Strain identifier

BacDive ID: 12518

Type strain: Yes

Species: Barnesiella viscericola

Strain Designation: C46

Strain history: M. Sakamoto <-- P. T. N. Lan C46.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
880074strain
397865species

strain history

@refhistory
7411<- M. Sakamoto; C46 <- P. T. N. Lan
67770M. 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31956negative6.35 µm1.2 µmrod-shapedno
69480no91.408
69480negative99.999

colony morphology

@refincubation period
74112-3 days
606602 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

@refnamegrowthlinkcomposition
7411COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
7411CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: 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

@refgrowthtypetemperaturerange
7411positivegrowth37mesophilic
60660positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7411anaerobe
31956anaerobe
60660anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
31956no
69481no100
69480no100

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3195630089acetate+carbon source
3195617057cellobiose+carbon source
3195617234glucose+carbon source
3195617306maltose+carbon source
3195637684mannose+carbon source
3195616634raffinose+carbon source
3195630031succinate+carbon source
3195617992sucrose+carbon source
319564853esculin+hydrolysis
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-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

@refvalueactivityec
31956alkaline phosphatase+3.1.3.1
31956alpha-galactosidase+3.2.1.22
31956gelatinase+
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380glutamate decarboxylase+4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyA
7411-+/-++-++/---+--++--+--+----+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7411chicken caecumJapanJPNAsia
67770Chicken cecum

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Barnesiella viscericola DSM 18177 C46, DSM 18177GCA_000512915completencbi880074
66792Barnesiella viscericola DSM 18177 strain C46, DSM 18177880074.29completepatric880074
66792Barnesiella viscericola C46, DSM 181772509276067completeimg880074

GC content

@refGC-contentmethod
741152.0
3195652
6777052high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.884yes
flagellatedno96.289yes
gram-positiveno97.108yes
anaerobicyes99.171yes
halophileno81.04no
spore-formingno96.483yes
thermophileno96.145no
glucose-utilyes87.207no
aerobicno98.809yes
glucose-fermentyes56.522no

External links

@ref: 7411

culture collection no.: CCUG 55593, DSM 18177, JCM 13660

straininfo link

  • @ref: 81737
  • straininfo: 294005

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267976Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum.Sakamoto M, Lan PTN, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64709-02007Anaerobiosis, 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 AcidEnzymology
Pathogenicity35806099Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.Sabater C, Calvete-Torre I, Ruiz L, Margolles AInt J Mol Sci10.3390/ijms231370932022*Crohn Disease/drug therapy, Dysbiosis, Humans, *Microbiota, Pectins, XylansMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18177)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18177
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31956Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2821228776041
60660Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55593)https://www.ccug.se/strain?id=55593
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81737Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294005.1StrainInfo: A central database for resolving microbial strain identifiers