Name: Mycobacterium innocens MK13
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 166497

Type strain:

Species: Mycobacterium innocens

Strain Designation: MK13

Culture col. no.: CCUG 72126, DSM 107161

Strain history: <- F. Tagini, Lausanne University Hospital; MK13

NCBI tax ID(s): 2341083 (species)

SI-ID 408014

DSM 107161

Special Collections

Section

When using BacDive for research please cite our paper

Mycobacterium innocens MK13 is a mesophilic bacterium that was isolated from expectoration of a patient.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Mycobacteriaceae*
	Genus	*Mycobacterium*
	Species	**Mycobacterium innocens**
	Full Scientific Name (LPSN)	Mycobacterium innocens Tagini et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %94.4

[Ref.: #67931]	Colony color	beige
[Ref.: #67931]	Incubation period	14 days
[Ref.: #67931]	Cultivation medium used	7H10

[Ref.: #67931]	Pigment production	yes
[Ref.: #67931]	Pigment name	Photochrome

Information on culture and growth conditions Culture and growth conditions

[Ref.: #69048]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #69048]

Culture medium growth

[Ref.: #69048]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #67931]		optimum	37 °C
[Ref.: #67931]	negative	growth	25 °C
[Ref.: #67931]	negative	growth	45 °C
[Ref.: #69048]		growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %98.7

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67931]		potassium tellurite ChEBI	-	reduction
[Ref.: #67931]		tween 80 ChEBI	+	hydrolysis

	Enzyme	Enzyme activity	EC number
[Ref.: #67931]	arylsulfatase	-	3.1.6.1
[Ref.: #67931]	catalase	+	1.11.1.6
[Ref.: #67931]	nitrate reductase	+	1.7.99.4
[Ref.: #67931]	urease	+	3.5.1.5

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

[Ref.: #67931]	Sample type/isolated from	expectoration of a patient
[Ref.: #67931]	Geographic location (country and/or sea, region)	Lausanne University Hospital
[Ref.: #67931]	Country	Switzerland
[Ref.: #67931]	Country ISO 3 Code	CHE
[Ref.: #67931]	Continent	Europe

[Ref.: #69048]	Sample type/isolated from	Expectoration (Human)
[Ref.: #69048]	Geographic location (country and/or sea, region)	Lausanne
[Ref.: #69048]	Country	Switzerland
[Ref.: #69048]	Country ISO 3 Code	CHE
[Ref.: #69048]	Continent	Europe
[Ref.: #69048]	Geographic location	46.5200°/6.6336°
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence LS999933 (>99% sequence identity) for Mycobacterium from Microbeatlas

Aquatic Samples	382
Soil Samples	881
Animal Samples	203
Plant Samples	54
Total Samples	1520

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.: #67931]	Mycobacterium sp. MK13 partial 16S rRNA gene, strain MK13, isolate MK13, clone MK13=CCUG 72126=DSM 107161	LS999933	1527	GenBank ENA	2341083 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mycobacterium innocens MK13	GCA_900566055	contig	GenBank ENA	2341083 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium innocens MK13 NCBI: GCA_900566055.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	87.367	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.986	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	78.242	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	59.117	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.119	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium innocens MK13 NCBI: GCA_900566055
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	56.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	84.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	94.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.7

Availability in culture collections External links

[Ref.: #67931]

Culture collection no.

CCUG 72126, DSM 107161

[Ref.: #114802]

SI-ID 408014

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov.	Tagini F, Aeby S, Bertelli C, Droz S, Casanova C, Prod'hom G, Jaton K, Greub G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003378	2019	*

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 )

#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) .

#67931

Florian Tagini, Sébastien Aeby, Claire Bertelli, Sara Droz, Carlo Casanova, Guy Prod'hom, Katia Jaton, Gilbert Greub: Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov.. IJSEM 69: 1696 - 1704 2019 ( DOI 10.1099/ijsem.0.003378 )

#69048

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107161

#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 .

#114802

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-ID408014.1 )

#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 .

* These data were automatically processed and therefore are not curated

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