Name: Microbacterium yannicii G72
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7462

Type strain:

Species: Microbacterium yannicii

Strain Designation: G72

Culture col. no.: DSM 23203, LMG 25521, JCM 18959

Strain history: LMG 25521 <-- S. Karojet G72.

NCBI tax ID(s): 671622 (species)

SI-ID 368519

LMG 25521, DSM 23203, JCM 18959

Special Collections

Section

Microbacterium yannicii G72 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from roots of Arabidopsis thaliana.

Gram-positive
rod-shaped
microaerophile
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	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium yannicii**
	Full Scientific Name (LPSN)	Microbacterium yannicii Karojet et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #29931]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %92.019

[Ref.: #29931]	Cell length	1.5-3.0 µm

[Ref.: #29931]	Cell width	0.5-0.6 µm

[Ref.: #29931]	Cell shape	rod-shaped

[Ref.: #29931]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.5

[Ref.: #29931]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16747]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #16747]

Culture medium growth

[Ref.: #16747]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16747]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16747]	growth	28 °C
[Ref.: #29931]	growth	04-37 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29931]

Oxygen tolerance

microaerophile

[Ref.: #69481]

Ability of spore formation

no Confidence in %96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29931]		NaCl		growth	<2	%

[Ref.: #67770]

Observation

quinones: MK-13, MK-12, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29931]	arabinose ChEBI	+	carbon source
[Ref.: #29931]	lactate ChEBI	+	carbon source
[Ref.: #29931]	sucrose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #29931]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29931]		catalase	+	1.11.1.6
[Ref.: #29931]		gelatinase	+

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

[Ref.: #16747]	Sample type/isolated from	roots of Arabidopsis thaliana
[Ref.: #16747]	Host species	Arabidopsis thaliana
[Ref.: #16747]	Geographic location (country and/or sea, region)	Potsdam-Golm (52° 24' 57'' N 12° 58' 18'' E)
[Ref.: #16747]	Country	Germany
[Ref.: #16747]	Country ISO 3 Code	DEU
[Ref.: #16747]	Continent	Europe
[Ref.: #16747]	Geographic location	52.4158°/12.9717°

[Ref.: #67770]	Sample type/isolated from	Roots of Arabidopsis thaliana in the fields of Golm
[Ref.: #67770]	Host species	Arabidopsis thaliana
[Ref.: #67770]	Geographic location (country and/or sea, region)	area around Potsdam
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

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

[Ref.: #16747]

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.: #16747]	Microbacterium yannicii partial 16S rRNA gene, strain G72	FN547412	1466	GenBank ENA	671622 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbacterium yannicii JCM 18959	GCA_015278355	contig	GenBank ENA	671622 tax ID	*
[Ref.: #66792]	Microbacterium yannicii strain JCM 18959	671622.3	wgs	PATRIC	671622 tax ID	*
[Ref.: #66792]	Microbacterium yannicii DSM 23203	GCA_024055635	contig	GenBank ENA	671622 tax ID	*

[Ref.: #16747]	GC-content	70.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29931]	GC-content	70.1 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: Microbacterium yannicii strain JCM 18959 PATRIC: 671622.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	96	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium yannicii strain JCM 18959 PATRIC: 671622.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	92.019	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.052	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	80.059	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.394	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92.5	no

Availability in culture collections External links

[Ref.: #16747]

Culture collection no.

DSM 23203, LMG 25521, JCM 18959

[Ref.: #76908]

SI-ID 368519

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria.	Xie F, Niu S, Lin X, Pei S, Jiang L, Tian Y, Zhang G	J Microbiol	10.1007/s12275-021-1186-5	2021	*
Phylogeny	Microbacterium ureisolvens sp. nov., isolated from a Yellow River sample.	Cheng LJ, Ming H, Zhao ZL, Ji WL, Zhang LY, Li LY, Meng XL, Li M, Niu MM, Nie GX	Int J Syst Evol Microbiol	10.1099/ijsem.0.003203	2018	*
Phylogeny	Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.).	Yan ZF, Lin P, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002167	2017	*
Phylogeny	Microbacterium yannicii sp. nov., isolated from Arabidopsis thaliana roots.	Karojet S, Kunz S, van Dongen JT	Int J Syst Evol Microbiol	10.1099/ijs.0.026955-0	2011	*

References

#16747

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23203

#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 )

#29931

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 #26302 (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;

#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 )

#76908

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-ID368519.1 )

#26302

IJSEM 822 2012 ( DOI 10.1099/ijs.0.026955-0 , PubMed 21571929 )

* These data were automatically processed and therefore are not curated

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Microbacterium yannicii strain JCM 18959

Microbacterium yannicii strain JCM 18959

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