Name: Vibrio rarus RW22
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17342

Type strain:

Species: Vibrio rarus

Strain Designation: RW22

Culture col. no.: DSM 19662, LMG 23674, NBRC 102084, CIP 109638

Strain history: CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain RW22

NCBI tax ID(s): 1219063 (strain), 413403 (species)

SI-ID 307807

LMG 23674, NBRC 102084, DSM 19662, CIP 109638

Special Collections

Section

When using BacDive for research please cite our paper

Vibrio rarus RW22 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of abalone Haliotis rufescens.

Gram-negative
rod-shaped
facultative anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Vibrio*
	Species	**Vibrio rarus**
	Full Scientific Name (LPSN)	Vibrio rarus Sawabe et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32001]	Gram stain	negative
[Ref.: #122140]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %100

[Ref.: #32001]	Cell length	1.5 µm

[Ref.: #32001]	Cell width	0.75 µm

[Ref.: #32001]	Cell shape	rod-shaped
[Ref.: #122140]	Cell shape	rod-shaped

[Ref.: #32001]	Motility	no
[Ref.: #122140]	Motility	no

[Ref.: #32001]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8239]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #8239]

Culture medium growth

[Ref.: #8239]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8239]

Culture medium composition

expand / minimize

[Ref.: #37653]

Culture medium

Marine agar (MA)

[Ref.: #37653]

Culture medium growth

[Ref.: #37653]

Culture medium composition

expand / minimize

[Ref.: #122140]

Culture medium

CIP Medium 13

[Ref.: #122140]

Culture medium growth

[Ref.: #122140]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8239]	growth	28 °C
[Ref.: #32001]	growth	15-30 °C
[Ref.: #37653]	growth	20 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32001]

Oxygen tolerance

facultative anaerobe

[Ref.: #32001]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.1
[Ref.: #125438]	Ability of spore formation	no Confidence in %97.03

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32001]		NaCl		growth	<6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32001]	acetate ChEBI	+	carbon source
[Ref.: #32001]	cellobiose ChEBI	+	carbon source
[Ref.: #32001]	gluconate ChEBI	+	carbon source
[Ref.: #32001]	glucose ChEBI	+	carbon source
[Ref.: #32001]	glutamate ChEBI	+	carbon source
[Ref.: #32001]	maltose ChEBI	+	carbon source
[Ref.: #32001]	mannitol ChEBI	+	carbon source
[Ref.: #32001]	mannose ChEBI	+	carbon source
[Ref.: #32001]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32001]	nitrate ChEBI	+	reduction
[Ref.: #122140]	nitrate ChEBI	+	reduction
[Ref.: #122140]	nitrite ChEBI	-	reduction
[Ref.: #32001]	proline ChEBI	+	carbon source
[Ref.: #32001]	pyruvate ChEBI	+	carbon source
[Ref.: #32001]	sorbitol ChEBI	+	carbon source
[Ref.: #32001]	succinate ChEBI	+	carbon source
[Ref.: #32001]	sucrose ChEBI	+	carbon source
[Ref.: #32001]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #32001]		indole ChEBI	yes
[Ref.: #122140]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #32001]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32001]	catalase	+	1.11.1.6
[Ref.: #122140]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32001]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122140]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122140]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122140]	12020	-	+	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8239]	Sample type/isolated from	gut of abalone Haliotis rufescens
[Ref.: #8239]	Host species	Haliotis rufescens
[Ref.: #8239]	Geographic location (country and/or sea, region)	La Jolla
[Ref.: #8239]	Country	USA
[Ref.: #8239]	Country ISO 3 Code	USA
[Ref.: #8239]	Continent	North America

[Ref.: #122140]	Sample type/isolated from	Gut, Californian abalone Haliotis rufescence
[Ref.: #122140]	Geographic location (country and/or sea, region)	La Jolla, California
[Ref.: #122140]	Country	United States of America
[Ref.: #122140]	Country ISO 3 Code	USA
[Ref.: #122140]	Continent	North America
[Ref.: #122140]	Isolation date	2005
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681696 (>99% sequence identity) for Vibrio rarus subclade from Microbeatlas

Aquatic Samples	141
Soil Samples	6
Animal Samples	233
Plant Samples	6
Total Samples	386

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8239]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122140]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8239]	Vibrio rarus strain RW22 16S ribosomal RNA gene, partial sequence	DQ914239	1403	GenBank ENA	413403 tax ID
[Ref.: #20218]	Vibrio rarus gene for 16S rRNA, partial sequence, strain: NBRC 102084	AB681696	1495	GenBank ENA	413403 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio rarus LMG 23674	GCA_024347075	complete	GenBank ENA	413403 tax ID	*

[Ref.: #32001]

GC-content

43.8 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio rarus LMG 23674 NCBI: GCA_024347075.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.264	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	68.935	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	97.03	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.436	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	68.022	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio rarus LMG 23674 NCBI: GCA_024347075
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	57.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	75.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	89.7

Availability in culture collections External links

[Ref.: #8239]

Culture collection no.

DSM 19662, LMG 23674, NBRC 102084, CIP 109638

[Ref.: #86342]

SI-ID 307807

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens.	Sawabe T, Fujimura Y, Niwa K, Aono H	Int J Syst Evol Microbiol	10.1099/ijs.0.64789-0	2007	*

References

#8239

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19662

#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 )

#32001

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 #28255 (see below)

#37653 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 .

#86342

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID307807.1 )

#122140 Collection of Institut Pasteur ; Curators of the CIP; CIP 109638

#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 .

#28255

IJSEM 916 2007 ( DOI 10.1099/ijs.0.64789-0 , PubMed 17473233 )

* These data were automatically processed and therefore are not curated

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Vibrio rarus LMG 23674

Vibrio rarus LMG 23674

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