Strain identifier
BacDive ID: 12641
Type strain:
Species: Cutibacterium avidum
Strain Designation: 1689B
Strain history: CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 0179 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1689B
NCBI tax ID(s): 997355 (strain), 33010 (species)
General
@ref: 1868
BacDive-ID: 12641
DSM-Number: 4901
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped
description: Cutibacterium avidum 1689B is an anaerobe, mesophilic, Gram-positive bacterium of the family Propionibacteriaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
33010 | species |
997355 | strain |
strain history
@ref | history |
---|---|
1868 | <- ATCC <- W.E.C. Moore, VPI 0179 <- A.R. Prévot, 1689B |
116665 | CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 0179 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1689B |
doi: 10.13145/bacdive12641.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Propionibacteriaceae
- genus: Cutibacterium
- species: Cutibacterium avidum
- full scientific name: Cutibacterium avidum (Eggerth 1935) Scholz and Kilian 2016
synonyms
@ref synonym 20215 Bacteroides avidus 20215 Propionibacterium avidum
@ref: 1868
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Propionibacteriaceae
genus: Cutibacterium
species: Cutibacterium avidum
full scientific name: Cutibacterium avidum (Eggerth 1935) Scholz and Kilian 2016 emend. Nouioui et al. 2018
strain designation: 1689B
type strain: yes
Morphology
cell morphology
- @ref: 116665
- gram stain: positive
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 53372
- incubation period: 2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1868 | 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 |
42202 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
1868 | 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 |
116665 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1868 | positive | growth | 37 | mesophilic |
42202 | positive | growth | 37 | mesophilic |
53372 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
1868 | anaerobe |
53372 | anaerobe |
53372 | microaerophile |
116665 | anaerobe |
compound production
- @ref: 1868
- compound: LL diaminopimelic acid
murein
- @ref: 1868
- murein short key: A41.01
- type: A3gamma LL-Dpm-Gly
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | + | builds acid from | 24265 |
68371 | L-arabitol | + | builds acid from | 18403 |
68371 | D-arabitol | + | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | + | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | + | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | + | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | + | builds acid from | 17113 |
68371 | glycerol | + | builds acid from | 17754 |
116665 | nitrate | - | reduction | 17632 |
116665 | nitrite | - | reduction | 16301 |
68380 | urea | - | hydrolysis | 16199 |
68380 | arginine | - | hydrolysis | 29016 |
68380 | D-mannose | + | fermentation | 16024 |
68380 | raffinose | - | fermentation | 16634 |
68380 | L-glutamate | - | degradation | 29985 |
68380 | nitrate | - | reduction | 17632 |
68380 | tryptophan | - | energy source | 27897 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
116665 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | + | 3.2.1.55 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
116665 | oxidase | - | |
116665 | catalase | + | 1.11.1.6 |
116665 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116665 | - | + | + | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116665 | + | + | - | + | + | - | - | + | - | + | + | + | + | - | - | - | + | - | - | - | - | + | - | - | - | - | - | + | - | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | + | + | + | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1868 | - | - | - | +/- | - | + | +/- | + | - | - | + | - | - | - | - | - | - | +/- | + | +/- | - | - | - | - | + | + | - | - | + |
1868 | - | - | - | +/- | - | + | +/- | + | - | +/- | + | - | - | - | - | - | - | - | + | +/- | - | - | - | - | +/- | +/- | - | - | +/- |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_868.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_410;97_598;98_687;99_868&stattab=map
- Last taxonomy: Cutibacterium avidum subclade
- 16S sequence: KF906606
- Sequence Identity:
- Total samples: 29908
- soil counts: 847
- aquatic counts: 1592
- animal counts: 27061
- plant counts: 408
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1868 | 2 | Risk group (German classification) |
116665 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Propionibacterium avidum strain ATCC 25577 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence | AF386071 | 284 | ena | 997355 |
20218 | Propionibacterium avidum ATCC 25577 16S rRNA gene, partial sequence | U02905 | 385 | ena | 997355 |
20218 | Propionibacterium avidum ATCC 25577 16S ribosomal RNA gene, partial sequence | KF906606 | 1462 | ena | 997355 |
1868 | Propionibacterium avidum DSM 4901 16S rRNA gene | AJ003055 | 1504 | ena | 997355 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Propionibacterium avidum ATCC 25577 | 997355.3 | wgs | patric | 997355 |
66792 | Cutibacterium avidum VPI 0179 | 2518285596 | draft | img | 997355 |
66792 | Cutibacterium avidum VPI 0179 | 2513237389 | draft | img | 997355 |
66792 | Cutibacterium avidum ATCC 25577 | GCA_000227295 | scaffold | ncbi | 997355 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 94.872 | no |
flagellated | no | 98.196 | no |
gram-positive | yes | 92.244 | no |
anaerobic | no | 55.086 | no |
aerobic | no | 86.098 | yes |
halophile | no | 86.679 | no |
spore-forming | no | 91.912 | no |
thermophile | no | 84.726 | yes |
glucose-util | yes | 90.7 | no |
glucose-ferment | yes | 78.477 | no |
External links
@ref: 1868
culture collection no.: DSM 4901, ATCC 25577, CCUG 36754, VPI 0179, CIP 103261, NCDO 2585, NCTC 11864, PCM 2467, NBRC 15671
straininfo link
- @ref: 81854
- straininfo: 38601
literature
- topic: Phylogeny
- Pubmed-ID: 824484
- title: Mitogenic activity of the cell walls of mycobacteria, nocardia, corynebacteria and anaerobic coryneforms.
- authors: Azuma I, Taniyama T, Sugimura K, Aladin A, Yamamura Y
- journal: Jpn J Microbiol
- DOI: 10.1111/j.1348-0421.1976.tb00987.x
- year: 1976
- mesh: Animals, B-Lymphocytes/immunology, *BCG Vaccine, Bacterial Proteins/analysis, Cell Wall/immunology, Corynebacterium diphtheriae/*immunology, Female, *Lymphocyte Activation, Male, Mice, *Mitogens, Mucoproteins, Mycobacterium bovis/*immunology, Mycolic Acids/immunology, Nocardia/*immunology, Polysaccharides, Bacterial, Propionibacterium/*immunology, Species Specificity, Spleen/immunology, T-Lymphocytes/immunology
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1868 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4901) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4901 | |||
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 | |
42202 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15039 | ||||
53372 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 36754) | https://www.ccug.se/strain?id=36754 | |||
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) | |||
68371 | Automatically annotated from API 50CH acid | |||||
68380 | Automatically annotated from API rID32A | |||||
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 | |||
81854 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38601.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116665 | Curators of the CIP | Collection of Institut Pasteur (CIP 103261) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103261 |