Strain identifier

BacDive ID: 4971

Type strain: Yes

Species: Enterobacter intermedius

Strain Designation: E86

Strain history: CIP <- 1979, H. Leclerc, INSERM, Villeneuve-d'Ascq, France: strain CUETM 77-130 <- F. Gavini, INSERM, France: strain E86

NCBI tax ID(s): 1218113 (strain), 61648 (species)

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General

@ref: 1779

BacDive-ID: 4971

DSM-Number: 4581

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

description: Enterobacter intermedius E86 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Water,surface.

NCBI tax id

NCBI tax idMatching level
1218113strain
61648species

strain history

@refhistory
1779<- CIP <- H. Leclerc, CUETM <- F. Gavini, E86
67770R. Sakazaki 256 <-- H. Leclerc CUETM 77-130 <-- F. Gavini E 86.
120145CIP <- 1979, H. Leclerc, INSERM, Villeneuve-d'Ascq, France: strain CUETM 77-130 <- F. Gavini, INSERM, France: strain E86

doi: 10.13145/bacdive4971.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Enterobacter
  • species: Enterobacter intermedius
  • full scientific name: Enterobacter intermedius corrig. Izard et al. 1980

  • synonyms

    @refsynonym
    20215Enterobacter intermedium
    20215Kluyvera cochleae
    20215Kluyvera intermedia

@ref: 1779

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Kluyvera

species: Kluyvera intermedia

full scientific name: Kluyvera intermedia (Izard et al. 1980) Pavan et al. 2005

strain designation: E86

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120145negativerod-shapedyes
125438negative99.5
125439negative93.4

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1779REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37713MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120145CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
1779positivegrowth30
37713positivegrowth30
46037positivegrowth37
67770positivegrowth37
120145positivegrowth10-37
120145nogrowth5
120145nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
46037aerobe
120145facultative anaerobe
125439aerobe95.1

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 91

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12014529864mannitol+fermentation
12014516947citrate+carbon source
12014517234glucose+fermentation
12014517716lactose+fermentation
12014517632nitrate+reduction
12014516301nitrite-reduction
12014515792malonate+assimilation
120145132112sodium thiosulfate-builds gas from
12014517234glucose+degradation
68371Potassium 5-ketogluconate+builds acid from
6837118305arbutin+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

antibiotic resistance

  • @ref: 120145
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
12014535581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12014515688acetoin+
12014517234glucose-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
120145oxidase-
120145beta-galactosidase+3.2.1.23
120145alcohol dehydrogenase-1.1.1.1
120145gelatinase-
120145catalase+1.11.1.6
120145lysine decarboxylase-4.1.1.18
120145ornithine decarboxylase+4.1.1.17
120145phenylalanine ammonia-lyase-4.3.1.24
120145tryptophan deaminase-
120145urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382alpha-glucosidase+3.2.1.20
68382lipase (C 14)-
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120145-+-+-+----++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1779+--++----+-++-++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120145+--+++---++++-++/--++-+++/-+++++++++--+---++/--+/--+/---+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120145+++++-+++-++-+++-+++++-+-----+++-++-+----+-++----+---+++++-++++++----------+---++-+---+--++--++----

Isolation, sampling and environmental information

isolation

@refsample type
46037Water,surface
67770Surface water
120145Environment, Surface water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Surface water

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17792Risk group (German classification)
1201452Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterobacter intermedius 16S ribosomal RNA gene, partial sequenceAF3102171453nuccore61648
20218Kluyvera intermedia gene for 16S ribosomal RNA, partial sequenceAB0047471438nuccore61648
20218Kluyvera intermedia gene for 16S rRNA, partial sequence, strain: NBRC 102594AB6818711465nuccore61648
124043Kluyvera intermedia partial 16S rRNA gene, strain HAMBI 1299LT8999781516nuccore61648

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kluyvera intermedia NCTC12125GCA_900635475completencbi61648
66792Kluyvera intermedia NBRC 102594 = ATCC 331101218113.4wgspatric1218113
66792Kluyvera intermedia strain NCTC1212561648.17completepatric61648
66792Kluyvera intermedia NBRC 1025942731957696draftimg1218113
67770Kluyvera intermedia NBRC 102594 = ATCC 33110GCA_001598315contigncbi1218113

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe95.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative93.4
125439BacteriaNetmotilityAbility to perform movementyes69.7
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.301yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no62.339no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.018no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99yes
125438motile2+flagellatedAbility to perform flagellated movementyes76.503no

External links

@ref: 1779

culture collection no.: CCUG 14183, CIP 79-27, NCTC 12125, LMG 2785, DSM 4581, ATCC 33110, CIP 79.27, CUETM 77.130, IAM 14238, JCM 1238, BCRC 14808, CCM 3433, CUETM 77-130, HAMBI 1299, HUT 8114, NBRC 102594, NCIMB 13626, VTT E-97862

straininfo link

  • @ref: 74467
  • straininfo: 389410

literature

  • topic: Phylogeny
  • Pubmed-ID: 15653915
  • title: Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius Izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia.
  • authors: Pavan ME, Franco RJ, Rodriguez JM, Gadaleta P, Abbott SL, Janda JM, Zorzopulos J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63071-0
  • year: 2005
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Enterobacter/*classification/genetics/metabolism, Enterobacteriaceae/classification/genetics/metabolism, Kluyvera/*classification/genetics/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminology as Topic
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1779Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4581)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4581
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
37713Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11053
46037Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14183)https://www.ccug.se/strain?id=14183
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74467Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389410.1StrainInfo: A central database for resolving microbial strain identifiers
120145Curators of the CIPCollection of Institut Pasteur (CIP 79.27)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2079.27
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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