Strain identifier

BacDive ID: 17439

Type strain: Yes

Species: Xanthobacter viscosus

Strain Designation: 7d

Strain history: CIP <- 2004, VKM <- N.V. Doronina, Russian Academ. Scien., Moscow, Russia: strain 7d

NCBI tax ID(s): 110 (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: 15636

BacDive-ID: 17439

DSM-Number: 21355

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

description: Xanthobacter viscosus 7d is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of a sewage purification system of the Baikal paper mill.

NCBI tax id

  • NCBI tax id: 110
  • Matching level: species

strain history

@refhistory
15636<- KCTC <- J. S. Lee <- VKM
123876CIP <- 2004, VKM <- N.V. Doronina, Russian Academ. Scien., Moscow, Russia: strain 7d

doi: 10.13145/bacdive17439.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Xanthobacter
  • species: Xanthobacter viscosus
  • full scientific name: Xanthobacter viscosus Doronina and Trotsenko 2003

@ref: 15636

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Xanthobacter

species: Xanthobacter viscosus

full scientific name: Xanthobacter viscosus Doronina and Trotsenko 2003

strain designation: 7d

type strain: yes

Morphology

cell morphology

  • @ref: 123876
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 123876
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15636NUTRIENT 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
36739MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123876CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123876CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15636positivegrowth30mesophilic
36739positivegrowth30mesophilic
123876positivegrowth15-30
123876nogrowth10psychrophilic
123876nogrowth37mesophilic
123876nogrowth41thermophilic
123876nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123876
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123876NaClpositivegrowth0 %
123876NaClnogrowth2 %
123876NaClnogrowth4 %
123876NaClnogrowth6 %
123876NaClnogrowth8 %
123876NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12387616947citrate+carbon source
1238764853esculin-hydrolysis
123876606565hippurate-hydrolysis
12387617632nitrate+reduction
12387616301nitrite-reduction
12387617632nitrate-respiration

antibiotic resistance

  • @ref: 123876
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123876
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12387615688acetoin-
12387617234glucose-

enzymes

@refvalueactivityec
123876oxidase+
123876beta-galactosidase-3.2.1.23
123876alcohol dehydrogenase-1.1.1.1
123876gelatinase-
123876amylase-
123876DNase-
123876caseinase-3.4.21.50
123876catalase+1.11.1.6
123876tween esterase-
123876gamma-glutamyltransferase+2.3.2.2
123876lecithinase-
123876lipase-
123876lysine decarboxylase-4.1.1.18
123876ornithine decarboxylase-4.1.1.17
123876phenylalanine ammonia-lyase-4.3.1.24
123876protease-
123876tryptophan deaminase-
123876urease-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
123876--+--+----+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123876-+-----------------------------------------------+----------+-+------+------------+-----+--------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15636activated sludge of a sewage purification system of the Baikal paper millBaikalRussiaRUSAsia
123876Environment, Activated sludgeRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Industrial wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_4714.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_1529;97_2844;98_3536;99_4714&stattab=map
  • Last taxonomy: Xanthobacter
  • 16S sequence: AF399970
  • Sequence Identity:
  • Total samples: 208
  • soil counts: 34
  • aquatic counts: 110
  • animal counts: 32
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
156361Risk group (German classification)
1238761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15636
  • description: Xanthobacter viscosus 16S ribosomal RNA gene, partial sequence
  • accession: AF399970
  • length: 1384
  • database: ena
  • NCBI tax ID: 110

Genome sequences

  • @ref: 66792
  • description: Xanthobacter viscosus DSM 21355
  • accession: 2928234723
  • assembly level: draft
  • database: img
  • NCBI tax ID: 110

GC content

  • @ref: 15636
  • GC-content: 66.3

External links

@ref: 15636

culture collection no.: DSM 21355, ATCC BAA 298, KCTC 12306, VKM B-2253, CIP 108462

straininfo link

  • @ref: 86435
  • straininfo: 101068

literature

  • topic: Phylogeny
  • Pubmed-ID: 12656170
  • title: Reclassification of 'Blastobacter viscosus' 7d and 'Blastobacter aminooxidans' 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov.
  • authors: Doronina NV, Trotsenko YA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02231-0
  • year: 2003
  • mesh: Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic, Xanthobacter/*classification/genetics/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
15636Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21355)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21355
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
36739Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6087
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)
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
86435Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101068.1StrainInfo: A central database for resolving microbial strain identifiers
123876Curators of the CIPCollection of Institut Pasteur (CIP 108462)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108462