Strain identifier

BacDive ID: 4938

Type strain: Yes

Species: Hafnia alvei

Strain Designation: Type 32011

Strain history: CIP <- 1957, NCTC <- 1950, C.A. Stuart, Rhode Island

NCBI tax ID(s): 910996 (strain), 569 (species)

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General

@ref: 9173

BacDive-ID: 4938

DSM-Number: 30163

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Hafnia alvei Type 32011 is a facultative anaerobe, mesophilic, Gram-negative human pathogen of the family Hafniaceae.

NCBI tax id

NCBI tax idMatching level
910996strain
569species

strain history

@refhistory
9173<- ATCC; ATCC 13337 <- NCTC; NCTC 8105 <- C. A. Stuart; NCDC 434-68
67770Y. Kosako 82061 <-- R. Sakazaki 286 <-- ATCC 13337 <-- NCTC 8105 <-- C. A. Stuart (type 32011).
116316CIP <- 1957, NCTC <- 1950, C.A. Stuart, Rhode Island

doi: 10.13145/bacdive4938.20250331.9.3

Name and taxonomic classification

LPSN

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

@ref: 9173

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Hafniaceae

genus: Hafnia

species: Hafnia alvei

full scientific name: Hafnia alvei Møller 1954

strain designation: Type 32011

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116316negativerod-shapedyes
125438negative99.985
125439negative99.1

multimedia

  • @ref: 9173
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_30163.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9173COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
9173TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
41708MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116316CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
9173positivegrowth30
41708positivegrowth30
67770positivegrowth37
116316positivegrowth10-41
116316nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
116316facultative anaerobe
125439aerobe90.1

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11631629864mannitol+fermentation
11631616947citrate-carbon source
11631617234glucose+fermentation
11631617716lactose-fermentation
11631617632nitrate+reduction
11631616301nitrite-reduction
11631615792malonate+assimilation
116316132112sodium thiosulfate-builds gas from
11631617234glucose+degradation
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: 116316
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
11631635581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
11631615688acetoin+
11631617234glucose+
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
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
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116316oxidase-
116316beta-galactosidase+3.2.1.23
116316alcohol dehydrogenase-1.1.1.1
116316gelatinase-
116316catalase+1.11.1.6
116316lysine decarboxylase+4.1.1.18
116316ornithine decarboxylase+4.1.1.17
116316tryptophan deaminase-
116316urease+3.5.1.5
68382alpha-mannosidase-3.2.1.24
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
116316-++--+----++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
9173+-+++-+--+-++--+--++-
9173+-+++-+--+-++--+--++-
9173+-+++-+--+-++--+--++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116316+++++----++-----++++++-+-------+-+---------------+---++++--+++----------+--+---++-+---+--++++++---+

Isolation, sampling and environmental information

isolation

  • @ref: 116316
  • isolation date: 1919

taxonmaps

  • @ref: 69479
  • File name: preview.99_934.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_324;98_734;99_934&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: AB519795
  • Sequence Identity:
  • Total samples: 27485
  • soil counts: 2075
  • aquatic counts: 4333
  • animal counts: 18887
  • plant counts: 2190

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
9173yesyes2Risk group (German classification)
1163161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hafnia alvei ATCC 13337 16S ribosomal RNA gene, partial sequenceM591551488nuccore910996
20218Hafnia alvei gene for 16S ribosomal RNA, partial sequenceAB5197951473nuccore569
124043Hafnia alvei gene for 16S rRNA, partial sequence, strain: NBRC 105685.AB6822611468nuccore569
124043Hafnia alvei strain GD35 16S ribosomal RNA gene, partial sequence.KF9287911496nuccore569

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hafnia alvei ATCC 13337910996.5wgspatric910996
66792Hafnia alvei ATCC 13337910996.3wgspatric910996
66792Hafnia alvei strain NCTC8105569.79wgspatric569
66792Hafnia alvei Stuart 32011, ATCC 133372588253788draftimg910996
67770Hafnia alvei ATCC 13337GCA_000735375contigncbi910996
67770Hafnia alvei ATCC 13337GCA_003668715contigncbi910996
67770Hafnia alvei NCTC8105GCA_900451105contigncbi569

