Name: Actibacterium naphthalenivorans NS6
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132960

Type strain:

Species: Actibacterium naphthalenivorans

Strain Designation: NS6

Culture col. no.: DSM 105040, JCM 30828, KCTC 18418

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; NS6.

NCBI tax ID(s): 1614693 (species)

SI-ID 396553

DSM 105040

Special Collections

Section

Actibacterium naphthalenivorans NS6 is a Gram-negative bacterium that was isolated from sea-tidal-flat sediment, crude-oil contaminated.

Gram-negative
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Actibacterium*
	Species	**Actibacterium naphthalenivorans**
	Full Scientific Name (LPSN)	Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020

Synonym

Confluentimicrobium naphthalenivorans

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24748]

Culture medium

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

[Ref.: #24748]

Culture medium growth

[Ref.: #24748]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24748]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24748]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %96

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #24748]	24590	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+

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

[Ref.: #24748]	Sample type/isolated from	sea-tidal-flat sediment, crude-oil contaminated
[Ref.: #24748]	Geographic location (country and/or sea, region)	Yeosu coastel area
[Ref.: #24748]	Country	Republic of Korea
[Ref.: #24748]	Country ISO 3 Code	KOR
[Ref.: #24748]	Continent	Asia
[Ref.: #24748]	Geographic location	34.8092°/127.7240°

[Ref.: #67770]	Sample type/isolated from	Sea-tidal-flat sediment
[Ref.: #67770]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP272155 (>99% sequence identity) for Actibacterium naphthalenivorans subclade from Microbeatlas

Aquatic Samples	3015
Soil Samples	100
Animal Samples	171
Plant Samples	9
Total Samples	3295

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

[Ref.: #24748]

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.: #24748]	Actibacterium naphthalenivorans strain NS6 16S ribosomal RNA gene, partial sequence	KP272155	1453	GenBank ENA	1614693 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Actibacterium naphthalenivorans DSM 105040	GCA_014196965	contig	GenBank ENA	1614693 tax ID	*
[Ref.: #66792]	Confluentimicrobium naphthalenivorans strain DSM 105040	1614693.4	wgs	PATRIC	1614693 tax ID	*
[Ref.: #66792]	Actibacterium naphthalenivorans DSM 105040	2830026743	draft	JGI IMG/M	1614693 tax ID	*

[Ref.: #24748]	GC-content	64.5 mol%
[Ref.: #67770]	GC-content	64.5 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Confluentimicrobium naphthalenivorans strain DSM 105040 PATRIC: 1614693.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	96	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Confluentimicrobium naphthalenivorans strain DSM 105040 PATRIC: 1614693.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	88.179	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.145	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	80.343	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.875	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	58.232	no

Availability in culture collections External links

[Ref.: #24748]

Culture collection no.

DSM 105040, JCM 30828, KCTC 18418

[Ref.: #91237]

SI-ID 396553

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015.	Jeong HI, Jin HM, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.000561	2015	*

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 )

#24748

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105040

#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;

#68369

Automatically annotated from API 20NE .

#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 )

#91237

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-ID396553.1 )

* These data were automatically processed and therefore are not curated

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Confluentimicrobium naphthalenivorans strain DSM 105040

Confluentimicrobium naphthalenivorans strain DSM 105040

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