Wenxinia marina (DSM 24838, CGMCC 1.6105, JCM 14017)

Name: Wenxinia marina (DSM 24838, CGMCC 1.6105, JCM 14017)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13839

Type strain

Strain Designation HY34

Culture col. no. DSM 24838 CGMCC 1.6105 JCM 14017 HY34 CIP 109725

NCBI tax ID(s) 1123501 390641

Special Collections DSMZ JCM CIP Literature strains

Links

Wenxinia marina HY34 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from marine sediment.

Gram-negative ovoid-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309515

CGMCC 1.6105,JCM 14017,CIP 109725,DSM 24838

@ref 20215

Last LPSN update 2025-12-16 09:50:11

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Wenxinia

Species Wenxinia marina

Full scientific name Wenxinia marina Ying et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
32022	negative	1.3 µm	0.75 µm	ovoid-shaped
125439	negative					91.1

Colony morphology

17784

Incubation period1-2 days

Pigmentation

32022

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17784	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)	Range
17784	positive	growth	30	mesophilic
32022	positive	growth	15-42
32022	positive	optimum	36	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32022	positive	optimum	7.75
32022	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32022	aerobe
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
32022
125439		95.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32022	NaCl	positive	growth	0.5-9 %
32022	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32022	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
32022	16449 ChEBI	alanine	+	carbon source
32022	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
32022	28885 ChEBI	butanol	+	carbon source
32022	17057 ChEBI	cellobiose	+	carbon source
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
32022	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
32022	15740 ChEBI	formate	+	carbon source
32022	28757 ChEBI	fructose	+	carbon source
32022	33984 ChEBI	fucose	+	carbon source
32022	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
32022	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
32022	17234 ChEBI	glucose	+	carbon source
32022	29987 ChEBI	glutamate	+	carbon source
32022	17754 ChEBI	glycerol	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
32022	24996 ChEBI	lactate	+	carbon source
32022	17716 ChEBI	lactose	+	carbon source
32022	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
32022	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
32022	29864 ChEBI	mannitol	+	carbon source
32022	37684 ChEBI	mannose	+	carbon source
32022	28053 ChEBI	melibiose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
32022	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
32022	26271 ChEBI	proline	+	carbon source
32022	15361 ChEBI	pyruvate	+	carbon source
32022	16634 ChEBI	raffinose	+	carbon source
32022	26546 ChEBI	rhamnose	+	carbon source
32022	33942 ChEBI	ribose	+	carbon source
32022	30911 ChEBI	sorbitol	+	carbon source
32022	30031 ChEBI	succinate	+	carbon source
32022	17992 ChEBI	sucrose	+	carbon source
32022	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
32022	53424 ChEBI	tween 20	+	carbon source
32022	53423 ChEBI	tween 40	+	carbon source
32022	53426 ChEBI	tween 80	+	carbon source
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
32022	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
32022	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
17784	catalase	+	1.11.1.6
32022	catalase	+	1.11.1.6
32022	cytochrome oxidase	+	1.9.3.1
17784	cytochrome-c oxidase	+	1.9.3.1
32022	gelatinase	+
68369	gelatinase	-		from API 20NE
32022	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	starch degradation	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	glycogen biosynthesis	100	4 of 4
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B12 metabolism	82.35	28 of 34
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	76.6	72 of 94
66794	pyrimidine metabolism	75.56	34 of 45
66794	lactate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	methionine metabolism	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	phenol degradation	65	13 of 20
66794	oxidative phosphorylation	64.84	59 of 91
66794	heme metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	carnitine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	degradation of pentoses	60.71	17 of 28
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	glycolysis	58.82	10 of 17
66794	histidine metabolism	58.62	17 of 29
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of hexoses	55.56	10 of 18
66794	cysteine metabolism	55.56	10 of 18
66794	sulfate reduction	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	gluconeogenesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	ascorbate metabolism	45.45	10 of 22
66794	carotenoid biosynthesis	45.45	10 of 22
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	cholesterol biosynthesis	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	polyamine pathway	26.09	6 of 23
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9
66794	chlorophyll metabolism	22.22	4 of 18
66794	daunorubicin biosynthesis	22.22	2 of 9

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
17784	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17784	marine sediment	Xijiang oilfield in the South China Sea near Fujian province	China	CHN	Asia
67770	Sediment of the Xijiang oilfield in the South China Sea		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ640643 (>99% sequence identity) for Wenxinia marina from Microbeatlas

Aquatic Samples	935
Soil Samples	150
Animal Samples	115
Plant Samples	34
Total Samples	1234

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17784	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
67770	ASM83669v1 assembly for Wenxinia marina DSM 24838	scaffold	GCA_000836695	1123501.16	2806310715	1123501	73.98
66792	ASM1464507v1 assembly for Wenxinia marina CGMCC 1.6105	contig	GCA_014645075	390641.3	8063538181	390641	72.83
67770	ASM37948v1 assembly for Wenxinia marina DSM 24838	scaffold	GCA_000379485	1123501.3	2515154190	1123501	71.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17784	Wenxinia marina strain HY34 16S ribosomal RNA gene, partial sequence	DQ640643	1428		390641

GC content

@ref	GC-content (mol%)	Method
17784	69.4	thermal denaturation, midpoint method (Tm)
32022	69.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Wenxinia marina DSM 24838
IMG: 2806310715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no
125439	gram_stain	BacteriaNetⓘ	negative	91.10	no
125439	motility	BacteriaNetⓘ	yes	68.30	no
125439	spore_formation	BacteriaNetⓘ	no	95.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin.	Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R.	PLoS One	10.1371/journal.pone.0063422	2013
Genetics	Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments.	Riedel T, Fiebig A, Han J, Huntemann M, Spring S, Petersen J, Ivanova NN, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.5601028	2014
Phylogeny	Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea.	Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.64825-0	2007

References

#17784	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24838
#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 )
#32022	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 #28274 (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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#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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Wenxinia marina (DSM 24838, CGMCC 1.6105, JCM 14017)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000836695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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