Name: Mycobacterium avium subsp. silvaticum 6409
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 8445

Type strain:

Species: Mycobacterium avium subsp. silvaticum

Strain Designation: 6409

Culture col. no.: DSM 44175, ATCC 49884, CCUG 47446, CIP 103317, KCTC 19633

Strain history: CIP <- 1989, M.F. Thorel, CNEVA, Maisons-Alfort, France: strain 6409

NCBI tax ID(s): 1401690 (strain), 44282 (subspecies)

SI-ID 42732

ATCC 49884, CIP 103317, DSM 44175, CCUG 47446

Special Collections

Section

When using BacDive for research please cite our paper

Mycobacterium avium subsp. silvaticum 6409 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from wood pigeon.

Gram-positive
rod-shaped
aerobe
human pathogen
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 avium subsp. silvaticum**
	Full Scientific Name (LPSN)	Mycobacterium avium subsp. silvaticum Thorel et al. 1990

Information on morphological and physiological properties Morphology

[Ref.: #116683]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %92.6

[Ref.: #116683]	Cell shape	rod-shaped

[Ref.: #116683]	Motility	no

[Ref.: #57693]

Incubation period

12-17 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11573]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #11573]

Culture medium growth

[Ref.: #11573]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11573]

Culture medium composition

expand / minimize

[Ref.: #116683]

Culture medium

CIP Medium 93

[Ref.: #116683]

Culture medium growth

[Ref.: #116683]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #11573]		growth	37 °C
[Ref.: #57693]		growth	37 °C
[Ref.: #116683]		growth	30-37 °C
[Ref.: #116683]	negative	growth	10 °C
[Ref.: #116683]	negative	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #57693]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116683]	citrate ChEBI	-	carbon source
[Ref.: #116683]	esculin ChEBI	-	hydrolysis
[Ref.: #116683]	hippurate ChEBI	-	hydrolysis
[Ref.: #116683]	nitrate ChEBI	-	reduction
[Ref.: #116683]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #116683]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #116683]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116683]	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.: #116683]	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.: #116683]	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.: #116683]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116683]	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.: #116683]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116683]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116683]	tryptophan deaminase	-
[Ref.: #116683]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #116683]	392	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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.: #116683]	7496	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #11573]	Sample type/isolated from	wood pigeon
[Ref.: #11573]	Geographic location (country and/or sea, region)	Maisons-Alfort
[Ref.: #11573]	Country	France
[Ref.: #11573]	Country ISO 3 Code	FRA
[Ref.: #11573]	Continent	Europe

[Ref.: #57693]	Sample type/isolated from	Wood pigeon liver and spleen,Columba palumbus
[Ref.: #57693]	Sampling date	1978
[Ref.: #57693]	Geographic location (country and/or sea, region)	Val d'Oise
[Ref.: #57693]	Country	France
[Ref.: #57693]	Country ISO 3 Code	FRA
[Ref.: #57693]	Continent	Europe

[Ref.: #116683]	Sample type/isolated from	Wood pigeon
[Ref.: #116683]	Geographic location (country and/or sea, region)	Maisons Alfort
[Ref.: #116683]	Country	France
[Ref.: #116683]	Country ISO 3 Code	FRA
[Ref.: #116683]	Continent	Europe
[Ref.: #116683]	Isolation date	1978
* marker position based on {}

Isolation sources categories

#Host

#Birds

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF521891 (>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.: #11573]	Pathogenicity (human)	yes
[Ref.: #11573]	Pathogenicity (animal)	yes
[Ref.: #11573]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #116683]	Biosafety level	2	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.: #20218]	Mycobacterium avium subsp. silvaticum strain ATCC 49884 16S ribosomal RNA gene, partial sequence	EF521891	1442	GenBank ENA	1401690 tax ID	*
[Ref.: #20218]	Mycobacterium avium subsp. silvaticum strain ATCC 49884 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	EF521899	438	GenBank ENA	1401690 tax ID	*
[Ref.: #20218]	Mycobacterium avium subsp. silvaticum strain CIP 103317 16S ribosomal RNA gene, partial sequence	AF547900	554	GenBank ENA	1401690 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mycobacterium avium subsp. silvaticum ATCC 49884	1401690.3	wgs	PATRIC	1401690 tax ID	*
[Ref.: #66792]	Mycobacterium avium silvaticum ATCC 49884	2568526319	draft	JGI IMG/M	1401690 tax ID	*
[Ref.: #66792]	Mycobacterium avium subsp. silvaticum ATCC 49884	GCA_000504975	contig	GenBank ENA	1401690 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 avium subsp. silvaticum ATCC 49884 PATRIC: 1401690.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	87.549	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.291	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	65.311	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	79.575	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	88	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium avium subsp. silvaticum ATCC 49884 NCBI: GCA_000504975
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	77.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	63.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	92.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.6

Availability in culture collections External links

[Ref.: #11573]

Culture collection no.

DSM 44175, ATCC 49884, CCUG 47446, CIP 103317, KCTC 19633

[Ref.: #77843]

SI-ID 42732

References

#11573

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44175

#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 )

#57693 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 47446

#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) .

#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 .

#77843

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-ID42732.1 )

#116683 Collection of Institut Pasteur ; Curators of the CIP; CIP 103317

#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 avium subsp. silvaticum ATCC 49884

Mycobacterium avium subsp. silvaticum ATCC 49884

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