Name: Litoreibacter arenae GA2-M15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13858

Type strain:

Species: Litoreibacter arenae

Strain Designation: GA2-M15

Culture col. no.: DSM 19593, KACC 12675

Strain history: <- S.-W. Kwon, KACC; GA2-M15

NCBI tax ID(s): 1123360 (strain), 491388 (species)

SI-ID 400074

DSM 19593

Section

Litoreibacter arenae GA2-M15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea sand.

Gram-negative
motile
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Litoreibacter*
	Species	**Litoreibacter arenae**
	Full Scientific Name (LPSN)	Litoreibacter arenae (Kim et al. 2009) Kim et al. 2012

Synonym

Thalassobacter arenae

Information on morphological and physiological properties Morphology

[Ref.: #32648]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #32648]	Cell length	1.2-2.4 µm

[Ref.: #32648]	Cell width	0.7-1.2 µm

[Ref.: #32648]	Motility	yes

[Ref.: #8197]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8197]

Culture medium

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

[Ref.: #8197]

Culture medium growth

[Ref.: #8197]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8197]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8197]	growth	28 °C
[Ref.: #32648]	growth	05-35 °C
[Ref.: #32648]	optimum	30 °C

[Ref.: #8197]	Temperature range	mesophilic
[Ref.: #32648]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32648]			optimum	7
[Ref.: #32648]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32648]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32648]		NaCl		growth	0.85-8	%
[Ref.: #32648]		NaCl		optimum	4.425	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32648]	citrate ChEBI	+	carbon source
[Ref.: #32648]	esculin ChEBI	+	hydrolysis
[Ref.: #32648]	fructose ChEBI	+	carbon source
[Ref.: #32648]	galactose ChEBI	+	carbon source
[Ref.: #32648]	glucose ChEBI	+	carbon source
[Ref.: #32648]	glutamate ChEBI	+	carbon source
[Ref.: #32648]	glycerol ChEBI	+	carbon source
[Ref.: #32648]	mannitol ChEBI	+	carbon source
[Ref.: #32648]	mannose ChEBI	+	carbon source
[Ref.: #32648]	melibiose ChEBI	+	carbon source
[Ref.: #32648]	propionate ChEBI	+	carbon source
[Ref.: #32648]	pyruvate ChEBI	+	carbon source
[Ref.: #32648]	serine ChEBI	+	carbon source
[Ref.: #32648]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32648]		catalase	+	1.11.1.6
[Ref.: #32648]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	allantoin degradation	100	9 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	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]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #8197]	Sample type/isolated from	sea sand
[Ref.: #8197]	Geographic location (country and/or sea, region)	Pohang city, Homi Cape
[Ref.: #8197]	Country	Republic of Korea
[Ref.: #8197]	Country ISO 3 Code	KOR
[Ref.: #8197]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU342372 (>99% sequence identity) for Litoreibacter from Microbeatlas

Aquatic Samples	1543
Soil Samples	80
Animal Samples	244
Plant Samples	29
Total Samples	1896

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

[Ref.: #8197]

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.: #8197]	Thalassobacter arenae strain GA2-M15 16S ribosomal RNA gene, partial sequence	EU342372	1396	ENA	1123360 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Litoreibacter arenae DSM 19593	GCA_000442275	scaffold	GenBank	1123360 tax ID	*
[Ref.: #66792]	Thalassobacter arenae DSM 19593	1123360.3	wgs	PATRIC	1123360 tax ID	*

[Ref.: #8197]	GC-content	56.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32648]	GC-content	56 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: Litoreibacter arenae DSM 19593 DSM 19593 NCBI: GCA_000442275.2
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Litoreibacter arenae DSM 19593 DSM 19593 NCBI: GCA_000442275.1
[Ref.: #69480]	motile	no	57.249	no
[Ref.: #69480]	flagellated	no	90.539	no
[Ref.: #69480]	gram-positive	no	98.712	no
[Ref.: #69480]	anaerobic	no	98.656	yes
[Ref.: #69480]	aerobic	yes	92.825	yes
[Ref.: #69480]	halophile	yes	83.729	no
[Ref.: #69480]	spore-forming	no	97.037	no
[Ref.: #69480]	thermophile	no	93.95	yes
[Ref.: #69480]	glucose-util	yes	52.298	yes
[Ref.: #69480]	glucose-ferment	no	93.579	no
[Ref.: #69480]	motile	no	57.249	no
[Ref.: #69480]	flagellated	no	90.539	no
[Ref.: #69480]	gram-positive	no	98.712	no
[Ref.: #69480]	anaerobic	no	98.656	yes
[Ref.: #69480]	aerobic	yes	92.825	yes
[Ref.: #69480]	halophile	yes	83.729	no
[Ref.: #69480]	spore-forming	no	97.037	no
[Ref.: #69480]	thermophile	no	93.95	yes
[Ref.: #69480]	glucose-util	yes	52.298	yes
[Ref.: #69480]	glucose-ferment	no	93.579	no

Availability in culture collections External links

[Ref.: #8197]

Culture collection no.

DSM 19593, KACC 12675

[Ref.: #83034]

SI-ID 400074

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member of the Roseobacter clade isolated from sea sand.	Riedel T, Fiebig A, Petersen J, Gronow S, Kyrpides NC, Goker M, Klenk HP	Stand Genomic Sci	10.4056/sigs.4258318	2013	*
Phylogeny	Description of Litoreibacter meonggei sp. nov., isolated from the sea squirt Halocynthia roretzi, reclassification of Thalassobacter arenae as Litoreibacter arenae comb. nov. and emended description of the genus Litoreibacter Romanenko et al. 2011.	Kim YO, Park S, Nam BH, Kang SJ, Hur YB, Kim DG, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.035113-0	2011	*
Phylogeny	Thalassobacter arenae sp. nov., isolated from sea sand in Korea.	Kim BY, Weon HY, Son JA, Lee CM, Hong SB, Jeon YA, Koo BS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.65841-0	2009	*

References

#8197

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19593

#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 )

#32648

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 #28859 (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 )

#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 .

#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 )

#83034

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-ID400074.1 )

#28859

IJSEM 487 2009 ( DOI 10.1099/ijs.0.65841-0 , PubMed 19244427 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Litoreibacter arenae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Litoreibacter arenae DSM 19593 DSM 19593

Litoreibacter arenae DSM 19593 DSM 19593

Change proposal

Change proposal