Arthrobacter pigmenti (DSM 16403, LMG 22284, R-5117)

Name: Arthrobacter pigmenti (DSM 16403, LMG 22284, R-5117)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7605

Type strain

Strain Designation R-5117

Culture col. no. DSM 16403 LMG 22284 R-5117 IAM 15322 CIP 108899 1 more

NCBI tax ID(s) 271432

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History <- J. Heyrman, R-5117 2005, DSMZ IAM 15322 <-- LMG 22284 <-- J. Heyrman R-5117. CIP <- 2005, DSMZ

Links

Arthrobacter pigmenti R-5117 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from Mural painting, biofilm.

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

Name and taxonomic classification

SI-ID 362265

LMG 22284,DSM 16403,JCM 21771,CIP 108899,IAM 15322

@ref 20215

Last LPSN update 2026-02-09 11:19:30

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter pigmenti

Full scientific name Arthrobacter pigmenti Heyrman et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
31342	positive	0.9 µm	coccus-shaped
121830	positive		coccus-shaped
125438	positive			90.455

Colony morphology

@ref	Colony color	Incubation period	Medium used
18402	Lemon yellow (1012)	10-14 days	ISP 2
18402	Lemon yellow (1012)	10-14 days	ISP 3
18402	Lemon yellow (1012)	10-14 days	ISP 4
18402	Lemon yellow (1012)	10-14 days	ISP 5
18402	Lemon yellow (1012)	10-14 days	ISP 6
18402	Lemon yellow (1012)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18402		ISP 2
18402		ISP 3
18402		ISP 4
18402		ISP 5
18402		ISP 6
18402		ISP 7

Pigmentation

31342

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6432	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
18402	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18402	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18402	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18402	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18402	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18402	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37304	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121830	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6432	positive	growth	28
18402	positive	optimum	28
31342	positive	growth	10-37
31342	positive	optimum	26
37304	positive	growth	25
67770	positive	growth	28
121830	positive	growth	15-37
121830	negative	growth	10
121830	negative	growth	41
121830	negative	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
31342	positive	optimum	8.5
31342	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31342	aerobe
121830	obligate aerobe
125438	aerobe	90.058
125439	obligate aerobe	90.1

Spore formation

31342

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31342	NaCl	positive	growth	05-15 %
31342	NaCl	positive	optimum	10 %
121830	NaCl	positive	growth	0-10 %

Murein

@ref	Murein short key	Type
6432	A11.07	A3alpha L-Lys-L-Ala₄

Observation

@ref	Observation
31342	aggregates in chains
67770	quinones: MK-9(H₂), MK-7(H₂), MK-10(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18402	22599 ChEBI	arabinose	+
18402	62968 ChEBI	cellulose	-
121830	16947 ChEBI	citrate	-	carbon source
31342	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
121830	4853 ChEBI	esculin	-	hydrolysis
18402	28757 ChEBI	fructose	+
31342	5291 ChEBI	gelatin	+	carbon source
18402	17234 ChEBI	glucose	+
31342	17234 ChEBI	glucose	+	carbon source
121830	606565 ChEBI	hippurate	+	hydrolysis
31342	17306 ChEBI	maltose	+	carbon source
18402	29864 ChEBI	mannitol	+
31342	37684 ChEBI	mannose	+	carbon source
18402	17268 ChEBI	myo-inositol	+
31342	17632 ChEBI	nitrate	+	reduction
121830	17632 ChEBI	nitrate	+	reduction
121830	17632 ChEBI	nitrate	-	respiration
121830	16301 ChEBI	nitrite	-	reduction
18402	16634 ChEBI	raffinose	+
18402	26546 ChEBI	rhamnose	-
18402	17992 ChEBI	sucrose	+
31342	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
18402	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121830	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121830	15688 ChEBI	acetoin	-
121830	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
31342	acid phosphatase	+	3.1.3.2
121830	alcohol dehydrogenase	-	1.1.1.1
31342	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
31342	alpha-galactosidase	+	3.2.1.22
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	+	3.2.1.24	from API zym
121830	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
121830	beta-galactosidase	+	3.2.1.23
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68379	beta-glucuronidase	+	3.2.1.31	from API Coryne
121830	caseinase	+	3.4.21.50
31342	catalase	+	1.11.1.6
121830	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121830	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121830	gamma-glutamyltransferase	-	2.3.2.2
31342	gelatinase	+
121830	gelatinase	+/-
121830	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121830	lipase	-
68382	lipase (C 14)	-		from API zym
121830	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121830	ornithine decarboxylase	-	4.1.1.17
121830	oxidase	-
121830	phenylalanine ammonia-lyase	-	4.3.1.24
121830	protease	+
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	+	3.4.21.4	from API zym
121830	tryptophan deaminase	-
121830	tween esterase	-
121830	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18402	not determinedn.d.	-	-	+	+	+	+	-	-	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	+	not determinedn.d.	not determinedn.d.

