Archive BacDiveID:10.13145/bacdive11282.20230509.8.1

Strain identifier

BacDive ID: 11282

Type strain:

Species: Neptunomonas japonica

Strain history: M. Miyazaki JAMM 0745.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 7797

BacDive-ID: 11282

DSM-Number: 18939

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, rod-shaped

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

NCBI tax id

NCBI tax id	Matching level
417574	species
1122599	strain

strain history

@ref	history
7797	<- M. Miyazaki, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; JAMM 0745
67770	M. Miyazaki JAMM 0745.

doi: 10.13145/bacdive11282.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Oceanospirillales
family: Oceanospirillaceae
genus: Neptunomonas
species: Neptunomonas japonica
full scientific name: Neptunomonas japonica Miyazaki et al. 2008

@ref: 7797

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Neptunomonas

species: Neptunomonas japonica

full scientific name: Neptunomonas japonica Miyazaki et al. 2008

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32444	negative	1.7 µm	0.9 µm	rod-shaped	yes
69480					yes	98.795
69480	negative					100

pigmentation

@ref: 32444
production: yes

Culture and growth conditions

culture medium

@ref: 7797
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: 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	range
7797	positive	growth	20	psychrophilic
32444	positive	growth	05-25
32444	positive	optimum	20	psychrophilic
67770	positive	growth	20	psychrophilic

culture pH

@ref	ability	type	pH	PH range
32444	positive	growth	07-09	alkaliphile
32444	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 32444
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
32444	no
69481	no	100
69480	no	99.977

halophily

@ref	salt	growth	tested relation	concentration
32444	NaCl	positive	growth	01-05 %
32444	NaCl	positive	optimum	2 %

observation

@ref: 67770
observation: quinones: Q-8

metabolite utilization

@ref: 32444
Chebi-ID: 17632
metabolite: nitrate
utilization activity: +
kind of utilization tested: reduction

enzymes

@ref	value	activity	ec
32444	catalase	+	1.11.1.6
32444	gelatinase	+
32444	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	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

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_43610.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_1716;97_3735;98_31648;99_43610&stattab=map
Last taxonomy: Neptunomonas
16S sequence: AB288092
Sequence Identity:
Total samples: 5578
soil counts: 131
aquatic counts: 5203
animal counts: 211
plant counts: 33

Safety information

risk assessment

@ref: 7797
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7797
description: Neptunomonas japonica gene for 16S rRNA, partial sequence, strain: JAMM 0745
accession: AB288092
length: 1498
database: ena
NCBI tax ID: 1122599

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Neptunomonas japonica DSM 18939	1122599.8	wgs	patric	1122599
66792	Neptunomonas japonica DSM 18939	2523533624	draft	img	1122599
67770	Neptunomonas japonica DSM 18939	GCA_000422765	scaffold	ncbi	1122599

GC content

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

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	91.264	no
flagellated	yes	92.227	no
gram-positive	no	99.262	yes
anaerobic	no	98.654	no
aerobic	no	53.161	yes
halophile	yes	59.12	no
spore-forming	no	95.654	yes
glucose-util	yes	54.395	no
thermophile	no	99.738	yes
glucose-ferment	no	86.58	no

External links

@ref: 7797

culture collection no.: DSM 18939, JCM 14595, JAMM 0745

straininfo link

@ref: 80515
straininfo: 402057

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18398184	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	Animals, Annelida/microbiology, Base Composition, DNA, Bacterial/chemistry/genetics, Ecosystem, Fatty Acids/metabolism, Genes, Bacterial, Japan, Microscopy, Electron, Transmission, Molecular Sequence Data, Oceanospirillaceae/classification/genetics/isolation & purification/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Symbiosis, Terminology as Topic, Whales/microbiology	Metabolism
Phylogeny	19801396	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	DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/microbiology, Molecular Sequence Data, Oceanospirillaceae/classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics	Metabolism
Phylogeny	22199221	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	Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oceanospirillaceae/classification/genetics/isolation & purification, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysis	Genetics
Phylogeny	22904225	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	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oceanospirillaceae/classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Silicon Dioxide	Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7797	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18939)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-18939
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32444	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28666	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
80515	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID402057.1	StrainInfo: A central database for resolving microbial strain identifiers