Mycobacterium kyorinense (DSM 45166, JCM 15038, KUM 060204)

Name: Mycobacterium kyorinense (DSM 45166, JCM 15038, KUM 060204)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8580

Type strain

Culture col. no. DSM 45166 JCM 15038 KUM 060204

NCBI tax ID(s) 487514

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- M. Okazaki; KUM 060204 JCM <-- M. Okazaki; Kyorin Univ. Sch. of Med., Japan; KUM060204.

Links

Mycobacterium kyorinense DSM 45166 is a rod-shaped bacterium that was isolated from sputum of a patient with pneumonia.

rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398395

JCM 15038,DSM 45166

@ref 20215

Last LPSN update 2026-05-29 08:26:54

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium kyorinense

Full scientific name Mycobacterium kyorinense Okazaki et al. 2009

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Confidence	Gram stain
28896	3 µm	0.3 µm	rod-shaped
125439				94.089
125439				97.175	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19918	grey white	10-14 days	ISP 3
19918		10-14 days	ISP 4
19918		10-14 days	ISP 5
19918		10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19918		ISP 3
19918		ISP 4
19918		ISP 5
19918		ISP 7

Pigmentation

28896

Productionno

Multimedia

@ref:	15638
multimedia content:	DSM_45166-1.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45166-1.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	15638
multimedia content:	DSM_45166-2.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45166-2.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	15638
multimedia content:	DSM_45166.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45166.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
15638	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
19918	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19918	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19918	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
19918	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:

Culture temp

@ref	Growth	Type	Temperature (°C)
15638	positive	growth	37
19918	positive	optimum	37
28896	positive	growth	28-42
28896	positive	optimum	35
67770	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.436

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19918	22599 ChEBI	arabinose	-
19918	62968 ChEBI	cellulose	-
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
19918	28757 ChEBI	fructose	-
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
19918	17234 ChEBI	glucose	-
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
19918	29864 ChEBI	mannitol	-
19918	17268 ChEBI	myo-inositol	-
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
19918	16634 ChEBI	raffinose	-
19918	26546 ChEBI	rhamnose	-
19918	17992 ChEBI	sucrose	-
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
19918	18222 ChEBI	xylose	-

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
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
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
28896	arylsulfatase	+	3.1.6.1
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
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
28896	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
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	-	3.4.11.1	from API zym
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
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
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
19918	-	-	-	-	-	-	-	-	-	-	-	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
19918	not determinedn.d.	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Inflammation	-
#Infection	#Patient	-
#Host Body-Site	#Oral cavity and airways	#Airways
#Host Body Product	#Fluids	#Sputum

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
15638	sputum of a patient with pneumonia	Homo sapiens	Kyorin Univ. Hospital, Mitaka City, Tokyo	Japan	JPN	Asia
67770	Sputum in a 62-year-old Japanese man with pneumonia at Kyorin Univ. Hosp.	Homo sapiens	Mitaka City, Tokyo	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15638	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM210173v1 assembly for Mycobacterium kyorinense DSM 45166	contig	GCA_002101735	487514.26	8111196881	487514	42.16
67770	ASM75969v1 assembly for Mycobacterium kyorinense KUM060204T	contig	GCA_000759695	487514.3	2630968205	487514	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Mycobacterium kyorinense strain DSM 45166 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	JQ582666	363		487514
15638	Mycobacterium kyorinense gene for 16S ribosomal RNA, partial sequence, strain: KUM 060204	AB370111	1470		487514

GC content

@ref	GC-content (mol%)	Method
67770	66.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM210173v1 assembly for Mycobacterium kyorinense DSM 45166
NCBI: GCA_002101735

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.44	no
125439	gram_stain	BacteriaNetⓘ	positive	97.18	no
125439	motility	BacteriaNetⓘ	no	94.09	no
125439	spore_formation	BacteriaNetⓘ	yes	60.39	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium kyorinense strain DSM 45166
PATRIC: 487514.26

