Strain identifier
BacDive ID: 5661
Type strain:
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)
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 id | Matching level |
---|---|
1014 | species |
865938 | strain |
strain history
@ref | history |
---|---|
6644 | <- CIP <- B. Holmes, NCTC London; CL345/78 <- CDC |
67770 | IAM 14551 <-- NCTC 11634 <-- B. Holmes. |
123871 | CIP <- 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.987 | ||
123871 | negative | rod-shaped | no |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
6644 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
40514 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
123871 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
123871 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6644 | positive | growth | 30 | mesophilic |
40514 | positive | growth | 30 | mesophilic |
50137 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
50137 | obligate aerobe |
123871 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.979 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123871 | 17632 | nitrate | - | reduction |
123871 | 16301 | nitrite | - | reduction |
68377 | 17634 | D-glucose | - | builds acid from |
68377 | 15824 | D-fructose | - | builds acid from |
68377 | 17306 | maltose | - | builds acid from |
68377 | 17992 | sucrose | - | builds acid from |
68377 | 18257 | ornithine | - | degradation |
68377 | 16199 | urea | + | hydrolysis |
metabolite production
- @ref: 123871
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68377 | gamma-glutamyltransferase | + | 2.3.2.2 |
68377 | proline-arylamidase | - | 3.4.11.5 |
68377 | beta-galactosidase | - | 3.2.1.23 |
68377 | alkaline phosphatase | - | 3.1.3.1 |
68377 | lipase | + | |
68377 | urease | + | 3.5.1.5 |
68377 | ornithine decarboxylase | - | 4.1.1.17 |
68377 | beta-lactamase | + | 3.5.2.6 |
123871 | oxidase | + | |
123871 | catalase | + | 1.11.1.6 |
123871 | urease | + | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123871 | - | + | + | + | - | + | + | - | + | - | + | + | - | - | - | - | - | - | - | - |
API NH
@ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT |
---|---|---|---|---|---|---|---|---|---|---|---|---|
6644 | + | - | - | - | - | - | + | + | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6644 | human urine | North Carolina | USA | USA | North America |
50137 | Human urine | ||||
67770 | Human urine | NC | USA | USA | North America |
123871 | Human, Urine | North Carolina | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Urine |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
6644 | yes, in single cases | 1 | Risk group (German classification) |
123871 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacteroides sp. CIP103040 16S ribosomal RNA gene, partial sequence | AF133539 | 1479 | ena | 107580 |
6644 | Weeksella virosa 16S ribosomal RNA gene, partial sequence | M93152 | 1465 | ena | 1014 |
67770 | Weeksella virosa gene for 16S rRNA, partial sequence, strain: NBRC 16016 | AB681031 | 1445 | ena | 1014 |
67770 | Weeksella virosa strain DSM _16922 16S ribosomal RNA gene, partial sequence | MH789422 | 1441 | ena | 1014 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Weeksella virosa NCTC11634 | GCA_900637795 | complete | ncbi | 1014 |
66792 | Weeksella virosa DSM 16922 | GCA_000189415 | complete | ncbi | 865938 |
66792 | Weeksella virosa DSM 16922 | 865938.3 | complete | patric | 865938 |
66792 | Weeksella virosa strain NCTC11634 | 1014.5 | complete | patric | 1014 |
66792 | Weeksella virosa 9751, DSM 16922 | 650377986 | complete | img | 865938 |
GC content
@ref | GC-content | method |
---|---|---|
6644 | 37.3 | |
6644 | 35.9 | sequence analysis |
67770 | 35.92 | genome sequence analysis |
67770 | 37 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.891 | no |
flagellated | no | 96.557 | no |
gram-positive | no | 97.707 | no |
anaerobic | no | 97.141 | no |
aerobic | yes | 81.329 | yes |
halophile | no | 86.99 | no |
spore-forming | no | 96.373 | no |
glucose-util | yes | 64.6 | no |
thermophile | no | 99.291 | yes |
glucose-ferment | no | 91.648 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6644 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16922) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16922 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40514 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14793 | ||||
50137 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 30538) | https://www.ccug.se/strain?id=30538 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68377 | Automatically annotated from API NH | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75143 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7272.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123871 | Curators of the CIP | Collection of Institut Pasteur (CIP 103040) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103040 |