Name: Luteibaculum oceani CC-AMWY-103B
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134069

Type strain:

Species: Luteibaculum oceani

Strain Designation: CC-AMWY-103B

Culture col. no.: JCM 18817, BCRC 80551

Strain history: C.-C. Young CC-AMWY-103B.

NCBI tax ID(s): 1294296 (species)

Section

Luteibaculum oceani CC-AMWY-103B is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

Gram-negative
motile
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Cryomorphaceae*
	Genus	*Luteibaculum*
	Species	**Luteibaculum oceani**
	Full Scientific Name (LPSN)	Luteibaculum oceani Shahina et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31167]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #31167]	Cell length	1.6 µm

[Ref.: #31167]	Cell width	0.4 µm

[Ref.: #31167]	Cell shape	rod-shaped

[Ref.: #31167]	Motility	yes

[Ref.: #31167]	Flagellum arrangement	gliding

[Ref.: #31167]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31167]	growth	20-35 °C
[Ref.: #31167]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #31167]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31167]			optimum	7
[Ref.: #31167]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31167]

Oxygen tolerance

aerobe

[Ref.: #31167]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31167]		NaCl		growth	01-05	%
[Ref.: #31167]		NaCl		optimum	2	%

[Ref.: #31167]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31167]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #31167]	esculin ChEBI	+	hydrolysis
[Ref.: #31167]	glutamate ChEBI	+	carbon source
[Ref.: #31167]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #31167]	nitrate ChEBI	+	reduction
[Ref.: #31167]	trehalose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31167]	acid phosphatase	+	3.1.3.2
[Ref.: #31167]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31167]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	serine metabolism	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]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arginine metabolism	33.33	8 of 24
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	valine metabolism	22.22	2 of 9
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #31167]	Sample type/isolated from	seawater

[Ref.: #67770]	Sample type/isolated from	Surface seawater at Kending
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

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.: #31167]	Luteibaculum oceani strain CC-AMWY-103B 16S ribosomal RNA gene, partial sequence	KC169812	1453	GenBank	1294296 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Luteibaculum oceani JCM 18817	GCA_007995015	contig	GenBank	1294296 tax ID	*
[Ref.: #66792]	Luteibaculum oceani strain JCM 18817	1294296.4	wgs	PATRIC	1294296 tax ID	*
[Ref.: #66792]	Luteibaculum oceani JCM 18817	2886904261	draft	JGI IMG/M	1294296 tax ID	*

[Ref.: #31167]	GC-content	44.2 mol%
[Ref.: #67770]	GC-content	43.9-44.5 mol%	thermal denaturation, midpoint method (Tm)

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: Luteibaculum oceani strain JCM 18817 PATRIC: 1294296.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Luteibaculum oceani strain JCM 18817 PATRIC: 1294296.4
[Ref.: #69480]	motile	no	87.716	no
[Ref.: #69480]	gram-positive	no	98.895	no
[Ref.: #69480]	anaerobic	no	99.026	no
[Ref.: #69480]	aerobic	yes	89.755	yes
[Ref.: #69480]	halophile	no	53.653	no
[Ref.: #69480]	spore-forming	no	95.877	yes
[Ref.: #69480]	glucose-util	yes	80.119	no
[Ref.: #69480]	flagellated	no	95.68	yes
[Ref.: #69480]	thermophile	no	94.379	yes
[Ref.: #69480]	glucose-ferment	no	89.977	no

Availability in culture collections External links

[Ref.: #31167]

Culture collection no.

JCM 18817, BCRC 80551

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vicingus serpentipes gen. nov., sp. nov., a new member of the Flavobacteriales from the North Sea.	Wiese J, Saha M, Wenzel-Storjohann A, Weinberger F, Schmaljohann R, Imhoff JF	Int J Syst Evol Microbiol	10.1099/ijsem.0.002509	2017	*
Phylogeny	Luteibaculum oceani gen. nov., sp. nov., a carotenoid-producing, lipolytic bacterium isolated from surface seawater, and emended description of the genus Owenweeksia Lau et al. 2005.	Shahina M, Hameed A, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.054635-0	2013	*

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 )

#31167

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 #27495 (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;

#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 )

#27495

IJSEM 4765 2013 ( DOI 10.1099/ijs.0.054635-0 , PubMed 23990655 )

* These data were automatically processed and therefore are not curated

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Luteibaculum oceani strain JCM 18817

Luteibaculum oceani strain JCM 18817

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