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.985no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.879no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no60.046no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.657no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.42no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.6
125439BacteriaNetmotilityAbility to perform movementyes77.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe90.1

External links

@ref: 9173

culture collection no.: DSM 30163, ATCC 13337, CIP 57.31, NCDC 434-68, NCTC 8105, WDCM 00095, JCM 1666, CCUG 15720, CCUG 41547, CECT 158, CGMCC 1.2026, HAMBI 1876, LMG 10392, NBRC 105685, NCIMB 11999, NCIMB 13060, NRRL B-4260, VTT E-022142, VTT E-991294

straininfo link

  • @ref: 74434
  • straininfo: 92428

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny1718234Structural studies on Hafnia alvei 114-60 O-antigen.Katzenellenbogen E, Romanowska E, Witkowska D, Bogulska M, Dabrowski JArch Immunol Ther Exp (Warsz)1990Antigens, Bacterial/*chemistry, Carbohydrate Sequence, Cross Reactions, Enterobacteriaceae/classification/*immunology, Lipopolysaccharides/chemistry/immunology, Magnetic Resonance Spectroscopy, Methylation, Molecular Sequence Data, Molecular Structure, O Antigens, Species SpecificityGenetics
Genetics2606108O-specific polysaccharides of Hafnia alvei lipopolysaccharides isolated from two serologically related strains: ATCC 13337 and 1187. A serological and structural study using chemical methods, gas chromatography/mass spectrometry and NMR spectroscopy at 500 MHz.Gamian A, Romanowska E, Opferkuch HJ, Hauck M, Dabrowski JEur J Biochem1989Carbohydrate Conformation, Carbohydrate Sequence, Enterobacteriaceae/*immunology, Gas Chromatography-Mass Spectrometry, *Lipopolysaccharides, Magnetic Resonance Spectroscopy, Methylation, Molecular Sequence Data, Polysaccharides/*isolation & purificationEnzymology10.1111/j.1432-1033.1989.tb15251.x
Genetics7535188Lipopolysaccharide core region of Hafnia alvei: structure elucidation using chemical methods, gas chromatography-mass spectrometry, and NMR spectroscopy.Gamian A, Katzenellenbogen E, Romanowska E, Dabrowski U, Dabrowski JCarbohydr Res1995Carbohydrate Sequence, Enterobacteriaceae/*chemistry/immunology, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Methylation, Molecular Sequence Data, O Antigens, Phosphorylation, Polysaccharides, Bacterial/*chemistry10.1016/0008-6215(94)00266-i
Genetics7653161Structural and serological characterization of Hafnia alvei lipopolysaccharide core region.Lugowski C, Niedziela T, Jachymek W, Klonowska A, Czarny A, Rowinski S, Petersson C, Kenne LActa Biochim Pol1995Carbohydrate Sequence, Chromatography, Gel, Enterobacteriaceae/*chemistry, Gas Chromatography-Mass Spectrometry, Glucose/chemistry, Heptoses/chemistry, Lipopolysaccharides/*chemistry/*immunology, Magnetic Resonance Spectroscopy, Mannose/chemistry, Methylation, Molecular Sequence Data, Oxidation-Reduction, Tetanus Toxoid/immunology
Genetics7719279Lipopolysaccharide core region of Hafnia alvei: serological characterization.Lugowski C, Jachymek W, Niedziela T, Romanowska A, Witkowska D, Romanowska EFEMS Immunol Med Microbiol1995Animals, Carbohydrate Sequence, Enterobacteriaceae/*immunology, Immune Sera/immunology, Immunoblotting, Lipopolysaccharides/*immunology, Molecular Sequence Data, Oligosaccharides/immunology, Rabbits10.1111/j.1574-695X.1995.tb00020.x
Genetics8156055Serological and structural features of Hafnia alvei lipopolysaccharides containing D-3-hydroxybutyric acid.Romanowska A, Gamian A, Witkowska D, Katzenellenbogen E, Romanowska EFEMS Immunol Med Microbiol19943-Hydroxybutyric Acid, Animals, Antibodies, Bacterial/immunology, Antigens, Bacterial/*chemistry/immunology, Carbohydrate Sequence, Cross Reactions, Enterobacteriaceae/*chemistry/immunology, Hydroxybutyrates/*chemistry/immunology, Immunoblotting, Immunoelectrophoresis, Lipopolysaccharides/*chemistry/immunology, Molecular Sequence Data, RabbitsEnzymology10.1111/j.1574-695X.1994.tb00429.x
