Strain identifier

BacDive ID: 132418

Type strain: Yes

Species: Chryseobacterium frigidum

Strain Designation: D07

Strain history: <- Fang Peng, CCTCC

NCBI tax ID(s): 1593234 (species)

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General

@ref: 24207

BacDive-ID: 132418

DSM-Number: 100383

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Chryseobacterium frigidum D07 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from high-Arctic tundra soil.

NCBI tax id

  • NCBI tax id: 1593234
  • Matching level: species

strain history

@refhistory
24207<- M. Kim, CCTCC; D07 <- T. Kim
67771<- Fang Peng, CCTCC

doi: 10.13145/bacdive132418.20230509.8.1

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 frigidum
  • full scientific name: Chryseobacterium frigidum Kim et al. 2016

@ref: 24207

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium frigidum

full scientific name: Chryseobacterium frigidum Kim et al. 2016

strain designation: D07

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
44024negative0.63-1.08 µm0.53-0.63 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 44024
  • colony size: 1.0-2.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

pigmentation

  • @ref: 44024
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
44024BHIno
44024MacConkeyno
44024MBno
44024Nutrient agar (NA)yes
44024Reasoner's 2A agar (R2A)yes
44024TSByes
24207R2A 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

culture temp

@refgrowthtypetemperaturerange
44024positivegrowth4-37
44024positiveoptimum28-30mesophilic
44024mesophilic
24207positivegrowth28mesophilic
67771positivegrowth28-30mesophilic

culture pH

@refabilitytypepHPH range
44024positivegrowth6.0-9.0alkaliphile
44024positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44024aerobe
67771aerobe

spore formation

  • @ref: 44024
  • spore formation: no

halophily

  • @ref: 44024
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.0 %

observation

@refobservation
44024budding reproduction
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4402417234glucose-fermentation
4402485146carboxymethylcellulose-hydrolysis
4402417029chitin-hydrolysis
4402416991dna-hydrolysis
4402417895L-tyrosine-hydrolysis
4402453426tween 80-hydrolysis
4402416199urea-hydrolysis
4402417632nitrate-reduction
4402417634D-glucose+builds acid from
4402416024D-mannose+builds acid from
440244853esculin+builds acid from
4402428087glycogen+builds acid from
4402417716lactose+builds acid from
4402417306maltose+builds acid from
4402428053melibiose+builds acid from
44024506227N-acetylglucosamine+builds acid from
4402428017starch+builds acid from
44024167632-oxobutanoate+carbon source
4402417925alpha-D-glucose+carbon source
4402417057cellobiose+carbon source
4402415824D-fructose+carbon source
4402412936D-galactose+carbon source
4402414314D-glucose 6-phosphate+carbon source
4402416024D-mannose+carbon source
4402423652dextrin+carbon source
4402429042glucose 1-phosphate+carbon source
4402428087glycogen+carbon source
4402473804glycyl L-aspartic acid+carbon source
4402417596inosine+carbon source
4402473786L-alanylglycine+carbon source
4402429991L-aspartate+carbon source
4402429985L-glutamate+carbon source
4402417203L-proline+carbon source
4402416857L-threonine+carbon source
4402417716lactose+carbon source
440246359lactulose+carbon source
4402417306maltose+carbon source
4402428053melibiose+carbon source
4402451850methyl pyruvate+carbon source
4402475146monomethyl succinate+carbon source
4402428037N-acetylgalactosamine+carbon source
44024506227N-acetylglucosamine+carbon source
4402473784glycyl-l-glutamate+carbon source
4402416634raffinose+carbon source
4402417748thymidine+carbon source
4402432528turanose+carbon source
4402416704uridine+carbon source
44024casein+hydrolysis
440244853esculin+hydrolysis
440245291gelatin+hydrolysis
4402428017starch+hydrolysis
4402453424tween 20+hydrolysis
4402453423tween 40+hydrolysis
4402453425tween 60+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
44024474053cefazolinyesyes
440247731ofloxacinyesyes
440243534cephalexinyesyes
4402428001vancomycinyesyes
440245195furazolidoneyesyes
440243515cefuroximeyesyes
440243493cefoperazoneyesyes
440248232piperacillinyesyes
4402463598levofloxacinyesyes
44024100246norfloxacinyesyes
4402448923erythromycinyesyes
440246104kanamycinyesyes
44024135817cefminoxyesyes
4402427902tetracyclineyesyes
44024209807cefoxitinyesyes
44024204928cefotaximeyesyes
440246472lincomycinyesyes
4402429007ceftriaxoneyesyes
44024102484sulfisoxazoleyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4402416136hydrogen sulfideno
4402415688acetoinyes
4402435581indoleyes

