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BacDive ID 10458
Type strain
Strain Designation 333/54-55
Culture col. no. DSM 8340 ATCC 23834 KCTC 15198 CCUG 2138 333/54-55 NCTC 10596 LMG 7827 LMG 3978 LMG 15557 CIP 70.75 JCM 12952 6 more
NCBI tax ID(s) 546274 539
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 3257

BacDive-ID: 10458

DSM-Number: 8340

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Eikenella corrodens 333/54-55 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
539species
546274strain

strain history

@refhistory
3257<- ATCC; ATCC 23834 <- S. D. Henriksen; 333/54-55 (Bacteroides corrodens) <- P. Holm; <- M. Eiken;
67770DSM 8340 <-- ATCC 23834 <-- S. D. Henriksen 333/54-55 <-- P. Holm <-- M. Eiken.
118756CIP <- 1970, NCTC <- 1968, S.D. Henriksen: strain 333/54-55, Bacteroides corrodens <- P. Holm <- M. Eiken

doi: 10.13145/bacdive10458.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: Eikenella
  • species: Eikenella corrodens
  • full scientific name: Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides corrodens

@ref: 3257

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Neisseriaceae

genus: Eikenella

species: Eikenella corrodens

full scientific name: Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972

strain designation: 333/54-55

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118756negativerod-shapedno
125439positive95.7
125439no93.2
125438negative99

colony morphology

  • @ref: 118756

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33476MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118756CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
3257COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

@refgrowthtypetemperature
3257positivegrowth37
33476positivegrowth37
67770positivegrowth37
118756positivegrowth25-37
118756nogrowth5
118756nogrowth15
118756nogrowth41
118756nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98.8

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 92.423

halophily

@refsaltgrowthtested relationconcentration
118756NaClpositivegrowth0 %
118756NaClnogrowth2 %
118756NaClnogrowth4 %
118756NaClnogrowth6 %
118756NaClnogrowth8 %
118756NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837727897tryptophan-energy source
6837716199urea-hydrolysis
6837717634D-glucose-builds acid from
6837715824D-fructose-builds acid from
1187564853esculin-hydrolysis
118756606565hippurate+hydrolysis
11875617632nitrate-builds gas from
11875617632nitrate+reduction
11875616301nitrite-builds gas from
11875616301nitrite-reduction
11875615792malonate-assimilation
11875617234glucose-degradation
11875617632nitrate+respiration
6837717306maltose-builds acid from

antibiotic resistance

  • @ref: 118756
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
11875635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
11875615688acetoin-
11875617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
118756oxidase+
118756beta-galactosidase+3.2.1.23
118756alcohol dehydrogenase-1.1.1.1
118756gelatinase-
118756catalase-1.11.1.6
118756gamma-glutamyltransferase-2.3.2.2
118756lysine decarboxylase+4.1.1.18
118756ornithine decarboxylase+4.1.1.17
118756phenylalanine ammonia-lyase-4.3.1.24
118756tryptophan deaminase-
118756urease-3.5.1.5
68382beta-galactosidase-3.2.1.23
68382esterase lipase (C 8)+
68377tryptophan deaminase-4.1.99.1
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377beta-lactamase-3.5.2.6

fatty acid profile

  • @reffatty acidpercentageECL
    44497C12:06.112
    44497C14:01.814
    44497C16:026.816
    44497C18:02.518
    44497C12:0 3OH6.713.455
    44497C16:0 3OH117.52
    44497C16:1 ω7c21.315.819
    44497C18:1 ω7c /12t/9t29.717.824
    44497C18:1 ω9c1.817.769
    44497C18:2 ω6,9c/C18:0 ANTE2.417.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    44497C12:08.212
    44497C14:0214
    44497C16:024.816
    44497C18:01.118
    44497C12:0 3OH8.913.455
    44497C16:1 ω7c24.515.819
    44497C18:1 ω7c /12t/9t25.917.824
    44497C18:1 ω9c1.617.769
    44497C18:2 ω6,9c/C18:0 ANTE2.817.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118756--++-+-----+---+----

