Mycobacterium avium subsp. silvaticum (DSM 44175, ATCC 49884, CCUG 47446)

Name: Mycobacterium avium subsp. silvaticum (DSM 44175, ATCC 49884, CCUG 47446)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8445

Type strain

Strain Designation 6409

Culture col. no. DSM 44175 ATCC 49884 CCUG 47446 CIP 103317 6409 1 more

NCBI tax ID(s) 1401690 44282

Special Collections DSMZ CCUG CIP KCTC

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

Links

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

Gram-positive rod-shaped aerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42732

ATCC 49884,CIP 103317,DSM 44175,CCUG 47446

@ref 20215

Last LPSN update 2026-05-29 08:26:52

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium avium subsp. silvaticum

Full scientific name Mycobacterium avium subsp. silvaticum Thorel et al. 1990

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
116683	positive	rod-shaped

Colony morphology

57693

Incubation period12-17 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
11573	MIDDLEBROOK MEDIUM (DSMZ Medium 645)		Medium recipe at MediaDive	Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
116683	CIP Medium 93		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11573	positive	growth	37
57693	positive	growth	37
116683	positive	growth	30-37
116683	negative	growth	10
116683	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
57693	aerobe
125439	obligate aerobe	99.557

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116683	16947 ChEBI	citrate	-	carbon source
116683	4853 ChEBI	esculin	-	hydrolysis
116683	606565 ChEBI	hippurate	-	hydrolysis
116683	17632 ChEBI	nitrate	-	reduction
116683	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116683	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
116683	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116683	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
116683	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116683	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116683	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116683	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116683	ornithine decarboxylase	-	4.1.1.17
116683	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
116683	tryptophan deaminase	-
116683	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116683	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	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
116683	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Birds

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
11573	wood pigeon		Maisons-Alfort	France	FRA	Europe
57693	Wood pigeon liver and spleen,Columba palumbus	1978	Val d'Oise	France	FRA	Europe
116683	Wood pigeon		Maisons Alfort	France	FRA	Europe	1978

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
11573			2	Risk group (German classification) According to TRBA 466
116683			2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	MAS 49884 version 1 assembly for Mycobacterium avium subsp. silvaticum ATCC 49884	contig	GCA_000504975	1401690.3	2568526319	1401690	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium avium subsp. silvaticum strain ATCC 49884 16S ribosomal RNA gene, partial sequence	EF521891	1442	1401690
20218	Mycobacterium avium subsp. silvaticum strain ATCC 49884 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	EF521899	438	1401690
20218	Mycobacterium avium subsp. silvaticum strain CIP 103317 16S ribosomal RNA gene, partial sequence	AF547900	554	1401690

