Elizabethkingia miricola (CCUG 58416, JCM 11413, DSM 14571)

Name: Elizabethkingia miricola (CCUG 58416, JCM 11413, DSM 14571)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5507

Type strain

Strain Designation W3-B1

Culture col. no. CCUG 58416 JCM 11413 DSM 14571 CIP 108250 GTC 862 3 more

NCBI tax ID(s) 172045

Special Collections DSMZ CCUG JCM KCTC CIP

History <- T. Ezaki; W3-B1 T. Ezaki W3-B1. CIP <- 2004, JCM <- 2001, T. Ezaki: strain W3-B1

Links

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

Gram-negative rod-shaped aerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 131416

DSM 14571,JCM 11413,LMG 22470,BCRC 17371,CCRC 17371,CIP 108250,KCTC 12492,CCUG 58416T

@ref 20215

Last LPSN update 2026-02-09 11:18:59

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 (1)

Chryseobacterium miricola

BacDive ID	Other strains from **Elizabethkingia miricola** (11)	Type strain
139445	E. miricola CIP 111038
139610	E. miricola LDVH 337.01, CIP 108653
139611	E. miricola CIP 111047
156902	E. miricola CCUG 66552
176804	E. miricola Dres_ElizMir_03, DSM 101869
176805	E. miricola Dres_ElizMir_06, DSM 105705
176806	E. miricola Dres_ElizMir_02, DSM 111608
176807	E. miricola Dres_ElizMir_05, DSM 113910
176808	E. miricola Dres_ElizMir_07, DSM 114280
176809	E. miricola Dres_ElizSp_39, DSM 115351
176810	E. miricola Dres_ElzabMir_15, DSM 120181

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120972	negative	rod-shaped
125438			92
125438	negative		98.5
125439	negative		99.3

Colony morphology

Pigmentation

@ref	Production	Name
120972		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5389	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
5389	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
41929	MEDIUM 112 - for Janibacter		Distilled 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
120972	CIP Medium 112	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5389	positive	growth	30
41929	positive	growth	30
61683	positive	growth	30
67770	positive	growth	30
120972	positive	growth	15-37
120972	negative	growth	5
120972	negative	growth	41
120972	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
61683	aerobe
120972	obligate aerobe
125439	obligate aerobe	95.6

Spore formation

@ref	Spore formation	Confidence
125438		90.2
125439		98.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120972	NaCl	positive	growth	0-6 %
120972	NaCl		growth	8 %
120972	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120972	16947 ChEBI	citrate	-	carbon source
120972	4853 ChEBI	esculin	+	hydrolysis
120972	606565 ChEBI	hippurate	+	hydrolysis
120972	15792 ChEBI	malonate	-	assimilation
120972	17632 ChEBI	nitrate	-	builds gas from
120972	17632 ChEBI	nitrate	-	reduction
120972	17632 ChEBI	nitrate	-	respiration
120972	16301 ChEBI	nitrite	-	builds gas from
120972	16301 ChEBI	nitrite	+	reduction
120972	35020 ChEBI	tributyrin	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120972	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
120972	15688 ChEBI	acetoin	-
120972	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120972	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
120972	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120972	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120972	caseinase	+	3.4.21.50
120972	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120972	DNase	+
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
120972	gamma-glutamyltransferase	+	2.3.2.2
120972	gelatinase	+
120972	lecithinase	+
68382	leucine arylamidase	-	3.4.11.1	from API zym
120972	lipase	-
68382	lipase (C 14)	-		from API zym
120972	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120972	ornithine decarboxylase	-	4.1.1.17
120972	oxidase	+
120972	phenylalanine ammonia-lyase	+	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
120972	tryptophan deaminase	-
120972	tween esterase	-
120972	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120972	-	+	-	-	-	-	+	-	+	-	+	+	-	-	-	+	-	+	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120972	not determinedn.d.	+	+	-	+	+	-	-	-	-	+	+	+	-	-	-	-	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5389	condensation water	Russian Space station Mir
61683	Water,condensation	Russion space laboratory Mir	Space
67770	Condensation water in the Russian space laboratory Mir
120972	Environment, Water	Mir space laboratory	Russian Federation	RUS	Europe

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
5389			2	Risk group (German classification) According to TRBA 466
120972			1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM90009204v1 assembly for Elizabethkingia miricola	contig	GCA_900092045	172045.52	2850371549	172045	68.38
67770	ASM812455v1 assembly for Elizabethkingia miricola DSM 14571	scaffold	GCA_008124555	172045.68	2593339301	172045	67.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Elizabethkingia miricola gene for 16S rRNA, partial sequence	AB071953	1312		172045

GC content

@ref	GC-content (mol%)	Method
67770	35	high performance liquid chromatography (HPLC)
67770	34.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Elizabethkingia miricola DSM 14571
NCBI: GCA_008124555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	no	74.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Elizabethkingia miricola strain DSM 14571
PATRIC: 172045.68

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	97.64	yes
125438	spore-forming	spore-formingⓘ	no	90.20	no
125438	aerobic	aerobicⓘ	yes	88.74	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Molecular 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 Microbiol	10.3389/fmicb.2025.1582121	2025
Phylogeny	Evaluation 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 Microbiol	10.1128/jcm.00157-08	2008
	Lung 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 Cases	10.12998/wjcc.v12.i1.169	2024
	Validation 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 Sci	10.3390/ijms241613007	2023
Phylogeny	Determination of Elizabethkingia Diversity by MALDI-TOF Mass Spectrometry and Whole-Genome Sequencing.	Eriksen HB, Gumpert H, Faurholt CH, Westh H.	Emerg Infect Dis	10.3201/eid2302.161321	2017
Genetics	Comparative 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 Rep	10.1038/s41598-019-55795-3	2019
Phylogeny	Transfer 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 ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63541-0	2005
Genetics	Revisiting 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 Leeuwenhoek	10.1007/s10482-017-0926-3	2018
Phylogeny	Elizabethkingia argenteiflava sp. nov., isolated from the pod of soybean, Glycine max.	Hwang JH, Kim J, Kim JH, Mo S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004767	2021
Phylogeny	Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelisKampfer et al. 2011.	Kampfer P, Busse HJ, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.000236	2015
Phylogeny	Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae.	Kampfer P, Matthews H, Glaeser SP, Martin K, Lodders N, Faye I	Int J Syst Evol Microbiol	10.1099/ijs.0.026393-0	2010
Phylogeny	Chryseobacterium 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 T	Syst Appl Microbiol	10.1078/072320203770865828	2003

References

#5389	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14571
#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#41929	; Curators of the CIP;
#61683	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58416
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#120972	Collection of Institut Pasteur ; Curators of the CIP; CIP 108250
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. 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. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Elizabethkingia miricola (CCUG 58416, JCM 11413, DSM 14571)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900092045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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