Name: Mycobacterium colombiense 10B
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 8550

Type strain:

Species: Mycobacterium colombiense

Strain Designation: 10B, B10

Culture col. no.: DSM 45105, CECT 3035, CIP 108962, CCUG 55633, JCM 16228

Strain history: CIP <- 2005, M.J. Garcia, Madrid Univ., Madrid, Spain: strain B10

NCBI tax ID(s): 1041522 (strain), 339268 (species)

SI-ID 297257

CECT 3035, CIP 108962, DSM 45105, JCM 16228, CCUG 55633

Special Collections

Section

When using BacDive for research please cite our paper

Mycobacterium colombiense 10B is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from blood of an HIV positive patient.

rod-shaped
mesophilic
obligate aerobe
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 colombiense**
	Full Scientific Name (LPSN)	Mycobacterium colombiense Murcia et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %91.9

[Ref.: #118706]	Cell shape	rod-shaped

[Ref.: #118706]	Motility	no

Multimedia content

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Caption:

Medium 645 37°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

MEDIUM 55 - for Mycobacterium

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Culture medium growth

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Culture medium

CIP Medium 55

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #12347]	growth	37 °C
[Ref.: #42061]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #118706]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.5

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118706]		nitrate ChEBI	+	reduction
[Ref.: #118706]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118706]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118706]	alcohol dehydrogenase	-	1.1.1.1
[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.: #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.: #118706]	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.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118706]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118706]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118706]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118706]	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.: #118706]	11579	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #12347]	Sample type/isolated from	blood of an HIV positive patient
[Ref.: #12347]	Country	Colombia
[Ref.: #12347]	Country ISO 3 Code	COL
[Ref.: #12347]	Continent	Middle and South America

[Ref.: #60679]	Sample type/isolated from	Human blood,AIDS patient
[Ref.: #60679]	Sampling date	1995
[Ref.: #60679]	Geographic location (country and/or sea, region)	Bogota
[Ref.: #60679]	Country	Colombia
[Ref.: #60679]	Country ISO 3 Code	COL
[Ref.: #60679]	Continent	Middle and South America

[Ref.: #67770]	Sample type/isolated from	Blood of an HIV-positive patient
[Ref.: #67770]	Country	Colombia
[Ref.: #67770]	Country ISO 3 Code	COL
[Ref.: #67770]	Continent	Middle and South America

[Ref.: #118706]	Sample type/isolated from	Blood culture
[Ref.: #118706]	Geographic location (country and/or sea, region)	Bogota
[Ref.: #118706]	Country	Colombia
[Ref.: #118706]	Country ISO 3 Code	COL
[Ref.: #118706]	Continent	Middle and South America
[Ref.: #118706]	Isolation date	1995
* marker position based on {}

Isolation sources categories

#Infection	#Patient	-
#Host Body Product	#Fluids	#Blood

What are isolation sources categories?

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Global distribution of 16S sequence GQ153275 (>99% sequence identity) for Mycobacterium from Microbeatlas

Aquatic Samples	4789
Soil Samples	12779
Animal Samples	3677
Plant Samples	2833
Total Samples	24078

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

[Ref.: #12347]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #118706]	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.: #12347]	Mycobacterium colombiense partial 16S rRNA gene and ITS1, type strain:10B	AM062764	1807	GenBank ENA	1041522 tax ID
[Ref.: #20218]	Mycobacterium colombiense strain CIP108962 16S ribosomal RNA gene, partial sequence	GQ153275	1495	GenBank ENA	1041522 tax ID	*
[Ref.: #124043]	Mycobacterium colombiense CECT 3035 16S ribosomal RNA gene, partial sequence.	OK539011	833	GenBank ENA	1041522 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium colombiense CECT 3035	GCA_000222105	contig	GenBank ENA	1041522 tax ID
[Ref.: #66792]	Mycobacterium colombiense CECT 3035	GCA_002105755	complete	GenBank ENA	1041522 tax ID	*
[Ref.: #66792]	Mycobacterium colombiense CECT 3035	1041522.3	wgs	PATRIC	1041522 tax ID	*
[Ref.: #66792]	Mycobacterium colombiense CECT 3035 strain CECT 3035	1041522.28	complete	PATRIC	1041522 tax ID	*
[Ref.: #66792]	Mycobacterium colombiense CECT 3035	2562617111	draft	JGI IMG/M	1041522 tax ID	*

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GC-content

68.1 mol%

genome sequence analysis

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 colombiense CECT 3035 CECT 3035 NCBI: GCA_002105755.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	88.304	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.066	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	79.163	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	64.118	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium colombiense CECT 3035 NCBI: GCA_002105755
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	91.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	68.3
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	76.9

Availability in culture collections External links

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Culture collection no.

DSM 45105, CECT 3035, CIP 108962, CCUG 55633, JCM 16228

[Ref.: #77934]

SI-ID 297257

Literature:

	Title	Authors	Journal	DOI	Year
Biotechnology	Sliding Motility, Biofilm Formation, and Glycopeptidolipid Production in Mycobacterium colombiense Strains.	Maya-Hoyos M, Leguizamon J, Marino-Ramirez L, Soto CY	Biomed Res Int	10.1155/2015/419549	2015	*
Pathogenicity	Identification of potential biomarkers to distinguish Mycobacterium colombiense from other mycobacterial species.	Leguizamon J, Hernandez J, Murcia MI, Soto CY	Mol Cell Probes	10.1016/j.mcp.2012.08.009	2012	*
Genetics	Genome sequence of the Mycobacterium colombiense type strain, CECT 3035.	Gonzalez-Perez M, Murcia MI, Landsman D, Jordan IK, Marino-Ramirez L	J Bacteriol	10.1128/JB.05928-11	2011	*
Phylogeny	Mycobacterium colombiense sp. nov., a novel member of the Mycobacterium avium complex and description of MAC-X as a new ITS genetic variant.	Murcia MI, Tortoli E, Menendez MC, Palenque E, Garcia MJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64190-0	2006	*
	In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035.	Hamde F, Dinka H, Naimuddin M	J Genet Eng Biotechnol	10.1186/s43141-022-00331-6	2022	*

References

#12347

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45105

#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 )

#42061 ; Curators of the CIP;
#60679 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55633

#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 .

#77934

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-ID297257.1 )

#118706 Collection of Institut Pasteur ; Curators of the CIP; CIP 108962

#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 .

* These data were automatically processed and therefore are not curated

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Mycobacterium colombiense CECT 3035

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