Strain identifier
BacDive ID: 17681
Type strain: 
Species: Papillibacter cinnamivorans
Strain Designation: CIN1
Strain history: <- J.-L. Garcia, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; CIN1 <- S. Defnoun {1998}
NCBI tax ID(s): 1122930 (strain), 100176 (species)
version 9.1 (current version)
General
@ref: 4833
BacDive-ID: 17681
DSM-Number: 12816
keywords: genome sequence, 16S sequence, Bacteria, anaerobe
description: Papillibacter cinnamivorans CIN1 is an anaerobe bacterium that was isolated from anaerobic shea cake digester.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122930 | strain |
| 100176 | species |
strain history
- @ref: 4833
- history: <- J.-L. Garcia, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; CIN1 <- S. Defnoun {1998}
doi: 10.13145/bacdive17681.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Papillibacter
- species: Papillibacter cinnamivorans
- full scientific name: Papillibacter cinnamivorans Defnoun et al. 2000
@ref: 4833
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Papillibacter
species: Papillibacter cinnamivorans
full scientific name: Papillibacter cinnamivorans Defnoun et al. 2000
strain designation: CIN1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 4833
- name: PAPILLIBACTER MEDIUM (DSMZ Medium 872)
- growth: yes
- link: https://mediadive.dsmz.de/medium/872
- composition: Name: PAPILLIBACTER MEDIUM (DSMZ Medium 872) Composition: Trypticase peptone 4.99501 g/l Yeast extract 4.99501 g/l Na2CO3 1.998 g/l NaCl 0.999001 g/l trans-Cinnamic acid 0.749251 g/l L-Cysteine HCl x H2O 0.499501 g/l Na2S x 9 H2O 0.499501 g/l KCl 0.499501 g/l MgCl2 x 6 H2O 0.3996 g/l NH4Cl 0.2997 g/l K2HPO4 0.1998 g/l CaCl2 x 2 H2O 0.0999001 g/l HCl 0.0024975 g/l FeCl2 x 4 H2O 0.0014985 g/l Sodium resazurin 0.0004995 g/l CoCl2 x 6 H2O 0.00018981 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l Na2MoO4 x 2 H2O 3.5964e-05 g/l NiCl2 x 6 H2O 2.3976e-05 g/l H3BO3 5.99401e-06 g/l CuCl2 x 2 H2O 1.998e-06 g/l Distilled water
culture temp
- @ref: 4833
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 4833
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 4833
- sample type: anaerobic shea cake digester
- country: Burkina Faso
- origin.country: BFA
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Anaerobic digestor |
| #Engineered | #Industrial | |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_6545.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_580;96_3103;97_3804;98_4832;99_6545&stattab=map
- Last taxonomy: Papillibacter cinnamivorans subclade
- 16S sequence: AF167711
- Sequence Identity:
- Total samples: 15953
- soil counts: 301
- aquatic counts: 1183
- animal counts: 14388
- plant counts: 81
Safety information
risk assessment
- @ref: 4833
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4833
- description: Papillibacter cinnaminovorans 16S ribosomal RNA gene, partial sequence
- accession: AF167711
- length: 1491
- database: nuccore
- NCBI tax ID: 100176
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Papillibacter cinnamivorans DSM 12816 | GCA_900176335 | scaffold | ncbi | 1122930 |
| 66792 | Papillibacter cinnamivorans DSM 12816 strain DSM 12816 | 1122930.3 | wgs | patric | 1122930 |
| 66792 | Papillibacter cinnamivorans DSM 12816 | 2588254267 | draft | img | 1122930 |
GC content
- @ref: 4833
- GC-content: 56
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 72 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 62.322 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 88.161 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 91.954 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 51.561 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 75.653 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 66.234 | no |
External links
@ref: 4833
culture collection no.: DSM 12816, ATCC 700879
straininfo link
- @ref: 86672
- straininfo: 6781
literature
- topic: Phylogeny
- Pubmed-ID: 10843066
- title: Papillibacter cinnamivorans gen. nov., sp. nov., a cinnamate-transforming bacterium from a shea cake digester.
- authors: Defnoun S, Labat M, Ambrosio M, Garcia JL, Patel BK
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-50-3-1221
- year: 2000
- mesh: Anaerobiosis, Bacteria, Anaerobic/*classification/genetics/growth & development/metabolism, Bioreactors, Cinnamates/*metabolism, Culture Media, DNA, Bacterial/chemistry/genetics, Genes, rRNA, Gram-Positive Asporogenous Rods/*classification/genetics/*growth & development/metabolism, Hydrocarbons, Aromatic/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tannins/metabolism, Trees
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4833 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12816) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12816 | |||
| 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 | |||
| 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) | |||
| 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 | |
| 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 | |||
| 86672 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID6781.1 | StrainInfo: A central database for resolving microbial strain identifiers |