Name: Mycobacterium shimoidei E4796
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8442

Type strain:

Species: Mycobacterium shimoidei

Strain Designation: E4796

Culture col. no.: CCUG 37517, JCM 12376, DSM 44152, ATCC 27962

Strain history: CCUG 37517 <-- DSM 44152 <-- ATCC 27962 <-- M. Tsukamura E4796.

NCBI tax ID(s): 29313 (species)

SI-ID 44801

ATCC 27962, DSM 44152, CCUG 37517, JCM 12376, CNCTC 7293

Other strains from Mycobacterium shimoidei

M. shimoidei CCUG 47517

Section

Mycobacterium shimoidei E4796 is a mesophilic bacterium that was isolated from sputum of patient with tuberculosis-like disease.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Mycobacteriaceae*
	Genus	*Mycobacterium*
	Species	**Mycobacterium shimoidei**
	Full Scientific Name (LPSN)	Mycobacterium shimoidei (ex Tsukamura et al. 1975) Tsukamura 1982

Information on morphological and physiological properties Morphology

[Ref.: #53711]

Incubation period

10 days

Multimedia content

[Ref.: #11552]

Caption:

Medium 645 37°C

[Ref.: #11552]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11552]

Culture medium

LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)

[Ref.: #11552]

Culture medium growth

[Ref.: #11552]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11552]

Culture medium composition

expand / minimize

[Ref.: #11552]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #11552]

Culture medium growth

[Ref.: #11552]

Culture medium link

Medium recipe at MediaDive

[Ref.: #11552]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #11552]	growth	37 °C
[Ref.: #53711]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #11552]	Temperature range	mesophilic
[Ref.: #53711]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #53711]

Fatty acid	Percentage	ECL
C18:1 ω9c	39.7	17.769
C16:0	30	16
C18:2 ω6,9c/C18:0 ANTE	12.1	17.724
C18:0	3.8	18
C16:1 ω7c	2.9	15.819
C18:1 ω7c /12t/9t	2.3	17.824
TBSA 10Me18:0	2.2	18.392
C20:0 alcohol (C20:0 2OH alc)	2	18.835
C16:1 ω9c	1.6	15.774
C20:4 ω6,9,12,15c	1.3	19.395
C14:0	1	14
C16:0 2OH	0.3	17.233
C17:0	0.3	17
C15:0	0.3	15
Unidentified	0.3	16.904

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #11552]	Sample type/isolated from	sputum of patient with tuberculosis-like disease

[Ref.: #53711]	Sample type/isolated from	Human sputum,patient w/tuberculosis-like disease

[Ref.: #67770]	Sample type/isolated from	Sputum of a patient
* marker position based on {}

Isolation sources categories

#Infection	#Disease	-
#Infection	#Patient	-
#Host Body Product	#Fluids	#Sputum

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X82459 (>99% sequence identity) for Mycobacterium shimoidei subclade from Microbeatlas

Aquatic Samples	394
Soil Samples	3022
Animal Samples	297
Plant Samples	219
Total Samples	3932

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #11552]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Mycobacterium shimoidei 16S rRNA gene and internal transcribed spacer	AJ005005	1805	ENA	29313 tax ID	*
[Ref.: #20218]	M.shimoidei 16S rRNA gene	X82459	1428	ENA	29313 tax ID	*
[Ref.: #20218]	M.shimoidei internal transcribed spacer between 16S and 23S rRNA, genomic sequence	X99219	274	ENA	29313 tax ID	*
[Ref.: #20218]	Mycobacterium shimoidei strain DSM 44152 16S ribosomal RNA gene, partial sequence	AF547965	556	ENA	29313 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium shimoidei DSM 44152	GCA_002101905	contig	GenBank	29313 tax ID
[Ref.: #66792]	Mycobacterium shimoidei strain DSM 44152	29313.4	wgs	PATRIC	29313 tax ID	*
[Ref.: #66792]	Mycobacterium shimoidei DSM 44152	GCA_025822885	scaffold	GenBank	29313 tax ID	*

[Ref.: #67770]

GC-content

65.8 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mycobacterium shimoidei strain DSM 44152 PATRIC: 29313.4
[Ref.: #69480]	gram-positive	yes	90.245	no
[Ref.: #69480]	anaerobic	no	98.682	no
[Ref.: #69480]	halophile	no	90.65	no
[Ref.: #69480]	spore-forming	no	89.775	no
[Ref.: #69480]	thermophile	no	94.706	yes
[Ref.: #69480]	glucose-util	yes	64.418	no
[Ref.: #69480]	motile	no	95.025	no
[Ref.: #69480]	flagellated	no	99.088	no
[Ref.: #69480]	aerobic	yes	89.344	no
[Ref.: #69480]	glucose-ferment	no	93.274	no

Availability in culture collections External links

[Ref.: #11552]

Culture collection no.

CCUG 37517, JCM 12376, DSM 44152, ATCC 27962

[Ref.: #77841]

SI-ID 44801

References

#11552

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44152

#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 )

#53711 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 37517

#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;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#77841

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID44801.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Mycobacterium shimoidei in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Mycobacterium shimoidei strain DSM 44152

Change proposal

Change proposal