Strain identifier

BacDive ID: 5507

Type strain: Yes

Species: Elizabethkingia miricola

Strain Designation: W3-B1

Strain history: CIP <- 2004, JCM <- 2001, T. Ezaki: strain W3-B1

NCBI tax ID(s): 172045 (species)

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

@ref: 5389

BacDive-ID: 5507

DSM-Number: 14571

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

description: Elizabethkingia miricola W3-B1 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from condensation water.

NCBI tax id

  • NCBI tax id: 172045
  • Matching level: species

strain history

@refhistory
5389<- T. Ezaki; W3-B1
67770T. Ezaki W3-B1.
120972CIP <- 2004, JCM <- 2001, T. Ezaki: strain W3-B1

doi: 10.13145/bacdive5507.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Elizabethkingia
  • species: Elizabethkingia miricola
  • full scientific name: Elizabethkingia miricola (Li et al. 2004) Kim et al. 2005
  • synonyms

    • @ref: 20215
    • synonym: Chryseobacterium miricola

@ref: 5389

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Elizabethkingia

species: Elizabethkingia miricola

full scientific name: Elizabethkingia miricola (Li et al. 2004) Kim et al. 2005 emend. Nicholson et al. 2018

strain designation: W3-B1

type strain: yes

Morphology

cell morphology

  • @ref: 120972
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120972

pigmentation

  • @ref: 120972
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5389NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
5389BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
41929MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
120972CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
5389positivegrowth30mesophilic
41929positivegrowth30mesophilic
61683positivegrowth30mesophilic
67770positivegrowth30mesophilic
120972positivegrowth15-37
120972nogrowth5psychrophilic
120972nogrowth41thermophilic
120972nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61683aerobe
120972obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120972NaClpositivegrowth0-6 %
120972NaClnogrowth8 %
120972NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12097216947citrate-carbon source
1209724853esculin+hydrolysis
120972606565hippurate+hydrolysis
12097217632nitrate-builds gas from
12097217632nitrate-reduction
12097216301nitrite-builds gas from
12097216301nitrite+reduction
12097235020tributyrin+hydrolysis
12097215792malonate-assimilation
12097217632nitrate-respiration

metabolite production

  • @ref: 120972
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12097215688acetoin-
12097217234glucose-

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
120972oxidase+
120972beta-galactosidase+3.2.1.23
120972alcohol dehydrogenase-1.1.1.1
120972gelatinase+
120972amylase-
120972DNase+
120972caseinase+3.4.21.50
120972catalase+1.11.1.6
120972tween esterase-
120972gamma-glutamyltransferase+2.3.2.2
120972lecithinase+
120972lipase-
120972lysine decarboxylase-4.1.1.18
120972ornithine decarboxylase-4.1.1.17
120972phenylalanine ammonia-lyase+4.3.1.24
120972tryptophan deaminase-
120972urease-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
120972-+----+-+-++---+-+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120972++-++----+++----+-+-----+------+-+-------------------++----+-+------------------------+--+++-++--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5389condensation waterRussian Space station Mir
61683Water,condensationRussion space laboratory MirSpace
67770Condensation water in the Russian space laboratory Mir
120972Environment, WaterMir space laboratoryRussian FederationRUSEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
5389yesyes2Risk group (German classification)
1209721Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Elizabethkingia miricola gene for 16S rRNA, partial sequence
  • accession: AB071953
  • length: 1312
  • database: ena
  • NCBI tax ID: 172045

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Elizabethkingia miricola Elizabethkingia miricola KCTC 12492GCA_900092045contigncbi172045
66792Elizabethkingia miricola strain DSM 14571172045.68wgspatric172045
66792Elizabethkingia miricola strain Elizabethkingia miricola KCTC 12492172045.52wgspatric172045
66792Elizabethkingia miricola DSM 145712593339301draftimg172045
67770Elizabethkingia miricola DSM 14571GCA_008124555scaffoldncbi172045

GC content

@refGC-contentmethod
6777035high performance liquid chromatography (HPLC)
6777034.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.993no
gram-positiveno98.026no
anaerobicno99.717yes
aerobicyes91.393no
halophileno95.394no
spore-formingno94.592no
glucose-utilyes87.273no
thermophileno99.485yes
flagellatedno94.785no
glucose-fermentno91.664no

External links

@ref: 5389

culture collection no.: CCUG 58416, JCM 11413, DSM 14571, CIP 108250, GTC 862, KCTC 12492, BCRC 17371

straininfo link

  • @ref: 74992
  • straininfo: 131416

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14666980Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir.Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki TSyst Appl Microbiol10.1078/0723202037708658282003Base Composition, Chryseobacterium/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/chemistry, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Spacecraft, Spores, Bacterial, Vitamin K 2/analysis/chemistry, *Water MicrobiologyEnzymology
Phylogeny15879269Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov.Kim KK, Kim MK, Lim JH, Park HY, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63541-02005Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/cytology/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flavobacteriaceae/*classification/cytology/physiology, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny21169462Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae.Kampfer P, Matthews H, Glaeser SP, Martin K, Lodders N, Faye IInt J Syst Evol Microbiol10.1099/ijs.0.026393-02010Animals, Anopheles/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny25858248Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelisKampfer et al. 2011.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.0002362015Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyGenetics
Phylogeny33835912Elizabethkingia argenteiflava sp. nov., isolated from the pod of soybean, Glycine max.Hwang JH, Kim J, Kim JH, Mo SInt J Syst Evol Microbiol10.1099/ijsem.0.0047672021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soybeans/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5389Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14571)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14571
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
41929Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5852
61683Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58416)https://www.ccug.se/strain?id=58416
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/
68382Automatically annotated from API zym
74992Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131416.1StrainInfo: A central database for resolving microbial strain identifiers
120972Curators of the CIPCollection of Institut Pasteur (CIP 108250)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108250