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: MAS 49884 version 1 assembly for Mycobacterium avium subsp. silvaticum ATCC 49884
BV-BRC: 1401690.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.56	no
125439	gram_stain	BacteriaNetⓘ	positive	82.87	no
125439	motility	BacteriaNetⓘ	no	72.21	no
125439	spore_formation	BacteriaNetⓘ	no	89.00	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.55	no
125438	anaerobic	anaerobicⓘ	no	96.29	yes
125438	spore-forming	spore-formingⓘ	no	65.31	no
125438	aerobic	aerobicⓘ	yes	79.58	yes
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A novel real-time PCR assay for specific detection and quantification of Mycobacterium avium subsp. paratuberculosis in milk with the inherent possibility of differentiation between viable and dead cells.	Dzieciol M, Volgger P, Khol J, Baumgartner W, Wagner M, Hein I.	BMC Res Notes	10.1186/1756-0500-3-251	2010
Enzymology	Highly specific and quick detection of Mycobacterium avium subsp. paratuberculosis in feces and gut tissue of cattle and humans by multiple real-time PCR assays.	Imirzalioglu C, Dahmen H, Hain T, Billion A, Kuenne C, Chakraborty T, Domann E.	J Clin Microbiol	10.1128/jcm.01492-10	2011
Genetics	First whole-genome sequence of Mycobacterium avium subsp. silvaticum isolated from a diseased Egyptian goose (Alopochen aegyptiaca)	Barth S, Peters M, Mormann S, Mobius P, Calvelage S, Brangsch H.	BMC Genomics		2025
Proteome	Detection and accurate identification of Mycobacterium species by flow injection tandem mass spectrometry (FIA-MS/MS) analysis of mycolic acids.	Rafal S, Magdalena D, Karol M, Bartlomiej S, Konrad K.	Sci Rep	10.1038/s41598-025-96867-x	2025
	Molecular Characterization of Mycobacterium avium subsp. hominissuis of Two Groups of Lymph Nodes, Being Intradermal Tuberculin or Interferon-Gamma Test Positive and Negative, Isolated from Swiss Cattle at Slaughter.	Scherrer S, Landolt P, Carroli N, Stephan R.	Front Vet Sci	10.3389/fvets.2018.00032	2018
	The Homologous Gene of Chromosomal Virulence D (chvD) Presents High Resolution as a Novel Biomarker in Mycobacterium Species Identification.	Yu X, He Y, Gu Y, Zhang T, Huo F, Liang Q, Wu J, Hu Y, Wang X, Tang W, Huang H, Liu G.	Infect Drug Resist	10.2147/idr.s422191	2023
	The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium.	Yano H, Suzuki H, Maruyama F, Iwamoto T.	BMC Genomics	10.1186/s12864-019-6078-2	2019
Phylogeny	Molecular identification of Mycobacterium avium subsp. silvaticum by duplex high-resolution melt analysis and subspecies-specific real-time PCR.	Ronai Z, Csivincsik A, Csivincsik A, Dan A.	J Clin Microbiol	10.1128/jcm.03556-14	2015
Genetics	Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences.	Bannantine JP, Conde C, Bayles DO, Branger M, Biet F.	Front Microbiol	10.3389/fmicb.2020.01701	2020
Enzymology	Characterization and Differentiation of Mycobacterium avium subsp. paratuberculosis from Other Mycobacteria Using Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.	Ravva SV, Harden LA, Sarreal CZ.	Front Cell Infect Microbiol	10.3389/fcimb.2017.00297	2017
Enzymology	Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing.	Higgins J, Camp P, Farrell D, Bravo D, Pate M, Robbe-Austerman S.	BMC Vet Res	10.1186/1746-6148-7-77	2011
Pathogenicity	Association of ISMav6 with the Pattern of Antibiotic Resistance in Korean Mycobacterium avium Clinical Isolates but No Relevance between Their Genotypes and Clinical Features.	Kim SY, Jeong BH, Park HY, Jeon K, Han SJ, Shin SJ, Koh WJ.	PLoS One	10.1371/journal.pone.0148917	2016
Phylogeny	Rapid identification and differentiation of Mycobacterium avium subspecies paratuberculosis types by use of real-time PCR and high-resolution melt analysis of the MAP1506 locus.	Castellanos E, Aranaz A, De Buck J.	J Clin Microbiol	10.1128/jcm.02484-09	2010
	Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4.	Dedrick RM, Guerrero Bustamante CA, Garlena RA, Pinches RS, Cornely K, Hatfull GF.	Tuberculosis (Edinb)	10.1016/j.tube.2019.01.002	2019
Phylogeny	Comparison of a variable-number tandem-repeat (VNTR) method for typing Mycobacterium avium with mycobacterial interspersed repetitive-unit-VNTR and IS1245 restriction fragment length polymorphism typing.	Inagaki T, Nishimori K, Yagi T, Ichikawa K, Moriyama M, Nakagawa T, Shibayama T, Uchiya K, Nikai T, Ogawa K.	J Clin Microbiol	10.1128/jcm.02373-08	2009
Phylogeny	Efficient differentiation of Mycobacterium avium complex species and subspecies by use of five-target multiplex PCR.	Shin SJ, Lee BS, Koh WJ, Manning EJ, Anklam K, Sreevatsan S, Lambrecht RS, Collins MT.	J Clin Microbiol	10.1128/jcm.00904-10	2010
Enzymology	Development and evaluation of a novel multicopy-element-targeting triplex PCR for detection of Mycobacterium avium subsp. paratuberculosis in feces.	Sevilla IA, Garrido JM, Molina E, Geijo MV, Elguezabal N, Vazquez P, Juste RA.	Appl Environ Microbiol	10.1128/aem.01026-14	2014
	Monoclonal Antibodies Bind A SNP-Sensitive Epitope that is Present Uniquely in Mycobacterium avium Subspecies Paratuberculosis.	Bannantine JP, Stabel JR, Lamont EA, Briggs RE, Sreevatsan S.	Front Microbiol	10.3389/fmicb.2011.00163	2011
	Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms.	Semret M, Turenne CY, de Haas P, Collins DM, Behr MA.	J Clin Microbiol	10.1128/jcm.44.3.881-887.2006	2006
Enzymology	Rapid mycobacterial liquid culture-screening method for Mycobacterium avium complex based on secreted antigen-capture enzyme-linked immunosorbent assay.	Shin SJ, Anklam K, Manning EJ, Collins MT.	Clin Vaccine Immunol	10.1128/cvi.00461-08	2009
Genetics	Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates.	Paustian ML, Kapur V, Bannantine JP.	J Bacteriol	10.1128/jb.187.7.2406-2415.2005	2005
	Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.	Paustian ML, Zhu X, Sreevatsan S, Robbe-Austerman S, Kapur V, Bannantine JP.	BMC Genomics	10.1186/1471-2164-9-135	2008
	Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification.	Zimenkov DV, Kulagina EV, Antonova OV, Krasnova MA, Chernyaeva EN, Zhuravlev VY, Kuz'min AV, Popov SA, Zasedatelev AS, Gryadunov DA.	J Clin Microbiol	10.1128/jcm.02579-14	2015
Phylogeny	Identification of mycobacteria by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry.	Pignone M, Greth KM, Cooper J, Emerson D, Tang J.	J Clin Microbiol	10.1128/jcm.01959-05	2006
Phylogeny	Sequencing of hsp65 distinguishes among subsets of the Mycobacterium avium complex.	Turenne CY, Semret M, Cousins DV, Collins DM, Behr MA.	J Clin Microbiol	10.1128/jcm.44.2.433-440.2006	2006
Phylogeny	Mycobacterium avium in the postgenomic era.	Turenne CY, Wallace R, Behr MA.	Clin Microbiol Rev	10.1128/cmr.00036-06	2007

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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Mycobacterium avium subsp. silvaticum (DSM 44175, ATCC 49884, CCUG 47446)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000504975

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media