| Phyla | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| AC1 | Hugenholtz | Pace | NCBI | ||
| Acidobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Actinobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| AD3 | Hugenholtz | (Chloroflexi) | |||
| Aquificae | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Bacteroidetes | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| BD1-5 | (OD2) | Pace | (Proteobacteria) | ||
| BRC1 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Caldicellulosiruptor | Hugenholtz | (Firmicutes) | (Firmicutes) | (Thermoanerobacteria) | |
| Caldithrix | Hugenholtz | (CD7_NC3,CD8,KSB1_NC5,marine group A) | (Deferribacteres) | (Firmicutes) | Ludwig |
| Carboxydocella | Hugenholtz | (Firmicutes) | (Firmicutes) | (Firmicutes) | |
| CD11 | Hugenholtz | (Nitrospira) | (Nitrospira) | (Nitrospira) | |
| CD12 | Hugenholtz | Pace | (Firmicutes) | ||
| CD13 | (WS3) | Pace | (WS3) | (WS3) | (WS3) |
| CD14 | (WS3) | Pace | |||
| CD15 | Hugenholtz | Pace | (Proteobacteria) | (Proteobacteria) | |
| CD18 | (OD2) | Pace | (OP11) | (OP11) | (OP11) |
| CD19 | (OD2) | Pace | (Proteobacteria) | (OD1) | |
| CD2 | (DSS1, WS2) | Pace | (Cyanobacteria) | (Cyanobacteria) | |
| CD3 | (Firmicutes) | Pace | (Firmicutes) | (Firmicutes) | (Firmicutes) |
| CD4 | Pace | (Firmicutes, WS3) | |||
| CD5 | (WS4) | Pace | (Deinococcus-Thermus) | ||
| CD7_NC3 | (Caldithrix) | Pace | (Proteobacteria) | (Fimicutes) | (Caldithrix) |
| CD8 | (Caldithrix) | Pace | (Fimicutes) | (Bacteroidetess, Chlorobi) | |
| Cenibacterium | (Proteobacteria) | NCBI | (Proteobacteria) | ||
| Chlamydia | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Chlorobi | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Chloroflexi | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Chrysiogenetes | NCBI | RDP | |||
| Coprothermobacter | Hugenholtz | Pace | (Firmicutes) | (Aquificae) | Ludwig |
| Crenarchaeota | Hugenholtz | Pace | NCBI | Ludwig | |
| Cyanobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Deep Cyanobacteria | (Cyanobacteria, Spirochates) | Pace | (Fimicutes, Cyanobacteria) | (Cyanobacteria) | (Cyanobacteria) |
| Deferribacteres | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Dehalococcoides | (Chloroflexi) | (Chloroflexi) | RDP | (Thermomicrobia) | |
| Deinococcus-Thermus | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Denitromonas | (Proteobacteria) | (Proteobacteria) | NCBI | (Proteobacteria) | (Proteobacteria) |
| Desulfurobacterium | (Aquificae) | Pace | (Aquificae) | (Aquificae) | (Aquificae) |
| Dictyoglomi | Hugenholtz | Pace | NCBI | RDP | (Thermoanaerobacter) |
| DSS1 | Hugenholtz | (CD2) | (Firmicutes) | (Cyanobacteria) | |
| EM19 | Hugenholtz | Pace | (Aquificae) | Ludwig | |
| Entotheonella_CD10 | Hugenholtz | Pace | (Proteobacteria) | (Proterobacteria) | (Proteobacteria) |
| Euryarchaeota | Hugenholtz | Pace | NCBI | (Aquificae) | Ludwig |
| Ferribacter | Hugenholtz | (Deferribacteres) | NCBI | (Deferribacteres) | (Firmicutes) |
| Fibrobacteres | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Firmicutes | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Fusobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Gemmatimonadales_Gemmimonas_NC9 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Guaymas 1 | (Proteobacteria) | Pace | (Proteobacteria) | (Proteobacteria) | |
| Haloanaerobiales | Hugenholtz | Pace | (Firmicutes) | (Firmicutes) | Ludwig |
| KB1 | (NKB19,OP1) | (NKB19,OP1) | NCBI | (OP1) | |
| Korarchaeota | Hugenholtz | Pace | NCBI | Ludwig | |
| KSB1_NC5 | (Caldithrix) | Pace | NCBI | (Fimicutes) | (Caldithrix) |
| LC1 | Hugenholtz | (Firmicutes) | (Spriocheates) | ||
| Lentisphaerae | Hugenholtz | Pace | NCBI | (Victivalliaceae) | |
| Magnetics | (Proteobacteria) | (Proteobacteria) | (Proteobacteria) | (Proteobacteria) | Ludwig |
| MgA_SAR406 | Hugenholtz | Pace | (Proteobacteria) | (Firmicutes,Protoebacteria)) | (Caldithrix) |
| Moorella | Hugenholtz | (Firmicutes) | (Firmicutes) | (Firmicutes) | |
| MS1 | (Gemmatimonadales) | Pace | (Proteobacteria, Actinobacteria) | (Proteobacteria) | (Gemmatimonadales) |
| Nanoarchaeota | (Euryarchaeota) | NCBI | (Euryarchaeota) | ||
| Nanobacterium | (Proteobacteria) | (Proteobacteria) | NCBI | (Proteobacteria) | (Proteobacteria) |
