Strain identifier
BacDive ID: 12518
Type strain:
Species: Barnesiella viscericola
Strain Designation: C46
Strain history: M. Sakamoto <-- P. T. N. Lan C46.
NCBI tax ID(s): 880074 (strain), 397865 (species)
General
@ref: 7411
BacDive-ID: 12518
DSM-Number: 18177
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Barnesiella viscericola C46 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from chicken caecum.
NCBI tax id
NCBI tax id | Matching level |
---|---|
880074 | strain |
397865 | species |
strain history
@ref | history |
---|---|
7411 | <- M. Sakamoto; C46 <- P. T. N. Lan |
67770 | M. Sakamoto <-- P. T. N. Lan C46. |
doi: 10.13145/bacdive12518.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Barnesiellaceae
- genus: Barnesiella
- species: Barnesiella viscericola
- full scientific name: Barnesiella viscericola Sakamoto et al. 2007
@ref: 7411
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Barnesiellaceae
genus: Barnesiella
species: Barnesiella viscericola
full scientific name: Barnesiella viscericola Sakamoto et al. 2007
strain designation: C46
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31956 | negative | 6.35 µm | 1.2 µm | rod-shaped | no | |
69480 | no | 91.408 | ||||
69480 | negative | 99.999 |
colony morphology
@ref | incubation period |
---|---|
7411 | 2-3 days |
60660 | 2 days |
pigmentation
- @ref: 31956
- production: no
multimedia
- @ref: 66793
- multimedia content: EM_DSM_18177_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7411 | COLUMBIA BLOOD AGAR (DSMZ Medium 429) | yes | https://mediadive.dsmz.de/medium/429 | Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base |
7411 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7411 | positive | growth | 37 | mesophilic |
60660 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7411 | anaerobe | |
31956 | anaerobe | |
60660 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
31956 | no | |
69481 | no | 100 |
69480 | no | 100 |
observation
- @ref: 67770
- observation: quinones: MK-11, MK-12
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31956 | 30089 | acetate | + | carbon source |
31956 | 17057 | cellobiose | + | carbon source |
31956 | 17234 | glucose | + | carbon source |
31956 | 17306 | maltose | + | carbon source |
31956 | 37684 | mannose | + | carbon source |
31956 | 16634 | raffinose | + | carbon source |
31956 | 30031 | succinate | + | carbon source |
31956 | 17992 | sucrose | + | carbon source |
31956 | 4853 | esculin | + | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | + | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
31956 | alkaline phosphatase | + | 3.1.3.1 |
31956 | alpha-galactosidase | + | 3.2.1.22 |
31956 | gelatinase | + | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
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 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
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 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7411 | - | +/- | + | + | - | + | +/- | - | - | + | - | - | + | + | - | - | + | - | - | + | - | - | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
7411 | chicken caecum | Japan | JPN | Asia |
67770 | Chicken cecum |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Birds | #Chicken |
#Host Body-Site | #Gastrointestinal tract | #Large intestine |
taxonmaps
- @ref: 69479
- File name: preview.99_5595.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_530;96_2697;97_3313;98_4173;99_5595&stattab=map
- Last taxonomy: Barnesiella viscericola subclade
- 16S sequence: AB267809
- Sequence Identity:
- Total samples: 13231
- soil counts: 419
- aquatic counts: 558
- animal counts: 12135
- plant counts: 119
Safety information
risk assessment
- @ref: 7411
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7411
- description: Barnesiella viscericola gene for 16S ribosomal RNA, partial sequence
- accession: AB267809
- length: 1461
- database: ena
- NCBI tax ID: 880074
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Barnesiella viscericola DSM 18177 C46, DSM 18177 | GCA_000512915 | complete | ncbi | 880074 |
66792 | Barnesiella viscericola DSM 18177 strain C46, DSM 18177 | 880074.29 | complete | patric | 880074 |
66792 | Barnesiella viscericola C46, DSM 18177 | 2509276067 | complete | img | 880074 |
GC content
@ref | GC-content | method |
---|---|---|
7411 | 52.0 | |
31956 | 52 | |
67770 | 52 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.884 | yes |
flagellated | no | 96.289 | yes |
gram-positive | no | 97.108 | yes |
anaerobic | yes | 99.171 | yes |
halophile | no | 81.04 | no |
spore-forming | no | 96.483 | yes |
thermophile | no | 96.145 | no |
glucose-util | yes | 87.207 | no |
aerobic | no | 98.809 | yes |
glucose-ferment | yes | 56.522 | no |
External links
@ref: 7411
culture collection no.: CCUG 55593, DSM 18177, JCM 13660
straininfo link
- @ref: 81737
- straininfo: 294005
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17267976 | Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum. | Sakamoto M, Lan PTN, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64709-0 | 2007 | Anaerobiosis, Animals, Anti-Bacterial Agents/pharmacokinetics, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, Bile, Cecum/*microbiology, Chickens/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Gram-Negative Aerobic Rods and Cocci, Molecular Sequence Data, Movement, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Enzymology |
Pathogenicity | 35806099 | Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study. | Sabater C, Calvete-Torre I, Ruiz L, Margolles A | Int J Mol Sci | 10.3390/ijms23137093 | 2022 | *Crohn Disease/drug therapy, Dysbiosis, Humans, *Microbiota, Pectins, Xylans | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7411 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18177) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18177 | ||||
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 | ||||
31956 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28212 | 28776041 | ||
60660 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55593) | https://www.ccug.se/strain?id=55593 | ||||
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 | 28604660 | 35: 676-683 2017 | ||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68380 | Automatically annotated from API rID32A | ||||||
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 | ||||
81737 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID294005.1 | StrainInfo: A central database for resolving microbial strain identifiers |