Strain identifier

BacDive ID: 17406

Type strain: Yes

Species: Ancylobacter vacuolatus

Strain Designation: NP-300

Strain history: CIP <- 2006, DSMZ <- USSR Academ. Sci., Moscow, Russia: strain NP-300 "Renobacter vacuolatum"

NCBI tax ID(s): 223389 (species)

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General

@ref: 601

BacDive-ID: 17406

DSM-Number: 1277

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

description: Ancylobacter vacuolatus NP-300 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 223389
  • Matching level: species

strain history

@refhistory
601<- Inst. Microbiol., USSR Academy of Sciences, Moscow, NP-300 <- D.I. Nikitin (Renobacter vacuolatum)
123773CIP <- 2006, DSMZ <- USSR Academ. Sci., Moscow, Russia: strain NP-300 "Renobacter vacuolatum"

doi: 10.13145/bacdive17406.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Ancylobacter
  • species: Ancylobacter vacuolatus
  • full scientific name: Ancylobacter vacuolatus Xin et al. 2006

@ref: 601

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Ancylobacter

species: Ancylobacter vacuolatus

full scientific name: Ancylobacter vacuolatus Xin et al. 2006

strain designation: NP-300

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31720negative0.8-1 µmrod-shapedno
123773negativeoval-shapedno

pigmentation

  • @ref: 31720
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
601HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
601MINERAL 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
601ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)yeshttps://mediadive.dsmz.de/medium/7Name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled water
37505MEDIUM 364 - for SpirosomayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (1.000g);Yeast extract (1.000 g);Peptone (1.000 g)
123773CIP Medium 364yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=364

culture temp

@refgrowthtypetemperaturerange
601positivegrowth30mesophilic
31720positivegrowth28-30mesophilic
31720positiveoptimum28-30mesophilic
37505positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31720positivegrowth07-11alkaliphile
31720positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31720
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31720
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31720NaClpositivegrowth0-2.5 %
31720NaClpositiveoptimum0-2.5 %

observation

  • @ref: 31720
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3172030089acetate+carbon source
3172015963ribitol+carbon source
3172016449alanine+carbon source
3172022599arabinose+carbon source
3172029016arginine+carbon source
3172028757fructose+carbon source
3172024265gluconate+carbon source
3172017754glycerol+carbon source
3172025115malate+carbon source
3172029864mannitol+carbon source
3172037684mannose+carbon source
3172026271proline+carbon source
3172017272propionate+carbon source
3172033942ribose+carbon source
3172030911sorbitol+carbon source
317204853esculin+hydrolysis
3172017632nitrate+reduction
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
6837116899D-mannitol-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
12377317632nitrate+reduction
12377316301nitrite-reduction

metabolite production

  • @ref: 123773
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31720catalase+1.11.1.6
31720cytochrome oxidase+1.9.3.1
31720urease+3.5.1.5
123773oxidase+
123773catalase+1.11.1.6
123773urease+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
123773-+++-++-+-++----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123773------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
601soil
123773Environment, SoilRussian FederationRUSEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6269.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_2984;97_3669;98_4644;99_6269&stattab=map
  • Last taxonomy: Ancylobacter
  • 16S sequence: AY211515
  • Sequence Identity:
  • Total samples: 6101
  • soil counts: 1085
  • aquatic counts: 2318
  • animal counts: 1936
  • plant counts: 762

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6011Risk group (German classification)
1237731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31720
  • description: Ancylobacter vacuolatus strain DSM 1277 16S ribosomal RNA gene, partial sequence
  • accession: AY211515
  • length: 1391
  • database: nuccore
  • NCBI tax ID: 223389

Genome sequences

  • @ref: 66792
  • description: Ancylobacter vacuolatus DSM 1277
  • accession: 2926565872
  • assembly level: draft
  • database: img
  • NCBI tax ID: 223389

GC content

  • @ref: 31720
  • GC-content: 65.5

External links

@ref: 601

culture collection no.: DSM 1277, CIP 109300, AS 1.176

straininfo link

  • @ref: 86404
  • straininfo: 47347

literature

  • topic: Phylogeny
  • Pubmed-ID: 16738088
  • title: Ancylobacter polymorphus sp. nov. and Ancylobacter vacuolatus sp. nov.
  • authors: Xin YH, Zhou YG, Chen WX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64118-0
  • year: 2006
  • mesh: Alphaproteobacteria/*classification/cytology/*genetics/growth & development, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
601Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1277
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
31720Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2799628776041
37505Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7026
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)
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
86404Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47347.1StrainInfo: A central database for resolving microbial strain identifiers
123773Curators of the CIPCollection of Institut Pasteur (CIP 109300)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109300