Name: Mycobacterium sediminis DSM 45643
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24236

Type strain:

Species: Mycobacterium sediminis

Culture col. no.: DSM 45643, KCTC 19999, YIM M13028, JCM 17899

Strain history: <- S-K Tang, Yunnan Inst., China

NCBI tax ID(s): 1286180 (species)

SI-ID 407834

DSM 45643

Special Collections

Section

Mycobacterium sediminis DSM 45643 is an aerobe, Gram-positive, ovoid-shaped bacterium that was isolated from marine sediment.

Gram-positive
ovoid-shaped
aerobe
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 sediminis**
	Full Scientific Name (LPSN)	Mycobacterium sediminis Zhang et al. 2013

Synonym

Mycolicibacterium sediminis

Information on morphological and physiological properties Morphology

[Ref.: #31044]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.225

[Ref.: #31044]	Cell shape	ovoid-shaped

[Ref.: #31044]	Motility	no

[Ref.: #31044]

Pigment production

yes

Multimedia content

[Ref.: #20671]

Caption:

Medium 645 28°C

[Ref.: #20671]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20671]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #20671]

Culture medium growth

[Ref.: #20671]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20671]

Culture medium composition

expand / minimize

[Ref.: #20671]

Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #20671]

Culture medium growth

[Ref.: #20671]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20671]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20671]	growth	28 °C
[Ref.: #31044]	growth	05-37 °C
[Ref.: #31044]	optimum	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #31044]			optimum	7
[Ref.: #31044]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #31044]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31044]		NaCl		growth	0-4	%
[Ref.: #31044]		NaCl		optimum	1	%

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31044]		catalase	+	1.11.1.6
[Ref.: #31044]		urease	+	3.5.1.5

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

[Ref.: #20671]	Sample type/isolated from	marine sediment
[Ref.: #20671]	Geographic location (country and/or sea, region)	Yunnan, South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 m
[Ref.: #20671]	Country	China
[Ref.: #20671]	Country ISO 3 Code	CHN
[Ref.: #20671]	Continent	Asia
[Ref.: #20671]	Geographic location	19.5044°/111.0040°

[Ref.: #67770]	Sample type/isolated from	Sediment sample from the South China Sea at a depth of 42 m

[Ref.: #67771]	Sample type/isolated from	From marine sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Southe China Sea
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC010490 (>99% sequence identity) for Mycolicibacterium from Microbeatlas

Aquatic Samples	648
Soil Samples	1808
Animal Samples	1323
Plant Samples	680
Total Samples	4459

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

[Ref.: #20671]

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.: #67770]	Mycolicibacterium sediminis strain YIM M13028 16S-23S ribosomal RNA intergenic spacer, complete sequence	KC010492	490	GenBank ENA	1286180 tax ID
[Ref.: #20671]	Mycobacterium sediminis strain YIM M13028 16S ribosomal RNA gene, partial sequence	KC010490	1515	GenBank ENA	1286180 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mycolicibacterium sediminis JCM 17899	GCA_010731735	complete	GenBank ENA	1286180 tax ID	*
[Ref.: #66792]	Mycolicibacterium sediminis strain JCM 17899	1286180.8	complete	PATRIC	1286180 tax ID	*
[Ref.: #66792]	Mycolicibacterium sediminis JCM 17899	2888243993	complete	JGI IMG/M	1286180 tax ID	*
[Ref.: #66792]	Mycolicibacterium sediminis DSM 45643	GCA_025822985	scaffold	GenBank ENA	1286180 tax ID	*

[Ref.: #20671]	GC-content	64.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31044]	GC-content	64.1 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Mycolicibacterium sediminis JCM 17899 NCBI: GCA_010731735.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mycolicibacterium sediminis JCM 17899 NCBI: GCA_010731735.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.225	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.467	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.888	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	60.574	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.667	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88	yes

Availability in culture collections External links

[Ref.: #20671]

Culture collection no.

DSM 45643, KCTC 19999, YIM M13028, JCM 17899

[Ref.: #88179]

SI-ID 407834

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.	Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.050567-0	2013	*

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 )

#20671

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45643

#31044

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 #27374 (see below)

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88179

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-ID407834.1 )

#27374

IJSEM 4081 2013 ( DOI 10.1099/ijs.0.050567-0 , PubMed 23728378 )

* These data were automatically processed and therefore are not curated

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Mycolicibacterium sediminis JCM 17899

Mycolicibacterium sediminis JCM 17899

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