Mycobacterium shinjukuense (DSM 45663, CCUG 53584, JCM 14233)

Cell morphology

Colony morphology

Multimedia

• @ref:	18021
  multimedia content:	DSM_45663.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45663.jpg
  caption:	Medium 645 37°C
  intellectual property rights:	© Leibniz-Institut DSMZ
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
18021	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

Culture temp

Oxygen tolerance

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	phenylmercury acetate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	aerobactin biosynthesis	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	IAA biosynthesis	100	3 of 3
66794	taurine degradation	100	1 of 1
66794	cyanate degradation	100	3 of 3
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	citric acid cycle	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	lactate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of sugar alcohols	68.75	11 of 16
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	enterobactin biosynthesis	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	pyrimidine metabolism	64.44	29 of 45
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	glycine betaine biosynthesis	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	arachidonate biosynthesis	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	oxidative phosphorylation	54.95	50 of 91
66794	cholesterol biosynthesis	54.55	6 of 11
66794	sphingosine metabolism	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	arginine metabolism	50	12 of 24
66794	Entner Doudoroff pathway	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	degradation of pentoses	50	14 of 28
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	vitamin B12 metabolism	35.29	12 of 34
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	chlorophyll metabolism	22.22	4 of 18

Isolation source categories

Isolation

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1073005v1 assembly for Mycobacterium shinjukuense JCM 14233	complete	GCA_010730055	398694.15	8110384092	398694	95.99
124043	MshiDSM45663v1 assembly for Mycobacterium shinjukuense DSM 45663	complete	GCA_963853675			398694	90.12
66792	ASM2582228v1 assembly for Mycobacterium shinjukuense DSM 45663	scaffold	GCA_025822285	398694.18	8115269272	398694	58.92
67770	ASM208675v1 assembly for Mycobacterium shinjukuense CCUG 53584	contig	GCA_002086755	398694.3	2865597299	398694	42.05

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18021	Mycobacterium shinjukuense gene for 16S rRNA, partial sequence, strain: GTC 2738	AB268503	1505		398694

