Woesearchaeota Archaea A Thaumarchaeota Archaea Euryarchaeota Diapherotrites CP Verstraetaerchaeota CP Parvarchaeota CP Pacearchaeota CP Bathyarchaeota CP Altiarchaeota CP Aenigmarchaeota Verrucomicrobia V6 Verrucomicrobia V4 Verrucomicrobia V3 Verrucomicrobia V2 Verrucomicrobia V1 Planctomycetes Phycisphaerae Nitrospirae Lentisphaerae Kirimatiellacea Ignavibacteria Gs Gemmatimonadetes A Gammaproteobacteria Firmicutes Fibrobacteres acidobacteria Deltaproteobacteria Cyanobacteria CP Zixibacteria CP Ziwabacteria CP WWE3 CP WWE1 y of 523 M CP WOR−3 n CP WOR−2 Omnitrophica CP Urhbacteria CP TM6 Bacte Bacte CP Tectomicrobia CP Tanganyikabacteria axono CP Staskawiczbacteria T CP Shapirobacteria r r CP Saccharibacteria ia ia CP Rokubacteria ual CP Poribacteria n CP Perigrinibacteria CP Peribacteria Ma CP Nealsonbacteria CP Moranbacteria CP Liptonbacteria CP Kaiserbacteria CP Hydrogenedentes CP Harrisonbacteria CP Handelsmanbacteria CP Gribaldobacteria CP Gottesmanbacteria CP Eisenbacteria CP BRC1 CP Aminicemantes (OP8) Chloroflexi Chlorobi Chlamydiae Calditrichaeota Betaproteobacteria Bacteroidetes Armatimonadetes Alphaproteobacteria non LD12 Alphaproteobacteria LD12 Actinobacteria Acidobacteria 0 50 60 70 80 90 20 40 60 100 Count Genome completeness (CheckM) (%) B Not a match, Thaumarchaeota are named Crenarchaeota Not a match, only classified to Bacteria in GTDB Not a match, Lentisphaerae are lumped with Kiritimatiellae in GTDB−tk Not a match - renamed y (RP16) Not a match, Deltaproteobacteria are renamed into Desulfobacterota in GTDB m Not a match, Deltaproteobacteria are broken down into UBP10 in GTDB−tk y (GTDB−tk) m Not a match, Deltaproteobacteria are broken down into Myxococcota phylum Not a match, but in Patescibacteria ual taxono n Not a match, but in Cyanobacteria Not a match, Archaea classified as Bacteria in GTDB Not a match ison of ma r Match, but Nitrospirae are renamed Nitrospirota Match, but Kirimatiellae are within Verrucomicrobia in GTDB−tk and automated taxono Compa Match, but here GTDB puts Chlamydia within Verrucomicrobia Match but here GTDB puts Chlorobi within Bacteroidetes Match 50 60 70 80 90 100 Genome Completeness (%) Supplementary Figure 6. A. Comparison of manual RP16 taxonomy versus the GTDB-tk automated taxonomy, and distribution of completeness levels on for each taxonomy group. B. Distribution of completeness values among categories. The colors in panel B is the legend for the colors in the bar plot of panel A. There were matches across the range of completeness values (“Match”). However, when there is a mismatch, it is not always because the genome is less complete..