Name: Amphritea balenae JCM 14781
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134369

Type strain:

Species: Amphritea balenae

Culture col. no.: JCM 14781, ATCC BAA-1529, JAMM 1525

Strain history: M. Miyazaki JAMM 1525.

NCBI tax ID(s): 1278310 (strain), 452629 (species)

Section

Amphritea balenae JCM 14781 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from sediment adjacent to sperm whale carcasses.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Oceanospirillales*
	Family	*Oceanospirillaceae*
	Genus	*Amphritea*
	Species	**Amphritea balenae**
	Full Scientific Name (LPSN)	Amphritea balenae Miyazaki et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32637]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #32637]	Cell length	1.3-2 µm

[Ref.: #32637]	Cell width	0.6-0.9 µm

[Ref.: #32637]	Cell shape	rod-shaped

[Ref.: #32637]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.289

[Ref.: #32637]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #32637]	growth	04-28 °C
[Ref.: #32637]	optimum	20-22 °C
[Ref.: #67770]	growth	20 °C

[Ref.: #32637]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #32637]			optimum	7
[Ref.: #32637]			growth	6.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32637]

Oxygen tolerance

facultative anaerobe

[Ref.: #32637]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.968

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32637]		NaCl		growth	02-03	%
[Ref.: #32637]		NaCl		optimum	3	%

[Ref.: #32637]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32637]	alanine ChEBI	+	carbon source
[Ref.: #32637]	asparagine ChEBI	+	carbon source
[Ref.: #32637]	malate ChEBI	+	carbon source
[Ref.: #32637]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #32637]	nitrate ChEBI	+	reduction
[Ref.: #32637]	serine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32637]	catalase	+	1.11.1.6
[Ref.: #32637]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32637]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	benzoyl-CoA degradation	100	7 of 7
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor 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]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		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.: #32637]	Sample type/isolated from	sediment adjacent to sperm whale carcasses

[Ref.: #67770]	Sample type/isolated from	Sediment adjacent to a sperm whale carcass off Kagoshima
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Sediment
#Host	#Other	#Decomposing animal
#Host	#Mammals	#Aquatic mammal

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB330883 (>99% sequence identity) for Amphritea from Microbeatlas

Aquatic Samples	129
Soil Samples	5
Animal Samples	1
Plant Samples
Total Samples	135

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.: #32637]	Amphritea balenae gene for 16S ribosomal RNA, partial sequence, strain: JAMM 1525	AB330883	1463	GenBank	452629 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amphritea balenae JAMM 1525	GCA_003858655	contig	GenBank	452629 tax ID
[Ref.: #66792]	Amphritea balenae JCM 14781	GCA_014646975	scaffold	GenBank	452629 tax ID	*
[Ref.: #66792]	Amphritea balenae strain JCM 14781	452629.5	wgs	PATRIC	452629 tax ID	*

[Ref.: #32637]	GC-content	46.7 mol%
[Ref.: #67770]	GC-content	46.7 mol%	high performance liquid chromatography (HPLC)

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: Amphritea balenae strain JCM 14781 PATRIC: 452629.5
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amphritea balenae JCM 14781 NCBI: GCA_014646975.1
[Ref.: #69480]	flagellated	yes	91.183	no
[Ref.: #69480]	gram-positive	no	99.069	no
[Ref.: #69480]	anaerobic	no	97.21	yes
[Ref.: #69480]	aerobic	no	72.187	yes
[Ref.: #69480]	halophile	yes	75.538	no
[Ref.: #69480]	spore-forming	no	94.039	no
[Ref.: #69480]	thermophile	no	99.065	no
[Ref.: #69480]	glucose-util	yes	69.992	no
[Ref.: #69480]	motile	yes	92.654	yes
[Ref.: #69480]	glucose-ferment	no	85.038	no

Availability in culture collections External links

[Ref.: #32637]

Culture collection no.

JCM 14781, ATCC BAA-1529, JAMM 1525

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amphritea opalescens sp. nov., isolated from sediment adjacent to Fildes Peninsula, Antarctica.	Han X, Zhang J, Zhang Y, Liu J, Fang W, Fang Z, Xiao Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003359	2019	*
Phylogeny	Amphritea japonica sp. nov. and Amphritea balenae sp. nov., isolated from the sediment adjacent to sperm whale carcasses off Kagoshima, Japan.	Miyazaki M, Nogi Y, Fujiwara Y, Kawato M, Nagahama T, Kubokawa K, Horikoshi K	Int J Syst Evol Microbiol	10.1099/ijs.0.65826-0	2008	*

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 )

#32637

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 #28848 (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;

#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 )

#28848

IJSEM 2815 2008 ( DOI 10.1099/ijs.0.65826-0 , PubMed 19060065 )

* These data were automatically processed and therefore are not curated

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Amphritea balenae strain JCM 14781

Amphritea balenae JCM 14781

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