Mycobacterium arabiense (DSM 45768, JCM 18538, YIM 121001)

Name: Mycobacterium arabiense (DSM 45768, JCM 18538, YIM 121001)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24237

Type strain

Culture col. no. DSM 45768 JCM 18538 YIM 121001

NCBI tax ID(s) 1286181

Special Collections DSMZ JCM Literature strains

Links

Mycobacterium arabiense DSM 45768 is a mesophilic, Gram-positive, ovoid-shaped prokaryote that was isolated from coastal sand.

Gram-positive ovoid-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406386

JCM 18538,DSM 45768

@ref 20215

Last LPSN update 2025-12-16 09:52:48

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium arabiense

Full scientific name Mycobacterium arabiense Zhang et al. 2013

Synonyms (1)

Mycolicibacterium arabiense

Morphology

Cell morphology

@ref	Gram stain	Cell shape
31044	positive	ovoid-shaped
125438	positive
125439	positive

Pigmentation

31044

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20672	MIDDLEBROOK MEDIUM (DSMZ Medium 645)		Medium recipe at MediaDive	Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20672	positive	growth	28	mesophilic
31044	positive	growth	05-37
31044	positive	optimum	31	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
31044	positive	optimum	7
31044	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.3

Spore formation

31044

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31044	NaCl	positive	growth	0-5 %
31044	NaCl	positive	optimum	1.5 %

Enzymes

@ref	Value	Activity	Ec
31044	catalase	+	1.11.1.6
31044	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20672	coastal sand	Dubai shore	United Arab Emirates	ARE	Asia
67770	Coastal zone sand	Dubai	United Arab Emirates	ARE	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC010491 (>99% sequence identity) for Mycolicibacterium from Microbeatlas

Aquatic Samples	312
Soil Samples	382
Animal Samples	227
Plant Samples	63
Total Samples	984

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20672	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1073181v2 assembly for Mycolicibacterium arabiense JCM 18538	complete	GCA_010731815	1286181.11	2888232652	1286181	97.13
66792	Mycolicibacterium arabiense strain JCM 18538	contig		1286181.8		1286181	78.06
66792	ASM2582322v1 assembly for Mycolicibacterium arabiense DSM 45768	contig	GCA_025823225	1286181.10	8115541261	1286181	70.31

Genome browser: GCA_010731815

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20672	Mycolicibacterium arabiense strain YIM 121001 16S ribosomal RNA gene, partial sequence	KC010491	1535		1286181
67770	Mycolicibacterium arabiense strain YIM 121001 16S-23S ribosomal RNA intergenic spacer, complete sequence	KC010493	433		1286181

GC content

@ref	GC-content (mol%)	Method
20672	62.8	high performance liquid chromatography (HPLC)
31044	62.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycolicibacterium arabiense JCM 18538
IMG: 2888232652

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no
125439	gram_stain	BacteriaNetⓘ	positive	98.80	no
125439	motility	BacteriaNetⓘ	no	72.90	no
125439	spore_formation	BacteriaNetⓘ	no	57.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium arabiense JCM 18538
NCBI: GCA_010731815.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.63	yes
125438	anaerobic	anaerobicⓘ	no	97.64	no
125438	aerobic	aerobicⓘ	yes	87.09	no
125438	spore-forming	spore-formingⓘ	no	58.13	yes
125438	thermophilic	thermophileⓘ	no	96.67	yes
125438	flagellated	motile2+ⓘ	no	88.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbiological features and clinical relevance of new species of the genus Mycobacterium.	Tortoli E.	Clin Microbiol Rev	10.1128/cmr.00035-14	2014
Phylogeny	Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.	Gupta RS, Lo B, Son J.	Front Microbiol	10.3389/fmicb.2018.00067	2018
	Consequences of Climate Change on the Emergence of Pathogenic, Environmentally Acquired Nontuberculous Mycobacteria.	Koch TN, Banta JA, Wilsey RN, Chan ED, Crooks JL, Honda JR.	Open Forum Infect Dis	10.1093/ofid/ofaf232	2025
Genetics	Characterization of Mycobacterium salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection.	Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P.	Front Microbiol	10.3389/fmicb.2022.992610	2022
Phylogeny	Mycolicibacterium lacusdiani sp. nov., an Attached Bacterium of Microcystis aeruginosa.	Xiao Y, Chen J, Chen M, Deng SJ, Xiong ZQ, Tian BY, Zhang BH	Front Microbiol	10.3389/fmicb.2022.861291	2022
Phylogeny	Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.	Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.050567-0	2013

References

#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 )
#20672	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45768
#31044	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 #27374 (see below)
#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;
#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 .
#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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Mycobacterium arabiense (DSM 45768, JCM 18538, YIM 121001)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010731815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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