Arthrobacter rhombi (DSM 15838, CCUG 38813, CIP 107337)

Name: Arthrobacter rhombi (DSM 15838, CCUG 38813, CIP 107337)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132694

Type strain

Strain Designation F.98.3HR.69

Culture col. no. DSM 15838 CCUG 38813 CIP 107337 JCM 11678 F.98.3HR.69 2 more

NCBI tax ID(s) 71253

Special Collections DSMZ CCUG JCM CIP

History <- JCM <- M. D. Collins; F.98.3HR.69 <- C. R. Osorio and J. L. Barja CCUG 38813 <-- M. D. Collins F.98.3HR.69 <-- C. R. Osorio and J. L. Barja. CIP <- 2002, CCUG <- 1997, M.D. Collins, IFR, Reading, UK <- C.R. Osori and J.L. Barja, Santiago di Compostela, Spain

Links

Arthrobacter rhombi F.98.3HR.69 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from organs of Greenland halibut .

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 100511

CCUG 38813,CIP 107337,JCM 11678,LMG 22201,NCIMB 13909,DSM 15838

@ref 20215

Last LPSN update 2026-02-09 11:31:46

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter rhombi

Full scientific name Arthrobacter rhombi Osorio et al. 1999

BacDive ID	Other strains from **Arthrobacter rhombi** (1)	Type strain
149993	A. rhombi CCUG 38812

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
122231	positive	rod-shaped

Colony morphology

122231

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
24484	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
37306	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122231	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
24484	positive	growth	28
37306	positive	growth	30
54484	positive	growth	30
54484	negative	growth	37
67770	positive	growth	30
122231	negative	growth	41
122231	negative	growth	37
122231	negative	growth	15
122231	negative	growth	10
122231	positive	growth	25-30
122231	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
54484	aerobe
122231	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122231	NaCl	positive	growth	0-4 %
122231	NaCl		growth	6 %
122231	NaCl		growth	8 %
122231	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122231	16947 ChEBI	citrate	-	carbon source
122231	4853 ChEBI	esculin	+	hydrolysis
122231	17632 ChEBI	nitrate	-	reduction
122231	17632 ChEBI	nitrate	+	respiration
122231	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122231	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122231	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122231	15688 ChEBI	acetoin	-
122231	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
122231	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
122231	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
122231	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122231	caseinase	+	3.4.21.50
122231	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
122231	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122231	gamma-glutamyltransferase	-	2.3.2.2
122231	gelatinase	+/-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122231	lysine decarboxylase	+	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
122231	ornithine decarboxylase	+	4.1.1.17
122231	oxidase	-
122231	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122231	tryptophan deaminase	-
122231	tween esterase	-
122231	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	methylglyoxal degradation	100	5 of 5
66794	lipoate biosynthesis	100	5 of 5
66794	phenylmercury acetate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	denitrification	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	lactate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	glycolysis	70.59	12 of 17
66794	tryptophan metabolism	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	oxidative phosphorylation	63.74	58 of 91
66794	metabolism of disaccharids	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	vitamin B1 metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	creatinine degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	glutathione metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	d-xylose degradation	54.55	6 of 11
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	quinate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	phenol degradation	50	10 of 20
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycine metabolism	50	5 of 10
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	vitamin B6 metabolism	45.45	5 of 11
66794	tyrosine metabolism	42.86	6 of 14
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	ascorbate metabolism	40.91	9 of 22
66794	myo-inositol biosynthesis	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	degradation of sugar acids	32	8 of 25
66794	carotenoid biosynthesis	31.82	7 of 22
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

54484

Fatty acid	Percentage	ECL
C15:0 ANTEISO	77.9	14.711
Unidentified	10.2	15.029
C15:0 ISO	7.3	14.621
C17:0 anteiso	1.7	16.722
Unidentified	0.9	14.928
C16:0	0.7	16
C14:0	0.4	14
C16:0 iso	0.4	15.626
Unidentified	0.3	17.026
C14:0 ISO	0.2	13.618

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122231	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122231	not determinedn.d.	+	+	+	+	+	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	+	-	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	+	-	-	-	-	+	-	+	+	+	-	+	+	+	+	-	-	-	+	+	+	-	+	-	-	+	+	+	-	+	-	-	-	+	-	+	-	+	+	-	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Host Body-Site	#Organ

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Host species
24484	organs of Greenland halibut (Reinhardtius hippoglossoides)	NW Atlantic, Newfoundland, Flemish Cap				Reinhardtius hippoglossoides
54484	Greenland halibut (Reinhardtius hippoglossoides)	NW,Newfoundland,Flemish Cap	Atlantic Ocean
67770	Spleen of Greenland halibut (Reinhardtius hippoglossoides)					Reinhardtius hippoglossoides
122231	Greenland halibut	Atlantic, Newfoundland	Canada	CAN	North America

Taxonmaps

69479

Global distribution of 16S sequence Y15885 (>99% sequence identity) for Arthrobacter rhombi subclade from Microbeatlas

Aquatic Samples	101
Soil Samples	324
Animal Samples	451
Plant Samples	274
Total Samples	1150

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24484	1	Risk group (German classification)
122231	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4167928v1 assembly for Arthrobacter rhombi DSM 15838	contig	GCA_041679285	71253	71.21
124043	ASM3952624v1 assembly for Arthrobacter rhombi JCM 11678	scaffold	GCA_039526245	71253	64.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24484	Arthrobacter rhombi 16S rRNA gene, strain F58.3CB57	Y15884	1423		71253
67770	Arthrobacter rhombi 16S rRNA gene, strain F98.3HR69	Y15885	1423		71253

GC content

@ref	GC-content (mol%)	Method
24484	61
67770	61	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arthrobacter rhombi sp. nov., isolated from Greenland halibut (Reinhardtius hippoglossoides).	Osorio CR, Barja JL, Hutson RA, Collins MD	Int J Syst Bacteriol	10.1099/00207713-49-3-1217	1999

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 )
#24484	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15838
#37306	; Curators of the CIP;
#54484	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38813
#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;
#68382	Automatically annotated from API zym .
#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 .
#122231	Collection of Institut Pasteur ; Curators of the CIP; CIP 107337
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 rhombi (DSM 15838, CCUG 38813, CIP 107337)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Fatty acid profile

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_041679285

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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