Bizionia echini (DSM 23925, KCTC 22015, KMM 6177)

Name: Bizionia echini (DSM 23925, KCTC 22015, KMM 6177)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5715

Type strain

Culture col. no. DSM 23925 KCTC 22015 KMM 6177 LMG 25220

NCBI tax ID(s) 649333

Special Collections DSMZ KCTC Literature strains

History DSMZ <- KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia KCTC <- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia

Links

Bizionia echini DSM 23925 is an aerobe, Gram-negative, motile bacterium that was isolated from sea urchin Strongylocentrotus intermedius.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 264738

LMG 25220,KCTC 22015,DSM 23925

@ref 20215

Last LPSN update 2026-05-29 08:26:14

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Bizionia

Species Bizionia echini

Full scientific name Bizionia echini Nedashkovskaya et al. 2010

Synonyms (1)

"Algorimicrobium echini"

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
29440	negative	1.4-3.5 µm	0.4-0.5 µm	rod-shaped	gliding
67771				rod-shaped
67771	negative
125439	negative					95.569
125438						93
125438	negative					98.875

Pigmentation

29440

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17308	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17308	positive	growth	28
29440	positive	growth	04-39
29440	positive	optimum	30-37
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29440	aerobe
67771	aerobe
125439	obligate aerobe	94.181

Spore formation

@ref	Spore formation	Confidence
125439		99.421
125438		90.833

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29440	NaCl	positive	growth	01-08 %
29440	NaCl	positive	optimum	02-03 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29440	16947 ChEBI	citrate	+	carbon source
29440	17234 ChEBI	glucose	+	carbon source
29440	37684 ChEBI	mannose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29440	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29440	alkaline phosphatase	+	3.1.3.1
29440	catalase	+	1.11.1.6
29440	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Echinodermata
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17308	sea urchin Strongylocentrotus intermedius	Strongylocentrotus intermedius	Sea of Japan, Gulf of Peter the Great, Troitsa Bay	Russia	RUS	Asia
67771	From sea urchin `Strongylocentrotus intermedius`	Strongylocentrotus intermedius	Troitsa Bay, Gulf of Peter the Great, East Sea	Russia	RUS	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ716799 (>99% sequence identity) for Bizionia from Microbeatlas

Aquatic Samples	616
Soil Samples	12
Animal Samples	125
Plant Samples	7
Total Samples	760

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17308	1	Risk group (German 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	IMG-taxon 2622736504 annotated assembly for Bizionia echini DSM 23925	scaffold	GCA_900115185	649333.4	2622736504	649333	73.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17308	Bizionia echini 16S ribosomal RNA gene, partial sequence	FJ716799	1478		649333

GC content

@ref	GC-content (mol%)	Method
17308	34.4	thermal denaturation, midpoint method (Tm)
29440	34.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2622736504 annotated assembly for Bizionia echini DSM 23925
NCBI: GCA_900115185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.18	no
125439	gram_stain	BacteriaNetⓘ	negative	95.57	no
125439	motility	BacteriaNetⓘ	no	79.93	no
125439	spore_formation	BacteriaNetⓘ	no	99.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bizionia echini DSM 23925
NCBI: GCA_900115185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.88	no
125438	anaerobic	anaerobicⓘ	no	96.72	yes
125438	aerobic	aerobicⓘ	yes	87.23	no
125438	spore-forming	spore-formingⓘ	no	90.83	no
125438	thermophilic	thermophileⓘ	no	96.95	yes
125438	flagellated	motile2+ⓘ	no	93.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.	Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Goker M.	Front Microbiol	10.3389/fmicb.2019.02083	2019
Genetics	Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis.	Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, Smidt H, Sipkema D.	BMC Genomics	10.1186/s12864-020-06971-7	2020
Phylogeny	Pseudobizionia ponticola gen. nov., sp. nov., isolated from seawater.	Park S, Choi J, Choi SJ, Yoon JH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002691	2018
Phylogeny	Arcticiflavibacter luteus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from intertidal sand.	Liu C, Zhang XY, Wen XR, Shi M, Chen XL, Su HN.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000681	2016
Phylogeny	Geojedonia litorea gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from coastal seawater.	Park S, Lee JS, Lee KC, Yoon JH.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9904-6	2013
Phylogeny	Hanstruepera crassostreae sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from an oyster.	He RH, Liang QY, Zhao JX, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003053	2018
Phylogeny	Bizionia psychrotolerans sp. nov., a psychrophilic bacterium isolated from the intestine of a sea cucumber (Apostichopus japonicus).	Song EJ, Lee MH, Seo MJ, Yim KJ, Hyun DW, Bae JW, Park SL, Roh SW, Nam YD	Antonie Van Leeuwenhoek	10.1007/s10482-014-0253-x	2014
Phylogeny	Bizionia echini sp. nov., isolated from a sea urchin.	Nedashkovskaya OI, Vancanneyt M, Kim SB	Int J Syst Evol Microbiol	10.1099/ijs.0.013193-0	2009

References

#17308	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23925
#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 )
#25846	IJSEM 928 2010 ( DOI 10.1099/ijs.0.013193-0 , PubMed 19661492 )
#29440	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25846
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#69479	João 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 beta .
#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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Bizionia echini (DSM 23925, KCTC 22015, KMM 6177)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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