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.00	no
125438	anaerobic	anaerobicⓘ	no	95.13	no
125438	spore-forming	spore-formingⓘ	no	65.12	no
125438	aerobic	aerobicⓘ	yes	74.67	no
125438	thermophilic	thermophileⓘ	no	94.25	no
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbiological features and clinical relevance of new species of the genus Mycobacterium.	Tortoli E.	Clin Microbiol Rev	10.1128/cmr.00035-14	2014
	Pleuritis Complicating Pulmonary Infection of Mycobacterium kyorinense: A Case Report.	Sakamoto S, Takeda M, Goshima S, Takita Y, Izumiya Y, Okuda Y, Sano M, Sato K, Nakayama K.	Intern Med	10.2169/internalmedicine.5845-25	2025
	Cavitary Pulmonary Disease Caused by Mycobacterium kyorinense: A Case Report on a 3-Year Clinical Course.	Yanagi M.	Respirol Case Rep	10.1002/rcr2.70142	2025
	Dust to Disease: Cavitary Lung Lesion With Mycobacterium kansasii in a Black Lung Patient.	Machineni NVK, Gullapalli D, Tangutoori S, Tipparthi A, Lahori S, Khater F, Ganti SS.	J Investig Med High Impact Case Rep	10.1177/23247096251348906	2025
	Pulmonary Mycobacterium kyorinense infection secondary to cavitary pulmonary tuberculosis.	Nagao G, Okuzumi S, Kakimoto T, Minematsu N.	IDCases	10.1016/j.idcr.2022.e01476	2022
Phylogeny	Pulmonary Mycobacterium kyorinense disease: A case report and review of literature.	Saranathan R, Padmapriyadarsini C, Sivaramakrishnan GN, Perumal BK, Kannayan S, Joseph B, Gopalan N, Hanna LE.	Indian J Med Microbiol	10.4103/ijmm.ijmm_19_94	2019
Enzymology	Profile of patients with pulmonary non-tuberculous mycobacterial disease mimicking pulmonary tuberculosis.	Gomathy NS, Padmapriyadarsini C, Silambuchelvi K, Nabila A, Tamizhselvan M, Banurekha VV, Lavanya J, Chandrasekar C.	Indian J Tuberc	10.1016/j.ijtb.2019.04.013	2019
	Proposal of reclassification of Mycobacterium celatum type 2 as Mycobacterium kyorinense	Ohnishi H, Tortoli E, Ramos JP, Kazumi Y, Yonetani S, Matsushima S, Ohtsuka K, Watanabe T.	Ann Microbiol	10.1007/s13213-014-0860-9	2014
	[Fatal nontuberculous mycobacterial lung disease caused by Mycobacterium kyorinense: a case report with five years of follow-up].	Sakakibara Y, Kishimoto K, Kojima K, Fujie T, Inase N.	Kekkaku		2014
	Pleuritis Caused by Mycobacterium kyorinense without Pulmonary Involvement.	Ikeue T, Yoshida H, Tanaka E, Ohi I, Noguchi S, Fukao A, Terashita S, Horikawa S, Sugita T.	Intern Med	10.2169/internalmedicine.8699-16	2017
	Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.	Greninger AL, Cunningham G, Chiu CY, Miller S.	Genome Announc	10.1128/genomea.00930-15	2015
	Moso bamboo (Phyllostachys edulis (Carrière) J. Houzeau) invasion affects soil microbial communities in adjacent planted forests in the Lijiang River basin, China.	Sun H, Hu W, Dai Y, Ai L, Wu M, Hu J, Zuo Z, Li M, Yang H, Ma J.	Front Microbiol	10.3389/fmicb.2023.1111498	2023
	Whole-Genome Sequence of Mycobacterium kyorinense.	Ohtsuka K, Ohnishi H, Nozaki E, Pais Ramos J, Tortoli E, Yonetani S, Matsushima S, Tateishi Y, Matsumoto S, Watanabe T.	Genome Announc	10.1128/genomea.01062-14	2014
	Pulmonary Mycobacterium kyorinense disease showed clinical improvement following combined therapy with clarithromycin and levofloxacin.	Kobashi Y, Mouri K, Obase Y, Kato S, Oka M.	Intern Med	10.2169/internalmedicine.51.6431	2012
	Pulmonary cavitary Mycobacterium kyorinense (M. kyorinense) infection in an Australian woman.	Muruganandan S, Jayaram L, Wong JS, Guy S.	IDCases	10.1016/j.idcr.2015.02.001	2015
Phylogeny	First isolation of Mycobacterium kyorinense from clinical specimens in Brazil.	Campos CE, Caldas PC, Ohnishi H, Watanabe T, Ohtsuka K, Matsushima S, Ferreira NV, da Silva MV, Redner P, de Carvalho LD, Medeiros RF, Abbud Filho JA, Montes FC, Galvao TC, Ramos JP.	J Clin Microbiol	10.1128/jcm.00023-12	2012
	Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity.	Ma Z, Caldas Nogueira ML, Marchi-Salvador DP, Davidson VL.	ACS Omega	10.1021/acsomega.0c03338	2020
	A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein.	Seo H, Kim S, Mahmud HA, Islam MI, Yoon Y, Cho HD, Nam KW, Choi J, Gil YS, Lee BE, Song HY.	PLoS Biol	10.1371/journal.pbio.3001648	2022
	Characterization of Mycolic Acids in Total Fatty Acid Methyl Ester Fractions from Mycobacterium Species by High Resolution MALDI-TOFMS.	Teramoto K, Suga M, Sato T, Wada T, Yamamoto A, Fujiwara N.	Mass Spectrom (Tokyo)	10.5702/massspectrometry.a0035	2015
	High Mortality of Disseminated Non-Tuberculous Mycobacterial Infection in HIV-Infected Patients in the Antiretroviral Therapy Era.	Kobayashi T, Nishijima T, Teruya K, Aoki T, Kikuchi Y, Oka S, Gatanaga H.	PLoS One	10.1371/journal.pone.0151682	2016
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Phylogeny	Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens.	Ramos JP, Campos CED, Caldas PCS, Ferreira NV, Boas da Silva MV, Redner P, Campelo CL, Vale SF, Barroso EC, Medeiros RFM, Montes FCOF, Galvao TC, Tortoli E.	Int J Syst Evol Microbiol	10.1099/ijs.0.046862-0	2013
Phylogeny	Mycobacterium kyorinense sp. nov., a novel, slow-growing species, related to Mycobacterium celatum, isolated from human clinical specimens.	Okazaki M, Ohkusu K, Hata H, Ohnishi H, Sugahara K, Kawamura C, Fujiwara N, Matsumoto S, Nishiuchi Y, Toyoda K, Saito H, Yonetani S, Fukugawa Y, Yamamoto M, Wada H, Sejimo A, Ebina A, Goto H, Ezaki T, Watanabe T	Int J Syst Evol Microbiol	10.1099/ijs.0.000760-0	2009

References

#15638	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45166
#19918	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 )
#25336	IJSEM 1336 2009 ( DOI 10.1099/ijs.0.000760-0 , PubMed 19502312 )
#28896	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25336
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 kyorinense (DSM 45166, JCM 15038, KUM 060204)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002101735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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