| Origin | Code | Comment | Supplementary Taxo |
|---|
| Bacillus amyloliquefaciens | ISBamy | | |
| Bacillus anthracis | ISBan | | |
| Bacillus cereus | ISBce | | |
| Bacillus circulans | ISBci | | |
| Bacillus clausei | ISBcl | | |
| Bacillus coagulans | ISBco | | |
| Bacillus coahuilensis | ISBch | | |
| Bacillus cytotoxicus | ISBcy | | |
| Bacillus halodurans | ISBha | | |
| Bacillus hisashii | ISBhi | | |
| Bacillus koreensis | ISBko | | |
| Bacillus licheniformis | ISBali | | |
| Bacillus megaterium | ISBame | | |
| Bacillus pseudofirmus | ISBpse | | |
| Bacillus pseudomycoides | ISBaps | | |
| Bacillus pumilus | ISBpu | | |
| Bacillus selenitireducens | ISBse | | |
| Bacillus smithii | ISBsm | | |
| Bacillus sp. | ISBsp | | |
| Bacillus sphaericus | ISBsph | | |
| Bacillus stearothermophilus | ISBst | | |
| Bacillus subtilis | ISBsu | | |
| Bacillus thermotolerans | ISBath | | |
| Bacillus thuringiensis | ISBth | | |
| Bacillus weihenstephanensis | ISBwe | | |
| Bacteriophage c-st : specific_host Clostridium botulinum | ISCbt | Predefined common nomenclature | |
| Bacteroides finegoldii | ISBfi | | |
| Bacteroides fragilis | ISBf | Predefined common nomenclature | |
| Bacteroides ovatus | ISBaov | | |
| Bacteroides plebeius | ISBpl | | |
| Bacteroides salanitronis | ISBasa | | |
| Bacteroides sp. | ISBias | | |
| Bacteroides thetaiotaomicron | ISBthe | | |
| Bacteroides uniformis | ISBun | | |
| Bacteroides vulgatus | ISBvu | | |
| Bacteroidetes bacterium | ISBaba | | |
| Bartonella tamiae | ISBta | | |
| Bathymodiolus azoricus | ISBaz | | Bathymodiolus azoricus thioautotrophic gill symbiont |
| Bdellovibrionales bacterium | ISBdb | | |
| Beggiatoa sp. | ISBeg | | |
| Beijerinckia indica | ISBin | | |
| Belliella baltica | ISBeba | | |
| Belnapia moabensis | ISBmo | | |
| Betaproteobacteria bacterium | ISBeb | | |
| Bifidobacterium adolescentis | ISBad | | |
| Bifidobacterium animalis | ISBian | | |
| Bifidobacterium asteroides | ISBast | | |
| Bifidobacterium bifidum | ISBbi | | |
| Bifidobacterium breve | ISBibr | | |
| Bifidobacterium longum | ISBlo | | |
| Bifidobacterium sp | ISBisp | | |
| Bifidobacterium thermophilum | ISBith | | |
| Blastococcus saxobsidens | ISBsa | | |
| Blastopirellula marina | ISBlma | | |
| Blautia producta | ISBpr | | |
| Bordetella holmesii | ISBho | | |
| Bordetella parapertussis | ISBpa | | |
| Bordetella pertussis | ISBpe | | |
| Bordetella petrii | ISBope | | |
| Bordetella sp. | ISBosp | | |
| Bosea sp. | ISBos | | |
| Brachyspira hyodysenteriae | ISBhy | | |
| Bradyrhizobium diazoefficiens | ISBdi | | |
| Bradyrhizobium japonicum | ISBj | Predefined common nomenclature | |
| Bradyrhizobium neotropicale | ISBne | | |
| Bradyrhizobium retamae | ISBra | | |
| Bradyrhizobium sp. | ISBrsp | | |
| Bradyrhizobium valentinum | ISBva | | |
| Brenneria salicis | ISBrsa | | |
| Brevibacillus brevis | ISBbr | | |
| Brevibacterium casai | ISBca | | |
| Brevibacterium fuscum | ISBfu | | |
| Brevibacterium lactofermentum | ISBla | | |
| Brevibacterium linens | ISBli | | |
| Brevundimonas sp | ISBesp | | |
| Brocadia sinica | ISBsi | | Candidatus Brocadia sinica |
| Brucella abortus | ISBab | | |
| Brucella melitensis | ISBm | Predefined common nomenclature | |
| Brucella ovis | ISBov | | |
| Brucella suis | ISBrsu | | |
| Bryobacteraceae bacterium | ISBrba | | |
| Burkholderia ambifaria | ISBam | | |
| Burkholderia cenocepacia | ISBcen | | |
| Burkholderia cepacia | ISBuce | | |
| Burkholderia dolosa | ISBdo | | |
| Burkholderia fungorum | ISBfun | | |
| Burkholderia glumae | ISBugl | Predefined common nomenclature | |
| Burkholderia humi | ISBhu | | |
| Burkholderia hypogeia | ISBuhy | | |
| Burkholderia mallei | ISBma | | |
| Burkholderia multivorans | ISBmu | | |
| Burkholderia phymatum | ISBph | | |
| Burkholderia phytofirmans | ISBuph | | |
| Burkholderia pseudomallei | ISBps | | |
| Burkholderia rhizoxinica | ISBrh | | |
| Burkholderia sp. | ISBusp | | |
| Burkholderia terrae | ISBte | | |
| Burkholderia thailandensis | ISButh | | |
| Burkholderia vietnamiensis | ISBvi | | |
| Burkholderia xenovorans | ISBxe | | |
| Burkholderiaceae bacterium | ISBba | | |
| Burkholderiales bacterium | ISBuba | | |