Strain identifier

BacDive ID: 17445

Type strain: Yes

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

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
370776species
1121013strain

strain history

@refhistory
7329<- K. K. Kim, KAIST; TR7-09 <- L. Jin
67771<- ST Lee, KAIST
118716CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31836negative1.4 µm0.45 µmrod-shapedyes
67771negative
69480negative99.95
118716negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7329REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: 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
37839MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118716CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7329positivegrowth30mesophilic
31836positivegrowth20-42
31836positiveoptimum30mesophilic
37839positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31836positivegrowth06-09alkaliphile
31836positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31836no
69481no99
69480no99.988

halophily

  • @ref: 31836
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31836161933-hydroxybenzoate+carbon source
31836581435-dehydro-D-gluconate+carbon source
3183630089acetate+carbon source
3183628087glycogen+carbon source
3183615792malonate+carbon source
3183626546rhamnose+carbon source
3183617822serine+carbon source
318369300suberic acid+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11871617632nitrate-reduction
11871616301nitrite+reduction

metabolite production

  • @ref: 118716
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31836cytochrome oxidase+1.9.3.1
31836urease+3.5.1.5
118716oxidase+
118716catalase-1.11.1.6
118716urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118716-+++-+---+++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118716-----------------+/--------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7329compostDaejeonRepublic of KoreaKORAsia
67771From compostRepublic of KoreaKORAsia
118716Environment, CompostDaejeonRepublic of KoreaKORAsia

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

@refbiosafety levelbiosafety level comment
73291Risk group (German classification)
1187161Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenimonas composti TR7-09 = DSM 18010GCA_000426365scaffoldncbi1121013
66792Arenimonas composti TR7-09 = DSM 18010GCA_000747175contigncbi1121013
66792Arenimonas composti DSM 180101121013.3wgspatric1121013
66792Arenimonas composti TR7-09 = DSM 180101121013.4wgspatric1121013
66792Arenimonas composti TR7-09, DSM 180102630968769draftimg1121013
66792Arenimonas composti TR7-09, DSM 180102524614513draftimg1121013

GC content

@refGC-contentmethod
732970.8high performance liquid chromatography (HPLC)
3183670.95
6777170.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno81.315yes
flagellatedno97.225no
gram-positiveno98.495yes
anaerobicno99.422no
aerobicyes92.527no
halophileno93.595no
spore-formingno97.41no
glucose-utilyes86.863no
thermophileno97.18yes
glucose-fermentno92.462no

External links

@ref: 7329

culture collection no.: DSM 18010, CIP 109794, KCTC 12666, KCTC 12557

straininfo link

  • @ref: 86441
  • straininfo: 309429

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684274Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae.Jin L, Kim KK, Im WT, Yang HC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64472-02007DNA, 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 & purificationGenetics
Phylogeny19628604Arenimonas 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 YRInt J Syst Evol Microbiol10.1099/ijs.0.006031-02009Agriculture/methods, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, *Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny22493175Arenimonas 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 HMInt J Syst Evol Microbiol10.1099/ijs.0.035410-02012Bacterial 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 & purificationGenetics
Phylogeny25731739Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NMAntonie Van Leeuwenhoek10.1007/s10482-015-0409-32015Bacterial 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/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7329Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18010)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18010
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31836Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2810228776041
37839Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7577
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86441Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309429.1StrainInfo: A central database for resolving microbial strain identifiers
118716Curators of the CIPCollection of Institut Pasteur (CIP 109794)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109794