Escherichia coli K12 DH1 is a facultative anaerobe, mesophilic, Gram-negative prokaryote of the family Enterobacteriaceae.
Gram-negative motile rod-shaped facultative anaerobe mesophilic genome sequence| @ref 20215 |
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| Domain Bacteria |
| Phylum Pseudomonadota |
| Class Gammaproteobacteria |
| Order Enterobacterales |
| Family Enterobacteriaceae |
| Genus Escherichia |
| Species Escherichia coli |
| Full scientific name Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980) |
| Synonyms (1) |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 1622 | LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) | Medium recipe at MediaDive | Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water | ||
| 35667 | MEDIUM 3 - Columbia agar | Columbia agar (39.000 g);distilled water (1000.000 ml) | |||
| 118351 | CIP Medium 3 | Medium recipe at CIP |
| @ref | Spore formation | Confidence | |
|---|---|---|---|
| 125439 | 91.7 |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 68371 | 27613 ChEBI | amygdalin | - | builds acid from | from API 50CH acid |
| 68368 | 27613 ChEBI | amygdalin | - | fermentation | from API 20E |
| 68371 | 18305 ChEBI | arbutin | - | builds acid from | from API 50CH acid |
| 68371 | 17057 ChEBI | cellobiose | - | builds acid from | from API 50CH acid |
| 118351 | 16947 ChEBI | citrate | - | carbon source | |
| 68368 | 16947 ChEBI | citrate | - | assimilation | from API 20E |
| 68371 | 17108 ChEBI | D-arabinose | - | builds acid from | from API 50CH acid |
| 68371 | 18333 ChEBI | D-arabitol | - | builds acid from | from API 50CH acid |
| 68371 | 15824 ChEBI | D-fructose | + | builds acid from | from API 50CH acid |
| 68371 | 28847 ChEBI | D-fucose | - | builds acid from | from API 50CH acid |
| 68371 | 12936 ChEBI | D-galactose | + | builds acid from | from API 50CH acid |
| 68371 | 17634 ChEBI | D-glucose | + | builds acid from | from API 50CH acid |
| 68368 | 17634 ChEBI | D-glucose | + | fermentation | from API 20E |
| 68371 | 62318 ChEBI | D-lyxose | - | builds acid from | from API 50CH acid |
| 68371 | 16899 ChEBI | D-mannitol | + | builds acid from | from API 50CH acid |
| 68368 | 16899 ChEBI | D-mannitol | + | fermentation | from API 20E |
| 68371 | 16024 ChEBI | D-mannose | + | builds acid from | from API 50CH acid |
| 68371 | 16988 ChEBI | D-ribose | + | builds acid from | from API 50CH acid |
| 68371 | 17924 ChEBI | D-sorbitol | + | builds acid from | from API 50CH acid |
| 68371 | 16443 ChEBI | D-tagatose | - | builds acid from | from API 50CH acid |
| 68371 | 65327 ChEBI | D-xylose | + | builds acid from | from API 50CH acid |
| 68371 | 17113 ChEBI | erythritol | - | builds acid from | from API 50CH acid |
| 118351 | 4853 ChEBI | esculin | + | hydrolysis | |
| 68371 | 4853 ChEBI | esculin | - | builds acid from | from API 50CH acid |
| 68371 | 16813 ChEBI | galactitol | - | builds acid from | from API 50CH acid |
| 68368 | 5291 ChEBI | gelatin | - | hydrolysis | from API 20E |
| 68371 | 28066 ChEBI | gentiobiose | - | builds acid from | from API 50CH acid |
| 68371 | 24265 ChEBI | gluconate | + | builds acid from | from API 50CH acid |
| 118351 | 17234 ChEBI | glucose | + | fermentation | |
| 118351 | 17234 ChEBI | glucose | + | degradation | |
| 68371 | 17754 ChEBI | glycerol | + | builds acid from | from API 50CH acid |
| 68371 | 28087 ChEBI | glycogen | - | builds acid from | from API 50CH acid |
| 68371 | 15443 ChEBI | inulin | - | builds acid from | from API 50CH acid |
| 68371 | 30849 ChEBI | L-arabinose | + | builds acid from | from API 50CH acid |
| 68368 | 30849 ChEBI | L-arabinose | + | fermentation | from API 20E |
| 68371 | 18403 ChEBI | L-arabitol | - | builds acid from | from API 50CH acid |
| 68371 | 18287 ChEBI | L-fucose | + | builds acid from | from API 50CH acid |
| 68371 | 62345 ChEBI | L-rhamnose | + | builds acid from | from API 50CH acid |
| 68368 | 62345 ChEBI | L-rhamnose | + | fermentation | from API 20E |
| 68371 | 17266 ChEBI | L-sorbose | - | builds acid from | from API 50CH acid |
| 68371 | 65328 ChEBI | L-xylose | - | builds acid from | from API 50CH acid |
| 118351 | 17716 ChEBI | lactose | + | fermentation | |
