Cite the latest
BacDive paper
×

Rate our new design

Thank you!
BacDive D3
Content
Advanced search Isolation sources API ® test finder TAXplorer Statistics Special collections Download selection Web services SPARQL
About us
About Team Contact Tutorials News Mailinglist
BacDive ID 5507
Type strain
Strain Designation W3-B1
Culture col. no. CCUG 58416 JCM 11413 DSM 14571 CIP 108250 GTC 862 KCTC 12492 W3-B1 BCRC 17371 3 more
NCBI tax ID(s) 172045
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 5389

BacDive-ID: 5507

DSM-Number: 14571

keywords: genome sequence, 16S sequence, 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/bacdive5507.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/pseudomonadati
  • keyword: phylum/bacteroidota
  • 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

@refgram staincell shapemotilityconfidence
120972negativerod-shapedno
125438no92
125438negative98.5
125439negative99.3

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

@refgrowthtypetemperature
5389positivegrowth30
41929positivegrowth30
61683positivegrowth30
67770positivegrowth30
120972positivegrowth15-37
120972negativegrowth5
120972negativegrowth41
120972negativegrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
61683aerobe
120972obligate aerobe
125439obligate aerobe95.6

spore formation

@refspore formationconfidence
125438no90.2
125439no98.2

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
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
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

Interaction and safety

risk assessment

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

Sequence information

Genome sequences

@refdescriptionassembly levelINSDC accessionBV-BRC accessionIMG accessionNCBI tax IDscore
66792ASM90009204v1 assembly for Elizabethkingia miricolacontigGCA_900092045172045.52285037154917204568.38
67770ASM812455v1 assembly for Elizabethkingia miricola DSM 14571scaffoldGCA_008124555172045.68259333930117204567.76

16S sequences

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

GC content

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

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.639yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.2no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.741no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementno92no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.2
125439BacteriaNetmotilityAbility to perform movementno74.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.6

Literature

@ref: 5389

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

straininfo link

  • @ref: 126262
  • 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
Phylogeny18400920Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria.Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, Dunn J, Hall G, Wilson D, Lasala P, Kostrzewa M, Harmsen D.J Clin Microbiol10.1128/jcm.00157-082008classification, metabolism, genetics, methods, Bacterial Typing Techniques, methodsMetabolism
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
Phylogeny28098550Determination of Elizabethkingia Diversity by MALDI-TOF Mass Spectrometry and Whole-Genome Sequencing.Eriksen HB, Gumpert H, Faurholt CH, Westh H.Emerg Infect Dis10.3201/eid2302.1613212017Bacteria, 16S rRNA, Nomenclature, Multidrug resistance, Antimicrobial resistance, MALDI-TOF, Septic Arthritis, Carbapenemase, Nosocomial Infections, Matrix-assisted Laser Desorption/ionization Time-of-flight Mass Spectrometry, Etest, Elizabethkingia Miricola, Elizabethkingia Species, Gob-1, classification, genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Genome, Bacterial, Whole Genome SequencingGenetics
Genetics28856455Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J, Emery B, Bell M, Loparev V, Juieng P, Gartin J, Bizet C, Clermont D, Criscuolo A, Brisse S, McQuiston JR.Antonie Van Leeuwenhoek10.1007/s10482-017-0926-32018Taxonomy, SNPs, MALDI-TOF, Aai, Ani, Elizabethkingia, classification, genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Genomics, Genome, Bacterial, Whole Genome SequencingPhylogeny
Genetics31844108Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence.Liang CY, Yang CH, Lai CH, Huang YH, Lin JN.Sci Rep10.1038/s41598-019-55795-32019genetics, Genomics, Genome, Bacterial, Genetic Variation, Whole Genome Sequencing
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
37629190Validation of 16S rRNA and Complete rpoB Gene Sequence Analysis for the Identification of Elizabethkingia Species.Lin JN, Lai CH, Yang CH, Huang YH.Int J Mol Sci10.3390/ijms2416130072023Phylogenetic analysis, Species identification, Elizabethkingia Miricola Cluster, Flavobacteriaceae Infections
38292629Lung imaging characteristics in a patient infected with Elizabethkingia miricola following cerebral hemorrhage surgery: A case report.Qi PQ, Zeng YJ, Peng W, Kuai J.World J Clin Cases10.12998/wjcc.v12.i1.1692024Case Report, Imaging Features, Elizabethkingia Miricola, Postoperative Pulmonary Infection, Cerebral Hemorrhage Surgery
Genetics40703244Molecular characterization, comparative genome analysis and resistance determinants of three clinical Elizabethkingia miricola strains isolated from Michigan.Chen S, Agah G, Blom J, Walker ED.Front Microbiol10.3389/fmicb.2025.15821212025Genome analysis, Molecular identification, Antimicrobial resistance, Elizabethkingia Miricola, Pangenomes

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
120972Curators of the CIPCollection of Institut Pasteur (CIP 108250)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108250
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

BacDive

About Team News Mailinglist

Help

How to cite Tutorials Contact Help

Social Media

BlueskyBluesky linkedin de.NBI Survey
DSMZ Global core biodata resource deNBI Elixis core data resource DZIF NFDI4 Biodiversity NFDI4 Microbiota
© DSMZ 2026 Imprint Privacy Statement Copyright & License License