| Origin | Code | Comment | Supplementary Taxo |
|---|
| Dechloromonas aromatica | ISDar | | |
| Dehalococcoides ethenogenes | ISDet | | |
| Dehalococcoides sp. | ISDsp | | |
| Deinococcus deserti | ISDds | | |
| Deinococcus geothermalis | ISDge | | |
| Deinococcus radiodurans | ISDra | | |
| Delftia acidovorans | ISDeac | | |
| Delftia sp. | ISDlsp | | |
| Delta proteobacterium | ISDpr | | |
| Deltaproteobacteria bacterium | ISDebc | | |
| Desantisbacteria bacterium | ISDaba | | |
| Desulfatibacillum alkenivorans | ISDal | | |
| Desulfitobacterium hafniense | ISDha | | |
| Desulfitobacterium sp. | ISDesp | | |
| Desulfobacterales bacterium | ISDbac | | |
| Desulfobacterium autotrophicum | ISDau | | |
| Desulfobacterium sp. | ISDssp | | |
| Desulfobulbaceae bacterium | ISDeba | | |
| Desulfobulbus sp. | ISDes | | |
| Desulfococcus oleovorans | ISDol | | |
| Desulfohalobium retbaense | ISDere | | |
| Desulfomicrobium baculatum | ISDba | | |
| Desulfomicrobium orale | ISDeor | | |
| Desulfonatronospira thiodismutans | ISDth | | |
| Desulfopila aestuarii | ISDeae | | |
| Desulforhopalus singaporensis | ISDsi | | |
| Desulfosporosinus acidiphilus | ISDsac | | |
| Desulfosporosinus sp | ISDess | | |
| Desulfotalea psychrophila | ISDps | | |
| Desulfotignum phosphitoxidans | ISDph | | |
| Desulfotomaculum acetoxidans | ISDce | | |
| Desulfotomaculum gibsoniae | ISDgi | | |
| Desulfotomaculum kuznetsovii | ISDku | | |
| Desulfotomaculum reducens | ISDre | | |
| Desulfovibrio aespoeensis | ISDae | | |
| Desulfovibrio alaskensis | ISDala | | |
| Desulfovibrio desulfuricans | ISDde | | |
| Desulfovibrio litoralis | ISDli | | |
| Desulfovibrio sp. | ISDeul | | |
| Desulfovibrio vulgaris | ISDvu | | |
| Desulfurobacterium thermolithotrophum | ISDeth | | |
| Desulfurococcus kamchatkensis | ISDka | | |
| Desulfuromonadales bacterium | ISDsba | | |
| Desulfuromonas acetoxidans | ISDac | | |
| Desulfuromonas sp. | ISDesu | | |
| Dethiobacter alkaliphilus | ISDeal | | |
| Devosia sp. | ISDev | | |
| Dialister invisus | ISDin | | |
| Dialister succinatiphilus | ISDsu | | |
| Diaphorobacter sp. | ISDisp | | |
| Dichelobacter nodosus | ISDno | | |
| Dickeya dadantii | ISEch | | Erwinia chrysanthemi |
| Dictyoglomus thermophilum | ISDith | | |
| Dinoroseobacter shibae | ISDsh | | |
| Dorea sp. | ISDosp | | |
| Draconibacterium orientale | ISDor | | |
| Duganella phyllosphaerae | ISDuph | | |