Mycobacterium pyrenivorans (DSM 44605, CIP 108596, NRRL B-24349)

Name: Mycobacterium pyrenivorans (DSM 44605, CIP 108596, NRRL B-24349)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8535

Type strain

Strain Designation 17A3, ID 705-01

Culture col. no. DSM 44605 CIP 108596 NRRL B-24349 17A3 ID 705-01 2 more

NCBI tax ID(s) 1305860 187102

Special Collections DSMZ JCM CIP

Links

Mycobacterium pyrenivorans 17A3 is an obligate aerobe, mesophilic, rod-shaped prokaryote that was isolated from soil.

rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 362273

DSM 44605,NRRL B-24349,CIP 108596,JCM 15927

@ref 20215

Last LPSN update 2025-12-16 09:48:51

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium pyrenivorans

Full scientific name Mycobacterium pyrenivorans Derz et al. 2004

Synonyms (1)

Mycolicibacterium pyrenivorans

Morphology

Cell morphology

@ref	Cell shape	Confidence	Gram stain
122087	rod-shaped
125438		94.5
125439		99	positive
125439		90

Multimedia

@ref:	11920
multimedia content:	DSM_44605.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44605.jpg
caption:	Medium 645 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11920	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
36343	MEDIUM 93 - for Mycobacterium avium subsp. sylvaticum		Distilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)
122087	CIP Medium 93	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11920	positive	growth	28	mesophilic
36343	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
122087	positive	growth	22-30
122087	negative	growth	10
122087	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
122087	obligate aerobe
125439	obligate aerobe	98.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122087	606565 ChEBI	hippurate	-	hydrolysis
122087	17632 ChEBI	nitrate	+	reduction
122087	17632 ChEBI	nitrate	-	respiration
122087	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
122087	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122087	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
122087	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
122087	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
122087	caseinase	-	3.4.21.50
122087	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
122087	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122087	gamma-glutamyltransferase	+	2.3.2.2
122087	gelatinase	-
122087	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122087	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122087	oxidase	-
122087	protease	+
68382	trypsin	-	3.4.21.4	from API zym
122087	tween esterase	+
122087	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
122087	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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
122087	not determinedn.d.	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11920	soil	Übach-Palenberg	Germany	DEU	Europe
67770	Contaminated soil of a former coking plant	Übach-Palenberg	Germany	DEU	Europe
122087	Environment, Soil		Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11920	1	Risk group (German classification) According to TRBA 466
122087	1	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	ASM2582162v1 assembly for Mycolicibacterium pyrenivorans DSM 44605	scaffold	GCA_025821625	187102.4	8047362685	187102	12.73
66792	ASM131410v1 assembly for Mycolicibacterium pyrenivorans JCM 15927	contig	GCA_001314105	1305860.4	2734481971	1305860

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Mycobacterium pyrenivorans strain DSM 44605 16S ribosomal RNA gene, partial sequence	DQ124113	536		187102
11920	Mycobacterium sp. DSM 44605 16S rRNA gene, strain DSM 44605	AJ431371	1481		187102

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycolicibacterium pyrenivorans DSM 44605
NCBI: GCA_025821625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	59.90	no
125439	motility	BacteriaNetⓘ	no	90.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium pyrenivorans JCM 15927
PATRIC: 1305860.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	79.61	no
125438	anaerobic	anaerobicⓘ	no	95.01	yes
125438	spore-forming	spore-formingⓘ	no	71.14	no
125438	aerobic	aerobicⓘ	yes	81.66	yes
125438	thermophilic	thermophileⓘ	no	96.74	yes
125438	flagellated	motile2+ⓘ	no	94.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.	Gupta RS, Lo B, Son J.	Front Microbiol	10.3389/fmicb.2018.00067	2018
	A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
Phylogeny	Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species.	Cheng Y, Lei W, Wang X, Tian Z, Liu H, Yang J, Lu S, Lai XH, Pu J, Huang Y, Zhang S, Yang C, Lian X, Bai Y, Wan K, Wang S, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.005019	2021
Phylogeny	Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species.	Derz K, Klinner U, Schuphan I, Stackebrandt E, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/ijs.0.03003-0	2004

References

#11920	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44605
#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 )
#36343	; 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 .
#122087	Collection of Institut Pasteur ; Curators of the CIP; CIP 108596
#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 )

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Mycobacterium pyrenivorans (DSM 44605, CIP 108596, NRRL B-24349)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025821625

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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