Mycobacterium kubicae (DSM 44627, ATCC 700732, CDC 941078)

Name: Mycobacterium kubicae (DSM 44627, ATCC 700732, CDC 941078)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8512

Type strain

Strain Designation 941078

Culture col. no. DSM 44627 ATCC 700732 CDC 941078 CIP 106428 CCUG 55639 2 more

NCBI tax ID(s) 120959

Special Collections DSMZ CCUG JCM CIP

History <- CIP <- W. R. Butler, CDC 2000, W.R. Butler, CDC, Atlanta, USA: strain 941078 CIP 106428 <-- W. R. Butler CDC 941078. CIP <- 2000, W.R. Butler, CDC, Atlanta, USA: strain 941078

Links

Mycobacterium kubicae 941078 is a mesophilic, rod-shaped prokaryote that was isolated from human sputum.

rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 44109

CT2025-00091,ATCC 700732,CIP 106428,DSM 44627,JCM 13573,CCUG 55639

@ref 20215

Last LPSN update 2025-12-16 09:48:51

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium kubicae

Full scientific name Mycobacterium kubicae Floyd et al. 2000

Morphology

Cell morphology

@ref	Cell shape	Gram stain	Confidence
120508	rod-shaped
125438		positive	90.814
125439		positive	92

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11939	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
36256	MEDIUM 55 - for Mycobacterium
120508	CIP Medium 55	Medium recipe at CIP
120508	CIP Medium 96	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11939	positive	growth	37	mesophilic
36256	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
120508	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120508	606565 ChEBI	hippurate	-	hydrolysis
120508	17632 ChEBI	nitrate	-	reduction
120508	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120508	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
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
120508	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120508	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120508	gamma-glutamyltransferase	-	2.3.2.2
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120508	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
120508	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
120508	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Sputum

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11939	human sputum	South Carolina	USA	USA	North America
60684	Human sputum
67770	Human sputum
120508	Sputum

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11939	2	Risk group (German classification) According to TRBA 466
120508	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	ASM1568917v1 assembly for Mycobacterium kubicae JCM 13573	complete	GCA_015689175	120959.24	8110833118	120959	96.13
66792	ASM1072313v1 assembly for Mycobacterium kubicae JCM 13573	contig	GCA_010723135	120959.18	8112484662	120959	75.36
67770	ASM210174v1 assembly for Mycobacterium kubicae CIP 106428	contig	GCA_002101745	120959.3	8115158849	120959	54.27
66792	ASM2582182v1 assembly for Mycobacterium kubicae DSM 44627	contig	GCA_025821825	120959.28	8113887403	120959	39.26

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene, partial sequence	AF547941	542	120959
20218	Mycobacterium kubicae 16S ribosomal RNA gene and internal transcribed spacer, partial sequence	DQ275612	266	120959
11939	Mycobacterium kubicae 16S ribosomal RNA gene, partial sequence	AF133902	1321	120959
11939	Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	HM022200	1792	120959

GC content

@ref	GC-content (mol%)	Method
67770	66	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium kubicae strain JCM 13573
PATRIC: 120959.24

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no
125439	gram_stain	BacteriaNetⓘ	positive	92.00	no
125439	motility	BacteriaNetⓘ	no	77.90	no
125439	spore_formation	BacteriaNetⓘ	no	52.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium kubicae JCM 13573
NCBI: GCA_015689175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.81	no
125438	anaerobic	anaerobicⓘ	no	96.99	no
125438	aerobic	aerobicⓘ	yes	80.84	no
125438	spore-forming	spore-formingⓘ	no	59.66	no
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates.	Hendrix J, Epperson LE, Durbin D, Honda JR, Strong M.	Microb Genom	10.1099/mgen.0.000497	2021
	Complete Genome Sequence of Mycobacterium sp. Strain 4858.	Bouam A, Levasseur A, Bonnet M, Borand L, Van Goethem C, Drancourt M, Godreuil S.	Genome Announc	10.1128/genomea.01604-17	2018
	The Presence of esat-6 and cfp10 and Other Gene Orthologs of the RD 1 Region in Non-Tuberculous Mycobacteria, Mycolicibacteria, Mycobacteroides and Mycolicibacter as Possible Impediments for the Diagnosis of (Animal) Tuberculosis	Gcebe N, Hlokwe T, Bouw A, Michel A, Rutten V.	Microorganisms		2024
Phylogeny	Mycobacterium kubicae sp. nov., a slowly growing, scotochromogenic Mycobacterium.	Floyd MM, Gross WM, Bonato DA, Silcox VA, Smithwick RW, Metchock B, Crawford JT, Butler WR	Int J Syst Evol Microbiol	10.1099/00207713-50-5-1811	2000

References

#11939	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44627
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#36256	; Curators of the CIP;
#60684	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55639
#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 .
#120508	Collection of Institut Pasteur ; Curators of the CIP; CIP 106428
#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 kubicae (DSM 44627, ATCC 700732, CDC 941078)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_015689175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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