Archaea Bacteria 100 100 90

90 80

80 70

70 60 50 60 Genome Completeness (%)

Genome completeness (CheckM) (%) Genome completeness (CheckM) Archaea Bacteria 60 50 ia ia ylum Match ia in GTDB ia in GTDB

anobacter ucomicrobia Not a match 40 atescibacter err ut in Cy obacterota in GTDB ut in P Not a match - renamed itimatiellae in GTDB−tk ucomicrobia in GTDB−tk wn into UBP10 in GTDB−tk err

ydia within V ae are renamed Nitrospirota

Count wn into Myxococcota ph 20 en do Not a match, b en do Not a match, b ut Nitrospir ia are brok ia are brok

ae are lumped with Kir ia are renamed into Desulf 0 Match, b Not a match, only classified to Bacter ut here GTDB puts Chlorobi within Bacteroidetes imatiellae are within V Not a match, Archaea classified as Bacter ut here GTDB puts Chlam ut Kir xi ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ae ae ae ites Match b A. Comparison of manual RP16 taxonomy versus the GTDB-tk automated taxonomy, and distribution of A. Comparison of manual RP16 taxonomy versus the GTDB-tk automated taxonomy, Not a match, Thaumarchaeota are named Crenarchaeota Not a match, Thaumarchaeota are named ydiae OR−3 ycetes micutes ia LD12 CP TM6 Chlorobi ichaeota ibacter ibacter ibacter abacter Match, b vibacter CP BRC1 archaeota archaeota archaeota inibacter Fir anbacter Chlorofle er or Match, b CP WWE3 CP WWE1 Nitrospir v y y CP W anobacter Chlam imatiellacea yikabacter ycisphaer ia non LD12 isonbacter wiczbacter ectomicrobia igr ar acearchaeota Acidobacter Bacteroidetes Igna r Diapherot ibaldobacter r Lentisphae Actinobacter aetaerchaeota Cy r Eu Kir Ph er oesearchaeota Calditr CP Zixibacter matimonadetes CP Urhbacter ucomicrobia V6 ucomicrobia V4 ucomicrobia V3 ucomicrobia V2 ucomicrobia V1 ucomicrobia CP P CP P Planctom CP Ziw CP Altiarchaeota W Thaumarchaeota CP Rokubacter CP Eisenbacter CP T Ar CP Liptonbacter CP Mor CP Kaiserbacter angan err err err err err CP P CP P erstr Betaproteobacter h CP Bat CP Shapirobacter V V V V V Deltaproteobacter OR−2 Omnitrophica Not a match, Lentisphaer CP P CP Nealsonbacter Gemmatimonadetes CP Harr CP Gr CP Sacchar CP Aenigmarchaeota CP Hydrogenedentes Gammaproteobacter CP Gottesmanbacter CP Staska CP T CP V Not a match, Deltaproteobacter

CP Handelsmanbacter

Not a match, Deltaproteobacter CP Aminicemantes (OP8) CP W

Alphaproteobacter

m taxono automated and Not a match, Deltaproteobacter (GTDB−tk) y

r Fibrobacteres acidobacte

r Compa n ma of ison m taxono ual y (RP16) (RP16) y n Ma T ual n axono A M 523 of y Gs Alphaproteobacter

B A

when there is a mismatch, it is not always because the genome is less complete. Supplementary Figure 6. the legend for the colors in the bar plot of panel A. There were matches across the range of completeness values (“Match”). However, There were matches across the range of completeness values (“Match”). However, A. the legend for the colors in the bar plot of panel completeness levels on for each taxonomy group. B. Distribution of completeness values among categories. The colors in panel B is completeness levels on for each taxonomy group. B. Distribution of completeness values among categories.