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
3257-----+----++/--
44497-----+----+--
3257----+----+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3257sputum
44497Human sputum
67770Sputum
118756SputumDenmarkDNKEurope

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_1242.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_721;97_844;98_982;99_1242&stattab=map
  • Last taxonomy: Eikenella corrodens
  • 16S sequence: AB525415
  • Sequence Identity:
  • Total samples: 24331
  • soil counts: 395
  • aquatic counts: 569
  • animal counts: 23214
  • plant counts: 153

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32572Risk group (German classification)
1187562Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218E.Corrodens (strain ATCC 23834) 16S ribosomal RNA, complete cdsM225121481nuccore539
20218Eikenella corrodens strain BCRC 14415 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014522734nuccore539
20218Eikenella corrodens 16S rRNA gene, partialAJ247212458nuccore539
20218E.corrodens (strain FDC 1073) 16S ribosomal RNA, complete cdsM225151476nuccore539
20218Eikenella corrodens gene for 16S ribosomal RNA, paertial sequence, strain: JCM 12952AB5254151503nuccore539
20218Eikenella corrodens strain NCTC 10596 16S ribosomal RNA gene, partial sequenceEF012271623nuccore539

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Eikenella corrodens NCTC10596GCA_900187105completencbi539
66792Eikenella corrodens ATCC 23834546274.4wgspatric546274
66792Eikenella corrodens strain FDAARGOS_1474539.195completepatric539
66792Eikenella corrodens strain NCTC10596539.20completepatric539
66792Eikenella corrodens NCTC 105962823405847completeimg539
66792Eikenella corrodens ATCC 23834643886208draftimg546274
67770Eikenella corrodens ATCC 23834GCA_000158615scaffoldncbi546274
66792Eikenella corrodens strain FDAARGOS_1474539.197completepatric539
66792Eikenella corrodens strain FDAARGOS_1474539.198completepatric539
66792Eikenella corrodens strain FDAARGOS_1474539.196completepatric539

GC content

@refGC-content
325756.4
6777057-58

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.059no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no53.018no
125438spore-formingspore-formingAbility to form endo- or exosporesno92.423no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.278no
125438motile2+flagellatedAbility to perform flagellated movementno83.984no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno83.9
125439BacteriaNetmotilityAbility to perform movementno93.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive95.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.8

External links

@ref: 3257

culture collection no.: DSM 8340, ATCC 23834, KCTC 15198, CCUG 2138, JCM 12952, CIP 70.75, LMG 15557, LMG 3978, LMG 7827, NCTC 10596

