Strain identifier
BacDive ID: 2318
Type strain:
Species: Brevundimonas aveniformis
Strain Designation: EMB102
Strain history: <- CO Jeon, Gyungsang Univ.
NCBI tax ID(s): 1121123 (strain), 370977 (species)
General
@ref: 7309
BacDive-ID: 2318
DSM-Number: 17977
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Brevundimonas aveniformis EMB102 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
370977 | species |
1121123 | strain |
strain history
@ref | history |
---|---|
7309 | <- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB102 |
67771 | <- CO Jeon, Gyungsang Univ. |
doi: 10.13145/bacdive2318.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Caulobacterales
- family: Caulobacteraceae
- genus: Brevundimonas
- species: Brevundimonas aveniformis
- full scientific name: Brevundimonas aveniformis Ryu et al. 2007
@ref: 7309
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Caulobacteraceae
genus: Brevundimonas
species: Brevundimonas aveniformis
full scientific name: Brevundimonas aveniformis Ryu et al. 2007
strain designation: EMB102
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31972 | negative | 1.5 µm | 0.35 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | negative | 99.974 |
Culture and growth conditions
culture medium
- @ref: 7309
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7309 | positive | growth | 25 | mesophilic |
31972 | positive | growth | 15-35 | |
31972 | positive | optimum | 30 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31972 | positive | growth | 6.0-9.0 | alkaliphile |
31972 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31972 | facultative aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 96 |
69480 | no | 99.993 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31972 | NaCl | positive | growth | 0.0-1.0 % |
31972 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 67771
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31972 | 21217 | L-alaninamide | + | carbon source |
31972 | 16449 | alanine | + | carbon source |
31972 | 22653 | asparagine | + | carbon source |
31972 | 35391 | aspartate | + | carbon source |
31972 | 29987 | glutamate | + | carbon source |
31972 | 28087 | glycogen | + | carbon source |
31972 | 29864 | mannitol | + | carbon source |
31972 | 37684 | mannose | + | carbon source |
31972 | 17268 | myo-inositol | + | carbon source |
31972 | 26271 | proline | + | carbon source |
31972 | 15361 | pyruvate | + | carbon source |
31972 | 16634 | raffinose | + | carbon source |
31972 | 17822 | serine | + | carbon source |
31972 | 30031 | succinate | + | carbon source |
31972 | 26986 | threonine | + | carbon source |
31972 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31972 | acid phosphatase | + | 3.1.3.2 |
31972 | alkaline phosphatase | + | 3.1.3.1 |
31972 | catalase | + | 1.11.1.6 |
31972 | gelatinase | + | |
31972 | cytochrome oxidase | + | 1.9.3.1 |
31972 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7309 | activated sludge | Pohang | Republic of Korea | KOR | Asia |
67771 | From activated sludge | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_6366.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_3023;97_3713;98_4705;99_6366&stattab=map
- Last taxonomy: Brevundimonas aveniformis subclade
- 16S sequence: DQ372984
- Sequence Identity:
- Total samples: 2796
- soil counts: 628
- aquatic counts: 1194
- animal counts: 830
- plant counts: 144
Safety information
risk assessment
- @ref: 7309
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7309
- description: Brevundimonas aveniformis strain EMB102 16S ribosomal RNA gene, partial sequence
- accession: DQ372984
- length: 1403
- database: ena
- NCBI tax ID: 370977
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Brevundimonas aveniformis DSM 17977 | GCA_000428765 | scaffold | ncbi | 1121123 |
66792 | Brevundimonas aveniformis DSM 17977 | 1121123.3 | wgs | patric | 1121123 |
66792 | Brevundimonas aveniformis DSM 17977 | 2524614798 | draft | img | 1121123 |
GC content
- @ref: 7309
- GC-content: 64.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | yes | 88.601 | yes |
flagellated | no | 85.595 | no |
gram-positive | no | 98.564 | no |
anaerobic | no | 98.13 | yes |
aerobic | yes | 79.247 | no |
halophile | no | 94.59 | yes |
spore-forming | no | 96.936 | no |
glucose-util | yes | 54.563 | no |
thermophile | no | 94.025 | yes |
glucose-ferment | no | 90.562 | no |
External links
@ref: 7309
culture collection no.: DSM 17977, KCTC 12609
straininfo link
- @ref: 71875
- straininfo: 401919
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17625194 | Brevundimonas aveniformis sp. nov., a stalked species isolated from activated sludge. | Ryu SH, Park M, Lee JR, Yun PY, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.64737-0 | 2007 | Bacterial Typing Techniques, Base Composition, Caulobacteraceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Names, Nucleic Acid Hybridization, Phospholipids/analysis, Phosphorus/metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Temperature | Genetics |
Phylogeny | 31596194 | Brevundimonas fluminis sp. nov., isolated from a river. | Lee YW, Lee KH, Lee SY, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003736 | 2020 | Bacterial Typing Techniques, Base Composition, Caulobacteraceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7309 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17977) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17977 | |||
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 | |||
31972 | 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 | 28227 | 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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
71875 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401919.1 | StrainInfo: A central database for resolving microbial strain identifiers |