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

Section

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

coccus-shaped
Gram-positive
aerobe
mesophilic
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 %100

[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

[Ref.: #6432]	Temperature range	mesophilic
[Ref.: #18402]	Temperature range	mesophilic
[Ref.: #31342]	Temperature range	mesophilic
[Ref.: #37304]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #121830]	Temperature range	psychrophilic
[Ref.: #121830]	Temperature range	thermophilic

	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.: #31342]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.747

	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	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	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	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	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arthrobacter pigmenti strain DSM 16403 PATRIC: 271432.3
[Ref.: #69480]	motile	yes	52.607	no
[Ref.: #69480]	gram-positive	yes	91.956	no
[Ref.: #69480]	anaerobic	no	99.566	no
[Ref.: #69480]	halophile	no	69.335	no
[Ref.: #69480]	spore-forming	no	88.763	no
[Ref.: #69480]	glucose-util	yes	84.778	yes
[Ref.: #69480]	aerobic	yes	95.453	no
[Ref.: #69480]	flagellated	no	92.32	no
[Ref.: #69480]	thermophile	no	99.18	yes
[Ref.: #69480]	glucose-ferment	no	87.575	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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Arthrobacter pigmenti in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Arthrobacter pigmenti strain DSM 16403

Arthrobacter pigmenti strain DSM 16403

Change proposal

Change proposal