Devosia naphthalenivorans (CGMCC 1.13553, JCM 32509, CM5-1)

Name: Devosia naphthalenivorans (CGMCC 1.13553, JCM 32509, CM5-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164276

Type strain

Strain Designation CM5-1

Culture col. no. CGMCC 1.13553 JCM 32509 CM5-1

NCBI tax ID(s) 2082392

Special Collections JCM Literature strains

History JCM <-- J. Chen; Zhejiang Wanli Univ., China; CM5-1.

Links

Devosia naphthalenivorans CM5-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Sediment sample from the East Pacific Ocean.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 133139

JCM 32509

@ref 20215

Last LPSN update 2026-05-29 08:45:22

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Devosiaceae

Genus Devosia

Species Devosia naphthalenivorans

Full scientific name Devosia naphthalenivorans Chen et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
67950	negative	0.6-0.7 µm	0.2-0.3 µm	rod-shaped
125438	negative					96.986

Colony morphology

@ref	Colony color	Colony shape	Medium used
67950	white	circular	Marine agar (MA)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	30
67950	positive	growth	5-30
67950	positive	optimum	25

Culture pH

@ref	Ability	Type	PH
67950	positive	optimum	7
67950	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67950	aerobe
125439	obligate aerobe	96.49

Spore formation

@ref	Spore formation	Confidence
125439		95.878
125438		91.438

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67950	NaCl	positive	growth	0-5 %(w/v)
67950	NaCl	positive	optimum	3-4 %(w/v)

Observation

@ref	Observation
67770	quinones: Q-10
67950	The major isoprenoid quinone is Q-10
67950	polar lipids include diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and four unidentified lipids

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
67950	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	degradation
67950	29016 ChEBI	arginine	+	reduction
67950		casein	-	hydrolysis
67950	4853 ChEBI	esculin	+	hydrolysis
67950	5291 ChEBI	gelatin	+	degradation
67950	17632 ChEBI	nitrate	+	reduction
67950	28017 ChEBI	starch	-	hydrolysis
67950	53424 ChEBI	tween 20	-	hydrolysis
67950	53423 ChEBI	tween 40	-	hydrolysis
67950	53425 ChEBI	tween 60	-	hydrolysis
67950	53426 ChEBI	tween 80	-	hydrolysis

Enzymes

@ref	Value	Activity	Ec
67950	acid phosphatase	+	3.1.3.2
67950	alkaline phosphatase	+	3.1.3.1
67950	alpha-glucosidase	+	3.2.1.20
67950	alpha-mannosidase	+	3.2.1.24
67950	beta-galactosidase	+	3.2.1.23
67950	beta-glucosidase	+	3.2.1.21
67950	catalase	+	1.11.1.6
67950	cytochrome oxidase	+	1.9.3.1
67950	esterase (C 4)	+
67950	esterase Lipase (C 8)	+
67950	leucine arylamidase	+	3.4.11.1
67950	lipase (C 14)	+
67950	naphthol-AS-BI-phosphohydrolase	+
67950	trypsin	+	3.4.21.4
67950	urease	+	3.5.1.5
67950	valine arylamidase	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Latitude	Longitude
67770	Sediment sample from the East Pacific Ocean
67950	sediment sample collected at a water depth of 5160 m	2011-10	Eastern Pacific Ocean	Pacific Ocean	10.049	-154.298 10.049/-154.298

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
67770	ASM305635v1 assembly for Devosia naphthalenivorans CM5-1	scaffold	GCA_003056355	2082392.3	2082392	65.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67950	Devosia naphthalenivorans 16S ribosomal RNA gene, partial sequence	MG230310	1404		2082392

GC content

@ref	GC-content (mol%)	Method
67770	61.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM305635v1 assembly for Devosia naphthalenivorans CM5-1
NCBI: GCA_003056355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.49	no
125439	gram_stain	BacteriaNetⓘ	negative	86.97	no
125439	motility	BacteriaNetⓘ	yes	42.30	no
125439	spore_formation	BacteriaNetⓘ	no	95.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Devosia naphthalenivorans CM5-1
NCBI: GCA_003056355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.99	yes
125438	anaerobic	anaerobicⓘ	no	97.45	no
125438	aerobic	aerobicⓘ	yes	83.24	yes
125438	spore-forming	spore-formingⓘ	no	91.44	no
125438	thermophilic	thermophileⓘ	no	95.53	yes
125438	flagellated	motile2+ⓘ	yes	60.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.	Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HR	Int J Syst Evol Microbiol	10.1099/ijsem.0.004995	2021
Phylogeny	Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment.	Chen Y, Zhu S, Lin D, Wang X, Yang J, Chen J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003410	2019

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67950	Yong Chen, Sidong Zhu, Danqiu Lin, Xing Wang, Jifang Yang, Jigang Chen: Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment. IJSEM 69: 1974 - 1979 2019 ( DOI 10.1099/ijsem.0.003410 )
#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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Devosia naphthalenivorans (CGMCC 1.13553, JCM 32509, CM5-1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003056355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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