| 68371 | 17716 ChEBI | lactose | + | builds acid from | from API 50CH acid |
| 68368 | 25094 ChEBI | lysine | - | degradation | from API 20E |
| 118351 | 15792 ChEBI | malonate | - | assimilation | |
| 68371 | 17306 ChEBI | maltose | + | builds acid from | from API 50CH acid |
| 118351 | 29864 ChEBI | mannitol | + | fermentation | |
| 68371 | 6731 ChEBI | melezitose | - | builds acid from | from API 50CH acid |
| 68371 | 28053 ChEBI | melibiose | + | builds acid from | from API 50CH acid |
| 68368 | 28053 ChEBI | melibiose | + | fermentation | from API 20E |
| 68371 | 320061 ChEBI | methyl alpha-D-glucopyranoside | - | builds acid from | from API 50CH acid |
| 68371 | 43943 ChEBI | methyl alpha-D-mannoside | - | builds acid from | from API 50CH acid |
| 68371 | 74863 ChEBI | methyl beta-D-xylopyranoside | - | builds acid from | from API 50CH acid |
| 68371 | 17268 ChEBI | myo-inositol | - | builds acid from | from API 50CH acid |
| 68368 | 17268 ChEBI | myo-inositol | - | fermentation | from API 20E |
| 68371 | 59640 ChEBI | N-acetylglucosamine | + | builds acid from | from API 50CH acid |
| 118351 | 17632 ChEBI | nitrate | + | reduction | |
| 118351 | 16301 ChEBI | nitrite | - | reduction | |
| 68368 | 18257 ChEBI | ornithine | - | degradation | from API 20E |
| 68371 | Potassium 2-ketogluconate | - | builds acid from | from API 50CH acid | |
| 68371 | Potassium 5-ketogluconate | + | builds acid from | from API 50CH acid | |
| 68371 | 16634 ChEBI | raffinose | - | builds acid from | from API 50CH acid |
| 68371 | 15963 ChEBI | ribitol | - | builds acid from | from API 50CH acid |
| 68371 | 17814 ChEBI | salicin | - | builds acid from | from API 50CH acid |
| 118351 | 132112 ChEBI | sodium thiosulfate | - | builds gas from | |
| 68368 | 30911 ChEBI | sorbitol | + | fermentation | from API 20E |
| 68371 | 28017 ChEBI | starch | - | builds acid from | from API 50CH acid |
| 68371 | 17992 ChEBI | sucrose | - | builds acid from | from API 50CH acid |
| 68368 | 17992 ChEBI | sucrose | - | fermentation | from API 20E |
| 68371 | 27082 ChEBI | trehalose | + | builds acid from | from API 50CH acid |
| 68368 | 27897 ChEBI | tryptophan | + | energy source | from API 20E |
| 68371 | 32528 ChEBI | turanose | - | builds acid from | from API 50CH acid |
| 68368 | 16199 ChEBI | urea | - | hydrolysis | from API 20E |
| 68371 | 17151 ChEBI | xylitol | - | builds acid from | from API 50CH acid |
| @ref | Metabolite | Is sensitive | Is resistant | |
|---|---|---|---|---|
| 118351 | 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate) |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 118351 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 68382 | alkaline phosphatase | + | 3.1.3.1 | from API zym |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 | from API zym |
| 68382 | alpha-fucosidase | - | 3.2.1.51 | from API zym |
| 68382 | alpha-galactosidase | + | 3.2.1.22 | from API zym |
| 68382 | alpha-glucosidase | + | 3.2.1.20 | from API zym |
| 68382 | alpha-mannosidase | - | 3.2.1.24 | from API zym |
| 68382 | beta-galactosidase | + | 3.2.1.23 | from API zym |
| 118351 | beta-galactosidase | + | 3.2.1.23 | |
| 68368 | beta-galactosidase | + | 3.2.1.23 | from API 20E |
| 68382 | beta-glucosidase | - | 3.2.1.21 | from API zym |
| 68382 | beta-glucuronidase | + | 3.2.1.31 | from API zym |
| 118351 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | - | 3.4.11.3 | from API zym |
| 68368 | cytochrome oxidase | - | 1.9.3.1 | from API 20E |
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | - | from API zym | |
| 118351 | gelatinase | - | ||
| 68368 | gelatinase | - | from API 20E | |
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 68382 | lipase (C 14) | - | from API zym | |
| 118351 | lysine decarboxylase | - | 4.1.1.18 | |
| 68368 | lysine decarboxylase | - | 4.1.1.18 | from API 20E |
| 68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | + | from API zym | |
| 118351 | ornithine decarboxylase | - | 4.1.1.17 | |
| 68368 | ornithine decarboxylase | - | 4.1.1.17 | from API 20E |
| 118351 | oxidase | - | ||
| 118351 | phenylalanine ammonia-lyase | - | 4.3.1.24 | |
