Cite this strain

Microbacterium yannicii (DSM 23203, LMG 25521, G72)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7462

Type strain

Strain Designation G72

Culture col. no. DSM 23203 LMG 25521 G72 JCM 18959

NCBI tax ID(s) 671622

Special Collections DSMZ JCM Literature strains

Links

Name and taxonomic classification

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

Gram-positive rod-shaped microaerophile mesophilic genome sequence 16S sequence Bacteria

SI-ID 368519

LMG 25521, DSM 23203, JCM 18959

Last LPSN update 2024-12-09 10:43:57

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium yannicii

Full scientific name Microbacterium yannicii Karojet et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
29931	positive	1.5-3.0 µm	0.5-0.6 µm	rod-shaped
125438
125438	positive

Pigmentation

29931

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16747	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16747	positive	growth	28	mesophilic
29931	positive	growth	04-37
67770	positive	growth	28	mesophilic

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29931	NaCl	positive	growth	<2 %

Observation

67770

Observationquinones: MK-13, MK-12, MK-11

Enzymes

@ref	Value	Activity	Ec
29931	catalase	+	1.11.1.6
29931	gelatinase	+

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29931	16136 ChEBI	hydrogen sulfide

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29931	22599 ChEBI	arabinose	+	carbon source
29931	24996 ChEBI	lactate	+	carbon source
29931	17992 ChEBI	sucrose	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
29931	microaerophile
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
16747	roots of Arabidopsis thaliana	Arabidopsis thaliana	Potsdam-Golm (52° 24' 57'' N 12° 58' 18'' E)	Germany	DEU	Europe	52.4158	12.9717 52.4158/12.9717
67770	Roots of Arabidopsis thaliana in the fields of Golm	Arabidopsis thaliana	area around Potsdam	Germany	DEU	Europe

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
16747	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
16747	70.1	high performance liquid chromatography (HPLC)
29931	70.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16747	Microbacterium yannicii partial 16S rRNA gene, strain G72	FN547412	1466		671622

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Microbacterium yannicii JCM 18959	GCA_015278355	contig		671622
66792	Microbacterium yannicii strain JCM 18959	671622.3	wgs	PATRIC	671622
66792	Microbacterium yannicii DSM 23203	GCA_024055635	contig		671622

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Microbacterium yannicii JCM 18959
NCBI: GCA_015278355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.60	no
125439	motility	BacteriaNetⓘ	no	54.60	no
125439	gram_stain	BacteriaNetⓘ	positive	89.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from Diaspora project based on:
Microbacterium yannicii strain JCM 18959
PATRIC: 671622.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.02	yes
125438	anaerobic	anaerobicⓘ	no	98.05	yes
125438	spore-forming	spore-formingⓘ	no	80.06	no
125438	aerobic	aerobicⓘ	yes	85.39	yes
125438	thermophilic	thermophileⓘ	no	97.00	no
125438	flagellated	motile2+ⓘ	no	92.50	no

External links

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

Straininfo Link

@ref	Straininfo	Culture collections
76908	368519	LMG 25521, DSM 23203, JCM 18959

Culture collection no.

Culture collection no.
DSM 23203
LMG 25521
G72
JCM 18959

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;
#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 )
#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 .

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