Genetics9658571Reinvestigation of the O-specific polysaccharides of Hafnia alvei lipopolysaccharides isolated from strains ATCC 13337 and 1187.Gamian A, Katzenellenbogen E, Romanowska E, Grosskurth H, Dabrowski JCarbohydr Res1998Carbohydrate Conformation, Carbohydrate Sequence, Enterobacteriaceae/*chemistry/immunology, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, O Antigens/*chemistry/isolation & purification, Oligosaccharides/chemistryEnzymology10.1016/s0008-6215(98)00035-4
Metabolism12132774Phenotypic and genotypic properties of the genus Hafnia.Janda JM, Abbott SL, Khashe S, Probert WJ Med Microbiol2002Adhesins, Bacterial/genetics, Animals, Arabinose/metabolism, Arbutin/metabolism, Bacterial Typing Techniques, Bangladesh, Benzyl Alcohols/metabolism, Carrier Proteins/genetics, Diarrhea/*microbiology, Electrophoresis, Gel, Pulsed-Field, Escherichia coli/classification/genetics, *Escherichia coli Proteins, Esculin/metabolism, Fermentation, Genes, Bacterial, Genotype, Glucosides, Hafnia alvei/*classification/*genetics, Humans, Hydrolysis, Phenotype, RNA, Ribosomal, 16S/genetics, beta-Glucosidase/metabolismPhylogeny10.1099/0022-1317-51-7-575
Phylogeny16000455Identification of two distinct hybridization groups in the genus Hafnia by 16S rRNA gene sequencing and phenotypic methods.Janda JM, Abbott SL, Bystrom S, Probert WSJ Clin Microbiol2005Bacterial 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, DNAPathogenicity10.1128/JCM.43.7.3320-3323.2005
Phylogeny18836891Immunochemical studies of the lipopolysaccharides of Hafnia alvei PCM 1219 and other strains with the O-antigens containing D-glucose 1-phosphate and 2-deoxy-2-[(R)-3-hydroxybutyramido]-D-glucose.Katzenellenbogen E, Kocharova NA, Korzeniowska-Kowal A, Gamian A, Bogulska M, Szostko B, Shashkov AS, Knirel YAArch Immunol Ther Exp (Warsz)2008Antigens, Bacterial/analysis/*immunology, Glucose/*analogs & derivatives/chemistry, Glucosephosphates/*chemistry, Glycosylation, Hafnia alvei/classification/*metabolism, Nuclear Magnetic Resonance, Biomolecular, O Antigens/chemistry/*immunology, Polysaccharides, Bacterial/chemistry/*immunology, StereoisomerismMetabolism10.1007/s00005-008-0034-1
Phylogeny19734282Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2.Huys G, Cnockaert M, Abbott SL, Janda JM, Vandamme PInt J Syst Evol Microbiol2009Bacterial Proteins/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Enterobacteriaceae Infections/microbiology, Feces/microbiology, Hafnia/*classification/enzymology/genetics/*isolation & purification, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, beta-Glucosidase/metabolismMetabolism10.1099/ijs.0.018606-0
Phylogeny25563917Hafnia psychrotolerans sp. nov., isolated from lake water.Gu Z, Liu Y, Shen L, Liu X, Xiao N, Jiao N, Liu H, Zhou Y, Zhang SInt J Syst Evol Microbiol2015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hafnia/*genetics/growth & development/isolation & purification, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics10.1099/ijs.0.000049

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9173Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30163
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
41708Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9616
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
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
74434Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92428.1StrainInfo: A central database for resolving microbial strain identifiers
116316Curators of the CIPCollection of Institut Pasteur (CIP 57.31)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2057.31
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