Strain identifier
BacDive ID: 210
Type strain:
Species: Varibaculum cambriense
Strain Designation: R12359
Strain history: CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359
NCBI tax ID(s): 1123488 (strain), 184870 (species)
General
@ref: 6116
BacDive-ID: 210
DSM-Number: 15806
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Varibaculum cambriense R12359 is an anaerobe, mesophilic bacterium that was isolated from human postauricular abscess, 27 years old male.
NCBI tax id
NCBI tax id | Matching level |
---|---|
184870 | species |
1123488 | strain |
strain history
@ref | history |
---|---|
6116 | <- E. Falsen, CCUG <- M. D. Collins, Univ. of Reading <- V. Hall |
117109 | CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359 |
doi: 10.13145/bacdive210.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Actinomycetales
- family: Actinomycetaceae
- genus: Varibaculum
- species: Varibaculum cambriense
- full scientific name: Varibaculum cambriense corrig. Hall et al. 2003
synonyms
- @ref: 20215
- synonym: Varibaculum cambriensis
@ref: 6116
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Actinomycetaceae
genus: Varibaculum
species: Varibaculum cambriense
full scientific name: Varibaculum cambriense Hall et al. 2003 emend. Nouioui et al. 2018
strain designation: R12359
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 92.907 | ||
69480 | 100 | positive | ||
117109 | no | rod-shaped |
colony morphology
- @ref: 117109
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_15806_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15806_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15806_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15806_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15806_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6116 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water |
6116 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
42112 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
117109 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6116 | positive | growth | 37 | mesophilic |
42112 | positive | growth | 37 | mesophilic |
56585 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
6116 | anaerobe | |
56585 | anaerobe | |
56585 | microaerophile | |
69480 | anaerobe | 97.849 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
117109 | 17108 | D-arabinose | - | degradation |
117109 | 15824 | D-fructose | + | degradation |
117109 | 17634 | D-glucose | - | degradation |
117109 | 65327 | D-xylose | - | degradation |
117109 | 17057 | cellobiose | - | degradation |
117109 | 17716 | lactose | - | degradation |
117109 | 17306 | maltose | - | degradation |
117109 | 17814 | salicin | - | degradation |
117109 | 17992 | sucrose | - | degradation |
117109 | 4853 | esculin | - | hydrolysis |
117109 | 17632 | nitrate | + | reduction |
117109 | 16301 | nitrite | - | reduction |
117109 | 35020 | tributyrin | + | hydrolysis |
metabolite production
- @ref: 117109
- Chebi-ID: 35581
- metabolite: indole
- production: no
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 |
117109 | oxidase | - | |
117109 | beta-galactosidase | - | 3.2.1.23 |
117109 | gelatinase | - | |
117109 | amylase | - | |
117109 | DNase | - | |
117109 | caseinase | - | 3.4.21.50 |
117109 | catalase | + | 1.11.1.6 |
117109 | tween esterase | - | |
117109 | lecithinase | - | |
117109 | lipase | - | |
117109 | protease | - | |
117109 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117109 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
6116 | human postauricular abscess, 27 years old male | London | United Kingdom | GBR | Europe | |
56585 | Human postauricular abscess,27-yr-old male | London | United Kingdom | GBR | Europe | 1998 |
117109 | Human | Cardiff | United Kingdom | GBR | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | #Male |
#Host Body-Site | #Other | #Abscess |
#Host Body-Site | #Organ | #Ear |
taxonmaps
- @ref: 69479
- File name: preview.99_5423.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_520;96_2630;97_3222;98_4047;99_5423&stattab=map
- Last taxonomy: Varibaculum cambriense
- 16S sequence: AM084231
- Sequence Identity:
- Total samples: 7892
- soil counts: 30
- aquatic counts: 56
- animal counts: 7804
- plant counts: 2
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6116 | 2 | Risk group (German classification) |
117109 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Varibaculum cambriensis partial 16S rRNA gene, strain CCUG 44998 | AJ428402 | 1510 | ena | 184870 |
20218 | Varibaculum cambriense partial 16S rRNA gene, isolate CCUG 44998T | AM084231 | 1509 | ena | 184870 |
6116 | Varibaculum cambriensis 16S rRNA gene, type strain CCUG 44998T | AJ491326 | 1510 | ena | 184870 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Varibaculum cambriense DSM 15806 | GCA_000420065 | contig | ncbi | 1123488 |
66792 | Varibaculum cambriense DSM 15806 | 1123488.3 | wgs | patric | 1123488 |
66792 | Varibaculum cambriense DSM 15806 | 2524614732 | draft | img | 1123488 |
GC content
- @ref: 6116
- GC-content: 51.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.191 | no |
flagellated | no | 96.825 | no |
gram-positive | yes | 91.42 | no |
anaerobic | yes | 73.491 | no |
aerobic | no | 98.368 | no |
halophile | no | 82.933 | no |
spore-forming | no | 97.122 | no |
thermophile | no | 95.453 | yes |
glucose-util | yes | 78.521 | no |
glucose-ferment | yes | 79.261 | no |
External links
@ref: 6116
culture collection no.: DSM 15806, CCUG 44998, CIP 107344
straininfo link
- @ref: 69893
- straininfo: 25796
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12574260 | Characterization of some actinomyces-like isolates from human clinical sources: description of Varibaculum cambriensis gen nov, sp nov. | Hall V, Collins MD, Lawson PA, Hutson RA, Falsen E, Inganas E, Duerden B | J Clin Microbiol | 10.1128/JCM.41.2.640-644.2003 | 2003 | Actinomycetaceae/classification/genetics/*isolation & purification, Humans, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics | Pathogenicity |
Phylogeny | 27745752 | Varibaculum anthropi sp. nov. represented by three genetically different genomovars isolated from clinical material and emended description of the genus Varibaculum. | Glaeser SP, Doijad S, Hijazin M, Chakraborty T, Falsen E, Hall V, Kampfer P | Syst Appl Microbiol | 10.1016/j.syapm.2016.09.002 | 2016 | Actinomycetaceae/*classification/*genetics/isolation & purification, Adolescent, Adult, Base Sequence, DNA, Bacterial/*genetics, Female, Genome, Bacterial/*genetics, Humans, Male, Middle Aged, Multilocus Sequence Typing, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6116 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15806) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15806 | |||
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 | |
42112 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4769 | ||||
56585 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 44998) | https://www.ccug.se/strain?id=44998 | |||
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 | |
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
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 | |||
69893 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID25796.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
117109 | Curators of the CIP | Collection of Institut Pasteur (CIP 107344) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107344 |