Actibacterium naphthalenivorans (DSM 105040, JCM 30828, KCTC 18418)

Name: Actibacterium naphthalenivorans (DSM 105040, JCM 30828, KCTC 18418)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132960

Type strain

Strain Designation NS6

Culture col. no. DSM 105040 JCM 30828 KCTC 18418 NS6

NCBI tax ID(s) 1614693

Special Collections DSMZ JCM KCTC

Links

Actibacterium naphthalenivorans NS6 is a mesophilic prokaryote that was isolated from sea-tidal-flat sediment, crude-oil contaminated.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 396553

JCM 30828,DSM 105040

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Actibacterium

Species Actibacterium naphthalenivorans

Full scientific name Actibacterium naphthalenivorans (Jeong et al. 2015) Hördt et al. 2020

Synonyms (1)

Confluentimicrobium naphthalenivorans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.5
125439	negative	97.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24748	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)	Range
24748	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	90.1

Spore formation

@ref	Spore formation	Confidence
125439		95.3

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
24748	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24748	sea-tidal-flat sediment, crude-oil contaminated	Yeosu coastel area	Republic of Korea	KOR	Asia	34.8092	127.724 34.8092/127.724
67770	Sea-tidal-flat sediment	South Sea	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24748	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419696v1 assembly for Actibacterium naphthalenivorans DSM 105040	contig	GCA_014196965	1614693.4	2830026743	1614693	69.48

Genome browser: GCA_014196965

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24748	Actibacterium naphthalenivorans strain NS6 16S ribosomal RNA gene, partial sequence	KP272155	1453		1614693

GC content

@ref	GC-content (mol%)
24748	64.5
67770	64.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actibacterium naphthalenivorans DSM 105040
NCBI: GCA_014196965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.30	no
125439	motility	BacteriaNetⓘ	yes	67.00	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Confluentimicrobium naphthalenivorans strain DSM 105040
PATRIC: 1614693.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	88.18	no
125438	spore-forming	spore-formingⓘ	no	86.15	no
125438	aerobic	aerobicⓘ	yes	80.34	no
125438	thermophilic	thermophileⓘ	no	97.88	yes
125438	flagellated	motile2+ⓘ	yes	58.23	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
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 .
#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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Actibacterium naphthalenivorans (DSM 105040, JCM 30828, KCTC 18418)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014196965

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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