Strain identifier
BacDive ID: 7462
Type strain: 
Species: Microbacterium yannicii
Strain Designation: G72
Strain history: LMG 25521 <-- S. Karojet G72.
NCBI tax ID(s): 671622 (species)
version 9.1 (current version)
General
@ref: 16747
BacDive-ID: 7462
DSM-Number: 23203
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, Gram-positive, rod-shaped
description: Microbacterium yannicii G72 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from roots of Arabidopsis thaliana.
NCBI tax id
- NCBI tax id: 671622
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16747 | <- S. Karojet, Max Planck Inst. Molecular Plant Physiology, Golm, Germany; G72 <- S. Karojet, S. Kunz and J. T. van Dongen |
| 67770 | LMG 25521 <-- S. Karojet G72. |
doi: 10.13145/bacdive7462.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium yannicii
- full scientific name: Microbacterium yannicii Karojet et al. 2012
@ref: 16747
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium yannicii
full scientific name: Microbacterium yannicii Karojet et al. 2012
strain designation: G72
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29931 | positive | 1.5-3.0 µm | 0.5-0.6 µm | rod-shaped | no | |
| 69480 | positive | 92.019 | ||||
| 69480 | no | 92.5 |
pigmentation
- @ref: 29931
- production: yes
Culture and growth conditions
culture medium
- @ref: 16747
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: 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 |
|---|---|---|---|
| 16747 | positive | growth | 28 |
| 29931 | positive | growth | 04-37 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 29931
- oxygen tolerance: microaerophile
spore formation
- @ref: 69481
- spore formation: no
- confidence: 96
halophily
- @ref: 29931
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <2 %
observation
- @ref: 67770
- observation: quinones: MK-13, MK-12, MK-11
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29931 | 22599 | arabinose | + | carbon source |
| 29931 | 24996 | lactate | + | carbon source |
| 29931 | 17992 | sucrose | + | carbon source |
metabolite production
- @ref: 29931
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29931 | catalase | + | 1.11.1.6 |
| 29931 | gelatinase | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | 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 |
| 67770 | Roots of Arabidopsis thaliana in the fields of Golm | Arabidopsis thaliana | area around Potsdam | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Safety information
risk assessment
- @ref: 16747
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16747
- description: Microbacterium yannicii partial 16S rRNA gene, strain G72
- accession: FN547412
- length: 1466
- database: nuccore
- NCBI tax ID: 671622
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microbacterium yannicii JCM 18959 | GCA_015278355 | contig | ncbi | 671622 |
| 66792 | Microbacterium yannicii strain JCM 18959 | 671622.3 | wgs | patric | 671622 |
| 66792 | Microbacterium yannicii DSM 23203 | GCA_024055635 | contig | ncbi | 671622 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16747 | 70.1 | high performance liquid chromatography (HPLC) |
| 29931 | 70.1 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 96 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 92.019 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.052 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 80.059 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.394 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 92.5 | no |
External links
@ref: 16747
culture collection no.: DSM 23203, LMG 25521, JCM 18959
straininfo link
- @ref: 76908
- straininfo: 368519
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21571929 | 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 | Actinomycetales/*classification/genetics/isolation & purification, Arabidopsis/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genotype, Germany, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Genetics |
| Phylogeny | 28875898 | 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 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 30575502 | 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 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 34491524 | 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 | Base Composition, Carotenoids/chemistry/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Microbacterium/classification/genetics/*isolation & purification/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16747 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23203) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23203 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29931 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26302 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 76908 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID368519.1 | StrainInfo: A central database for resolving microbial strain identifiers |