Vannielia litorea (DSM 29440, CCUG 62794, KCTC 32083)

Name: Vannielia litorea (DSM 29440, CCUG 62794, KCTC 32083)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130614

Type strain

Strain Designation M-M22

Culture col. no. DSM 29440 CCUG 62794 KCTC 32083 M-M22

NCBI tax ID(s) 1217970

Special Collections DSMZ CCUG KCTC

History DSMZ <- KCTC <- J.-H. Yoon, KRIBB; M-M22

Links

Vannielia litorea M-M22 is an aerobe bacterium that was isolated from seashore sediment.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408248

KCTC 32083,DSM 29440,CCUG 62794

@ref 20215

Last LPSN update 2026-05-29 08:37:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Vannielia

Species Vannielia litorea

Full scientific name Vannielia litorea (Park et al. 2013) Hördt et al. 2020

Synonyms (1)

Oceanicola litoreus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.494
125439	negative	91.199

Colony morphology

@ref	Incubation period
21708	1-2 days
62902	2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21708	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)
21708	positive	growth	30
62902	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
62902	aerobe
125439	obligate aerobe	94.911

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
21708	catalase	+	1.11.1.6
21708	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ethanol fermentation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	Entner Doudoroff pathway	100	10 of 10
66794	quinate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	leucine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	degradation of sugar acids	84	21 of 25
66794	purine metabolism	82.98	78 of 94
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	tryptophan metabolism	78.95	30 of 38
66794	tyrosine metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	lipid metabolism	77.42	24 of 31
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	arginine metabolism	75	18 of 24
66794	degradation of pentoses	75	21 of 28
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	lysine metabolism	69.05	29 of 42
66794	methane metabolism	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	propanol degradation	57.14	4 of 7
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	toluene degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	ascorbate metabolism	50	11 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	vitamin K metabolism	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	coenzyme M biosynthesis	30	3 of 10
66794	starch degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	biotin biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin B12 metabolism	23.53	8 of 34

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
21708	-	-	-	-	-	+	-	+	+	+	+	+	-	+	+	-	+/-	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
21708	seashore sediment		Geoje island, South Sea	Republic of Korea	KOR	Asia
62902	Seashore sediment	2009	Geoje Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX291104 (>99% sequence identity) for Vannielia litorea subclade from Microbeatlas

Aquatic Samples	497
Soil Samples	21
Animal Samples	65
Plant Samples	6
Total Samples	589

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21708	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2698536701 annotated assembly for Vannielia litorea DSM 29440	contig	GCA_900142295	1217970.3	2698536701	1217970	78.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21708	Oceanicola litoreus strain M-M22 16S ribosomal RNA gene, partial sequence	JX291104	1388		1217970

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2698536701 annotated assembly for Vannielia litorea DSM 29440
BV-BRC: 1217970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.91	no
125439	motility	BacteriaNetⓘ	yes	50.22	no
125439	gram_stain	BacteriaNetⓘ	negative	91.20	no
125439	spore_formation	BacteriaNetⓘ	no	89.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oceanicola litoreus strain DSM 29440
PATRIC: 1217970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.49	no
125438	anaerobic	anaerobicⓘ	no	97.72	yes
125438	spore-forming	spore-formingⓘ	no	85.37	no
125438	aerobic	aerobicⓘ	yes	87.31	yes
125438	thermophilic	thermophileⓘ	no	96.45	yes
125438	flagellated	motile2+ⓘ	yes	59.35	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Harenicola maris gen. nov., sp. nov. isolated from the Sea of Japan shallow sediments.	Romanenko LA, Kurilenko VV, Chernysheva NY, Tekutyeva LA, Velansky PV, Svetashev VI, Isaeva MP	Arch Microbiol	10.1007/s00203-021-02360-0	2021
Phylogeny	Oceanicola litoreus sp. nov., an alphaproteobacterium isolated from the seashore sediment.	Park S, Lee MH, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-012-9867-z	2012
Phylogeny	Nioella nitratireducens gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from Azorean Island.	Rajasabapathy R, Mohandass C, Yoon JH, Dastager SG, Liu Q, Khieu TN, Son CK, Li WJ, Colaco A	Antonie Van Leeuwenhoek	10.1007/s10482-014-0355-5	2014

References

#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 )
#21708	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29440
#62902	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62794
#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 )
#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 .
#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 )

Content

About us

Vannielia litorea (DSM 29440, CCUG 62794, KCTC 32083)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

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_900142295

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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