Mycobacterium hiberniae (CCUG 39184, JCM 13571, DSM 44241)

Name: Mycobacterium hiberniae (CCUG 39184, JCM 13571, DSM 44241)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8470

Type strain

Strain Designation Hi 11, 14 403 0001

Culture col. no. CCUG 39184 JCM 13571 DSM 44241 ATCC 49874 CIP 104537 3 more

NCBI tax ID(s) 29314

Special Collections DSMZ CCUG JCM CIP Wink compendium KCTC

History DSMZ <- A.F. Yassin <- ATCC <- J. Kazda, IR 103 [Hi 11] JCM <-- CIP 104537 <-- DSM 44241 <-- A. F. Yassin <-- ATCC 49874 <-- J. Kazda Hi 11. CIP <- 2002, DSMZ <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 403 0001 <- ATCC <- J. Kadza, Borstel, Germany: strain Hi 11

Links

Mycobacterium hiberniae Hi 11 is a rod-shaped bacterium that was isolated from moss .

rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42729

ATCC 49874,CCUG 39184,DSM 44241,CIP 104537,JCM 13571,KCTC 19638

@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 hiberniae

Full scientific name Mycobacterium hiberniae Kazda et al. 1993

Synonyms (1)

Mycolicibacter hiberniae

Morphology

Cell morphology

@ref	Cell shape	Confidence	Gram stain
119888	rod-shaped
125438		93.5
125438		91.695	positive
125439		94.8	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19855	Ivory	10-14 days	5006
19855	Ivory	10-14 days	MB7H10
19855	Ivory	10-14 days	MB7H11

Multimedia

@ref:	11616
multimedia content:	DSM_44241.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44241.jpg
caption:	Medium 645 37°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11616	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
19855	MB7H10		Name: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
19855	MB7H11		Name: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
19855	5006		Medium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
36391	MEDIUM 55 - for Mycobacterium
119888	CIP Medium 55	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11616	positive	growth	37
19855	positive	optimum	37
36391	positive	growth	37
67770	positive	growth	37
119888	positive	growth	22-37
119888	negative	growth	10
119888	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.913

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68379	16899 ChEBI	D-mannitol	+	fermentation	from API Coryne
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68379	16988 ChEBI	D-ribose	+	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	+	fermentation	from API Coryne
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68379	28087 ChEBI	glycogen	+	fermentation	from API Coryne
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68379	17716 ChEBI	lactose	+	fermentation	from API Coryne
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
119888	17632 ChEBI	nitrate	+	reduction
119888	16301 ChEBI	nitrite	-	reduction
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
119888	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
119888	oxidase	-
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	+	3.5.1.5	from API Coryne
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
19855	+	+	+	+	-	+	-	-	-	+	-	not determinedn.d.	+	+	+	+	+	+	+	+	not determinedn.d.

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
19855	not determinedn.d.	+	+	+	-	-	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	-
119888	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	-	+	-	-	-
11616	-	-	+/-	+	-	-	-	-	-	-	+	+/-	-	-	-	+/-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
11616	+/-	-	-	-	-	+/-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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
119888	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Moss

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
11616	moss (Ctenidium molluscum)	Ctenidium molluscum	Ireland	IRL	Europe
54691	Moss (Ctenidium molluscum)		Ireland	IRL	Europe
67770	Moss (Ctenidium molluscum)	Ctenidium molluscum
119888	Environment, Soil		Ireland	IRL	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11616	1	Risk group (German classification) According to TRBA 466
19855	1	Risk group (German classification) According to TRBA 466
119888	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	ASM1072948v1 assembly for Mycolicibacter hiberniae JCM 13571	complete	GCA_010729485	29314.9	8066193970	29314	96.43
67770	ASM210165v1 assembly for Mycolicibacter hiberniae ATCC 49874	contig	GCA_002101655	29314.3	2865376297	29314	67.55
66792	ASM2582160v1 assembly for Mycolicibacter hiberniae DSM 44241	scaffold	GCA_025821605	29314.18	8113859237	29314	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium hiberniae strain ATCC 49874 16S ribosomal RNA gene, partial sequence	JN571173	479	29314
20218	M.hiberniae 16S rRNA	X67096	1419	29314
20218	Mycobacterium hiberniae 16S ribosomal RNA gene, partial sequence	AY438069	556	29314

GC content

@ref	GC-content (mol%)	Method
67770	68.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1072948v1 assembly for Mycolicibacter hiberniae JCM 13571
BV-BRC: 29314.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.91	no
125439	gram_stain	BacteriaNetⓘ	positive	94.80	no
125439	motility	BacteriaNetⓘ	no	88.55	no
125439	spore_formation	BacteriaNetⓘ	yes	36.97	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacter hiberniae JCM 13571
NCBI: GCA_010729485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.70	no
125438	anaerobic	anaerobicⓘ	no	94.58	no
125438	aerobic	aerobicⓘ	yes	83.40	no
125438	spore-forming	spore-formingⓘ	no	71.57	no
125438	thermophilic	thermophileⓘ	no	94.90	no
125438	flagellated	motile2+ⓘ	no	93.50	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
Enzymology	Evaluation of the invader assay with the BACTEC MGIT 960 system for prompt isolation and identification of mycobacterial species from clinical specimens.	Ichimura S, Nagano M, Ito N, Shimojima M, Egashira T, Miyamoto C, Ohkusu K, Ezaki T.	J Clin Microbiol	10.1128/jcm.02289-06	2007
Enzymology	New PCR systems to confirm real-time PCR detection of Mycobacterium avium subsp. paratuberculosis.	Herthnek D, Bolske G.	BMC Microbiol	10.1186/1471-2180-6-87	2006
Phylogeny	Mycobacterium hiberniae sp. nov.	Kazda J, Cooney R, Monaghan M, Quinn PJ, Stackebrandt E, Dorsch M, Daffe M, Muller K, Cook BR, Tarnok ZS	Int J Syst Bacteriol	10.1099/00207713-43-2-352	1993

References

#11616	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44241
#19855	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#36391	; Curators of the CIP;
#54691	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 39184
#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;
#68369	Automatically annotated from API 20NE .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#119888	Collection of Institut Pasteur ; Curators of the CIP; CIP 104537
#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 hiberniae (CCUG 39184, JCM 13571, DSM 44241)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010729485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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