Arthrobacter oryzae (DSM 25586, JCM 15922, NBRC 102055)

Name: Arthrobacter oryzae (DSM 25586, JCM 15922, NBRC 102055)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7618

Type strain

Strain Designation KV-651

Culture col. no. DSM 25586 JCM 15922 NBRC 102055 NRRL B-24478 KV-651

NCBI tax ID(s) 409290

Special Collections DSMZ JCM Literature strains

Links

Arthrobacter oryzae KV-651 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from paddy soil.

Gram-positive motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404081

NBRC 102055,JCM 15922,DSM 25586

@ref 20215

Last LPSN update 2025-12-16 09:48:38

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter oryzae

Full scientific name Arthrobacter oryzae Kageyama et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
32047	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18052	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18052	positive	growth	28	mesophilic
32047	positive	growth	04-34
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32047	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32047	aerobe
125439	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32047	NaCl	positive	growth	<2 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32047	17234 ChEBI	glucose	+	carbon source
32047	29864 ChEBI	mannitol	+	carbon source
32047	28053 ChEBI	melibiose	+	carbon source
32047	17632 ChEBI	nitrate	+	reduction
32047	16634 ChEBI	raffinose	+	carbon source
32047	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32047	acid phosphatase	+	3.1.3.2
32047	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	teichoic acid biosynthesis	100	1 of 1
66794	phenylmercury acetate degradation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	metabolism of disaccharids	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	citric acid cycle	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	purine metabolism	80.85	76 of 94
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	tryptophan metabolism	73.68	28 of 38
66794	pyrimidine metabolism	73.33	33 of 45
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	gallate degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	glycine betaine biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	oxidative phosphorylation	58.24	53 of 91
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	lysine metabolism	54.76	23 of 42
66794	methionine metabolism	53.85	14 of 26
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	lactate fermentation	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	tyrosine metabolism	42.86	6 of 14
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	degradation of sugar alcohols	37.5	6 of 16
66794	d-xylose degradation	36.36	4 of 11
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	chlorophyll metabolism	22.22	4 of 18
66794	polyamine pathway	21.74	5 of 23
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
18052	paddy soil	Japan	JPN	Asia
67770	Paddy soil	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB279889 (>99% sequence identity) for Arthrobacter from Microbeatlas

Aquatic Samples	364
Soil Samples	2849
Animal Samples	580
Plant Samples	2017
Total Samples	5810

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18052	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	ASM363409v1 assembly for Arthrobacter oryzae DSM 25586	scaffold	GCA_003634095	409290.3	2757320374	409290	75.29

Genome browser: GCA_003634095

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18052	Arthrobacter oryzae gene for 16S rRNA, partial sequence	AB279889	1465		409290

GC content

@ref	GC-content (mol%)
18052	67
67770	67

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arthrobacter oryzae DSM 25586
NCBI: GCA_003634095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	79.50	no
125439	motility	BacteriaNetⓘ	no	52.70	no
125439	gram_stain	BacteriaNetⓘ	positive	87.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arthrobacter oryzae strain DSM 25586
PATRIC: 409290.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.81	yes
125438	anaerobic	anaerobicⓘ	no	98.32	yes
125438	spore-forming	spore-formingⓘ	no	65.86	no
125438	aerobic	aerobicⓘ	yes	87.86	yes
125438	thermophilic	thermophileⓘ	no	97.97	yes
125438	flagellated	motile2+ⓘ	no	74.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft genome sequence of Arthrobacter sp. strain B10-11 isolated from the tomato rhizosphere.	Chaboy-Cansado R, Cobeta P, Roscales G, Aguirre de Carcer D, Rastrojo A.	Microbiol Resour Announc	10.1128/mra.01220-23	2024
Enzymology	First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77.	Singh RN, Gaba S, Yadav AN, Gaur P, Gulati S, Kaushik R, Saxena AK.	Stand Genomic Sci	10.1186/s40793-016-0176-4	2016
	Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance.	Rosas-Diaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sanchez-Reyes A, Pardo-Lopez L.	Front Microbiol	10.3389/fmicb.2021.713702	2021
Phylogeny	Arthrobacter liuii sp. nov., resuscitated from Xinjiang desert soil.	Yu XY, Zhang L, Ren B, Yang N, Liu M, Liu XT, Zhang LX, Ding LX	Int J Syst Evol Microbiol	10.1099/ijs.0.000037	2014
Phylogeny	Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov.	Kageyama A, Morisaki K, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64875-0	2008

References

#18052	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25586
#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 )
#32047	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 #28297 (see below)
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Arthrobacter oryzae (DSM 25586, JCM 15922, NBRC 102055)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003634095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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