Strain identifier

BacDive ID: 2888

Type strain: Yes

Species: Acidovorax facilis

Strain history: CIP <- 1989, DSM <- ATCC, Pseudomonas facilis <- A. Schatz, Hydrogenomonas facilis

NCBI tax ID(s): 12917 (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: 347

BacDive-ID: 2888

DSM-Number: 649

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

description: Acidovorax facilis DSM 649 is an obligate aerobe, mesophilic, Gram-negative bacterium of the family Comamonadaceae.

NCBI tax id

  • NCBI tax id: 12917
  • Matching level: species

strain history

@refhistory
347<- ATCC <- A. Schatz (Hydrogenomonas facilis)
119161CIP <- 1989, DSM <- ATCC, Pseudomonas facilis <- A. Schatz, Hydrogenomonas facilis

doi: 10.13145/bacdive2888.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Acidovorax
  • species: Acidovorax facilis
  • full scientific name: Acidovorax facilis (Schatz and Bovell 1952) Willems et al. 1990

  • synonyms

    @refsynonym
    20215Hydrogenomonas facilis
    20215Pseudomonas facilis

@ref: 347

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax facilis

full scientific name: Acidovorax facilis (Schatz and Bovell 1952) Willems et al. 1990

type strain: yes

Morphology

cell morphology

  • @ref: 119161
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 119161
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
347MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
347NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40593MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119161CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
347positivegrowth30mesophilic
40593positivegrowth25mesophilic
44487positivegrowth30mesophilic
119161positivegrowth10-30
119161nogrowth5psychrophilic
119161nogrowth37mesophilic
119161nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119161
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119161NaClpositivegrowth0 %
119161NaClnogrowth2 %
119161NaClnogrowth4 %
119161NaClnogrowth6 %
119161NaClnogrowth8 %
119161NaClnogrowth10 %

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
11916116947citrate-carbon source
1191614853esculin-hydrolysis
11916117632nitrate+reduction
11916116301nitrite-reduction
11916117632nitrate-respiration

antibiotic resistance

  • @ref: 119161
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11916135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119161oxidase+
119161beta-galactosidase-3.2.1.23
119161alcohol dehydrogenase-1.1.1.1
119161gelatinase+/-
119161amylase-
119161DNase-
119161caseinase+3.4.21.50
119161catalase+1.11.1.6
119161tween esterase+
119161lecithinase+
119161lipase-
119161lysine decarboxylase-4.1.1.18
119161ornithine decarboxylase-4.1.1.17
119161protease+
119161tryptophan deaminase-
119161urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    44487C12:04.712
    44487C14:04.914
    44487C16:027.316
    44487C10:0 3OH411.423
    44487C16:1 ω7c44.515.819
    44487C18:1 ω7c /12t/9t12.417.824
    44487C18:2 ω6,9c/C18:0 ANTE1.317.724
    44487C8:0 3OH0.99.385
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
44487-+++-+----+---------
119161-+++-+----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
44487+-------------------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119161-++-----------------+---------------------------++------------+--+---------+---++-------++++-------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample type
40593USAUSANorth America
44487USAUSANorth AmericaLawn soil
119161United States of AmericaUSANorth AmericaEnvironment, Lawn soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden
#Engineered#Built environment
#Environmental#Terrestrial#Grassland

taxonmaps

  • @ref: 69479
  • File name: preview.99_1316.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_1041;99_1316&stattab=map
  • Last taxonomy: Acidovorax
  • 16S sequence: AF078765
  • Sequence Identity:
  • Total samples: 1276
  • soil counts: 254
  • aquatic counts: 364
  • animal counts: 150
  • plant counts: 508

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
3471Risk group (German classification)
1191611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidovorax facilis strain FC-208 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ360425622ena12917
20218Acidovorax facilis 16S ribosomal RNA gene, partial sequenceAF0787651511ena12917
20218Acidovorax facilis 16S rRNA gene, strain DSM 649AJ4203241311ena12917
20218P.facilis 16S rRNAX59169158ena12917
20218Acidovorax facilis strain LMG 2193 16S ribosomal RNA gene, partial sequenceEU0241331318ena12917

Genome sequences

  • @ref: 66792
  • description: Acidovorax facilis DSM 649
  • accession: GCA_023913775
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 12917

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes73.486no
gram-positiveno98.78no
anaerobicno98.817no
aerobicyes94.215no
halophileno96.537no
spore-formingno94.219no
motileyes89.666no
glucose-fermentno90.121no
thermophileno98.806yes
glucose-utilyes64.64yes

External links

@ref: 347

culture collection no.: DSM 649, ATCC 11228, CCUG 2113, LMG 6221, LMG 2193, CCM 4561, CIP 103302, NCIMB 9938

straininfo link

  • @ref: 72411
  • straininfo: 136

literature

  • topic: Phylogeny
  • Pubmed-ID: 2275854
  • title: Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov.
  • authors: Willems A, Falsen E, Pot B, Jantzen E, Hoste B, Vandamme P, Gillis M, Kersters K, De Ley J
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-40-4-384
  • year: 1990
  • mesh: Base Composition, Base Sequence, Chromatography, Gas, Cluster Analysis, DNA, Bacterial/analysis, Electrophoresis, Fatty Acids/analysis, Nucleic Acid Hybridization, Phenotype, Pseudomonas/*classification/genetics, Terminology as Topic
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
347Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 649)https://www.dsmz.de/collection/catalogue/details/culture/DSM-649
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
40593Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15084
44487Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2113)https://www.ccug.se/strain?id=2113
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)
68369Automatically annotated from API 20NE
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
72411Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID136.1StrainInfo: A central database for resolving microbial strain identifiers
119161Curators of the CIPCollection of Institut Pasteur (CIP 103302)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103302