| Origin | Code | Comment | Supplementary Taxo |
| Oceanicaulis sp. | ISOesp | | |
| Oceanicola batsensis | ISOba | | |
| Oceanicola granulosus | ISOgr | | |
| Oceanimonas smirnovii | ISOsm | | |
| Oceanobacillus iheyensis | ISOih | | |
| Oceanobacillus picturae | ISOpi | | |
| Oceanobacter sp. | ISOsp | | |
| Oceanospirillaceae bacterium | ISOcba | | |
| Ochrobactrum anthropi | ISOcan | | |
| Ochrobactrum sp. | ISOcsp | | |
| Octadecabacter antarcticus | ISOan | | |
| Octadecabacter arcticus | ISOar | | |
| Odoribacter splanchnicus | ISOdsp | | |
| Oligella urethralis | ISOur | | |
| Omnitrophica bacterium | ISOmba | | Candidatus Omnitrophica bacterium |
| Opitutaceae bacterium | ISOpb | | |
| Oribacterium sp. | ISOrsp | | |
| Orientia tsutsugamushi | ISOt | Predefined common nomenclature | |
| Oscillatoria nigro-viridis | ISOni | | |
| Oxalobacteraceae bacterium | ISOxba | | |