Strain identifier

BacDive ID: 133593

Type strain: Yes

Species: Hafnia paralvei

Strain Designation: 4510-73

Strain history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 4510-73

NCBI tax ID(s): 1354263 (strain), 546367 (species)

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General

@ref: 29679

BacDive-ID: 133593

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

description: Hafnia paralvei 4510-73 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from Human clinical specimen.

NCBI tax id

NCBI tax idMatching level
546367species
1354263strain

strain history

  • @ref: 121568
  • history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 4510-73

doi: 10.13145/bacdive133593.20230509.8.1

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 paralvei
  • full scientific name: Hafnia paralvei Huys et al. 2010

@ref: 29679

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Hafniaceae

genus: Hafnia

species: Hafnia paralvei

strain designation: 4510-73

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29679negativerod-shapedyes
121568negativerod-shapedyes

pigmentation

  • @ref: 29679
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41389MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121568CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
29679positivegrowth28-37mesophilic
29679positiveoptimum32.5mesophilic
41389positivegrowth30mesophilic
121568positivegrowth5-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29679facultative anaerobe
121568facultative anaerobe

spore formation

  • @ref: 29679
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2967922599arabinose+carbon source
2967917234glucose+carbon source
2967917754glycerol+carbon source
2967917306maltose+carbon source
2967929864mannitol+carbon source
2967927082trehalose+carbon source
2967918222xylose+carbon source
2967917632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-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
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+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
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12156829864mannitol+fermentation
12156816947citrate-carbon source
12156817234glucose+fermentation
12156817716lactose-fermentation
12156817632nitrate+reduction
12156816301nitrite-reduction
12156815792malonate-assimilation
121568132112sodium thiosulfate-builds gas from
12156817234glucose+degradation

antibiotic resistance

  • @ref: 121568
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121568
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12156815688acetoin+
12156817234glucose+

enzymes

@refvalueactivityec
121568oxidase-
121568beta-galactosidase+3.2.1.23
121568alcohol dehydrogenase-1.1.1.1
121568gelatinase-
121568catalase+1.11.1.6
121568lysine decarboxylase+4.1.1.18
121568ornithine decarboxylase+4.1.1.17
121568phenylalanine ammonia-lyase-4.3.1.24
121568tryptophan deaminase-
121568urease-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
121568-+++-++++-++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121568+-+/-+++---++++-+--+---+--+-++/-+--+------+----+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121568+++++----++----+++++++-++------+-+--------------++---++++--+++----------+--+---++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refsample type
29679Human clinical specimen
121568Human

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Infection#Patient
#Infection#Medical environment#Clinic
#Infection#Patient#Specimen

taxonmaps

  • @ref: 69479
  • File name: preview.99_2022.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_324;98_734;99_2022&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: FM179943
  • Sequence Identity:
  • Total samples: 7454
  • soil counts: 435
  • aquatic counts: 1050
  • animal counts: 4808
  • plant counts: 1161

Safety information

risk assessment

  • @ref: 121568
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29679
  • description: Hafnia paralvei genomosp. 2 partial 16S rRNA gene, type strain ATCC 29927T
  • accession: FM179943
  • length: 1495
  • database: nuccore
  • NCBI tax ID: 1354263

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hafnia paralvei ATCC 29927GCA_001655005contigncbi1354263
66792Hafnia paralvei ATCC 299271354263.4wgspatric1354263
66792Hafnia paralvei Stebra 1GCA_023698525scaffoldncbi546367

GC content

  • @ref: 29679
  • GC-content: 49.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.276yes
gram-positiveno98.141yes
anaerobicno95.633no
halophileno91.547no
spore-formingno95.541yes
thermophileno99.407no
glucose-utilyes94.388yes
flagellatedno52.821no
aerobicyes82.759yes
glucose-fermentyes91.932no

External links

@ref: 29679

culture collection no.: CDC 4510-73, LMG 24706, ATCC 29927, CIP 104950

straininfo link

  • @ref: 91517
  • straininfo: 45883

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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 Microbiol10.1099/ijs.0.018606-02009Bacterial 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/metabolismMetabolism
Phylogeny21553084A case of bacteremia caused by Hafnia paralvei.Osuka H, Hitomi S, Koganemaru H, Kaneko TJ Infect Chemother10.1007/s10156-011-0255-92011Aged, 80 and over, Anti-Bacterial Agents/therapeutic use, Bacteremia/blood/drug therapy/*microbiology, Base Sequence, Cholecystitis/blood/microbiology, Diagnosis, Differential, Enterobacteriaceae Infections/blood/drug therapy/*microbiology, Hafnia/genetics/*isolation & purification, Humans, Male, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry/geneticsPathogenicity
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 Microbiol10.1099/ijs.0.0000492015Bacterial 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, DNAGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
29679Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172606428776041
41389Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16915
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91517Reimer, 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-ID45883.1
121568Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104950Collection of Institut Pasteur (CIP 104950)