| 68382 | trypsin | + | 3.4.21.4 | from API zym |
| 118351 | tryptophan deaminase | - | ||
| 68368 | tryptophan deaminase | - | 4.1.99.1 | from API 20E |
| 118351 | urease | - | 3.5.1.5 | |
| 68368 | urease | - | 3.5.1.5 | from API 20E |
| 68382 | valine arylamidase | + | from API zym |
| @ref | ONPG | ADH (Arg) | LDC (Lys) | ODC | CIT | H2S productionH2S | URE | TDA (Trp) | IND | Acetoin production (Voges Proskauer test)VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | Nitrite productionNO2 | Reduction to N2N2 | MotilityMOB | Growth on MacConkey mediumMAC | OF-O | OF-F | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1622 | + | + | - | - | - | - | - | - | + | - | - | + | + | - | + | + | - | + | - | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | |
| 1622 | + | - | - | - | - | - | - | - | + | - | - | + | + | - | + | + | - | + | - | + | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. |
| @ref | ControlQ | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 118351 | not determinedn.d. | + | - | - | + | + | + | - | - | - | + | + | + | + | - | + | - | - | + | + | - | - | + | - | - | - | - | - | + | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | + |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | spore_formation | BacteriaNetⓘ | no | 91.70 | no |
| 125439 | motility | BacteriaNetⓘ | yes | 62.80 | no |
| 125439 | gram_stain | BacteriaNetⓘ | negative | 92.80 | no |
| 125439 | oxygen_tolerance | BacteriaNetⓘ | obligate aerobe | 97.20 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 99.75 | no |
| 125438 | anaerobic | anaerobicⓘ | no | 95.78 | yes |
| 125438 | aerobic | aerobicⓘ | no | 60.09 | yes |
| 125438 | spore-forming | spore-formingⓘ | no | 87.95 | no |
| 125438 | thermophilic | thermophileⓘ | no | 98.50 | no |
| 125438 | flagellated | motile2+ⓘ | yes | 75.36 | no |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Safety of lacto-N-fucopentaose I/2'-fucosyllactose (LNFP-I/2'-FL) mixture as a novel food pursuant to Regulation (EU) 2015/2283. | EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA), Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch-Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Aguilera-Gomez M, Cubadda F, Frenzel T, Heinonen M, Prieto Maradona M, Marchelli R, Neuhauser-Berthold M, Pelaez C, Poulsen M, Schlatter JR, Siskos A, van Loveren H, Colombo P, Noriega Fernandez E, Knutsen HK. | EFSA J | 10.2903/j.efsa.2023.8412 | 2023 | ||
| Safety of 3-fucosyllactose (3-FL) produced by a derivative strain of Escherichia coli K-12 DH1 as a novel food pursuant to Regulation (EU) 2015/2283. | EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA), Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch-Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pelaez C, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Aguilera-Gomez M, Cubadda F, Frenzel T, Heinonen M, Prieto Maradona M, Marchelli R, Neuhauser-Berthold M, Poulsen M, Schlatter JR, Siskos A, van Loveren H, Colombo P, Noriega Fernandez E, Knutsen HK. | EFSA J | 10.2903/j.efsa.2023.8026 | 2023 | ||
| Hijacking the Peptidoglycan Recycling Pathway of Escherichia coli to Produce Muropeptides. | Rousseau A, Michaud J, Pradeau S, Armand S, Cottaz S, Richard E, Fort S. | Chemistry | 10.1002/chem.202202991 | 2023 | ||
| Current status of the novel food ingredient safety evaluation system. | Heo S, Lee G, Na HE, Park JH, Kim T, Oh SE, Jeong DW. | Food Sci Biotechnol | 10.1007/s10068-023-01396-w | 2024 | ||
| Metabolism | Production of perdeuterated fucose from glyco-engineered bacteria. | Gajdos L, Forsyth VT, Blakeley MP, Haertlein M, Imberty A, Samain E, Devos JM. | Glycobiology | 10.1093/glycob/cwaa059 | 2021 | |
| Phylogeny | Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials. | Torok VA, Hughes RJ, Mikkelsen LL, Perez-Maldonado R, Balding K, MacAlpine R, Percy NJ, Ophel-Keller K. | Appl Environ Microbiol | 10.1128/aem.00165-11 | 2011 | |
| Genetics | Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. | Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. | mSystems | 10.1128/msystems.00537-21 | 2021 | |
| Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. | Kothari A, Wu YW, Chandonia JM, Charrier M, Rajeev L, Rocha AM, Joyner DC, Hazen TC, Singer SW, Mukhopadhyay A. | mBio | 10.1128/mbio.02899-18 | 2019 | ||