metabolite tests

  • @ref: 44024
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: -

enzymes

@refvalueactivityec
44024catalase+1.11.1.6
44024urease-3.5.1.5
44024beta-galactosidase-3.2.1.23
44024arginine dihydrolase-3.5.3.6
44024lysine decarboxylase-4.1.1.18
44024ornithine decarboxylase-4.1.1.17
44024tryptophan deaminase-4.1.99.1
44024cytochrome oxidase+1.9.3.1
44024alkaline phosphatase+3.1.3.1
44024esterase (C 4)+
44024esterase Lipase (C 8)+
44024acid phosphatase+3.1.3.2
44024leucine arylamidase+3.4.11.1
44024valine arylamidase+
44024trypsin+3.4.21.4
44024naphthol-AS-BI-phosphohydrolase+
44024alpha-galactosidase+3.2.1.22
44024alpha-glucosidase+3.2.1.20
44024N-acetyl-beta-glucosaminidase+3.2.1.52

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture temperatureisolation procedure
24207high-Arctic tundra soilSvalbard archipelago near the settlement Ny-Alesund (78° 55' N 11° 58' E)NorwayNOREurope78.916711.9667
44024soil sample in the high Artic tundraNy-Ålesund in the Svalbard archipelagoNorwayNOREurope78.916711.9667R2A agar28standard dilution plating technique on R2A agar (BD)
67771From soil in the high Arctic tundra near the settlement Ny-â„«lesundthe Svalbard archipelagoNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Climate#Cold#Polar
#Climate#Cold#Tundra
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Tundra

taxonmaps

  • @ref: 69479
  • File name: preview.99_69957.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_29970;97_37865;98_49123;99_69957&stattab=map
  • Last taxonomy: Chryseobacterium frigidum subclade
  • 16S sequence: KP408226
  • Sequence Identity:
  • Total samples: 2824
  • soil counts: 219
  • aquatic counts: 576
  • animal counts: 1902
  • plant counts: 127

Safety information

risk assessment

  • @ref: 24207
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24207
  • description: Chryseobacterium frigidum strain D07 16S ribosomal RNA gene, partial sequence
  • accession: KP408226
  • length: 1409
  • database: ena
  • NCBI tax ID: 1593234

GC content

@refGC-contentmethod
2420749.3high performance liquid chromatography (HPLC)
6777149.3

External links

@ref: 24207

culture collection no.: DSM 100383, CCTCC AB 2011160, KCTC 42897

straininfo link

  • @ref: 90758
  • straininfo: 397168

literature

  • topic: Phylogeny
  • Pubmed-ID: 26558703
  • title: Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense.
  • authors: Kim T, Kim M, Kang O, Jiang F, Chang X, Liu P, Zhang Y, Da X, Zheng C, Fang C, Peng F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000761
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24207Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100383Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100383)
44024TongRyul Kim, MyongChol Kim, OkChol Kang, Fan Jiang, Xulu Chang, Ping Liu, Yumin Zhang, Xuyang Da, Congyi Zheng, Chengxiang Fang, Fang PengChryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense10.1099/ijsem.0.000761IJSEM 66: 609-615 201626558703
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/
90758Reimer, 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-ID397168.1