Name: Mycobacterium mantenii 04-1474
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 8583

Type strain:

Species: Mycobacterium mantenii

Strain Designation: 04-1474, NLA000401474

Culture col. no.: DSM 45255, CIP 109863, JCM 18113

Strain history: CIP <- 2008, J. Van Inge, RIVM, Bilthoven, The Netherlands: strain NLA000401474 <- E. J. Kuijper, Leiden Univ., Leiden, The Netherlands

NCBI tax ID(s): 560555 (species)

SI-ID 364721

CIP 109863, DSM 45255, JCM 18113

Special Collections

Section

When using BacDive for research please cite our paper

Mycobacterium mantenii 04-1474 is a mesophilic, rod-shaped bacterium that was isolated from lymph node biopsy of a child.

rod-shaped
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 mantenii**
	Full Scientific Name (LPSN)	Mycobacterium mantenii van Ingen et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %94

[Ref.: #29294]	Cell shape	rod-shaped

[Ref.: #120782]	Motility	no

[Ref.: #29294]

Pigment production

yes

Multimedia content

[Ref.: #15933]

Caption:

Medium 645 37°C

[Ref.: #15933]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15933]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #15933]

Culture medium growth

[Ref.: #15933]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15933]

Culture medium composition

expand / minimize

[Ref.: #37864]

Culture medium

MEDIUM 55 - for Mycobacterium

[Ref.: #37864]

Culture medium growth

[Ref.: #120782]

Culture medium

CIP Medium 750

[Ref.: #120782]

Culture medium growth

[Ref.: #120782]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120782]

Culture medium

CIP Medium 55

[Ref.: #120782]

Culture medium growth

[Ref.: #120782]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15933]	growth	37 °C
[Ref.: #29294]	growth	25-45 °C
[Ref.: #29294]	optimum	36 °C
[Ref.: #37864]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %99.6

[Ref.: #29294]

Ability of spore formation

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120782]		nitrate ChEBI	-	reduction
[Ref.: #120782]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120782]		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.: #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.: #29294]	catalase	+	1.11.1.6
[Ref.: #120782]	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.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120782]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #29294]	urease	+	3.5.1.5
[Ref.: #120782]	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.: #120782]	12170	-	+	-	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #15933]	Sample type/isolated from	lymph node biopsy of a child
[Ref.: #15933]	Geographic location (country and/or sea, region)	Leiden
[Ref.: #15933]	Country	Netherlands
[Ref.: #15933]	Country ISO 3 Code	NLD
[Ref.: #15933]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Human, lymph node biopsy specimen
[Ref.: #67770]	Geographic location (country and/or sea, region)	Leiden
[Ref.: #67770]	Country	Netherlands
[Ref.: #67770]	Country ISO 3 Code	NLD
[Ref.: #67770]	Continent	Europe

[Ref.: #120782]	Sample type/isolated from	Human, Lymph node biopsy
[Ref.: #120782]	Geographic location (country and/or sea, region)	Leiden
[Ref.: #120782]	Country	Netherlands
[Ref.: #120782]	Country ISO 3 Code	NLD
[Ref.: #120782]	Continent	Europe
[Ref.: #120782]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Infection	#Patient	#Biopsy
#Infection	#Patient	-
#Host Body-Site	#Organ	#Lymph node
#Host	#Human	#Child

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ042897 (>99% sequence identity) for Mycobacterium from Microbeatlas

Aquatic Samples	300
Soil Samples	1602
Animal Samples	128
Plant Samples	202
Total Samples	2232

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

[Ref.: #15933]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #120782]	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.: #15933]	Mycobacterium mantenii strain NLA000401474 16S ribosomal RNA gene, partial sequence	FJ042897	1471	GenBank ENA	560555 tax ID
[Ref.: #67770]	Mycobacterium mantenii strain NLA000401474 16S-23S ribosomal RNA intergenic spacer, partial sequence	FJ232522	281	GenBank ENA	560555 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium mantenii DSM 45255	GCA_002086335	contig	GenBank ENA	560555 tax ID
[Ref.: #66792]	Mycobacterium mantenii JCM 18113	GCA_010731775	complete	GenBank ENA	560555 tax ID	*
[Ref.: #66792]	Mycobacterium mantenii strain DSM 45255	560555.3	wgs	PATRIC	560555 tax ID	*
[Ref.: #66792]	Mycobacterium mantenii strain JCM 18113	560555.10	complete	PATRIC	560555 tax ID	*
[Ref.: #66792]	Mycobacterium mantenii DSM 45255	GCA_025822645	scaffold	GenBank ENA	560555 tax ID	*

[Ref.: #67770]

GC-content

66.9 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 mantenii JCM 18113 NCBI: GCA_010731775.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	88.36	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.492	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	76.685	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	63.986	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.3	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium mantenii strain JCM 18113 PATRIC: 560555.10
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	65.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	77.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	94
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.6

Availability in culture collections External links

[Ref.: #15933]

Culture collection no.

DSM 45255, CIP 109863, JCM 18113

[Ref.: #77967]

SI-ID 364721

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species.	van Ingen J, Lindeboom JA, Hartwig NG, de Zwaan R, Tortoli E, Dekhuijzen PN, Boeree MJ, van Soolingen D	Int J Syst Evol Microbiol	10.1099/ijs.0.010405-0	2009	*

References

#15933

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45255

#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 )

#29294

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 #25710 (see below)

#37864 ; Curators of the CIP;

#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 .

#77967

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-ID364721.1 )

#120782 Collection of Institut Pasteur ; Curators of the CIP; CIP 109863

#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 .

#25710

IJSEM 2782 2009 ( DOI 10.1099/ijs.0.010405-0 , PubMed 19625425 )

* These data were automatically processed and therefore are not curated

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Mycobacterium mantenii JCM 18113

Mycobacterium mantenii strain JCM 18113

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