Name: Amphritea japonica JCM 14782
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134368

Type strain:

Species: Amphritea japonica

Culture col. no.: JCM 14782, ATCC BAA-1530, JAMM 1866

Strain history: M. Miyazaki JAMM 1866.

NCBI tax ID(s): 1278309 (strain), 452627 (species)

Section

Amphritea japonica JCM 14782 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 japonica**
	Full Scientific Name (LPSN)	Amphritea japonica Miyazaki et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32637]	Gram stain	negative

[Ref.: #32637]	Cell length	0.9-1.7 µm

[Ref.: #32637]	Cell width	0.6-0.9 µm

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

[Ref.: #32637]	Motility	yes

[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	22-24 °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	6.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32637]

Oxygen tolerance

facultative anaerobe

[Ref.: #32637]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32637]		NaCl		growth	02-05	%
[Ref.: #32637]		NaCl		optimum	3	%

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

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32637]		glycerol ChEBI	+	carbon source
[Ref.: #32637]		nitrate ChEBI	+	reduction

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

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 AB330881 (>99% sequence identity) for Amphritea japonica subclade from Microbeatlas

Aquatic Samples	2352
Soil Samples	35
Animal Samples	77
Plant Samples	81
Total Samples	2545

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 japonica gene for 16S ribosomal RNA, partial sequence, strain: JAMM 1866	AB330881	1463	GenBank	1278309 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amphritea japonica ATCC BAA-1530 JAMM 1866	GCA_000381785	scaffold	GenBank	1278309 tax ID
[Ref.: #66792]	Amphritea japonica JCM 14782	GCA_024347275	complete	GenBank	452627 tax ID	*

[Ref.: #32637]	GC-content	46.6-47 mol%
[Ref.: #67770]	GC-content	47 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 Diaspora project based on: Amphritea japonica JCM 14782 NCBI: GCA_024347275.1
[Ref.: #69480]	flagellated	yes	91.369	no
[Ref.: #69480]	gram-positive	no	99.245	no
[Ref.: #69480]	anaerobic	no	99.032	yes
[Ref.: #69480]	aerobic	yes	54.504	no
[Ref.: #69480]	halophile	yes	80.979	no
[Ref.: #69480]	spore-forming	no	94.442	yes
[Ref.: #69480]	motile	yes	90.763	yes
[Ref.: #69480]	glucose-ferment	no	84.034	no
[Ref.: #69480]	thermophile	no	99.016	yes
[Ref.: #69480]	glucose-util	yes	53.419	no

Availability in culture collections External links

[Ref.: #32637]

Culture collection no.

JCM 14782, ATCC BAA-1530, JAMM 1866

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	*
Phylogeny	Sinobacterium caligoides gen. nov., sp. nov., a new member of the family Oceanospirillaceae isolated from the South China Sea, and emended description of Amphritea japonica.	Su J, Zhou Y, Lai Q, Li X, Dong P, Yang X, Zhang B, Zhang J, Zheng X, Tian Y, Zheng T	Int J Syst Evol Microbiol	10.1099/ijs.0.030965-0	2012	*

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) .

#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) .

#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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