Strain identifier

BacDive ID: 5531

Type strain: Yes

Species: Flavobacterium hibernum

Strain Designation: LCI

Strain history: CIP <- 1998, JF. Bernardet, INRA, Jouy en Josas, France, "Flavobacterium ameridies" <- P. Franzmann <- Mc Cammon

NCBI tax ID(s): 37752 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4772

BacDive-ID: 5531

DSM-Number: 12611

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, psychrophilic, Gram-negative

description: Flavobacterium hibernum LCI is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from surface water.

NCBI tax id

  • NCBI tax id: 37752
  • Matching level: species

strain history

@refhistory
4772<- ACAM <- P. D. Franzmann; LCI
119890CIP <- 1998, JF. Bernardet, INRA, Jouy en Josas, France, "Flavobacterium ameridies" <- P. Franzmann <- Mc Cammon

doi: 10.13145/bacdive5531.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium hibernum
  • full scientific name: Flavobacterium hibernum McCammon et al. 1998

@ref: 4772

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium hibernum

full scientific name: Flavobacterium hibernum McCammon et al. 1998

strain designation: LCI

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.996
119890negativerod-shapedyes

colony morphology

  • @ref: 119890

pigmentation

  • @ref: 119890
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4772R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
32829MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119890CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119890CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4772positivegrowth20psychrophilic
32829positivegrowth25mesophilic
119890positivegrowth5-30
119890nogrowth37mesophilic
119890nogrowth41thermophilic
119890nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119890
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
119890NaClpositivegrowth0 %
119890NaClnogrowth2 %
119890NaClnogrowth4 %
119890NaClnogrowth6 %
119890NaClnogrowth8 %
119890NaClnogrowth10 %

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
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
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
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119890citrate-carbon source16947
119890esculin+hydrolysis4853
119890hippurate-hydrolysis606565
119890nitrate-builds gas from17632
119890nitrate+reduction17632
119890nitrite-builds gas from16301
119890nitrite-reduction16301
119890tributyrin-hydrolysis35020
119890malonate-assimilation15792
119890glucose+degradation17234

antibiotic resistance

  • @ref: 119890
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119890
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11989015688acetoin-
11989017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
119890oxidase-
119890beta-galactosidase+3.2.1.23
119890alcohol dehydrogenase+1.1.1.1
119890gelatinase+/-
119890amylase+
119890DNase-
119890caseinase+3.4.21.50
119890catalase+1.11.1.6
119890tween esterase+
119890gamma-glutamyltransferase+2.3.2.2
119890lecithinase-
119890lipase-
119890lysine decarboxylase-4.1.1.18
119890ornithine decarboxylase-4.1.1.17
119890phenylalanine ammonia-lyase-4.3.1.24
119890protease-
119890tryptophan deaminase-
119890urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119890-+++++++-+++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119890--++-+---++++--------+++-++++/--+++--++-++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119890--+-----++-----++++-++-+-------------------------------+---+--------------------------+---+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentlatitudelongitudecountryorigin.country
4772surface waterVestfold Hills, Crooked Lake, 68°38'S, 18°17'EAustralia and Oceania-68.633318.2833
119890Environment, Water, surfaceCrooked lakeAntarcticaAntarcticaATA

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47721Risk group (German classification)
1198901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Flavobacterium hibernum 16S ribosomal RNA gene, partial sequence
  • accession: L39067
  • length: 1461
  • database: ena
  • NCBI tax ID: 37752

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium hibernum DSM 12611GCA_000832125contigncbi37752
66792Flavobacterium hibernum ATCC 51468GCA_002217315scaffoldncbi37752
66792Flavobacterium hibernum DSM 1261137752.5wgspatric37752
66792Flavobacterium hibernum strain ATCC 5146837752.9wgspatric37752
66792Flavobacterium hibernum DSM 126112648501293draftimg37752

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.5no
gram-positiveno98.095no
anaerobicno99.785no
aerobicyes92.405no
halophileno97.863no
spore-formingno93.94no
thermophileno99.651yes
glucose-utilyes89.643no
motileno84.436no
glucose-fermentno87.724no

External links

@ref: 4772

culture collection no.: DSM 12611, ACAM 376, ATCC 51468, CIP 105745

straininfo link

  • @ref: 75014
  • straininfo: 46908

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828443Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake.McCammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ, Holloway PE, Skerratt JH, Nichols PD, Rankin LMInt J Syst Bacteriol10.1099/00207713-48-4-14051998Antarctic Regions, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Flavobacterium/*classification/enzymology/isolation & purification/physiology, Fresh Water/*microbiology, Lactose/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Terminology as Topic, *Water Microbiology, beta-Galactosidase/metabolismEnzymology
Phylogeny25313092Flavobacterium maotaiense sp. nov., isolated from freshwater.Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv JInt J Syst Evol Microbiol10.1099/ijs.0.064139-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny29804222Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil.Dahal RH, Kim JAntonie Van Leeuwenhoek10.1007/s10482-018-1105-x2018Bacterial Typing Techniques, Base Composition/genetics, Flavobacterium/*genetics/*metabolism, Genotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Urea/*metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4772Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12611)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12611
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
32829Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17798
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75014Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46908.1StrainInfo: A central database for resolving microbial strain identifiers
119890Curators of the CIPCollection of Institut Pasteur (CIP 105745)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105745