straininfo link

  • @ref: 79735
  • straininfo: 2189

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity1323951Identification of a streptomycin resistance gene and a partial Tn3 transposon coding for a beta-lactamase in a periodontal strain of Eikenella corrodens.Lacroix JM, Walker CBAntimicrob Agents Chemother10.1128/AAC.36.4.7401992DNA Transposable Elements, DNA, Bacterial/*analysis, Drug Resistance, Microbial/genetics, Eikenella corrodens/drug effects/*genetics, Sequence Homology, Nucleic Acid, Streptomycin/*pharmacology, beta-Lactamases/*genetics
Pathogenicity3530124Susceptibility of Eikenella corrodens to newer and older quinolones.Goldstein EJ, Citron DM, Vagvolgyi AE, Gombert MEAntimicrob Agents Chemother10.1128/AAC.30.1.1721986Bacteroides/*drug effects, Eikenella corrodens/*drug effects, Microbial Sensitivity Tests, Penicillin G/pharmacology, Quinolines/*pharmacology, Vancomycin/pharmacology
Pathogenicity6360893Biological activities of Eikenella corrodens outer membrane and lipopolysaccharide.Progulske A, Mishell R, Trummel C, Holt SCInfect Immun10.1128/iai.43.1.178-182.19841984Animals, Bacterial Outer Membrane Proteins, Bacterial Proteins/*pharmacology, Bacteroides/*pathogenicity, Biological Assay, Bone Resorption/drug effects, Eikenella corrodens/*pathogenicity, Limulus Test, *Lymphocyte Activation, Lymphocytes/immunology, Membrane Proteins/*pharmacology, Mice, Mice, Inbred Strains, *Mitogens
Pathogenicity7009539Transmission-scanning electron microscopic observations of selected Eikenella corrodens strains.Progulske A, Holt SCJ Bacteriol10.1128/jb.143.2.1003-1018.19801980Bacteroides/*ultrastructure, Eikenella corrodens/*ultrastructure, Humans, Microscopy, Electron, Microscopy, Electron, Scanning, Periodontitis/microbiology, Sputum/microbiology
Metabolism7675516Some observations on the nutritional requirements of Eikenella corrodens ATCC 23834T grown in continuous culture.Gully NJ, Rogers AHOral Microbiol Immunol10.1111/j.1399-302x.1995.tb00129.x1995Amino Acids/*metabolism, Cell Division, Culture Media, Eikenella corrodens/*growth & development/*metabolism, Glutamic Acid/metabolism, Hydrogen-Ion Concentration, Nitrates/metabolism, Serine/metabolism, Time FactorsCultivation
Pathogenicity7790076Characterization of an antiproliferative surface-associated protein from Actinobacillus actinomycetemcomitans which can be neutralized by sera from a proportion of patients with localized juvenile periodontitis.White PA, Wilson M, Nair SP, Kirby AC, Reddi K, Henderson BInfect Immun10.1128/iai.63.7.2612-2618.19951995Adolescent, Adult, Aggregatibacter actinomycetemcomitans/*pathogenicity, Aggressive Periodontitis/*microbiology, Antibodies, Bacterial/immunology, Antigens, Bacterial/immunology, Bacterial Proteins/immunology/*pharmacology, Child, Growth Inhibitors/chemistry/*pharmacology, Humans, Membrane Proteins/*immunology/pharmacology, Molecular Weight, Osteoblasts/*cytology
7877077Scanning electron microscopy of Eikenella corrodens colony morphology variants.Cobb CM, Helber JT, Hirschberg RJ Periodontal Res10.1111/j.1600-0765.1994.tb01242.x1994Eikenella corrodens/pathogenicity/*ultrastructure, Genetic Variation, Virulence
Pathogenicity8302938Development of a genetic system for Eikenella corrodens: transfer of plasmids pFM739 and pLES2.Rao VK, Whitlock JA, Progulske-Fox APlasmid10.1006/plas.1993.10621993*Conjugation, Genetic, DNA, Bacterial/metabolism, Eikenella corrodens/*genetics/pathogenicity, Escherichia coli/genetics, Gram-Negative Bacterial Infections/microbiology, Humans, *Plasmids, Species SpecificityPhylogeny
Enzymology8478080Sequence divergence in two tandemly located pilin genes of Eikenella corrodens.Tonjum T, Weir S, Bovre K, Progulske-Fox A, Marrs CFInfect Immun10.1128/iai.61.5.1909-1916.19931993Amino Acid Sequence, Bacterial Adhesion, Bacterial Outer Membrane Proteins/*genetics, Base Sequence, Blotting, Southern, Cloning, Molecular, Eikenella corrodens/*genetics, Fimbriae Proteins, *Genes, Bacterial, Microscopy, Electron, Molecular Sequence Data, Oligodeoxyribonucleotides/chemistry, Restriction Mapping, Sequence Homology, Amino AcidGenetics
