Strain identifier
BacDive ID: 17445
Type strain:
Species: Arenimonas composti
Strain Designation: TR7-09
Strain history: CIP <- 2008, DSMZ <- K.K. Kim, KAIST, Daejon, Korea: strain TR7-09 <- L. Jin, KAIST, Daejon, Korea
NCBI tax ID(s): 1121013 (strain), 370776 (species)
General
@ref: 7329
BacDive-ID: 17445
DSM-Number: 18010
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Arenimonas composti TR7-09 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from compost.
NCBI tax id
NCBI tax id | Matching level |
---|---|
370776 | species |
1121013 | strain |
strain history
@ref | history |
---|---|
7329 | <- K. K. Kim, KAIST; TR7-09 <- L. Jin |
67771 | <- ST Lee, KAIST |
118716 | CIP <- 2008, DSMZ <- K.K. Kim, KAIST, Daejon, Korea: strain TR7-09 <- L. Jin, KAIST, Daejon, Korea |
doi: 10.13145/bacdive17445.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Arenimonas
- species: Arenimonas composti
- full scientific name: Arenimonas composti (Jin et al. 2007) Aslam et al. 2009
synonyms
- @ref: 20215
- synonym: Aspromonas composti
@ref: 7329
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Arenimonas
species: Arenimonas composti
full scientific name: Arenimonas composti (Jin et al. 2007) Aslam et al. 2009
strain designation: TR7-09
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31836 | negative | 1.4 µm | 0.45 µm | rod-shaped | yes | |
67771 | negative | |||||
69480 | negative | 99.95 | ||||
118716 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7329 | REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) | yes | https://mediadive.dsmz.de/medium/830c | Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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 |
37839 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
118716 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7329 | positive | growth | 30 | mesophilic |
31836 | positive | growth | 20-42 | |
31836 | positive | optimum | 30 | mesophilic |
37839 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31836 | positive | growth | 06-09 | alkaliphile |
31836 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31836 | no | |
69481 | no | 99 |
69480 | no | 99.988 |
halophily
- @ref: 31836
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <3 %
observation
- @ref: 67771
- observation: quinones: Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31836 | 16193 | 3-hydroxybenzoate | + | carbon source |
31836 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
31836 | 30089 | acetate | + | carbon source |
31836 | 28087 | glycogen | + | carbon source |
31836 | 15792 | malonate | + | carbon source |
31836 | 26546 | rhamnose | + | carbon source |
31836 | 17822 | serine | + | carbon source |
31836 | 9300 | suberic acid | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 17634 | D-glucose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
118716 | 17632 | nitrate | - | reduction |
118716 | 16301 | nitrite | + | reduction |
metabolite production
- @ref: 118716
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31836 | cytochrome oxidase | + | 1.9.3.1 |
31836 | urease | + | 3.5.1.5 |
118716 | oxidase | + | |
118716 | catalase | - | 1.11.1.6 |
118716 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118716 | - | + | + | + | - | + | - | - | - | + | + | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118716 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7329 | compost | Daejeon | Republic of Korea | KOR | Asia |
67771 | From compost | Republic of Korea | KOR | Asia | |
118716 | Environment, Compost | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Biodegradation
- Cat3: #Composting
taxonmaps
- @ref: 69479
- File name: preview.99_7339.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_3434;97_4214;98_5382;99_7339&stattab=map
- Last taxonomy: Arenimonas
- 16S sequence: AM229324
- Sequence Identity:
- Total samples: 313
- soil counts: 151
- aquatic counts: 87
- animal counts: 50
- plant counts: 25
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7329 | 1 | Risk group (German classification) |
118716 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7329
- description: Aspromonas composti partial 16S rRNA gene, type strain TR7-09T
- accession: AM229324
- length: 1480
- database: ena
- NCBI tax ID: 1121013
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arenimonas composti TR7-09 = DSM 18010 | GCA_000426365 | scaffold | ncbi | 1121013 |
66792 | Arenimonas composti TR7-09 = DSM 18010 | GCA_000747175 | contig | ncbi | 1121013 |
66792 | Arenimonas composti DSM 18010 | 1121013.3 | wgs | patric | 1121013 |
66792 | Arenimonas composti TR7-09 = DSM 18010 | 1121013.4 | wgs | patric | 1121013 |
66792 | Arenimonas composti TR7-09, DSM 18010 | 2630968769 | draft | img | 1121013 |
66792 | Arenimonas composti TR7-09, DSM 18010 | 2524614513 | draft | img | 1121013 |
GC content
@ref | GC-content | method |
---|---|---|
7329 | 70.8 | high performance liquid chromatography (HPLC) |
31836 | 70.95 | |
67771 | 70.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 81.315 | yes |
flagellated | no | 97.225 | no |
gram-positive | no | 98.495 | yes |
anaerobic | no | 99.422 | no |
aerobic | yes | 92.527 | no |
halophile | no | 93.595 | no |
spore-forming | no | 97.41 | no |
glucose-util | yes | 86.863 | no |
thermophile | no | 97.18 | yes |
glucose-ferment | no | 92.462 | no |
External links
@ref: 7329
culture collection no.: DSM 18010, CIP 109794, KCTC 12666, KCTC 12557
straininfo link
- @ref: 86441
- straininfo: 309429
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17684274 | Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae. | Jin L, Kim KK, Im WT, Yang HC, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64472-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, *Soil Microbiology, Ubiquinone/analysis, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 19628604 | Arenimonas oryziterrae sp. nov., isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime, and reclassification of Aspromonas composti as Arenimonas composti comb. nov. | Aslam Z, Park JH, Kim SW, Jeon CO, Chung YR | Int J Syst Evol Microbiol | 10.1099/ijs.0.006031-0 | 2009 | Agriculture/methods, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, *Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolism | Genetics |
Phylogeny | 22493175 | Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir. | Huy H, Jin L, Lee YK, Lee KC, Lee JS, Yoon JH, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.035410-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 25731739 | Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China. | Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NM | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0409-3 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oryza/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolism | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7329 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18010) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18010 | ||||
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 | ||||
31836 | 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 | 28102 | 28776041 | ||
37839 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7577 | |||||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
86441 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309429.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
118716 | Curators of the CIP | Collection of Institut Pasteur (CIP 109794) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109794 |