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic and phenotypic characterization of Mycobacterium tuberculosis' closest-related non-tuberculous mycobacteria.	Sous C, Frigui W, Pawlik A, Sayes F, Ma L, Cokelaer T, Brosch R.	Microbiol Spectr	10.1128/spectrum.04126-23	2024
Pathogenicity	Evolution and emergence of Mycobacterium tuberculosis.	Orgeur M, Sous C, Madacki J, Brosch R.	FEMS Microbiol Rev	10.1093/femsre/fuae006	2024
Phylogeny	Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis.	Sapriel G, Brosch R.	Genome Biol Evol	10.1093/gbe/evz162	2019
Phylogeny	Microbiological features and clinical relevance of new species of the genus Mycobacterium.	Tortoli E.	Clin Microbiol Rev	10.1128/cmr.00035-14	2014
	The Presence of esat-6 and cfp10 and Other Gene Orthologs of the RD 1 Region in Non-Tuberculous Mycobacteria, Mycolicibacteria, Mycobacteroides and Mycolicibacter as Possible Impediments for the Diagnosis of (Animal) Tuberculosis	Gcebe N, Hlokwe T, Bouw A, Michel A, Rutten V.	Microorganisms		2024
	Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae.	Brenner E, Sreevatsan S.	Front Microbiol	10.3389/fmicb.2023.1204838	2023
	Rifampicin-Induced Lung Injury in Mycobacterium shinjukuense Infection: A Case Report.	Hachisu Y, Hanawa M, Hosino Y, Uno S, Onuki Y, Ezawa K, Horie T.	Respirol Case Rep	10.1002/rcr2.70208	2025
	Pulmonary Mycobacterium shinjukuense infection with cavitary lesion.	Sueda Y, Tokuyasu H, Sakai H, Yamasaki A.	Respirol Case Rep	10.1002/rcr2.1399	2024
	Mycobacterium shinjukuense infection successfully treated with clarithromycin, rifampicin, and ethambutol.	Nakamura K, Murakami E, Kishino D, Mashimo S, Kurioka Y, Shibata Y, Taniguchi A, Higo H, Hiramatsu Y, Maeda Y, Miyahara N.	Respir Med Case Rep	10.1016/j.rmcr.2023.101894	2023
	Two Cases of Mycobacterium shinjukuense Pulmonary Disease With a Long-Term Response to Treatment With Clarithromycin, Rifampicin, and Ethambutol.	Imakura T, Kakiuchi S, Kagawa H, Murakami N, Haku T.	Cureus	10.7759/cureus.52888	2024
	A universal, high-quality, and high-yield DNA purification method for mycobacteria, including Mycobacterium tuberculosis: large-scale assessment of the chloroform-bead method.	Murase Y, Hosoya M, Morishige Y, Shimomura Y, Nagai M, Tamaru A, Takaki A, Mitarai S, Japan Tuberculosis Genotyping Group (2023), Japan Tuberculosis Genotyping Group.	Microbiol Spectr	10.1128/spectrum.00765-25	2025
Phylogeny	Mycobacterium Shinjukuense Pulmonary Disease Progressed to Pleuritis after Iatrogenic Pneumothorax: A Case Report.	Taoka T, Shinohara T, Hatakeyama N, Iwamura S, Murase Y, Mitarai S, Ogushi F.	J Clin Tuberc Other Mycobact Dis	10.1016/j.jctube.2020.100160	2020
	Nontuberculous Mycobacterial Lung Disease Caused by Mycobacterium shinjukuense: The First Reported Case in Korea.	Moon SM, Kim SY, Chung MJ, Lee SH, Shin SJ, Koh WJ.	Tuberc Respir Dis (Seoul)	10.4046/trd.2015.78.4.416	2015
Pathogenicity	Mono- and multidomain defense toxins of the RelE/ParE superfamily.	Gerdes K.	mBio	10.1128/mbio.00258-25	2025
	Mycobacterium shinjukuense lung disease that was successfully treated with antituberculous drugs.	Watanabe K, Shinkai M, Yamaguchi N, Shinoda M, Hara Y, Ishigatsubo Y, Kaneko T.	Intern Med	10.2169/internalmedicine.52.1116	2013
	Diagnostic Utility of a Mycobacterium Multiplex PCR Detection Panel for Tuberculosis and Nontuberculous Mycobacterial Infections.	Uwamino Y, Aono A, Tomita Y, Morimoto K, Kawashima M, Kamata H, Sasaki Y, Nagai H, Hasegawa N, Mitarai S.	Microbiol Spectr	10.1128/spectrum.05162-22	2023
	Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital.	Xiao YH, Liu MF, Wu H, Xu DR, Zhao R.	Infect Drug Resist	10.2147/idr.s401707	2023
Phylogeny	Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.	Hall MB, Coin LJM.	Gigascience	10.1093/gigascience/giae010	2024
Genetics	Comparative Genomic and Transcriptomic Analyses of Mycobacterium kansasii Subtypes Provide New Insights Into Their Pathogenicity and Taxonomy.	Guan Q, Ummels R, Ben-Rached F, Alzahid Y, Amini MS, Adroub SA, van Ingen J, Bitter W, Abdallah AM, Pain A.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00122	2020
	Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense.	Guan Q, Garbati M, Mfarrej S, AlMutairi T, Laval T, Singh A, Fagbo S, Smyth A, Browne JA, urRahman MA, Alruwaili A, Hoosen A, Meehan CJ, Nakajima C, Suzuki Y, Demangel C, Bhatt A, Gordon SV, AlAsmari F, Pain A.	NAR Genom Bioinform	10.1093/nargab/lqab070	2021
Genetics	Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics.	Gupta RS.	High Throughput	10.3390/ht7040031	2018
	Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis.	Schwenk S, Moores A, Nobeli I, McHugh TD, Arnvig KB.	Nucleic Acids Res	10.1093/nar/gky226	2018
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 shinjukuense sp. nov., a slowly growing, non-chromogenic species isolated from human clinical specimens.	Saito H, Iwamoto T, Ohkusu K, Otsuka Y, Akiyama Y, Sato S, Taguchi O, Sueyasu Y, Kawabe Y, Fujimoto H, Ezaki T, Butler R	Int J Syst Evol Microbiol	10.1099/ijs.0.025478-0	2010