Name: Arthrobacter pigmenti R-5117
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7605

Type strain:

Species: Arthrobacter pigmenti

Strain Designation: R-5117

Culture col. no.: DSM 16403, LMG 22284, JCM 21771, CIP 108899, IAM 15322

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 271432 (species)

SI-ID 362265

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

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Micrococcaceae*
	Genus	*Arthrobacter*
	Species	**Arthrobacter pigmenti**
	Full Scientific Name (LPSN)	Arthrobacter pigmenti Heyrman et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31342]	Gram stain	positive
[Ref.: #121830]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.455

[Ref.: #31342]	Cell width	0.9 µm

[Ref.: #31342]	Cell shape	coccus-shaped
[Ref.: #121830]	Cell shape	coccus-shaped

[Ref.: #31342]	Motility	no
[Ref.: #121830]	Motility	no

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 2

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 3

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 4

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 5

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 6

[Ref.: #18402]	Colony color	Lemon yellow (1012)
[Ref.: #18402]	Incubation period	10-14 days
[Ref.: #18402]	Cultivation medium used	ISP 7

[Ref.: #31342]

Pigment production

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 2

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 3

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 4

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 5

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 6

[Ref.: #18402]	Multicellular complex forming ability	no
[Ref.: #18402]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6432]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6432]

Culture medium growth

[Ref.: #6432]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6432]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 2

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 3

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 4

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 5

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 6

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #18402]

Culture medium

ISP 7

[Ref.: #18402]

Culture medium growth

[Ref.: #18402]

Culture medium composition

expand / minimize

[Ref.: #37304]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37304]

Culture medium growth

[Ref.: #37304]

Culture medium composition

expand / minimize

[Ref.: #121830]

Culture medium

CIP Medium 72

[Ref.: #121830]

Culture medium growth

[Ref.: #121830]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6432]		growth	28 °C
[Ref.: #18402]		optimum	28 °C
[Ref.: #31342]		growth	10-37 °C
[Ref.: #31342]		optimum	26 °C
[Ref.: #37304]		growth	25 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #121830]		growth	15-37 °C
[Ref.: #121830]	no	growth	10 °C
[Ref.: #121830]	no	growth	41 °C
[Ref.: #121830]	no	growth	45 °C

	pH	Kind of pH		pH
[Ref.: #31342]			optimum	8.5
[Ref.: #31342]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31342]	Oxygen tolerance	aerobe
[Ref.: #121830]	Oxygen tolerance	obligate aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %90.058

[Ref.: #31342]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt		Salt conc.
[Ref.: #31342]	NaCl	growth	05-15	%
[Ref.: #31342]	NaCl	optimum	10	%
[Ref.: #121830]	NaCl	growth	0-10	%

[Ref.: #6432]	Murein short key	A11.07
[Ref.: #6432]	Murein types	A3alpha L-Lys-L-Ala₄

