Strain identifier

BacDive ID: 6165

Type strain: Yes

Species: Devosia limi

Strain history: CIP <- 2005, DSMZ <- LMG

NCBI tax ID(s): 1121477 (strain), 288995 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6784

BacDive-ID: 6165

DSM-Number: 17137

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Devosia limi DSM 17137 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from commercial nitrifying inoculum.

NCBI tax id

NCBI tax idMatching level
1121477strain
288995species

strain history

@refhistory
6784<- B. Vanparys, LMG
120599CIP <- 2005, DSMZ <- LMG

doi: 10.13145/bacdive6165.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia limi
  • full scientific name: Devosia limi Vanparys et al. 2005

@ref: 6784

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia limi

full scientific name: Devosia limi Vanparys et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31510negative2 µm0.75 µmrod-shapedno
69480yes93.996
69480negative99.985
120599negativerod-shapedyes

colony morphology

  • @ref: 120599

pigmentation

  • @ref: 31510
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6784TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
33275MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120599CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6784positivegrowth28mesophilic
31510positivegrowth28mesophilic
31510positiveoptimum28mesophilic
33275positivegrowth30mesophilic

culture pH

@refabilitytypepH
31510positivegrowth6.8
31510positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6784aerobe
31510aerobe
120599obligate aerobe

spore formation

@refspore formationconfidence
31510no
69481no100
69480no99.991

observation

  • @ref: 31510
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3151025017leucine+carbon source
315104853esculin+hydrolysis
12059917632nitrate-reduction
12059916301nitrite-reduction

metabolite production

  • @ref: 120599
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31510alkaline phosphatase+3.1.3.1
31510catalase+1.11.1.6
31510cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
120599oxidase+
120599alcohol dehydrogenase-1.1.1.1
120599catalase+1.11.1.6
120599lysine decarboxylase-4.1.1.18
120599ornithine decarboxylase-4.1.1.17
120599urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120599-+---+--------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6784commercial nitrifying inoculumGentBelgiumBELEurope
120599Commercial nitrifying inoculumBelgiumBELEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_5144.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1058;97_3056;98_3836;99_5144&stattab=map
  • Last taxonomy: Devosia limi subclade
  • 16S sequence: AJ786801
  • Sequence Identity:
  • Total samples: 1317
  • soil counts: 532
  • aquatic counts: 211
  • animal counts: 425
  • plant counts: 149

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67841Risk group (German classification)
1205991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6784
  • description: Devosia sp. R-21940 partial 16S rRNA gene, type strain R-21940T
  • accession: AJ786801
  • length: 1437
  • database: ena
  • NCBI tax ID: 288995

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia limi DSM 17137GCA_900128975scaffoldncbi1121477
66792Devosia limi DSM 17137GCA_000970435contigncbi1121477
66792Devosia limi DSM 171371121477.3wgspatric1121477
66792Devosia limi DSM 171371121477.5wgspatric1121477
66792Devosia limi DSM 171372627853739draftimg1121477
66792Devosia limi DSM 171372582580747draftimg1121477

GC content

  • @ref: 6784
  • GC-content: 61.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes76.773yes
flagellatedno82.561yes
gram-positiveno97.757no
anaerobicno97.299yes
aerobicyes90.253no
halophileno95.346no
spore-formingno96.34no
thermophileno97.957yes
glucose-utilyes92.366no
glucose-fermentno88.111no

External links

@ref: 6784

culture collection no.: DSM 17137, CIP 109005, LMG 22951

straininfo link

  • @ref: 75650
  • straininfo: 137492

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166701Devosia limi sp. nov., isolated from a nitrifying inoculum.Vanparys B, Heylen K, Lebbe L, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.63714-02005Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nitrites/*metabolism, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyEnzymology
Phylogeny34435948Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HRInt J Syst Evol Microbiol10.1099/ijsem.0.0049952021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17137)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17137
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
31510Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780628776041
33275Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6699
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
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
75650Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137492.1StrainInfo: A central database for resolving microbial strain identifiers
120599Curators of the CIPCollection of Institut Pasteur (CIP 109005)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109005