Name: Mycobacterium scrofulaceum 12238
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8369

Type strain:

Species: Mycobacterium scrofulaceum

Strain Designation: 12238, 1356 TMC/1323, 14 022 0001, L2238, 1356

Culture col. no.: DSM 43992, ATCC 19981, JCM 6381, NCTC 10803, TMC 1323, CCUG 29045, CIP 105416, KCTC 9519, RIMD 1331002

Strain history: CIP <- 1998, V. Vincent, Inst. Pasteur, Paris, France: strain 14 022 0001 <- ATCC <- P. Hauduroy: strain L2238 <- F. Prissick: strain 1356

NCBI tax ID(s): 1783 (species)

SI-ID 46570

ATCC 19981, NCTC 10803, CIP 105416, DSM 43992, JCM 6381, KCTC 9519, CCUG 29045, CNCTC 7291

Other strains from Mycobacterium scrofulaceum

M. scrofulaceum DSM 43226, SN 802
M. scrofulaceum DSM 43512, SN 801
M. scrofulaceum DSM 43513, SN 803
M. scrofulaceum CCUG 28003
M. scrofulaceum CCUG 28164
M. scrofulaceum CCUG 29020, ATCC 23413
M. scrofulaceum CCUG 29021, ATCC 23414
M. scrofulaceum CCUG 29036, ATCC 23429
M. scrofulaceum CCUG 29053, ATCC 15081
M. scrofulaceum CCUG 29055, ATCC 15978
M. scrofulaceum 140220091, Cardiff 2729, CRBIP7.163, ...

Section

Mycobacterium scrofulaceum 12238 is an obligate aerobe, mesophilic human pathogen that was isolated from cervical lymph node .

human pathogen
mesophilic
obligate aerobe
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 scrofulaceum**
	Full Scientific Name (LPSN)	Mycobacterium scrofulaceum Prissick and Masson 1956 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

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

[Ref.: #122529]	Cell shape	rod-shaped

[Ref.: #122529]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.857

Multimedia content

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Intellectual property rights:

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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

LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)

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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

[Ref.: #36316]

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

	Kind of temperature		Temperature
[Ref.: #11442]		growth	37 °C
[Ref.: #36316]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #122529]		growth	22-37 °C
[Ref.: #122529]	no	growth	10 °C
[Ref.: #122529]	no	growth	45 °C

[Ref.: #11442]	Temperature range	mesophilic
[Ref.: #36316]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #122529]	Temperature range	psychrophilic
[Ref.: #122529]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122529]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %93
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.694

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122529]	hippurate ChEBI	-	hydrolysis
[Ref.: #122529]	nitrate ChEBI	+	reduction
[Ref.: #122529]	nitrate ChEBI	-	respiration
[Ref.: #122529]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #122529]		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.: #122529]	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.: #122529]	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.: #122529]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122529]	gelatinase	-
[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.: #122529]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122529]	tryptophan deaminase	-
[Ref.: #122529]	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.: #122529]	8680	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #11442]	Sample type/isolated from	cervical lymph node (lymphadentitis of a child)

[Ref.: #49492]	Sample type/isolated from	Human cervical lymph node

[Ref.: #67770]	Sample type/isolated from	Lymphadenitis of a 3-year-old child
[Ref.: #67770]	Geographic location (country and/or sea, region)	Montreal
[Ref.: #67770]	Country	Canada
[Ref.: #67770]	Country ISO 3 Code	CAN
[Ref.: #67770]	Continent	North America

[Ref.: #122529]	Sample type/isolated from	Cervical lymph node
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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Global distribution of 16S sequence GQ153271 (>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.: #11442]	Pathogenicity (human)	yes
[Ref.: #11442]	Pathogenicity (animal)	yes
[Ref.: #11442]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #122529]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

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

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Mycobacterium scrofulaceum strain ATCC19981 16S ribosomal RNA (rrs) gene, partial sequence	AF059847	173	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum 16S ribosomal RNA gene, partial sequence	AF480604	1466	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum strain ATCC 19981 16S ribosomal RNA gene, partial sequence	GQ153271	1492	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum 16S ribosomal RNA and 23S ribosomal RNA gene fragments	L15622	396	ENA	1783 tax ID	*
[Ref.: #20218]	M.scrofulaceum 16S ribosomal RNA gene	M59268	145	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum 16S rRNA gene	X52924	1493	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum strain CIP 105416 16S ribosomal RNA gene, partial sequence	AF547962	551	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum 16S rRNA gene	AJ536034	1467	ENA	1783 tax ID	*
[Ref.: #20218]	Mycobacterium scrofulaceum DNA for 16S rRNA, internal transcribed spacer, 23S rRNA	AB026702	439	ENA	1783 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium scrofulaceum DSM 43992	GCA_002086735	contig	GenBank	1783 tax ID
[Ref.: #66792]	Mycobacterium scrofulaceum strain DSM 43992	1783.5	wgs	PATRIC	1783 tax ID	*
[Ref.: #66792]	Mycobacterium scrofulaceum DSM 43992	2865591264	draft	JGI IMG/M	1783 tax ID	*
[Ref.: #66792]	Mycobacterium scrofulaceum DSM 43992	GCA_025821325	scaffold	GenBank	1783 tax ID	*

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GC-content

68.4 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 scrofulaceum strain DSM 43992 PATRIC: 1783.3
[Ref.: #69481]	spore-forming	no	93	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mycobacterium scrofulaceum strain DSM 43992 PATRIC: 1783.5
[Ref.: #69480]	motile	no	93.858	no
[Ref.: #69480]	gram-positive	yes	89.957	no
[Ref.: #69480]	anaerobic	no	98.881	no
[Ref.: #69480]	aerobic	yes	88.279	no
[Ref.: #69480]	halophile	no	93.306	no
[Ref.: #69480]	spore-forming	no	85.12	no
[Ref.: #69480]	thermophile	no	97.913	no
[Ref.: #69480]	glucose-util	yes	66.598	no
[Ref.: #69480]	flagellated	no	98.679	no
[Ref.: #69480]	glucose-ferment	no	91.103	no

Availability in culture collections External links

[Ref.: #11442]

Culture collection no.

DSM 43992, ATCC 19981, JCM 6381, NCTC 10803, TMC 1323, CCUG 29045, CIP 105416, KCTC 9519, RIMD 1331002

[Ref.: #77768]

SI-ID 46570

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

#11442

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43992

#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 )

#36316 ; Curators of the CIP;
#49492 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 29045

#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 .

#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 )

#77768

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-ID46570.1 )

#122529 Collection of Institut Pasteur ; Curators of the CIP; CIP 105416
* These data were automatically processed and therefore are not curated

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Mycobacterium scrofulaceum strain DSM 43992

Mycobacterium scrofulaceum strain DSM 43992

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