[Ref.: #31342]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-9(H₂), MK-7(H₂), MK-10(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18402]	arabinose ChEBI	+
[Ref.: #18402]	cellulose ChEBI	-
[Ref.: #121830]	citrate ChEBI	-	carbon source
[Ref.: #31342]	esculin ChEBI	+	hydrolysis
[Ref.: #121830]	esculin ChEBI	-	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #18402]	fructose ChEBI	+
[Ref.: #31342]	gelatin ChEBI	+	carbon source
[Ref.: #18402]	glucose ChEBI	+
[Ref.: #31342]	glucose ChEBI	+	carbon source
[Ref.: #121830]	hippurate ChEBI	+	hydrolysis
[Ref.: #31342]	maltose ChEBI	+	carbon source
[Ref.: #18402]	mannitol ChEBI	+
[Ref.: #31342]	mannose ChEBI	+	carbon source
[Ref.: #18402]	myo-inositol ChEBI	+
[Ref.: #31342]	nitrate ChEBI	+	reduction
[Ref.: #121830]	nitrate ChEBI	+	reduction
[Ref.: #121830]	nitrate ChEBI	-	respiration
[Ref.: #121830]	nitrite ChEBI	-	reduction
[Ref.: #18402]	raffinose ChEBI	+
[Ref.: #18402]	rhamnose ChEBI	-
[Ref.: #18402]	sucrose ChEBI	+
[Ref.: #31342]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #18402]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121830]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121830]		acetoin ChEBI	-
[Ref.: #121830]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #31342]	acid phosphatase	+	3.1.3.2
[Ref.: #121830]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #31342]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #31342]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #121830]	amylase	+
[Ref.: #121830]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym, API Coryne
[Ref.: #121830]	caseinase	+	3.4.21.50
[Ref.: #31342]	catalase	+	1.11.1.6
[Ref.: #121830]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #121830]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121830]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #31342]	gelatinase	+
[Ref.: #121830]	gelatinase	+/-
[Ref.: #121830]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121830]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121830]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121830]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121830]	oxidase	-
[Ref.: #121830]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #121830]	protease	+
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #121830]	tryptophan deaminase	-
[Ref.: #121830]	tween esterase	-
[Ref.: #121830]	urease	-	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #18402]	87	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:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18402]	112	not determinedn.d.	+	+	+	-	+	-	-	+	-	+	+	-	+	+	+	-	-	+	-
[Ref.: #121830]	11537	-	+	+	+	-	+	-	-	+	-	-	+	-	+	+	-	-	-	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6432]	Sample type/isolated from	Mural painting, biofilm
[Ref.: #6432]	Geographic location (country and/or sea, region)	Herberstein
[Ref.: #6432]	Country	Austria
[Ref.: #6432]	Country ISO 3 Code	AUT
[Ref.: #6432]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Rosy biofilm overgrowing a mural painting in the Saint-Catherine chapel
[Ref.: #67770]	Geographic location (country and/or sea, region)	castle of Herberstein
[Ref.: #67770]	Country	Austria
[Ref.: #67770]	Country ISO 3 Code	AUT
[Ref.: #67770]	Continent	Europe

[Ref.: #121830]	Sample type/isolated from	Mural painting
[Ref.: #121830]	Geographic location (country and/or sea, region)	Herberstein castle, Himsdorf
[Ref.: #121830]	Country	Austria
[Ref.: #121830]	Country ISO 3 Code	AUT
[Ref.: #121830]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	-
#Engineered	#Other	#Painting
#Environmental	#Biofilm	-

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #18402]	Biosafety level	2
[Ref.: #6432]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121830]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6432]	Arthrobacter pigmenti partial 16S rRNA gene, type strain LMG 22284T	AJ639827	1489	GenBank ENA	271432 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Arthrobacter pigmenti DSM 16403	GCA_011927905	contig	GenBank ENA	271432 tax ID
[Ref.: #66792]	Arthrobacter pigmenti strain DSM 16403	271432.3	wgs	PATRIC	271432 tax ID	*
[Ref.: #66792]	Arthrobacter pigmenti DSM 16403	2831304190	draft	JGI IMG/M	271432 tax ID	*

[Ref.: #6432]	GC-content	61.6 mol%
[Ref.: #67770]	GC-content	61.6 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Arthrobacter pigmenti strain DSM 16403 PATRIC: 271432.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arthrobacter pigmenti strain DSM 16403 PATRIC: 271432.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.455	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.862	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	69.486	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.058	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.967	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	74.5	no

Availability in culture collections External links

[Ref.: #6432]

Culture collection no.

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

[Ref.: #77049]

SI-ID 362265

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#37304 ; Curators of the CIP;

#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;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#77049

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID362265.1 )

#121830 Collection of Institut Pasteur ; Curators of the CIP; CIP 108899

#27656

IJSEM 1457 2005 ( DOI 10.1099/ijs.0.63358-0 , PubMed 16014466 )

* These data were automatically processed and therefore are not curated

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Arthrobacter pigmenti strain DSM 16403

Arthrobacter pigmenti strain DSM 16403

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