Neptunomonas japonica (DSM 18939, JCM 14595, JAMM 0745)

Name: Neptunomonas japonica (DSM 18939, JCM 14595, JAMM 0745)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11282

Type strain

Culture col. no. DSM 18939 JCM 14595 JAMM 0745

NCBI tax ID(s) 1122599 417574

Special Collections DSMZ JCM Literature strains

History <- M. Miyazaki, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; JAMM 0745 M. Miyazaki JAMM 0745.

Links

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

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402057

JCM 14595,DSM 18939

@ref 20215

Last LPSN update 2026-02-09 11:20:30

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Oceanospirillaceae

Genus Neptunomonas

Species Neptunomonas japonica

Full scientific name Neptunomonas japonica Miyazaki et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32444	negative	1.7 µm	0.9 µm	rod-shaped
125438	negative				99
125439	negative				99.8

Pigmentation

32444

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7797	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7797	positive	growth	20
32444	positive	growth	05-25
32444	positive	optimum	20
67770	positive	growth	20

Culture pH

@ref	Ability	Type	PH	PH range
32444	positive	optimum	7.5
32444	positive	growth	07-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32444	facultative anaerobe
125439	obligate aerobe	94.7

Spore formation

@ref	Spore formation	Confidence
32444
125438		93.165
125439		99.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32444	NaCl	positive	growth	01-05 %
32444	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32444	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
32444	catalase	+	1.11.1.6
32444	cytochrome oxidase	+	1.9.3.1
32444	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment
#Host	#Other	#Decomposing animal
#Host	#Mammals	#Aquatic mammal

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7797	sediment adjacent to a sperm whale carcass	Kagoshima	Japan	JPN	Asia
67770	Sediment adjacent to a sperm whale carcass off Kagoshima		Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7797	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42276v1 assembly for Neptunomonas japonica DSM 18939	scaffold	GCA_000422765	1122599.8	2523533624	1122599	70.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7797	Neptunomonas japonica gene for 16S rRNA, partial sequence, strain: JAMM 0745	AB288092	1498		1122599

GC content

@ref	GC-content (mol%)	Method
32444	43.6-43.8
67770	43.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Neptunomonas japonica DSM 18939
NCBI: GCA_000422765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	yes	79.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Neptunomonas japonica DSM 18939
PATRIC: 1122599.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	94.67	yes
125438	spore-forming	spore-formingⓘ	no	93.17	no
125438	aerobic	aerobicⓘ	yes	65.68	yes
125438	thermophilic	thermophileⓘ	no	100.00	yes
125438	flagellated	motile2+ⓘ	yes	89.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Functional characterization of diverse type I-F CRISPR-associated transposons.	Roberts A, Nethery MA, Barrangou R.	Nucleic Acids Res	10.1093/nar/gkac985	2022
	Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms.	Goffredi SK, Yi H, Zhang Q, Klann JE, Struve IA, Vrijenhoek RC, Brown CT.	ISME J	10.1038/ismej.2013.201	2014
	Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms.	Moggioli G, Panossian B, Sun Y, Thiel D, Martin-Zamora FM, Tran M, Clifford AM, Goffredi SK, Rimskaya-Korsakova N, Jekely G, Tresguerres M, Qian PY, Qiu JW, Rouse GW, Henry LM, Martin-Duran JM.	Nat Commun	10.1038/s41467-023-38521-6	2023
Metabolism	Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses.	Miyamoto N, Yoshida MA, Koga H, Fujiwara Y.	BMC Evol Biol	10.1186/s12862-016-0844-4	2017
Enzymology	Complete characterization of new isolates of Neptunomonas phycophila leads to emend its description and opens possibilities of biotechnological applications.	Dieguez AL, Pichon P, Balboa S, Magnesen T, Romalde JL.	Microbiologyopen	10.1002/mbo3.519	2017
	First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing.	Najafi A, Moradinasab M, Nabipour I.	Front Microbiol	10.3389/fmicb.2018.01500	2018
Phylogeny	Characterization of the bacterial community of the chemically defended Hawaiian sacoglossan Elysia rufescens.	Davis J, Fricke WF, Hamann MT, Esquenazi E, Dorrestein PC, Hill RT.	Appl Environ Microbiol	10.1128/aem.01568-13	2013
	Temporal variation and lack of host specificity among bacterial endosymbionts of Osedax bone worms (Polychaeta: Siboglinidae).	Salathe RM, Vrijenhoek RC.	BMC Evol Biol	10.1186/1471-2148-12-189	2012
Phylogeny	Novel psychropiezophilic Oceanospirillales species Profundimonas piezophila gen. nov., sp. nov., isolated from the deep-sea environment of the Puerto Rico trench.	Cao Y, Chastain RA, Eloe EA, Nogi Y, Kato C, Bartlett DH.	Appl Environ Microbiol	10.1128/aem.02288-13	2014
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 )
#28666	IJSEM 866 2008 ( DOI 10.1099/ijs.0.65509-0 , PubMed 18398184 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Neptunomonas japonica (DSM 18939, JCM 14595, JAMM 0745)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000422765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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