Pathogenicity10093530Variable serum immunoglobulin G immune response to genetically distinct Eikenella corrodens strains coexisting in the human oral cavity.Chen C, Ashimoto AOral Microbiol Immunol10.1111/j.1399-302x.1998.tb00727.x1998Adolescent, Adult, Aggressive Periodontitis/blood/immunology/microbiology, Analysis of Variance, Antibodies, Bacterial/biosynthesis/blood, Antigenic Variation, Antigens, Bacterial/immunology, Child, Eikenella corrodens/classification/genetics/*immunology, Enzyme-Linked Immunosorbent Assay, Humans, Immunoglobulin G/biosynthesis/blood, Middle Aged, Mouth/microbiology, Periodontitis/blood/*immunology/*microbiology, SerotypingPhylogeny
Cultivation17584471Production of antagonistic substance by Eikenella corrodens isolated from the oral cavity of human beings with and without periodontal disease.Apolonio AC, Carvalho MA, Ribas RN, Sousa-Gaia LG, Santos KV, Lana MA, Nicoli JR, Farias LMJ Appl Microbiol10.1111/j.1365-2672.2006.03211.x2007Acute Disease, *Antibiosis, Bacteriocins/*biosynthesis, Bacteriological Techniques, Chronic Disease, Culture Media, Eikenella corrodens/*metabolism/physiology, Gingiva/microbiology, Humans, Microbial Sensitivity Tests/methods, Mouth/*microbiology, Periodontitis/*microbiologyPathogenicity
Enzymology28485212Purification and characterization of hemolysin from periodontopathogenic bacterium Eikenella corrodens strain 1073.Jasin Mansur F, Takahara S, Yamamoto M, Shimatani M, Minnatul Karim M, Noiri Y, Ebisu S, Azakami HBiosci Biotechnol Biochem10.1080/09168451.2017.12958072017Aminopeptidases/genetics/*isolation & purification/metabolism/pharmacology, Bacterial Proteins/genetics/*isolation & purification/metabolism/pharmacology, Cell Fractionation, Cloning, Molecular, Eikenella corrodens/*enzymology/genetics/isolation & purification/*pathogenicity, Erythrocytes/cytology/drug effects, Escherichia coli/genetics/metabolism, Gene Expression, Hemolysin Proteins/genetics/*isolation & purification/metabolism/pharmacology, Hemolysis/*drug effects, Homologous Recombination, Humans, Molecular Weight, Periodontitis/microbiology, Periodontium/microbiology, Recombinant Proteins/genetics/isolation & purification/metabolism/pharmacologyPhylogeny
Phylogeny31693476Eikenella exigua sp. nov., isolated from brain abscess and blood.Stormo KA, Nygaard RM, Bruvold TS, Dimmen G, Lindemann PC, Jordal S, Kommedal OInt J Syst Evol Microbiol10.1099/ijsem.0.0038272019Bacterial Typing Techniques, Base Composition, Blood Culture, Brain Abscess/*microbiology, DNA, Bacterial/genetics, Eikenella/*classification/isolation & purification, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Pathogenicity33903681Effect of respiratory inhibitors and quinone analogues on the aerobic electron transport system of Eikenella corrodens.Jaramillo-Lanchero RD, Suarez-Alvarez P, Teheran-Sierra LSci Rep10.1038/s41598-021-88388-02021Aerobiosis/drug effects, *Bacterial Proteins/antagonists & inhibitors/metabolism, Eikenella corrodens/*enzymology, Electron Transport/drug effects, *Electron Transport Complex I/antagonists & inhibitors/metabolism, NAD/metabolism, Oxygen Consumption/*drug effects, *Quinones/chemistry/pharmacology, *Uncoupling Agents/chemistry/pharmacologyMetabolism
Phylogeny34499598Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species.Hering S, Jansson MK, Buhl MEJInt J Syst Evol Microbiol10.1099/ijsem.0.0049772021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Eikenella/classification/isolation & purification, Fatty Acids/chemistry, Humans, *Pharynx/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3257Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8340)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8340
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33476Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10551
44497Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2138)https://www.ccug.se/strain?id=2138
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68377Automatically annotated from API NH
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
79735Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2189.1StrainInfo: A central database for resolving microbial strain identifiers
118756Curators of the CIPCollection of Institut Pasteur (CIP 70.75)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2070.75
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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