Name: Arthrobacter tumbae R-5305
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7607

Type strain:

Species: Arthrobacter tumbae

Strain Designation: R-5305

Culture col. no.: DSM 16406, LMG 19501, JCM 21773, CIP 108900, IAM 15324, VTT E-072668

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 163874 (species)

SI-ID 13191

LMG 19501, DSM 16406, JCM 21773, VTT E-072668, CIP 108900, IAM 15324

Special Collections

Section

Arthrobacter tumbae R-5305 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from Biofilm covering the Servilia tomb, Roman necropolis of Carmona.

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 tumbae**
	Full Scientific Name (LPSN)	Arthrobacter tumbae Heyrman et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31342]	Gram stain	positive
[Ref.: #123684]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %92.639

[Ref.: #31342]	Cell width	0.9 µm

[Ref.: #31342]	Cell shape	coccus-shaped
[Ref.: #123684]	Cell shape	coccus-shaped

[Ref.: #31342]	Motility	no
[Ref.: #123684]	Motility	no

[Ref.: #31342]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6435]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6435]

Culture medium growth

[Ref.: #6435]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6435]

Culture medium composition

expand / minimize

[Ref.: #6435]

Culture medium

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

[Ref.: #6435]

Culture medium growth

[Ref.: #6435]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6435]

Culture medium composition

expand / minimize

[Ref.: #37386]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37386]

Culture medium growth

[Ref.: #37386]

Culture medium composition

expand / minimize

[Ref.: #123684]

Culture medium

CIP Medium 72

[Ref.: #123684]

Culture medium growth

[Ref.: #123684]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6435]		growth	28 °C
[Ref.: #31342]		growth	04-37 °C
[Ref.: #31342]		optimum	26 °C
[Ref.: #37386]		growth	30 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #123684]		growth	10-30 °C
[Ref.: #123684]	no	growth	37 °C
[Ref.: #123684]	no	growth	41 °C
[Ref.: #123684]	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.: #123684]	Oxygen tolerance	obligate aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %90.693

[Ref.: #31342]

Ability of spore formation

	Salt	Tested relation		Salt conc.
[Ref.: #31342]	NaCl		growth	05-10	%
[Ref.: #31342]	NaCl		optimum	7.5	%
[Ref.: #123684]	NaCl		growth	0	%
[Ref.: #123684]	NaCl	no	growth	2	%
[Ref.: #123684]	NaCl	no	growth	4	%
[Ref.: #123684]	NaCl	no	growth	6	%
[Ref.: #123684]	NaCl	no	growth	8	%
[Ref.: #123684]	NaCl	no	growth	10	%

[Ref.: #6435]	Murein short key	A11.28
[Ref.: #6435]	Murein types	A3alpha L-Lys-L-Thr-L-Ala₃

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123684]	citrate ChEBI	-	carbon source
[Ref.: #123684]	esculin ChEBI	-	hydrolysis
[Ref.: #31342]	gelatin ChEBI	+	carbon source
[Ref.: #123684]	hippurate ChEBI	+	hydrolysis
[Ref.: #123684]	nitrate ChEBI	+	reduction
[Ref.: #123684]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #123684]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #123684]		acetoin ChEBI	-
[Ref.: #123684]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #123684]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #123684]	amylase	+
[Ref.: #123684]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123684]	caseinase	+	3.4.21.50
[Ref.: #31342]	catalase	+	1.11.1.6
[Ref.: #123684]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #123684]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #123684]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #31342]	gelatinase	+
[Ref.: #123684]	gelatinase	-
[Ref.: #123684]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #123684]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #123684]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #123684]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123684]	oxidase	-
[Ref.: #123684]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #123684]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123684]	tryptophan deaminase	-
[Ref.: #123684]	tween esterase	-
[Ref.: #123684]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #123684]	11538	-	-	+	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	+	-

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

[Ref.: #6435]	Sample type/isolated from	Biofilm covering the Servilia tomb, Roman necropolis of Carmona
[Ref.: #6435]	Geographic location (country and/or sea, region)	Carmona
[Ref.: #6435]	Country	Spain
[Ref.: #6435]	Country ISO 3 Code	ESP
[Ref.: #6435]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Biofilm overgrowing a mural painting in the Servilia tomb
[Ref.: #67770]	Geographic location (country and/or sea, region)	Roman necropolis of Carmona
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe

[Ref.: #123684]	Sample type/isolated from	Mural paintings sites
[Ref.: #123684]	Geographic location (country and/or sea, region)	Servilia tomb, Carmona
[Ref.: #123684]	Country	Spain
[Ref.: #123684]	Country ISO 3 Code	ESP
[Ref.: #123684]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Biofilm	-
#Environmental	#Terrestrial	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ315069 (>99% sequence identity) for Arthrobacter from Microbeatlas

Aquatic Samples	534
Soil Samples	2709
Animal Samples	1557
Plant Samples	851
Total Samples	5651

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

[Ref.: #6435]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123684]	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.: #6435]	Arthrobacter tumbae 16S rRNA gene, type strain LMG 19501	AJ315069	1475	GenBank ENA	163874 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arthrobacter tumbae DSM 16406	GCA_016907495	contig	GenBank ENA	163874 tax ID	*
[Ref.: #66792]	Arthrobacter tumbae strain DSM 16406	163874.3	wgs	PATRIC	163874 tax ID	*
[Ref.: #66792]	Arthrobacter tumbae DSM 16406	2893579105	draft	JGI IMG/M	163874 tax ID	*

[Ref.: #6435]	GC-content	64.7 mol%
[Ref.: #67770]	GC-content	64.7 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 tumbae strain DSM 16406 PATRIC: 163874.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	89	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arthrobacter tumbae strain DSM 16406 PATRIC: 163874.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	92.639	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.946	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	79.49	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.693	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.447	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89.5	no

Availability in culture collections External links

[Ref.: #6435]

Culture collection no.

DSM 16406, LMG 19501, JCM 21773, CIP 108900, IAM 15324, VTT E-072668

[Ref.: #77051]

SI-ID 13191

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.	Vaishampayan P, Moissl-Eichinger C, Pukall R, Schumann P, Sproer C, Augustus A, Roberts AH, Namba G, Cisneros J, Salmassi T, Venkateswaran K	Int J Syst Evol Microbiol	10.1099/ijs.0.047134-0	2012	*
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

#6435

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16406

#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)

#37386 ; 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;

#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 )

#77051

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-ID13191.1 )

#123684 Collection of Institut Pasteur ; Curators of the CIP; CIP 108900

#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 tumbae in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Arthrobacter tumbae strain DSM 16406

Arthrobacter tumbae strain DSM 16406

Change proposal

Change proposal