Strain identifier

BacDive ID: 1621

Type strain: Yes

Species: Bacteroides propionicifaciens

Strain Designation: SV434

Strain history: A. Ueki SV434.

NCBI tax ID(s): 1121099 (strain), 392838 (species)

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General

@ref: 15423

BacDive-ID: 1621

DSM-Number: 19291

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Bacteroides propionicifaciens SV434 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from methanogenic fermenter of cattle waste.

NCBI tax id

NCBI tax idMatching level
392838species
1121099strain

strain history

@refhistory
15423<- A. Ueki; SV434 {2007}
67770A. Ueki SV434.

doi: 10.13145/bacdive1621.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides propionicifaciens
  • full scientific name: Bacteroides propionicifaciens Ueki et al. 2008

@ref: 15423

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides propionicifaciens

full scientific name: Bacteroides propionicifaciens Ueki et al. 2008 emend. Hahnke et al. 2016

strain designation: SV434

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32432negative1.7 µm0.75 µmrod-shapedno
69480no92.888
69480negative99.989

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15423COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
15423CHOPPED 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
15423positivegrowth30mesophilic
32432positivegrowth05-35
32432positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 32432
  • ability: positive
  • type: optimum
  • pH: 7.9

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15423anaerobe
69480anaerobe98.649

spore formation

@refspore formationconfidence
32432no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32432NaClpositivegrowth0-4 %
32432NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3243222599arabinose+carbon source
3243217057cellobiose+carbon source
3243223652dextrin+carbon source
3243228757fructose+carbon source
3243228260galactose+carbon source
3243217234glucose+carbon source
3243228087glycogen+carbon source
3243224996lactate+carbon source
3243217716lactose+carbon source
3243217306maltose+carbon source
3243237684mannose+carbon source
3243215361pyruvate+carbon source
324324853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-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
32432catalase+1.11.1.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
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
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate+
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
15423---+++++-+/-+-----+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
15423methanogenic fermenter of cattle wasteJapanJPNAsia
62492Methanogenic fermenter of cattle wasteJapanJPNAsia2007
67770Rice-straw residue from a methanogenic reactor treating waste from cattle farms in Betsukai-machiJapanJPNAsiaHokkaido

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4200.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15892;96_2124;97_2559;98_3170;99_4200&stattab=map
  • Last taxonomy: Bacteroides propionicifaciens subclade
  • 16S sequence: AB510706
  • Sequence Identity:
  • Total samples: 12248
  • soil counts: 269
  • aquatic counts: 288
  • animal counts: 11553
  • plant counts: 138

Safety information

risk assessment

  • @ref: 15423
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides propionicifaciens gene for 16S ribosomal RNA, partial sequence, strain: JCM 14649AB5107061480ena392838
15423Bacteroides propionicifaciens gene for 16S ribosomal RNA, partial sequence, strain: SV434AB2646251428ena392838

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides propionicifaciens DSM 192911121099.3wgspatric1121099
66792Bacteroides propionicifaciens JCM 146491236495.3wgspatric1121099
66792Bacteroides propionicifaciens JCM 146492585427866draftimg1121099
66792Bacteroides propionicifaciens DSM 192912517093002draftimg1121099
67770Bacteroides propionicifaciens DSM 19291 = JCM 14649GCA_000375405contigncbi1121099
67770Bacteroides propionicifaciens DSM 19291 = JCM 14649GCA_000613745contigncbi1121099

GC content

@refGC-contentmethod
1542346.2-47.5high performance liquid chromatography (HPLC)
3243246.2-47.5
1542338.0sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.198yes
flagellatedno95.718yes
gram-positiveno95.489no
anaerobicyes96.004no
aerobicno96.68no
halophileno66.775no
spore-formingno95.199yes
thermophileno98.921yes
glucose-utilyes90.01yes
glucose-fermentyes63.84no

External links

@ref: 15423

culture collection no.: DSM 19291, JCM 14649, CCUG 60909

straininfo link

@refstraininfo
71266323949
71267408997

literature

  • topic: Phylogeny
  • Pubmed-ID: 18218929
  • title: Bacteroides propionicifaciens sp. nov., isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms.
  • authors: Ueki A, Abe K, Kaku N, Watanabe K, Ueki K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65486-0
  • year: 2008
  • mesh: Animal Husbandry/*methods, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, *Bioreactors, Cattle, DNA, Bacterial/analysis, Genes, rRNA, Methane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phenotype, Phylogeny, Propionates/*metabolism, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Species Specificity
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15423Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19291)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19291
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32432Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128654
62492Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60909)https://www.ccug.se/strain?id=60909
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)
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
71266Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323949.1StrainInfo: A central database for resolving microbial strain identifiers
71267Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408997.1StrainInfo: A central database for resolving microbial strain identifiers