| Metabolism | Improving microbial biogasoline production in Escherichia coli using tolerance engineering. | Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS, Leong S, Mukhopadhyay A. | mBio | 10.1128/mbio.01932-14 | 2014 | |
| Metabolism | Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. | Mohamed ET, Wang S, Lennen RM, Herrgard MJ, Simmons BA, Singer SW, Feist AM. | Microb Cell Fact | 10.1186/s12934-017-0819-1 | 2017 | |
| Comparison of sequence reads obtained from three next-generation sequencing platforms. | Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T. | PLoS One | 10.1371/journal.pone.0019534 | 2011 | ||
| Genetics | The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. | Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. | BMC Genomics | 10.1186/1471-2164-15-924 | 2014 | |
| Pathogenicity | Functional genomic study of exogenous n-butanol stress in Escherichia coli. | Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD. | Appl Environ Microbiol | 10.1128/aem.02323-09 | 2010 | |
| Genetics | Next generation models for storage and representation of microbial biological annotation. | Quest DJ, Land ML, Brettin TS, Cottingham RW. | BMC Bioinformatics | 10.1186/1471-2105-11-s6-s15 | 2010 | |
| Metabolism | Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes. | Recht MI, Puglisi JD. | Antimicrob Agents Chemother | 10.1128/aac.45.9.2414-2419.2001 | 2001 | |
| Enzymology | DNA probe technology for rapid detection of Haemophilus influenzae in clinical specimens. | Malouin F, Bryan LE, Shewciw P, Douglas J, Li D, Van den Elzen H, Lapointe JR. | J Clin Microbiol | 10.1128/jcm.26.10.2132-2138.1988 | 1988 | |
| Enzymology | Detection of Legionella species in respiratory specimens using PCR with sequencing confirmation. | Cloud JL, Carroll KC, Pixton P, Erali M, Hillyard DR. | J Clin Microbiol | 10.1128/jcm.38.5.1709-1712.2000 | 2000 | |
| Serodiagnosis of toxoplasmosis by using a recombinant form of the 54-kilodalton rhoptry antigen expressed in Escherichia coli. | van Gelder P, Bosman F, de Meuter F, van Heuverswyn H, Herion P. | J Clin Microbiol | 10.1128/jcm.31.1.9-15.1993 | 1993 | ||
| Enzymology | Chitinase determinants of Vibrio vulnificus: gene cloning and applications of a chitinase probe. | Wortman AT, Somerville CC, Colwell RR. | Appl Environ Microbiol | 10.1128/aem.52.1.142-145.1986 | 1986 | |
| Cloning and expression of genes responsible for altered penicillin-binding proteins 3a and 3b in Haemophilus influenzae. | Malouin F, Schryvers AB, Bryan LE. | Antimicrob Agents Chemother | 10.1128/aac.31.2.286 | 1987 | ||
| Gene transfer system for Rhodopseudomonas viridis. | Lang FS, Oesterhelt D. | J Bacteriol | 10.1128/jb.171.8.4425-4435.1989 | 1989 | ||
| Determination of the biomasses of small bacteria at low concentrations in a mixture of species with forward light scatter measurements by flow cytometry | Robertson BR, Button DK, Koch AL. | Appl Environ Microbiol | 10.1128/aem.64.10.3900-3909.1998 | 1998 | ||
| Metabolism | Determination of DNA content of aquatic bacteria by flow cytometry. | Button DK, Robertson BR. | Appl Environ Microbiol | 10.1128/aem.67.4.1636-1645.2001 | 2001 | |
| Pathogenicity | The ygaVP genes of Escherichia coli form a tributyltin-inducible operon. | Gueune H, Durand MJ, Thouand G, DuBow MS. | Appl Environ Microbiol | 10.1128/aem.02294-07 | 2008 |
| #1622 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4235 |
| #20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 ) |
| #35667 | ; Curators of the CIP; |
| #66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) . |
| #68368 | Automatically annotated from API 20E . |
| #68371 | Automatically annotated from API 50CH acid . |
| #68382 | Automatically annotated from API zym . |
| #118351 | Collection of Institut Pasteur ; Curators of the CIP; CIP 104745 |
| #125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 ) |
| #125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 . |
| #126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 ) |
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