Strain identifier

BacDive ID: 138457

Type strain: Yes

Species: Chryseobacterium hagamense

Strain Designation: RHA2-9

Strain history: CIP <- 2012, KCTC <- S.B. Kim, Chungnam Natl. Univ., Korea: strain RHA2-9

NCBI tax ID(s): 395935 (species)

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General

@ref: 39792

BacDive-ID: 138457

keywords: genome sequence, Bacteria, mesophilic, Gram-negative

description: Chryseobacterium hagamense RHA2-9 is a mesophilic, Gram-negative bacterium of the family Weeksellaceae.

NCBI tax id

  • NCBI tax id: 395935
  • Matching level: species

strain history

  • @ref: 39792
  • history: CIP <- 2012, KCTC <- S.B. Kim, Chungnam Natl. Univ., Korea: strain RHA2-9

doi: 10.13145/bacdive138457.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium hagamense
  • full scientific name: Chryseobacterium hagamense Cho et al. 2011

@ref: 39792

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Chryseobacterium

species: Chryseobacterium hagamense

strain designation: RHA2-9

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.984
39792negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39792MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
39792CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

  • @ref: 39792
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

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
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

enzymes

@refvalueactivityec
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
39792--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39792-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic location
39792Republic of KoreaKORAsia
39792Republic of KoreaKORAsiaEnvironment, Soil, rhizosphere of wild pea (Lathyrus japonica) growing in a coastal sand dune areaThe Tae-An area, Chungnam Province

Safety information

risk assessment

  • @ref: 39792
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium hagamense NBRC 105253GCA_007991455contigncbi395935
66792Chryseobacterium hagamense strain NBRC 105253395935.4wgspatric395935

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.179no
anaerobicno99.586no
halophileno93.186no
spore-formingno95.761no
glucose-utilyes87.231no
aerobicyes91.913no
motileno91.54no
thermophileno99.238yes
flagellatedno96.386no
glucose-fermentno92.446no

External links

@ref: 39792

culture collection no.: CIP 110400, KCTC 22545, NBRC 105253

straininfo link

  • @ref: 95180
  • straininfo: 413569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20185262Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov.Cho SH, Lee KS, Shin DS, Han JH, Park KS, Lee CH, Park KH, Kim SBSyst Appl Microbiol10.1016/j.syapm.2009.12.0042010Bacterial Typing Techniques, Chryseobacterium/chemistry/*classification/genetics/*isolation & purification, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny22707535Chryseobacterium rigui sp. nov., isolated from an estuarine wetland.Park SJ, Choi JH, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.040519-02012Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Estuaries, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Vitamin K 2/analogs & derivatives/analysis, *WetlandsGenetics

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
39792Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110400Collection of Institut Pasteur (CIP 110400)
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
95180Reimer, 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-ID413569.1