| Natronoanaerobium | Hugenholtz | (Fimicutes) | (Firmicutes) | (Firmicutes) | (Firmicutes) |
| Natronohydrobacter | (Proteobacteria) | (Proteobacteria) | NCBI | (Proteobacteria) | (Proteobacteria) |
| NB01 | Hugenholtz | (Proteobacteria) | |||
| NC10 | Hugenholtz | Pace | (Firmicutes) | (Nitrospira) | |
| Nitrospina | Hugenholtz | Pace | (Proteobacteria) | RDP | Ludwig |
| Nitrospira | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| NKB19 | Hugenholtz | Pace | NCBI | ||
| OD1 | Hugenholtz | Pace | NCBI | (OP11) | Ludwig |
| OD2 | Hugenholtz | (BD1-5, CD18, CD19) | (OP11,Proteobacteria) | (OP11) | (OD1) |
| ODP | Hugenholtz | (Firmicutes) | |||
| OP1 | Hugenholtz | Pace | NCBI | (OP10, OP11) | Ludwig |
| OP10 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| OP11 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| OP12 | (Symbiobacteria) | Pace | (Fimicutes) | (Fimicutes) | (Firmicutes) |
| OP2 | Pace | NCBI | Ludwig | ||
| OP3 | Hugenholtz | Pace | NCBI | Ludwig | |
| OP4 | (Spirocheates) | (Spirocheates) | NCBI | (Spirocheates) | |
| OP5 | Hugenholtz | Pace | NCBI | (Firmicutes, Nitrospira) | Ludwig |
| OP8 | Hugenholtz | Pace | NCBI | (Acidobacteria) | Ludwig |
| OP9_JS1_OPB46 | Hugenholtz | Pace | NCBI | (Firmicutes) | Ludwig |
| OPA2 | (Crenarchaeota) | Pace | (Crenarchaeota) | (Crenarchaeota) | |
| OPA3 | Pace | (Crenarchaeota) | (Crenarchaeota) | ||
| OPB7_EM3 | Hugenholtz | Pace | (Thermotogae) | Ludwig | |
| OS-K | Hugenholtz | Pace | NCBI | (Acidobacteria) | |
| OS-L | Hugenholtz | Pace | (OP10) | ||
| Planctomycetes | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Poribacteria | Hugenholtz | Pace | NCBI | ||
| Proteobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| SAM | (Chloroflexi) | NCBI | (Thermomicrobia) | ||
| SB1_ZB1 | (Chlorobi) | Pace | NCBI | (Chlorobi) | |
| SBR1093_1959 | Hugenholtz | Pace | NCBI | (Bacteriodes) | (Bacteriodes,Proteobacteria) |
| SC3 | Hugenholtz | Pace | |||
| SC4 | Hugenholtz | Pace | (OP10) | ||
| Smegmaraptor | (Proteobacteria) | (Proteobacteria) | NCBI | (Proteobacteria) | (Proteobacteria) |
| SPAM | Hugenholtz | Pace | NCBI | (Nitrospira) | |
| Sphaerobacter_Thermomicrobia | (Chloroflexi) | (Chloroflexi) | (Chloroflexi) | RDP | Ludwig |
| Spirochaetes | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| SR1 | Hugenholtz | Pace | NCBI | ||
| Sturt1 | Hugenholtz | (Firmicutes) | (Proteobacteria) | (Proteobacteria) | (Proteobacteria) |
| Sulfobacilli | Hugenholtz | Pace | (Firmicutes) | (Firmicutes) | (Firmicutes) |
| Symbiobacteria | Hugenholtz | (OP12, Sulfobacillus) | (Actinobacteria) | (Firmicutes) | (Firmicutes) |
| Synergistes_Desulfothiovibrio et rel | Hugenholtz | Pace | (Deferribacteres, Firmicutes) | (Firmicutes) | Ludwig |
| TG1 | Hugenholtz | Pace | NCBI | (Actinobacteria,Firmicutes,Proteobacteria) | (OP5) |
| TG2 | NCBI | ||||
| Thermoacetogenium | Hugenholtz | (Firmicutes) | (Firmicutes) | (Firmicutes) | |
| Thermoaerobacter | Hugenholtz | (Firmicutes) | (Firmicutes) | (Firmicutes) | |
| Thermoanaerobacter | Hugenholtz | Pace | (Firmicutes) | (Firmicutes) | Ludwig |
| Thermobaculum | (Chloroflexi) | (Chloroflexi) | NCBI | (Thermomicrobia) | |
| Thermodesulfobacteria | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Thermolithobacter | NCBI | (Fimicutes) | |||
| Thermoprotei | Hugenholtz | Pace | (Crenarchaeota) | (Aquificae) | (Crenarchaeota) |
| Thermotogae | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Thermovenabulum | Hugenholtz | (Fimicutes) | (Firmicutes) | (Fimicutes) | (Thermoanaerobacter) |
| TM6 | Hugenholtz | (Proteobacteria) | NCBI | (Proteobacteria) | Ludwig |
| TM7 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Verrucomicrobia | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| Victivalliaceae | (Lentisphaerae) | (Lentisphaerae, Proteobacteria) | (Lentisphaerae, Spirocheates, Verrucomicribia) | Ludwig | |
| WS1 | Hugenholtz | Pace | NCBI | (Fimicutes) | Ludwig |
| WS2 | Hugenholtz | (CD2) | NCBI | (Cyanobacteria) | |
| WS3 | Hugenholtz | Pace | NCBI | RDP | Ludwig |
| WS4 | Hugenholtz | (CD5) | NCBI | (Deinococcus-Thermus) | |
| WS5 | Hugenholtz | Pace | NCBI | ||
| WS6 | Hugenholtz | Pace | NCBI | Ludwig | |
| YNPFFA | Hugenholtz | Pace | (Crenarchaeota) | (Crenarchaeota) | |
| ZB3 | Hugenholtz | Pace | (Fimicutes) | (Fimicutes) | (Cyanobacteria) |