Strain identifier

BacDive ID: 2941

Type strain: Yes

Species: Delftia acidovorans

Strain Designation: 2167, 7

Strain history: CIP <- 1988, NCIMB <- T. Wiken, Pseudomonas acidovorans

NCBI tax ID(s): 1218107 (strain), 80866 (species)

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General

@ref: 2038

BacDive-ID: 2941

DSM-Number: 39

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, human pathogen

description: Delftia acidovorans 2167 is a mesophilic, motile human pathogen that was isolated from soil enriched with acetamide.

NCBI tax id

NCBI tax idMatching level
80866species
1218107strain

strain history

@refhistory
2038<- ATCC <- R. Hugh, 2167 <- Lab. Microbiol. Delft <- den Dooren de Jong, 7
67770Y. Kosako 85014 <-- Nissui Pharm. Co., Ltd. <-- ATCC 15668 <-- R. Hugh 2167 <-- Tech. Hogesch., Delft.
116024CIP <- 1988, NCIMB <- T. Wiken, Pseudomonas acidovorans

doi: 10.13145/bacdive2941.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Delftia
  • species: Delftia acidovorans
  • full scientific name: Delftia acidovorans (den Dooren de Jong 1926) Wen et al. 1999

  • synonyms

    @refsynonym
    20215Pseudomonas acidovorans
    20215Comamonas acidovorans

@ref: 2038

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Delftia

species: Delftia acidovorans

full scientific name: Delftia acidovorans (den Dooren de Jong 1926) Wen et al. 1999

strain designation: 2167, 7

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes95.627
6948099.994negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2038REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40510MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116024CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2038positivegrowth30mesophilic
40510positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.951

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2038+----------+--+-++-++

Isolation, sampling and environmental information

isolation

@refsample type
2038soil enriched with acetamide
67770Soil enriched with acetamide
116024Environment, Soil enriched with acetamide

isolation source categories

Cat1Cat2Cat3
#Engineered
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2038yes, in single cases1Risk group (German classification)
1160241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Delftia acidovorans 16S ribosomal RNA gene, partial sequenceAF0787741520ena80866
20218Delftia acidovorans strain BCRC 14819 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014532668ena80866
20218C.acidovorans 16S rRNAX59168158ena80866
20218Delftia acidovorans gene for 16S rRNA, strain: IAM 12409AB0214171522ena80866
20218Delftia acidovorans strain LMG 1226 16S ribosomal RNA gene, partial sequenceEU0241451318ena80866
20218Delftia acidovorans gene for 16S rRNA, partial sequence, strain: NBRC 14950AB6807191458ena80866

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Delftia acidovorans 2167GCA_000741825scaffoldncbi80866
66792Delftia acidovorans NBRC 149501218107.6wgspatric1218107
66792Delftia acidovorans NBRC 149502731957715draftimg1218107
66792Delftia acidovorans 21672609460141draftimg80866
67770Delftia acidovorans NBRC 14950GCA_001598795contigncbi1218107

GC content

@refGC-contentmethod
203866.6thermal denaturation, midpoint method (Tm)
6777067.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.422no
gram-positiveno98.649no
anaerobicno98.56no
aerobicyes92.623no
halophileno94.988no
spore-formingno94.84no
thermophileno99.533yes
glucose-utilno56.39yes
flagellatedyes69.515no
glucose-fermentno88.827yes

