Name: Vibrio xiamenensis G21
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17368

Type strain:

Species: Vibrio xiamenensis

Strain Designation: G21

Culture col. no.: DSM 22851, CGMCC 1.10228

Strain history: <- X. Xu, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; G21 <- Z. Gao

NCBI tax ID(s): 861298 (species)

SI-ID 397119

DSM 22851

Section

Vibrio xiamenensis G21 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from soil beneath mangrove.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Vibrio*
	Species	**Vibrio xiamenensis**
	Full Scientific Name (LPSN)	Vibrio xiamenensis Gao et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30329]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #30329]	Cell length	1.47 µm

[Ref.: #30329]	Cell width	0.75 µm

[Ref.: #30329]	Cell shape	rod-shaped

[Ref.: #30329]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.069

[Ref.: #30329]

Pigment production

yes

Multimedia content

[Ref.: #16489]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16489]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #16489]

Culture medium growth

[Ref.: #16489]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16489]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16489]	growth	28 °C
[Ref.: #30329]	growth	15-40 °C
[Ref.: #30329]	optimum	33.5 °C

[Ref.: #16489]	Temperature range	mesophilic
[Ref.: #30329]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30329]			optimum	7.25
[Ref.: #30329]			growth	5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30329]

Oxygen tolerance

facultative aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.978

[Ref.: #16489]

Name of produced compound

cellulase

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30329]		NaCl		growth	0.5-10	%
[Ref.: #30329]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30329]	arabinose ChEBI	+	carbon source
[Ref.: #30329]	cellobiose ChEBI	+	carbon source
[Ref.: #30329]	fructose ChEBI	+	carbon source
[Ref.: #30329]	galactose ChEBI	+	carbon source
[Ref.: #30329]	glucose ChEBI	+	carbon source
[Ref.: #30329]	glycerol ChEBI	+	carbon source
[Ref.: #30329]	maltose ChEBI	+	carbon source
[Ref.: #30329]	mannitol ChEBI	+	carbon source
[Ref.: #30329]	nitrate ChEBI	+	reduction
[Ref.: #30329]	rhamnose ChEBI	+	carbon source
[Ref.: #30329]	sucrose ChEBI	+	carbon source
[Ref.: #30329]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30329]		catalase	+	1.11.1.6
[Ref.: #30329]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #16489]	Sample type/isolated from	soil beneath mangrove
[Ref.: #16489]	Geographic location (country and/or sea, region)	Fujian province, Xiamen
[Ref.: #16489]	Country	China
[Ref.: #16489]	Country ISO 3 Code	CHN
[Ref.: #16489]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree

What are isolation sources categories?

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

[Ref.: #16489]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16489]	Vibrio xiamenensis strain G21 16S ribosomal RNA gene, partial sequence	GQ397859	1475	ENA	861298 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio xiamenensis CGMCC 1.10228	GCA_900100015	scaffold	GenBank	861298 tax ID	*
[Ref.: #66792]	Vibrio xiamenensis strain CGMCC 1.10228	861298.3	wgs	PATRIC	861298 tax ID	*
[Ref.: #66792]	Vibrio xiamenensis CGMCC 1.10228	2617270927	draft	JGI IMG/M	861298 tax ID	*

[Ref.: #16489]	GC-content	46.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30329]	GC-content	46 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Vibrio xiamenensis CGMCC 1.10228 NCBI: GCA_900100015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Vibrio xiamenensis CGMCC 1.10228 NCBI: GCA_900100015.1
[Ref.: #69480]	motile	yes	88.156	no
[Ref.: #69480]	flagellated	yes	89.962	no
[Ref.: #69480]	gram-positive	no	98.756	yes
[Ref.: #69480]	anaerobic	no	96.296	no
[Ref.: #69480]	aerobic	yes	55.053	yes
[Ref.: #69480]	halophile	no	52.017	no
[Ref.: #69480]	spore-forming	no	94.878	no
[Ref.: #69480]	glucose-ferment	yes	88.688	no
[Ref.: #69480]	thermophile	no	99.574	yes
[Ref.: #69480]	glucose-util	yes	94.137	yes

Availability in culture collections External links

[Ref.: #16489]

Culture collection no.

DSM 22851, CGMCC 1.10228

[Ref.: #86367]

SI-ID 397119

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil.	Gao ZM, Xiao J, Wang XN, Ruan LW, Chen XL, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.033597-0	2011	*

References

#16489

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22851

#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 )

#30329

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 #26670 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86367

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-ID397119.1 )

#26670

IJSEM 1958 2012 ( DOI 10.1099/ijs.0.033597-0 , PubMed 22039001 )

* These data were automatically processed and therefore are not curated

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Vibrio xiamenensis CGMCC 1.10228

Vibrio xiamenensis CGMCC 1.10228

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