Name: Mycobacterium noviomagense NLA000500338
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8578

Type strain:

Species: Mycobacterium noviomagense

Strain Designation: NLA000500338

Culture col. no.: DSM 45145, CIP 109766, JCM 16367

Strain history: CIP <- 2007, J. van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000500338 <- Laurentius Hosp., Roermond, The Netherlands

NCBI tax ID(s): 459858 (species)

SI-ID 362318

CIP 109766, DSM 45145, JCM 16367

Section

Mycobacterium noviomagense NLA000500338 is a mesophilic, Gram-positive, rod-shaped human pathogen that was isolated from sputum.

Gram-positive
rod-shaped
human pathogen
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 noviomagense**
	Full Scientific Name (LPSN)	Mycobacterium noviomagense van Ingen et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28917]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #28917]	Cell shape	rod-shaped

[Ref.: #121365]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.022

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15422]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #15422]

Culture medium growth

[Ref.: #15422]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15422]

Culture medium composition

expand / minimize

[Ref.: #36086]

Culture medium

MEDIUM 55 - for Mycobacterium

[Ref.: #36086]

Culture medium growth

[Ref.: #121365]

Culture medium

CIP Medium 55

[Ref.: #121365]

Culture medium growth

[Ref.: #121365]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15422]	growth	37 °C
[Ref.: #36086]	growth	30 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #15422]	Temperature range	mesophilic
[Ref.: #36086]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.81

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121365]		nitrate ChEBI	-	reduction
[Ref.: #121365]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #121365]		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.: #121365]	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.: #121365]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121365]	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.: #121365]	12097	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #15422]	Sample type/isolated from	sputum
[Ref.: #15422]	Geographic location (country and/or sea, region)	Weert
[Ref.: #15422]	Country	Netherlands
[Ref.: #15422]	Country ISO 3 Code	NLD
[Ref.: #15422]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Sputum
[Ref.: #67770]	Country	Netherlands
[Ref.: #67770]	Country ISO 3 Code	NLD
[Ref.: #67770]	Continent	Europe

[Ref.: #121365]	Sample type/isolated from	Human, Sputum
[Ref.: #121365]	Geographic location (country and/or sea, region)	Weert, Limburg
[Ref.: #121365]	Country	Netherlands
[Ref.: #121365]	Country ISO 3 Code	NLD
[Ref.: #121365]	Continent	Europe
[Ref.: #121365]	Isolation date	2005
* marker position based on {}

Isolation sources categories

#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.: #15422]	Pathogenicity (human)	yes, in single cases
[Ref.: #15422]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121365]	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.: #15422]	Mycobacterium noviomagense strain NLA000500338 16S ribosomal RNA gene, partial sequence	EU239955	1478	ENA	459858 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 noviomagense DSM 45145	GCA_002086415	contig	GenBank	459858 tax ID
[Ref.: #66792]	Mycobacterium noviomagense JCM 16367	GCA_010731635	complete	GenBank	459858 tax ID	*
[Ref.: #66792]	Mycobacterium noviomagense strain DSM 45145	459858.3	wgs	PATRIC	459858 tax ID	*
[Ref.: #66792]	Mycobacterium noviomagense strain JCM 16367	459858.9	complete	PATRIC	459858 tax ID	*
[Ref.: #66792]	Mycobacterium noviomagense DSM 45145	2865568667	draft	JGI IMG/M	459858 tax ID	*
[Ref.: #66792]	Mycobacterium noviomagense DSM 45145	GCA_025821305	contig	GenBank	459858 tax ID	*

[Ref.: #67770]

GC-content

65.8 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Mycobacterium noviomagense JCM 16367 NCBI: GCA_010731635.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mycobacterium noviomagense JCM 16367 NCBI: GCA_010731635.1
[Ref.: #69480]	motile	no	95.637	no
[Ref.: #69480]	flagellated	no	98.965	no
[Ref.: #69480]	gram-positive	yes	89.641	no
[Ref.: #69480]	anaerobic	no	99.029	no
[Ref.: #69480]	aerobic	yes	86.995	no
[Ref.: #69480]	halophile	no	94.795	no
[Ref.: #69480]	spore-forming	no	80.063	no
[Ref.: #69480]	glucose-util	yes	63.922	no
[Ref.: #69480]	thermophile	no	95.479	yes
[Ref.: #69480]	glucose-ferment	no	91.795	no

Availability in culture collections External links

[Ref.: #15422]

Culture collection no.

DSM 45145, CIP 109766, JCM 16367

[Ref.: #77962]

SI-ID 362318

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mycobacterium noviomagense sp. nov.; clinical relevance evaluated in 17 patients.	van Ingen J, Boeree MJ, de Lange WC, de Haas PE, van der Zanden AG, Mijs W, Rigouts L, Dekhuijzen PN, van Soolingen D	Int J Syst Evol Microbiol	10.1099/ijs.0.001511-0	2009	*

References

#15422

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45145

#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 )

#28917

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 #25356 (see below)

#36086 ; 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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#77962

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-ID362318.1 )

#121365 Collection of Institut Pasteur ; Curators of the CIP; CIP 109766

#25356

IJSEM 845 2009 ( DOI 10.1099/ijs.0.001511-0 , PubMed 19329618 )

* These data were automatically processed and therefore are not curated

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Mycobacterium noviomagense JCM 16367

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