 10247 uid188610
.   Halorubrum arcis JCM 13916 uid188617
.   Halorubrum litoreum JCM 13561 uid188613
.   Halorubrum aidingense JCM 13560 uid188616
.   Halorubrum lacusprofundi ATCC 49239 uid58807
.   Halorubrum saccharovorum DSM 1137 uid188612
.   Halorubrum kocurii JCM 14978 uid188615
.   Halorubrum lipolyticum DSM 21995 uid188614
.   halophilic archaeon DL31 uid72619
.   Halogranum salarium B 1 uid172007
.   Haloquadratum walsbyi C23 uid162019
.   Halogeometricum borinquense DSM 11551 uid54919
.   Halosarcina pallida JCM 14848 uid188609
.   Haloferax elongans ATCC BAA 1513 uid188630
.   Haloferax larsenii JCM 13917 uid188628
.   Haloferax alexandrinus JCM 10717 uid188631
.   Haloferax volcanii DS2 uid46845
.   Haloferax lucentense DSM 14919 uid188627
.   Haloferax prahovense DSM 18310 uid188626
.   Haloferax gibbonsii ATCC 33959 uid188629
.   Haloferax denitrificans ATCC 35960 uid188635
.   Haloferax sulfurifontis ATCC BAA 897 uid188632
.   Haloferax mediterranei ATCC 33500 uid167315
.   Haloferax mucosum ATCC BAA 1512 uid188633
.   Halalkalicoccus jeotgali B3 uid50305
.   Haladaptatus paucihalophilus DX253 uid62523
.   Halococcus hamelinensis 100A6 uid177808
.   Halococcus morrhuae DSM 1307 uid188645
.   Halomicrobium mukohataei DSM 12286 uid59107
.   Natronomonas moolapensis 8 8 11 uid190182
.   Natronomonas pharaonis DSM 2160 uid58435
.   Halosimplex carlsbadense 2 9 1 uid188608
.   Halorhabdus tiamatea SARL4B uid67927
.   Halorhabdus utahensis DSM 12940 uid59189
.   Halobacterium DL1 uid75121
.   Halobacterium NRC 1 uid57769
.   Halobacterium salinarum R1 uid61571
.   Halovivax ruber XH 70 uid184819
.   Natronococcus occultus SP4 uid184863
.   Natronococcus jeotgali DSM 18795 uid188591
.   Natronococcus amylolyticus DSM 10524 uid188592
.   Natrialba aegyptia DSM 13077 uid188603
.   Natrialba asiatica DSM 12278 uid188602
.   Natrialba taiwanensis DSM 12281 uid188599
.   Natrialba hulunbeirensis JCM 10989 uid188600
.   Natrialba magadii ATCC 43099 uid46245
.   Natrialba chahannaoensis JCM 10990 uid188601
.   Natronolimnobius innermongolicus JCM 12255 uid188590
.   Haloterrigena salina JCM 13891 uid188606
.   Haloterrigena turkmenica DSM 5511 uid43501
.   Halopiger xanaduensis SH 6 uid68105
.   Natronobacterium gregoryi SP2 uid74439
.   Halobiforma lacisalsi AJ5 uid157065
.   Halobiforma nitratireducens JCM 10879 uid188643
.   Haloterrigena limicola JCM 13563 uid188607
.   Natrinema pallidum DSM 3751 uid188596
.   Natrinema gari JCM 14663 uid188597
.   Natrinema altunense JCM 12890 uid188598
.   Natrinema versiforme JCM 10478 uid188594
.   Haloterrigena thermotolerans DSM 11522 uid188605
.   Natrinema pellirubrum DSM 15624 uid74437
.   Natronorubrum tibetense GA33 uid188587
.   Natronorubrum bangense JCM 10635 uid188589
.   Natronorubrum sulfidifaciens JCM 14089 uid188588

Jump to: Bacteroidetes, et al., Alpha proteobacteria, et al., Beta and Gamma Proteobacteria, Actinobacteria, Firmicutes, et al., Cyanobacteria, Archaea, and Eukaryotes.

12.8. Eukaryotes

This group contains the the Eukaryotes. Annotated pdfs with node numbers and family names are available for download for

The phylogeny of lower eukaryotes is significantly more difficult to understand than the rest of this tree, and we relied heavily on Ginger, et al., Koonin, and Adl, et al. in assembling this phylogeny.

