NCBI
NCBI Taxonomy taxdump · 2026-10-23taxid: 562
Bacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia > Escherichia coli
Escherichia coli
Species in genus Escherichia, family Enterobacteriaceae (order Enterobacterales). (from NCBI Taxonomy lineage)
Warning: This taxon splits 1→many across databases. Read the panels carefully.
Names over time
Loading the names
Cross-database view
GTDB
- Escherichia coli
- ECMA0423 sp047199055
- +49 more — see all names below
id: s__Escherichia coli / s__ECMA0423 sp047199055 · GTDB R232
At its weakest, linked by GTDB's own NCBI species id rather than the genome's raw one.
d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Warning: GTDB R232 places this taxon's 48712 genomes in 2 species.
Name differs between releases: Name differs across GTDB releases.
SILVA
Escherichia coli
id: JN048662 · SILVA 138.2
Linked by name — the SILVA table we ingest carries no NCBI taxid, so the binomial is the only join.
Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;
Greengenes2
- Escherichia ruysiae
- Shigella boydii
- Shigella dysenteriae
- +22 more — see all names below
id: Escherichia ruysiae / Shigella boydii / Shigella dysenteriae (+22) · Greengenes2 2024.09
Linked via GTDB R220 genome accessions — the same physical genomes, not a name match.
d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Enterobacterales_737866; f__Enterobacteriaceae_A_725029; g__Escherichia; s__Escherichia ruysiae
Warning: Greengenes2 2024.09 places this taxon's 1433 genomes in 11 species.
Name differs between releases: Name differs across Greengenes2 releases.
eHOMD
release 4.2Escherichia coli
id: HMT-574 · eHOMD 4.2
Linked by NCBI taxid — eHOMD records the same id NCBI does.
Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia
Only 1 genome — below the threshold for detecting a split, so “current” here means unverified, not confirmed.
Each panel shows one release. Switch a release to see how that database's answer changes — the taxon is held fixed by NCBI taxid, so every panel describes the same organism. Each panel also says how it was linked; how the databases are joined explains the routes.
Lineage by rank
| rank | NCBI | GTDB R232 | SILVA 138.2 | Greengenes2 2024.09 | eHOMD 4.2 |
|---|---|---|---|---|---|
| domain | Bacteria | Bacteria | Bacteria | Bacteria | Bacteria |
| phylum | Pseudomonadota | Pseudomonadota | Pseudomonadota | Pseudomonadota | Pseudomonadota |
| class | Gammaproteobacteria | Gammaproteobacteria | Gammaproteobacteria | Gammaproteobacteria | Gammaproteobacteria |
| order | Enterobacterales | Enterobacterales | Enterobacterales | first rank that differs from NCBI: Enterobacterales_737866 | Enterobacterales |
| family | Enterobacteriaceae | Enterobacteriaceae | Enterobacteriaceae | Enterobacteriaceae_A_725029 | Enterobacteriaceae |
| genus | Escherichia | Escherichia | first rank that differs from NCBI: Escherichia-Shigella | Escherichia | Escherichia |
| species | Escherichia coli | Escherichia coli | — | Escherichia ruysiae | — |
Each column is the release its box shows. marks the first rank at which a database's name differs from NCBI's, by exact text; a suffix such as _A counts. SILVA's path and eHOMD's columns end at genus, so their species row is blank; the box above names the species. Levels a source labels outside these seven ranks are in the API's ranks and not drawn here.
