Arthrobacter tumbae (DSM 16406, LMG 19501, R-5305)

Name: Arthrobacter tumbae (DSM 16406, LMG 19501, R-5305)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7607

Type strain

Strain Designation R-5305

Culture col. no. DSM 16406 LMG 19501 R-5305 VTT E-072668 IAM 15324 2 more

NCBI tax ID(s) 163874

Special Collections DSMZ JCM CIP Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 13191

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

@ref 20215

Last LPSN update 2025-12-16 09:48:37

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter tumbae

Full scientific name Arthrobacter tumbae Heyrman et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape
31342	positive	0.9 µm	coccus-shaped
123684	positive		coccus-shaped
125438	positive

Colony morphology

Pigmentation

31342

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6435	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
6435	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
37386	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123684	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6435	positive	growth	28	mesophilic
31342	positive	growth	04-37
31342	positive	optimum	26	mesophilic
37386	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
123684	positive	growth	10-30
123684	negative	growth	37
123684	negative	growth	41
123684	negative	growth	45

Culture pH

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31342	aerobe
123684	obligate aerobe
125438	aerobe
125439	obligate aerobe

Spore formation

31342

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31342	NaCl	positive	growth	05-10 %
31342	NaCl	positive	optimum	7.5 %
123684	NaCl	positive	growth	0 %
123684	NaCl		growth	2 %
123684	NaCl		growth	4 %
123684	NaCl		growth	6 %
123684	NaCl		growth	8 %
123684	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
6435	A11.28	A3alpha L-Lys-L-Thr-L-Ala₃

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123684	16947 ChEBI	citrate	-	carbon source
123684	4853 ChEBI	esculin	-	hydrolysis
31342	5291 ChEBI	gelatin	+	carbon source
123684	606565 ChEBI	hippurate	+	hydrolysis
123684	17632 ChEBI	nitrate	+	reduction
123684	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123684	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
123684	15688 ChEBI	acetoin	-
123684	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
123684	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
123684	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
123684	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
123684	caseinase	+	3.4.21.50
31342	catalase	+	1.11.1.6
123684	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
123684	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
123684	gamma-glutamyltransferase	-	2.3.2.2
31342	gelatinase	+
123684	gelatinase	-
123684	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
123684	lipase	-
68382	lipase (C 14)	-		from API zym
123684	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
123684	ornithine decarboxylase	-	4.1.1.17
123684	oxidase	-
123684	phenylalanine ammonia-lyase	-	4.3.1.24
123684	protease	+
68382	trypsin	-	3.4.21.4	from API zym
123684	tryptophan deaminase	-
123684	tween esterase	-
123684	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
123684	-	-	+	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Biofilm
#Environmental	#Terrestrial

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6435	Biofilm covering the Servilia tomb, Roman necropolis of Carmona	Carmona	Spain	ESP	Europe
67770	Biofilm overgrowing a mural painting in the Servilia tomb	Roman necropolis of Carmona	Spain	ESP	Europe
123684	Mural paintings sites	Servilia tomb, Carmona	Spain	ESP	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6435	1	Risk group (German classification) According to TRBA 466
123684	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
66792	ASM1690749v1 assembly for Arthrobacter tumbae DSM 16406	contig	GCA_016907495	163874.3	2893579105	163874	78.17

Genome browser: GCA_016907495

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6435	Arthrobacter tumbae 16S rRNA gene, type strain LMG 19501	AJ315069	1475		163874
124043	Arthrobacter tumbae strain LMG 19501 16S ribosomal RNA gene, partial sequence.	PQ524584	601		163874

GC content

@ref	GC-content (mol%)
6435	64.7
67770	64.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arthrobacter tumbae DSM 16406
NCBI: GCA_016907495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.90	no
125439	motility	BacteriaNetⓘ	no	72.70	no
125439	gram_stain	BacteriaNetⓘ	positive	81.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arthrobacter tumbae strain DSM 16406
PATRIC: 163874.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.64	yes
125438	anaerobic	anaerobicⓘ	no	97.95	yes
125438	spore-forming	spore-formingⓘ	no	79.49	yes
125438	aerobic	aerobicⓘ	yes	90.69	yes
125438	thermophilic	thermophileⓘ	no	96.45	no
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Identification of airborne microbiota in selected areas in a health-care setting in South Africa.	Setlhare G, Malebo N, Shale K, Lues R.	BMC Microbiol	10.1186/1471-2180-14-100	2014
	Temperature-Sensitive Lipids Reveal Intraspecific Diversity in Bacteria Isolated from an Ancient Antarctic Microbial Mat.	Lezcano MA, Carrizo D, Lominchar MA, Sanchez-Garcia L, Quesada A, Parro V.	Microb Ecol	10.1007/s00248-025-02583-4	2025
	Characterizing Peri-Implant and Sub-Gingival Microbiota through Culturomics. First Isolation of Some Species in the Oral Cavity. A Pilot Study.	Martellacci L, Quaranta G, Fancello G, D'Addona A, Sanguinetti M, Patini R, Masucci L.	Pathogens	10.3390/pathogens9050365	2020
	Indigenous oil-degrading bacteria more efficient in soil bioremediation than microbial consortium and active even in super oil-saturated soils.	Ali N, Khanafer M, Al-Awadhi H.	Front Microbiol	10.3389/fmicb.2022.950051	2022
	Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada.	Jroundi F, Gonzalez-Munoz MT, Sterflinger K, Pinar G.	PLoS One	10.1371/journal.pone.0132465	2015
Enzymology	Identification of causative pathogens in mouse eyes with bacterial keratitis by sequence analysis of 16S rDNA libraries.	Song HY, Qiu BF, Liu C, Zhu SX, Wang SC, Miao J, Jing J, Shao YX.	Exp Anim	10.1538/expanim.14-0046	2015
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
	Arthrobacter vasquezii sp. nov., isolated from a soil sample from Union Glacier, Antarctica.	Valenzuela-Ibaceta F, Carrasco V, Lagos-Moraga S, Dietz-Vargas C, Navarro CA, Perez-Donoso JM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006095	2023
Enzymology	Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea.	Chang HW, Bae JW, Nam YD, Kwon HY, Park JR, Shin KS, Kim KH, Quan ZX, Rhee SK, An KG, Park YH.	J Microbiol Biotechnol		2007
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

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 .
#123684	Collection of Institut Pasteur ; Curators of the CIP; CIP 108900
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 tumbae (DSM 16406, LMG 19501, R-5305)

Name and taxonomic classification

Morphology

Cell morphology

Colony 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 zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016907495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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