Strain identifier

BacDive ID: 139255

Type strain: No

Species: Hafnia alvei

Strain Designation: 5632-72

Strain history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 5632-72 <- Maine State Hlth. Dept., USA

NCBI tax ID(s): 569 (species)

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General

@ref: 41390

BacDive-ID: 139255

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Hafnia alvei 5632-72 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from Human.

NCBI tax id

  • NCBI tax id: 569
  • Matching level: species

strain history

  • @ref: 41390
  • history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 5632-72 <- Maine State Hlth. Dept., USA

doi: 10.13145/bacdive139255.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Hafniaceae
  • genus: Hafnia
  • species: Hafnia alvei
  • full scientific name: Hafnia alvei Møller 1954 (Approved Lists 1980)

@ref: 41390

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Hafniaceae

genus: Hafnia

species: Hafnia alvei

strain designation: 5632-72

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.303
6948099.982negative
41390yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41390MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
41390CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
41390positivegrowth30mesophilic
41390positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 41390
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.66

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
41390mannitol+fermentation29864
41390citrate+carbon source16947
41390glucose+fermentation17234
41390lactose-fermentation17716
41390nitrate+reduction17632
41390nitrite-reduction16301
41390malonate+assimilation15792
41390sodium thiosulfate-builds gas from132112
41390glucose+degradation17234

antibiotic resistance

  • @ref: 41390
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 41390
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4139015688acetoin+
4139017234glucose+

enzymes

@refvalueactivityec
41390oxidase-
41390beta-galactosidase+3.2.1.23
41390alcohol dehydrogenase-1.1.1.1
41390gelatinase-
41390catalase+1.11.1.6
41390lysine decarboxylase+4.1.1.18
41390ornithine decarboxylase+4.1.1.17
41390phenylalanine ammonia-lyase-4.3.1.24
41390tryptophan deaminase-
41390urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
41390-+++-+++--++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
41390+-+/-+++---++++-+--+---+----+/-+---+------+----+--++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
41390+++++----++----+-+-+++-++------+-+-------------------------+++----------++-+---++-++-----++++++----

Isolation, sampling and environmental information

isolation

  • @ref: 41390
  • sample type: Human

Safety information

risk assessment

  • @ref: 41390
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hafnia alvei ATCC 29926GCA_000980975contigncbi569
66792Hafnia alvei strain ATCC 29926569.29wgspatric569

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.158no
anaerobicno95.214no
halophileno91.644no
spore-formingno95.013no
glucose-utilyes95.122no
thermophileno99.284no
flagellatedyes52.064no
motileyes89.483no
aerobicyes81.744no
glucose-fermentyes93.671no

External links

@ref: 41390

culture collection no.: CIP 104949, ATCC 29926

straininfo link

  • @ref: 95800
  • straininfo: 44865

literature

  • topic: Phylogeny
  • Pubmed-ID: 16000455
  • title: Identification of two distinct hybridization groups in the genus Hafnia by 16S rRNA gene sequencing and phenotypic methods.
  • authors: Janda JM, Abbott SL, Bystrom S, Probert WS
  • journal: J Clin Microbiol
  • DOI: 10.1128/JCM.43.7.3320-3323.2005
  • year: 2005
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/*analysis, Enterobacteriaceae Infections/microbiology, Genes, rRNA, Hafnia/*classification/*genetics, Hafnia alvei/classification/genetics, Humans, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/*genetics, *Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
41390Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104949Collection of Institut Pasteur (CIP 104949)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
95800Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID44865.1