External links

@ref: 2038

culture collection no.: DSM 39, ATCC 15668, DSM 50251, JCM 5833, ACM 489, BCRC 14819, CCUG 12692, CCUG 14481, CECT 311, CIP 103021, IAM 12409, IFO 14950, JCM 6203, LMG 1226, LMG 6031, LMG 8910, LMG 8911, NBRC 14950, NCIMB 9681, NCTC 10683, IMET 10620, NCTC 10859

straininfo link

  • @ref: 72463
  • straininfo: 87460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2859843Phenylalanine hydroxylase and isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in relationship to the phylogenetic position of Pseudomonas acidovorans (Ps. sp. ATCC 11299a).Berry A, Johnson JL, Jensen RAArch Microbiol10.1007/BF0044673619853-Deoxy-7-Phosphoheptulonate Synthase/*genetics, Aldehyde-Lyases/*genetics, DNA, Bacterial/genetics, Isoenzymes/genetics, Phenylalanine Hydroxylase/*genetics, Phylogeny, Pseudomonas/*enzymology/genetics, Species SpecificityEnzymology
Phylogeny10319477Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov.Wen A, Fegan M, Hayward C, Chakraborty S, Sly LIInt J Syst Bacteriol10.1099/00207713-49-2-5671999DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Gram-Negative Aerobic Rods and Cocci/*classification/cytology/*genetics/physiology, Gram-Negative Bacteria/*classification/cytology/*genetics/physiology, Molecular Sequence Data, *Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny13130036Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludge.Shigematsu T, Yumihara K, Ueda Y, Numaguchi M, Morimura S, Kida KInt J Syst Evol Microbiol10.1099/ijs.0.02285-02003Base Composition, Base Sequence, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Delftia/classification/genetics/*isolation & purification/*metabolism, Molecular Sequence Data, Phenotype, Phthalic Acids/*metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Water Pollutants, Chemical/*metabolismMetabolism
Phylogeny22140156Delftia litopenaei sp. nov., a poly-beta-hydroxybutyrate-accumulating bacterium isolated from a freshwater shrimp culture pond.Chen WM, Lin YS, Sheu DS, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.037507-02011Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Delftia/*classification/genetics/isolation & purification/metabolism, Fatty Acids/analysis, Hydroxybutyrates/*metabolism, Molecular Sequence Data, Penaeidae, *Phylogeny, Polyesters/*metabolism, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Water MicrobiologyMetabolism
Metabolism24704165Engineering Delftia acidovorans DSM39 to produce polyhydroxyalkanoates from slaughterhouse waste.Romanelli MG, Povolo S, Favaro L, Fontana F, Basaglia M, Casella SInt J Biol Macromol10.1016/j.ijbiomac.2014.03.0492014*Abattoirs, *Biotransformation, Delftia acidovorans/*genetics/growth & development/*metabolism, Polyhydroxyalkanoates/*metabolism, *Waste ProductsBiotechnology
25237026Draft Genome Assembly of Delftia acidovorans Type Strain 2167.Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Palacios GF, Redden CL, Scholz MB, Teshima H, Johnson SLGenome Announc10.1128/genomeA.00917-142014
Phylogeny25842037Delftia deserti sp. nov., isolated from a desert soil sample.Li CT, Yan ZF, Chu X, Hussain F, Xian WD, Yunus Z, Hozzein WN, Abaydulla G, Li WJAntonie Van Leeuwenhoek10.1007/s10482-015-0440-42015Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Delftia/*classification/genetics/*isolation & purification/physiology, Desert Climate, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Metabolism29660658Nuclease expression in efficient polyhydroxyalkanoates-producing bacteria could yield cost reduction during downstream processing.Rodriguez Gamero JE, Favaro L, Pizzocchero V, Lomolino G, Basaglia M, Casella SBioresour Technol10.1016/j.biortech.2018.04.0212018*Cupriavidus necator, Deoxyribonucleases/metabolism, Polyhydroxyalkanoates/*metabolism, Staphylococcus aureus/metabolism, ViscosityBiotechnology
31516356Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa.Khalifa AYZ, AlMalki MSaudi J Biol Sci10.1016/j.sjbs.2018.05.0152018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2038Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 39)https://www.dsmz.de/collection/catalogue/details/culture/DSM-39
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40510Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14772
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
72463Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87460.1StrainInfo: A central database for resolving microbial strain identifiers
116024Curators of the CIPCollection of Institut Pasteur (CIP 103021)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103021