Name: Vibrio comitans GHG2-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17341

Type strain:

Species: Vibrio comitans

Strain Designation: GHG2-1

Culture col. no.: DSM 19668, LMG 23416, NBRC 102076, CCUG 56972, CIP 109637

Strain history: CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain GHG2-1

NCBI tax ID(s): 1219078 (strain), 413401 (species)

SI-ID 307799

LMG 23416, NBRC 102076, DSM 19668, CIP 109637, CCUG 56972

Special Collections

Section

When using BacDive for research please cite our paper

Vibrio comitans GHG2-1 is a facultative anaerobe, mesophilic, rod-shaped bacterium that was isolated from gut of abalone Haliotis gigantea.

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 comitans**
	Full Scientific Name (LPSN)	Vibrio comitans Sawabe et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #118711]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %100
[Ref.: #125439]	Gram stain	negative Confidence in %98.9

[Ref.: #118711]	Cell shape	oval-shaped
[Ref.: #32001]	Cell shape	rod-shaped

[Ref.: #118711]	Motility	no
[Ref.: #32001]	Motility	no

[Ref.: #32001]	Cell length	1.6 µm

[Ref.: #32001]	Cell width	0.75 µm

[Ref.: #32001]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8245]

Culture medium

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

[Ref.: #8245]

Culture medium growth

[Ref.: #8245]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8245]

Culture medium composition

expand / minimize

[Ref.: #37800]

Culture medium

Marine agar (MA)

[Ref.: #37800]

Culture medium growth

[Ref.: #37800]

Culture medium composition

expand / minimize

[Ref.: #118711]

Culture medium

CIP Medium 13

[Ref.: #118711]

Culture medium growth

[Ref.: #118711]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8245]	growth	28 °C
[Ref.: #32001]	growth	04-30 °C
[Ref.: #32001]	optimum	17 °C
[Ref.: #37800]	growth	20 °C
[Ref.: #61151]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32001]	Oxygen tolerance	facultative anaerobe
[Ref.: #61151]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.2

[Ref.: #32001]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %92.783
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32001]		NaCl		growth	01-06	%
[Ref.: #32001]		NaCl		optimum	3.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32001]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	gluconate ChEBI	+	carbon source
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	glucosamine ChEBI	+	carbon source
[Ref.: #32001]	glucose ChEBI	+	carbon source
[Ref.: #32001]	glutamate ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32001]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	mannitol ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32001]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	nitrate ChEBI	+	reduction
[Ref.: #118711]	nitrate ChEBI	+	reduction
[Ref.: #118711]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32001]	pyruvate ChEBI	+	carbon source
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #32001]	succinate ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32001]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118711]		indole ChEBI	no

	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.: #118711]	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.: #118711]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118711]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #118711]	11622	not determinedn.d.	-	-	-	-	-	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-	-	+	+	+	+	-	+	+	-	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	-

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.: #118711]	12019	-	+	+	-	-	+	-	-	-	-	+	+	-	+	-	-	-	+	-	-

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

[Ref.: #8245]	Sample type/isolated from	gut of abalone Haliotis gigantea
[Ref.: #8245]	Host species	Haliotis gigantea
[Ref.: #8245]	Geographic location (country and/or sea, region)	Goto Islands
[Ref.: #8245]	Country	Japan
[Ref.: #8245]	Country ISO 3 Code	JPN
[Ref.: #8245]	Continent	Asia

[Ref.: #61151]	Sample type/isolated from	Japanese abalone gut (Haliotis gigantea)
[Ref.: #61151]	Geographic location (country and/or sea, region)	Goto Island Nagasaki Prefecture
[Ref.: #61151]	Country	Japan
[Ref.: #61151]	Country ISO 3 Code	JPN
[Ref.: #61151]	Continent	Asia

[Ref.: #118711]	Sample type/isolated from	Gut, japanese abalone Haliotis gigantea
[Ref.: #118711]	Geographic location (country and/or sea, region)	Goto Island, Nagasaki
[Ref.: #118711]	Country	Japan
[Ref.: #118711]	Country ISO 3 Code	JPN
[Ref.: #118711]	Continent	Asia
[Ref.: #118711]	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 AB681688 (>99% sequence identity) for Vibrio comitans from Microbeatlas

Aquatic Samples	6346
Soil Samples	141
Animal Samples	1952
Plant Samples	41
Total Samples	8480

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

[Ref.: #8245]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118711]	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.: #8245]	Vibrio comitans strain GHG2-1 16S ribosomal RNA gene, partial sequence	DQ922915	1432	GenBank ENA	413401 tax ID
[Ref.: #32001]	Vibrio comitans strain GHD1-9 16S ribosomal RNA gene, partial sequence	DQ922914	1410	GenBank ENA	413401 tax ID
[Ref.: #20218]	Vibrio comitans gene for 16S rRNA, partial sequence, strain: NBRC 102076	AB681688	1477	GenBank ENA	413401 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio comitans NBRC 102076	GCA_006538565	contig	GenBank ENA	1219078 tax ID	*
[Ref.: #66792]	Vibrio comitans NBRC 102076	1219078.3	wgs	PATRIC	1219078 tax ID	*
[Ref.: #66792]	Vibrio comitans LMG 23416	GCA_024346835	complete	GenBank ENA	413401 tax ID	*

[Ref.: #32001]

GC-content

46.5 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 comitans LMG 23416 NCBI: GCA_024346835.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.127	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	62.82	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.783	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.35	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	67.962	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio comitans NBRC 102076 NCBI: GCA_006538565
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.7

Availability in culture collections External links

[Ref.: #8245]

Culture collection no.

DSM 19668, LMG 23416, NBRC 102076, CCUG 56972, CIP 109637

[Ref.: #86341]

SI-ID 307799

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

#8245

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19668

#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)

#37800 ; Curators of the CIP;
#61151 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56972

#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) .

#68371

Automatically annotated from API 50CH acid .

#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 .

#86341

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-ID307799.1 )

#118711 Collection of Institut Pasteur ; Curators of the CIP; CIP 109637

#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

Change proposal

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Search for species Vibrio comitans in external resources:
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PANGAEA
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Vibrio comitans LMG 23416

Vibrio comitans NBRC 102076

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Change proposal