Name: Mycobacterium kubicae 941078
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8512

Type strain:

Species: Mycobacterium kubicae

Strain Designation: 941078

Culture col. no.: DSM 44627, ATCC 700732, CDC 941078, CIP 106428, CCUG 55639, JCM 13573

Strain history: CIP <- 2000, W.R. Butler, CDC, Atlanta, USA: strain 941078

NCBI tax ID(s): 120959 (species)

SI-ID 44109

ATCC 700732, CIP 106428, DSM 44627, JCM 13573, CCUG 55639

Section

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

rod-shaped
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	*Mycobacteriales*
	Family	*Mycobacteriaceae*
	Genus	*Mycobacterium*
	Species	**Mycobacterium kubicae**
	Full Scientific Name (LPSN)	Mycobacterium kubicae Floyd et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #120508]	Cell shape	rod-shaped

[Ref.: #120508]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11939]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #11939]

Culture medium growth

[Ref.: #11939]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11939]

Culture medium composition

expand / minimize

[Ref.: #36256]

Culture medium

MEDIUM 55 - for Mycobacterium

[Ref.: #36256]

Culture medium growth

[Ref.: #120508]

Culture medium

CIP Medium 55

[Ref.: #120508]

Culture medium growth

[Ref.: #120508]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120508]

Culture medium

CIP Medium 96

[Ref.: #120508]

Culture medium growth

[Ref.: #120508]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #11939]	growth	37 °C
[Ref.: #36256]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #120508]	growth	37 °C

[Ref.: #11939]	Temperature range	mesophilic
[Ref.: #36256]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120508]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120508]	hippurate ChEBI	-	hydrolysis
[Ref.: #120508]	nitrate ChEBI	-	reduction
[Ref.: #120508]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120508]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[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.: #120508]	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.: #120508]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120508]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120508]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120508]	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.: #120508]	9491	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #11939]	Sample type/isolated from	human sputum
[Ref.: #11939]	Geographic location (country and/or sea, region)	South Carolina
[Ref.: #11939]	Country	USA
[Ref.: #11939]	Country ISO 3 Code	USA
[Ref.: #11939]	Continent	North America

[Ref.: #60684]	Sample type/isolated from	Human sputum

[Ref.: #67770]	Sample type/isolated from	Human sputum

[Ref.: #120508]	Sample type/isolated from	Sputum
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Fluids	#Sputum

What are isolation sources categories?

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

[Ref.: #11939]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #120508]	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.: #11939]	Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	HM022200	1792	ENA	120959 tax ID
[Ref.: #11939]	Mycobacterium kubicae 16S ribosomal RNA gene, partial sequence	AF133902	1321	ENA	120959 tax ID
[Ref.: #20218]	Mycobacterium kubicae 16S ribosomal RNA gene and internal transcribed spacer, partial sequence	DQ275612	266	ENA	120959 tax ID	*
[Ref.: #20218]	Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene, partial sequence	AF547941	542	ENA	120959 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium kubicae CIP 106428	GCA_002101745	contig	GenBank	120959 tax ID
[Ref.: #66792]	Mycobacterium kubicae JCM 13573	GCA_015689175	complete	GenBank	120959 tax ID	*
[Ref.: #66792]	Mycobacterium kubicae JCM 13573	GCA_010723135	contig	GenBank	120959 tax ID	*
[Ref.: #66792]	Mycobacterium kubicae strain CIP 106428	120959.3	wgs	PATRIC	120959 tax ID	*
[Ref.: #66792]	Mycobacterium kubicae strain JCM 13573	120959.24	complete	PATRIC	120959 tax ID	*
[Ref.: #66792]	Mycobacterium kubicae strain JCM 13573	120959.18	wgs	PATRIC	120959 tax ID	*

[Ref.: #67770]

GC-content

66 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mycobacterium kubicae JCM 13573 NCBI: GCA_015689175.1
[Ref.: #69480]	flagellated	no	98.953	no
[Ref.: #69480]	gram-positive	yes	90.627	no
[Ref.: #69480]	anaerobic	no	99.414	no
[Ref.: #69480]	aerobic	yes	92.909	no
[Ref.: #69480]	halophile	no	93.6	no
[Ref.: #69480]	spore-forming	no	78.281	no
[Ref.: #69480]	glucose-util	yes	65.522	no
[Ref.: #69480]	thermophile	no	99.089	no
[Ref.: #69480]	motile	no	95.118	no
[Ref.: #69480]	glucose-ferment	no	91.818	no

Availability in culture collections External links

[Ref.: #11939]

Culture collection no.

DSM 44627, ATCC 700732, CDC 941078, CIP 106428, CCUG 55639, JCM 13573

[Ref.: #77902]

SI-ID 44109

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#77902

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-ID44109.1 )

#120508 Collection of Institut Pasteur ; Curators of the CIP; CIP 106428
* These data were automatically processed and therefore are not curated

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Mycobacterium kubicae JCM 13573

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