Phylum Family Organism
Protozoa Alveolata Cryptosporidium parvum
(nodes 2401-2442) (nodes 2404-2416) Cryptosporidium muris
.   Theileria parva
.   Theileria annulata
.   Babesia bovis
.   Plasmodium vivax
.   Plasmodium knowlesi
.   Plasmodium falciparum
.   Plasmodium yoelii
.   Toxoplasma gondii
.   Neospora caninum
.   Perkinsus marinus
.   Cilophora
.   Paramecium tetraurelia
.   Tetrahymena thermophila
. Stramenopiles Thalassiosira pseudonana
. (nodes 2416-2417) Phaeodactylum tricornutum
.   Phytophthora infestans
. Cryptophyta Guillardia theta
.   Trypanosoma brucei
.   Leishmania donovani
.   Leishmania braziliensis
.   Naegleria gruberi
.   Giardia lamblia
.   Trichomonas vaginalis
.   Glycine max
.   Medicago truncatula
.   Cucumis sativus
.   Ricinus communis
.   Populus trichocarpa
.   Arabidopsis thaliana
.   Solanum lycopersicum
.   Vitis vinifera
.   Oryza sativa
.   Brachypodium distachyon
.   Sorghum bicolor
.   Selaginella moellendorffii
.   Physcomitrella patens
.   Micromonas sp.
.   Ostreococcus tauri
.   Ostreococcus lucimarinus
.   Chlorella unnamed
.   Chlamydomonas reinhardtii
Amoebozoa Mycetozoa Dictyostelium purpureum
(nodes 2444-2445) (node 2445) Dictyostelium discoideum
.   Entamoeba dispar
. Choanoflagellida Monosiga brevicollis
Metazoa Cnidaria Nematostella vectensis
(nodes 2448-2481) (node 2450 Hydra magnipapillata
. Porifera Amphimedon queenslandica
. Placozoa Trichoplax adhaerens
. Nematodes Trichinella spiralis
. (nodes 2453-2455) Caenorhabditis elegans
.   Loa loa
.   Brugia malayi
. Trematode Schistosoma mansoni
. Hemichordate Saccoglossus kowalevskii
. Echinodermata Strongylocentrotus prupuratus
. Arthropods Metaseiulus occidentalis
. (nodes 2458-2469) Ixodes unnamed
.   Tribolium castaneum
.   Pediculus humanus
.   Culex quinquefasciatus
.   Anopheles gambiae
.   Drosophila melanogaster
.   Megachile rotundata
.   Bombus impatiens
.   Apis mellifera
.   Nasonia vitripennis
. Chordates Ciona intestinalis
. (nodes 2470-2481) Oreochromis niloticus
.   Oryzias latipes
.   Danio rerio
.   Salmo salar
.   Takifugu rubripes
.   Xenopus tropicalis
.   Anolis carolinensis
.   Taeniopygia guttata
.   Gallus gallus
.   Sarcophilus harrisii
.   Mus musculus
.   Homo sapiens
Fungi Microsporidia Enterocytozoon bieneusi
(nodes 2482-2548) (nodes 2483-2486) Nosema ceranae
.   Encephalitozoon cuniculi
.   Encephalitozoon intestinalis
.   Encephalitozoon hellem
. Basidiomycota Puccinia graminis
. (nodes 2488-2493) Malassezia globosa
.   Schizophyllum commune
.   Coprinopsis cinerea
.   Laccaria bicolor
.   Ustilago maydis
.   Cryptococcus neoformans
. Basidiomycota Schizosaccharomyces pombe
. (node 2495) Schizosaccharomyces japonicus
. Saccharomycotina Yarrowia lipolytica
. (nodes 2497-2517) Lodderomyces elongisporus
.   Candida tropicalis
.   Candida dubliniensis
.   Debaryomyces hansenii
.   Meyerozyma guilliermondii
.   Scheffersomyces stipitis
.   Clavispora lusitaniae
.   Komagataella pastoris
.   Naumovozyma dairenensis
.   Naumovozyma castellii
.   Kazachstania africana
.   Saccharomyces cerevisiae
.   Candida glabrata
.   Torulaspora delbrueckii
.   Zygosaccharomyces rouxii
.   Vanderwaltozyma polyspora
.   Tetrapisispora phaffii
.   Lachancea thermotolerans
.   Eremothecium cymbalariae
.   Ashbya gossypii
.   Kluyveromyces lactis
. Pezizomycotina Zymoseptoria tritici
. (nodes 2518-2548) Pyrenophora tritici-repentis
.   Leptosphaeria maculans
.   Phaeosphaeria nodorum
.   Tuber melanosporum
.   Neosartorya fischeri
.   Aspergillus fumigatus
.   Aspergillus clavatus
.   Aspergillus niger
.   Aspergillus terreus
.   Aspergillus oryzae
.   Aspergillus flavus
.   Aspergillus nidulans
.   Penicillium chrysogenum
.   Talaromyces stipitatus
.   Uncinocarpus reesii
.   Coccidioides posadasii
.   Trichophyton rubrum
.   Arthroderma otae
.   Paracoccidioides sp.
.   Ajellomyces dermatitidis
.   Sclerotinia sclerotiorum
.   Botryotinia fuckeliana
.   Myceliophthora thermophila
.   Thielavia terrestris
.   Chaetomium globosum
.   Podospora anserina
.   Sordaria macrospora
.   Neurospora crassa
.   Magnaporthe oryzae
.   Verticillium albo-atrum
.   Nectria haematococca