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
18402	not determinedn.d.	+	+	+	-	+	-	-	+	-	+	+	-	+	+	+	-	-	+	-
121830	-	+	+	+	-	+	-	-	+	-	-	+	-	+	+	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Engineered	#Other	#Painting
#Environmental	#Biofilm	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6432	Mural painting, biofilm	Herberstein	Austria	AUT	Europe
67770	Rosy biofilm overgrowing a mural painting in the Saint-Catherine chapel	castle of Herberstein	Austria	AUT	Europe
121830	Mural painting	Herberstein castle, Himsdorf	Austria	AUT	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ639827 (>99% sequence identity) for Arthrobacter pigmenti from Microbeatlas

Aquatic Samples	7
Soil Samples	32
Animal Samples	86
Plant Samples	15
Total Samples	140

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6432	1	Risk group (German classification) According to TRBA 466
18402	2
121830	1	Risk group (French 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	ASM1192790v1 assembly for Arthrobacter pigmenti DSM 16403	contig	GCA_011927905	271432.3	2831304190	271432	79.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6432	Arthrobacter pigmenti partial 16S rRNA gene, type strain LMG 22284T	AJ639827	1489		271432

GC content

@ref	GC-content (mol%)	Method
6432	61.6
67770	61.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arthrobacter pigmenti DSM 16403
NCBI: GCA_011927905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.90	no
125439	motility	BacteriaNetⓘ	no	80.90	no
125439	gram_stain	BacteriaNetⓘ	positive	79.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arthrobacter pigmenti strain DSM 16403
PATRIC: 271432.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.46	yes
125438	anaerobic	anaerobicⓘ	no	96.86	yes
125438	spore-forming	spore-formingⓘ	no	69.49	yes
125438	aerobic	aerobicⓘ	yes	90.06	no
125438	thermophilic	thermophileⓘ	no	96.97	no
125438	flagellated	motile2+ⓘ	no	74.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
	Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota.	Winders TM, Holman DB, Schmidt KN, Luecke SM, Smith DJ, Neville BW, Dahlen CR, Swanson KC, Amat S.	Sci Rep	10.1038/s41598-023-35241-1	2023
	Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India.	Krishnan R, Menon RR, Tanaka N, Busse HJ, Krishnamurthi S, Rameshkumar N.	PLoS One	10.1371/journal.pone.0150322	2016
Phylogeny	Six novel Arthrobacter species isolated from deteriorated mural paintings.	Heyrman J, Verbeeren J, Schumann P, Swings J, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.63358-0	2005

References

#6432	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16403
#18402	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#27656	IJSEM 1457 2005 ( DOI 10.1099/ijs.0.63358-0 , PubMed 16014466 )
#31342	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 #27656
#37304	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#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 .
#121830	Collection of Institut Pasteur ; Curators of the CIP; CIP 108899
#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 pigmenti (DSM 16403, LMG 22284, R-5117)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011927905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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