Names in NCBI
from NCBI Taxonomy taxdump · 2026-10-23- Escherichia colicurrent
- Bacillus colisynonym
- Bacterium coli communesynonym
- Bacterium colisynonym
- Enterococcus colisynonym
- Escherichia/Shigella coliequivalent
Other names in these databases
GTDB R232
- Escherichia coli
- ECMA0423 sp047199055
- G047199095 sp047199095
- Enterobacter flexneri_A
- Escherichia coli_F
- Escherichia boydii
- Escherichia hormaechei_A
- Escherichia ruysiae
- G047199115 sp047199115
- Escherichia marmotae
- Klebsiella pneumoniae
- Escherichia coli_E
- Escherichia sp005843885
- Anaerotardibacter sp963591685
- Angelakisella sp900547385
- Aquipseudomonas pudica
- Atlantibacter hermannii
- CAG-115 sp963641955
- CAG-177 sp003514385
- CAG-390 sp000437015
- CAKRJP01 sp963589425
- Citrobacter freundii
- Citrobacter gillenii
- Citrobacter murliniae
- Cryptobacteroides sp963640185
- Enterobacter hormaechei_C
- Enterobacter roggenkampii
- Escherichia fergusonii
- Escherichia sp002965065
- F23-B02 sp963632825
- Fimenecus sp963590415
- Hafnia alvei
- Hominicoprocola fusiformis
- Klebsiella aerogenes
- Klebsiella michiganensis
- Klebsiella quasipneumoniae
- Klebsiella variicola
- Kluyvera sichuanensis
- Laedolimicola sp963656395
- Oribacterium sp963650995
- Ornithospirochaeta sp963626925
- Oscillibacter segnis
- Phascolarctobacterium_A sp963603005
- Phytobacter palmae
- Phytobacter ursingii
- Prevotella sp963593695
- Prevotella sp963601795
- Priestia flexa
- Providencia hangzhouensis
- Roseburia faecis
- UBA4951 sp963630675
SILVA 138.264 of 1,655
- Escherichia coli
- Escherichia coli O157:H7
- Escherichia coli K-12
- Escherichia coli str. K-12 substr. MG1655
- Escherichia coli str. K-12 substr. W3110
- Escherichia coli O6:H16
- Escherichia coli O104:H4 str. C227-11
- Escherichia coli O104:H4
- Escherichia coli O157
- Escherichia coli Nissle 1917
- Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775
- Escherichia coli O157:H7 str. EDL933
- Escherichia coli ATCC 8739
- Escherichia coli B
- Escherichia coli BL21(DE3)
- Escherichia coli DEC11D
- Escherichia coli DEC3F
- Escherichia coli DH1
- Escherichia coli KO11FL
- Escherichia coli O127:H6
- Escherichia coli O169:H41
- Escherichia coli W
- Escherichia coli B94
- Escherichia coli DEC1A
- Escherichia coli DEC1B
- Escherichia coli DEC4A
- Escherichia coli DEC4C
- Escherichia coli DEC5E
- Escherichia coli DEC6B
- Escherichia coli DEC6E
- Escherichia coli DEC9A
- Escherichia coli DEC9D
- Escherichia coli DEC10E
- Escherichia coli DEC11C
- Escherichia coli DEC12A
- Escherichia coli DEC1C
- Escherichia coli DEC2C
- Escherichia coli DEC4B
- Escherichia coli DEC4E
- Escherichia coli DEC7A
- Escherichia coli DEC8B
- Escherichia coli DEC8C
- Escherichia coli EPEC 32/73
- Escherichia coli 97.0246
- Escherichia coli DEC10C
- Escherichia coli DEC11E
- Escherichia coli DEC12C
- Escherichia coli DEC14B
- Escherichia coli DEC15B
- Escherichia coli DEC15D
- Escherichia coli DEC15E
- Escherichia coli DEC2E
- Escherichia coli DEC3A
- Escherichia coli DEC3C
- Escherichia coli DEC3D
- Escherichia coli DEC4F
- Escherichia coli DEC7C
- Escherichia coli DEC8A
- Escherichia coli DEC8D
- Escherichia coli DEC9B
- Escherichia coli EPEC C342-62
- Escherichia coli STEC_S1191
- Escherichia coli 2720900
- Escherichia coli 8-415-05_S3_C1
- …and 1,591 more, not listed — this taxon is a large placeholder bucket in SILVA 138.2.
Greengenes2 2024.09
- Escherichia ruysiae
- Shigella boydii
- Shigella dysenteriae
- Escherichia fergusonii
- Shigella sonnei
- Escherichia albertii
- Shigella flexneri
- Clostridioides_A difficile
- Mesomycoplasma sp012516495
- Proteus mirabilis
- Streptococcus suis
- Acinetobacter schindleri
- Agathobacter rectalis
- Bacillus_A cereus_U_306726
- Citrobacter_A_692098 werkmanii
- Clostridium_T beijerinckii
- Clostridium_T celatum
- Enterobacter_B_713587 hoffmannii
- Exiguobacterium_A indicum
- Mycoplasmopsis_A_271961 bovis
- Phocaeicola_A vulgatus
- Prevotella copri
- Streptococcus anginosus
- Sutterella wadsworthensis_A_565869
- Thomasclavelia ramosa