Strain identifier

BacDive ID: 5661

Type strain: Yes

Species: Weeksella virosa

Strain Designation: CL345/78, 9751

Strain history: CIP <- 1987, B. Holmes, London, UK: strain CL345/78 <- CDC: strain 9751

NCBI tax ID(s): 865938 (strain), 1014 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6644

BacDive-ID: 5661

DSM-Number: 16922

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, human pathogen

description: Weeksella virosa CL345/78 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from human urine.

NCBI tax id

NCBI tax idMatching level
1014species
865938strain

strain history

@refhistory
6644<- CIP <- B. Holmes, NCTC London; CL345/78 <- CDC
67770IAM 14551 <-- NCTC 11634 <-- B. Holmes.
123871CIP <- 1987, B. Holmes, London, UK: strain CL345/78 <- CDC: strain 9751

doi: 10.13145/bacdive5661.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Weeksella
  • species: Weeksella virosa
  • full scientific name: Weeksella virosa Holmes et al. 1987

@ref: 6644

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Weeksella

species: Weeksella virosa

full scientific name: Weeksella virosa Holmes et al. 1987 emend. Zhang et al. 2014 emend. Hahnke et al. 2016

strain designation: CL345/78, 9751

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.987
123871negativerod-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_16922_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6644CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40514MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123871CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123871CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6644positivegrowth30mesophilic
40514positivegrowth30mesophilic
50137positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50137obligate aerobe
123871obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.979

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12387117632nitrate-reduction
12387116301nitrite-reduction
6837717634D-glucose-builds acid from
6837715824D-fructose-builds acid from
6837717306maltose-builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea+hydrolysis

metabolite production

  • @ref: 123871
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
68377gamma-glutamyltransferase+2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase+
68377urease+3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase+3.5.2.6
123871oxidase+
123871catalase+1.11.1.6
123871urease+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
123871-+++-++-+-++--------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGT
6644+-----++---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6644human urineNorth CarolinaUSAUSANorth America
50137Human urine
67770Human urineNCUSAUSANorth America
123871Human, UrineNorth CarolinaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6644yes, in single cases1Risk group (German classification)
1238711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides sp. CIP103040 16S ribosomal RNA gene, partial sequenceAF1335391479ena107580
6644Weeksella virosa 16S ribosomal RNA gene, partial sequenceM931521465ena1014
67770Weeksella virosa gene for 16S rRNA, partial sequence, strain: NBRC 16016AB6810311445ena1014
67770Weeksella virosa strain DSM _16922 16S ribosomal RNA gene, partial sequenceMH7894221441ena1014

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Weeksella virosa NCTC11634GCA_900637795completencbi1014
66792Weeksella virosa DSM 16922GCA_000189415completencbi865938
66792Weeksella virosa DSM 16922865938.3completepatric865938
66792Weeksella virosa strain NCTC116341014.5completepatric1014
66792Weeksella virosa 9751, DSM 16922650377986completeimg865938

GC content

@refGC-contentmethod
664437.3
664435.9sequence analysis
6777035.92genome sequence analysis
6777037thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.891no
flagellatedno96.557no
gram-positiveno97.707no
anaerobicno97.141no
aerobicyes81.329yes
halophileno86.99no
spore-formingno96.373no
glucose-utilyes64.6no
thermophileno99.291yes
glucose-fermentno91.648no

External links

@ref: 6644

culture collection no.: DSM 16922, ATCC 43766, CDC 9751, CIP 103040, NCTC 11634, CCUG 30538, JCM 21250, IAM 14551, IFO 16016, LMG 12995, NBRC 16016

straininfo link

  • @ref: 75143
  • straininfo: 7272

literature

  • topic: Phylogeny
  • Pubmed-ID: 26310805
  • title: Algoriella xinjiangensis gen. nov., sp. nov., a new psychrotolerant bacterium of the family Flavobacteriaceae.
  • authors: Yang N, Zhang L, Sun C
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-015-0564-6
  • year: 2015
  • mesh: Bacterial Proteins/*genetics/metabolism, Bacterial Typing Techniques, Flavobacteriaceae/*classification/physiology/ultrastructure, Lipid Metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6644Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16922)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16922
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
40514Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14793
50137Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30538)https://www.ccug.se/strain?id=30538
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68377Automatically annotated from API NH
68382Automatically annotated from API zym
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
75143Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7272.1StrainInfo: A central database for resolving microbial strain identifiers
123871Curators of the CIPCollection of Institut Pasteur (CIP 103040)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103040