Name: Neptunomonas japonica DSM 18939
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11282

Type strain:

Species: Neptunomonas japonica

Culture col. no.: DSM 18939, JCM 14595, JAMM 0745

Strain history: M. Miyazaki JAMM 0745.

NCBI tax ID(s): 1122599 (strain), 417574 (species)

SI-ID 402057

DSM 18939

Section

Neptunomonas japonica DSM 18939 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from sediment adjacent to a sperm whale carcass.

Gram-negative
motile
rod-shaped
facultative anaerobe
psychrophilic
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	*Neptunomonas*
	Species	**Neptunomonas japonica**
	Full Scientific Name (LPSN)	Neptunomonas japonica Miyazaki et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32444]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #32444]	Cell length	1.7 µm

[Ref.: #32444]	Cell width	0.9 µm

[Ref.: #32444]	Cell shape	rod-shaped

[Ref.: #32444]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.795

[Ref.: #32444]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7797]

Culture medium

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

[Ref.: #7797]

Culture medium growth

[Ref.: #7797]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7797]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7797]	growth	20 °C
[Ref.: #32444]	growth	05-25 °C
[Ref.: #32444]	optimum	20 °C
[Ref.: #67770]	growth	20 °C

[Ref.: #7797]	Temperature range	psychrophilic
[Ref.: #32444]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #32444]			optimum	7.5
[Ref.: #32444]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32444]

Oxygen tolerance

facultative anaerobe

[Ref.: #32444]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.977

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32444]		NaCl		growth	01-05	%
[Ref.: #32444]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32444]		nitrate ChEBI	+	reduction

	Enzyme	Enzyme activity	EC number
[Ref.: #32444]	catalase	+	1.11.1.6
[Ref.: #32444]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32444]	gelatinase	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7797]	Sample type/isolated from	sediment adjacent to a sperm whale carcass
[Ref.: #7797]	Geographic location (country and/or sea, region)	Kagoshima
[Ref.: #7797]	Country	Japan
[Ref.: #7797]	Country ISO 3 Code	JPN
[Ref.: #7797]	Continent	Asia

[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 AB288092 (>99% sequence identity) for Neptunomonas from Microbeatlas

Aquatic Samples	5203
Soil Samples	131
Animal Samples	211
Plant Samples	33
Total Samples	5578

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

[Ref.: #7797]

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.: #7797]	Neptunomonas japonica gene for 16S rRNA, partial sequence, strain: JAMM 0745	AB288092	1498	ENA	1122599 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Neptunomonas japonica DSM 18939	GCA_000422765	scaffold	GenBank	1122599 tax ID
[Ref.: #66792]	Neptunomonas japonica DSM 18939	1122599.8	wgs	PATRIC	1122599 tax ID	*
[Ref.: #66792]	Neptunomonas japonica DSM 18939	2523533624	draft	JGI IMG/M	1122599 tax ID	*

[Ref.: #32444]	GC-content	43.6-43.8 mol%
[Ref.: #67770]	GC-content	43.6 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: Neptunomonas japonica DSM 18939 DSM 18939 NCBI: GCA_000422765.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Neptunomonas japonica DSM 18939 PATRIC: 1122599.8
[Ref.: #69480]	motile	yes	91.264	no
[Ref.: #69480]	flagellated	yes	92.227	no
[Ref.: #69480]	gram-positive	no	99.262	yes
[Ref.: #69480]	anaerobic	no	98.654	no
[Ref.: #69480]	aerobic	no	53.161	yes
[Ref.: #69480]	halophile	yes	59.12	no
[Ref.: #69480]	spore-forming	no	95.654	yes
[Ref.: #69480]	glucose-util	yes	54.395	no
[Ref.: #69480]	thermophile	no	99.738	yes
[Ref.: #69480]	glucose-ferment	no	86.58	no

Availability in culture collections External links

[Ref.: #7797]

Culture collection no.

DSM 18939, JCM 14595, JAMM 0745

[Ref.: #80515]

SI-ID 402057

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Neptunomonas qingdaonensis sp. nov., isolated from intertidal sand.	Liu A, Zhang XY, Chen CX, Xie BB, Qin QL, Liu C, Li GW, Li H, Xu Z, Chen XL, Zhou BC, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.041970-0	2012	*
Phylogeny	Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas.	Lee HW, Shin NR, Lee J, Roh SW, Whon TW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.037473-0	2011	*
Phylogeny	Neptunomonas antarctica sp. nov., isolated from marine sediment.	Zhang XY, Zhang YJ, Yu Y, Li HJ, Gao ZM, Chen XL, Chen B, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.017756-0	2009	*
Phylogeny	Neptunomonas japonica sp. nov., an Osedax japonicus symbiont-like bacterium isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan.	Miyazaki M, Nogi Y, Fujiwara Y, Kawato M, Kubokawa K, Horikoshi K	Int J Syst Evol Microbiol	10.1099/ijs.0.65509-0	2008	*

References

#7797

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18939

#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 )

#32444

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 #28666 (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) .

#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 )

#80515

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-ID402057.1 )

#28666

IJSEM 866 2008 ( DOI 10.1099/ijs.0.65509-0 , PubMed 18398184 )

* These data were automatically processed and therefore are not curated

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Neptunomonas japonica DSM 18939 DSM 18939

Neptunomonas japonica DSM 18939

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