Mycobacterium shigaense (DSM 46748, JCM 32072, UN-152)

Name: Mycobacterium shigaense (DSM 46748, JCM 32072, UN-152)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24231

Type strain

Strain Designation UN-152

Culture col. no. DSM 46748 JCM 32072 UN-152

NCBI tax ID(s) 722731

Special Collections DSMZ JCM Literature strains

History <- E. Tortoli, San Raffaele Scientific Inst., Milano, Italy; UN-152 <- K. Nakanaga, Leprosy Research Center, NIID, Tokyo, Japan; Y. Hoshino; Natl. Inst. of Infect. Dis., Japan; UN-152.

Links

Mycobacterium shigaense UN-152 is a mesophilic prokaryote that was isolated from cutaneous biopsy.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400471

JCM 32072,DSM 46748

@ref 20215

Last LPSN update 2025-12-16 09:52:48

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium shigaense

Full scientific name Mycobacterium shigaense Fukano et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	97.2
125438	positive	91.3

Colony morphology

@ref	Colony color	Incubation period	Medium used
66597	yellow	7-14 days	Middlebrook 7H10 agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20666	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
66597	egg slants
66597	Middlebrook 7H10 agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20666	positive	growth	37	mesophilic
66597	positive	growth	37	mesophilic
66597	negative	growth	42
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.7

Observation

66597

Observationaccumulation of niacin

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Biopsy
#Host Body-Site	#Organ	#Skin, Nail, Hair

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
20666	cutaneous biopsy		Shiga	Japan	JPN	Asia
66597	cutaneous lesions of a patient with NTM-associated infectious skin disease	2009	Shiga Prefecture	Japan	JPN	Asia
67770	Skin biopsies from a Japanese male patient with a history of Hodgkin's disease and severe cellular immunodeficiency		Shiga Pref.	Japan	JPN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM235631v1 assembly for Mycobacterium shigaense JCM 32072	complete	GCA_002356315	722731.3	2775507225	722731	96.75
67770	ASM298349v1 assembly for Mycobacterium shigaense UN-152	scaffold	GCA_002983495	722731.4	8008987092	722731	67.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20666	Mycobacterium shigaense gene for 16S ribosomal RNA, partial sequence	AB547401	1471		722731
67770	Mycobacterium shigaense genes for 16S ribosomal RNA, 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA	AB547404	429		722731

GC content

@ref	GC-content (mol%)	Method
67770	67.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium shigaense JCM 32072
NCBI: GCA_002356315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	66.70	no
125439	motility	BacteriaNetⓘ	no	79.40	no
125439	gram_stain	BacteriaNetⓘ	positive	97.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium shigaense JCM 32072
NCBI: GCA_002356315.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.30	no
125438	anaerobic	anaerobicⓘ	no	97.12	no
125438	aerobic	aerobicⓘ	yes	78.30	no
125438	spore-forming	spore-formingⓘ	no	60.22	no
125438	thermophilic	thermophileⓘ	no	94.89	no
125438	flagellated	motile2+ⓘ	no	87.00	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
Phylogeny	Mycobacterium shigaense sp. nov., a slow-growing, scotochromogenic species, is a member of the Mycobacterium simiae complex.	Fukano H, Yoshida M, Kazumi Y, Fujiwara N, Katayama K, Ogura Y, Hayashi T, Miyamoto Y, Fujimoto N, Hongsheng W, Mizumoto C, Koizumi Y, Maeda H, Hiranuma O, Mitarai S, Ishii N, Hoshino Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002845	2018

References

#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 )
#20666	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46748
#66597	Hanako Fukano, Mitsunori Yoshida, Yuko Kazumi, Nagatoshi Fujiwara, Kinya Katayama, Yoshitoshi Ogura, Tetsuya Hayashi, Yuji Miyamoto, Noriki Fujimoto, Wang Hongsheng, Chisaki Mizumoto, Yusuke Koizumi, Hiroyoshi Maeda, Osamu Hiranuma, Satoshi Mitarai, Norihisa Ishii and Yoshihiko Hoshino: Mycobacterium shigaense sp. nov., a slow-growing, scotochromogenic species, is a member of the Mycobacterium simiae complex. IJSEM 68: 2437 - 2442 2018 ( DOI 10.1099/ijsem.0.002845 , PubMed 29939124 )
#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;
#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 shigaense (DSM 46748, JCM 32072, UN-152)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002356315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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