Strain identifier

BacDive ID: 24336

Type strain: Yes

Species: Parabacteroides chinchillae

Strain Designation: ST166

Strain history: M. Kitahara ST166.

NCBI tax ID(s): 871327 (species)

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General

@ref: 20719

BacDive-ID: 24336

DSM-Number: 29073

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

description: Parabacteroides chinchillae ST166 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from faeces of Chinchilla lanigera.

NCBI tax id

  • NCBI tax id: 871327
  • Matching level: species

strain history

@refhistory
20719<- JCM <- M. Kitahara; ST166
67770M. Kitahara ST166.

doi: 10.13145/bacdive24336.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Tannerellaceae
  • genus: Parabacteroides
  • species: Parabacteroides chinchillae
  • full scientific name: Parabacteroides chinchillae Kitahara et al. 2013

@ref: 20719

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides chinchillae

full scientific name: Parabacteroides chinchillae Kitahara et al. 2013

strain designation: ST166

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31031negative8.5 µm1.2 µmrod-shapedno
69480negative94.908

colony morphology

@refincubation period
207191-2 days
627872 days

pigmentation

  • @ref: 31031
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20719
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: 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

@refgrowthtypetemperature
20719positivegrowth37
31031positiveoptimum37
62787positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20719anaerobe
31031anaerobe
62787anaerobe

spore formation

@refspore formationconfidence
31031no
69480no93.292
69481no100

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3103117234glucose+carbon source
3103117716lactose+carbon source
3103117306maltose+carbon source
3103137684mannose+carbon source
3103116634raffinose+carbon source
3103117992sucrose+carbon source
310314853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
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
31031alkaline phosphatase+3.1.3.1
31031alpha-galactosidase+3.2.1.22
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20719--++-++/---++/-+/-++--++-++/-+-+/-++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
20719faeces of Chinchilla lanigeraChinchilla lanigeraJapanJPNAsia
62787Feces,Chichilla lanigeraJapanJPNAsia
67770Feces of a chinchilla

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_34677.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_16667;97_20451;98_25585;99_34677&stattab=map
  • Last taxonomy: Parabacteroides chinchillae
  • 16S sequence: AB574482
  • Sequence Identity:
  • Total samples: 2550
  • soil counts: 27
  • aquatic counts: 50
  • animal counts: 2465
  • plant counts: 8

Safety information

risk assessment

  • @ref: 20719
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20719
  • description: Parabacteroides chinchillae gene for 16S rRNA, partial sequence
  • accession: AB574482
  • length: 1489
  • database: nuccore
  • NCBI tax ID: 871327

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides chinchillae DSM 29073GCA_900108035contigncbi871327
66792Parabacteroides chinchillae strain DSM 29073871327.5wgspatric871327
66792Parabacteroides chinchillae DSM 290732693429876draftimg871327

GC content

@refGC-contentmethod
3103142.8
6777042.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno94.908no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.788yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no91.602yes
69480spore-formingspore-formingAbility to form endo- or exosporesno93.292yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.964yes
69480flagellatedmotile2+Ability to perform flagellated movementno89yes

External links

@ref: 20719

culture collection no.: DSM 29073, CCUG 62154, JCM 17104

straininfo link

  • @ref: 88262
  • straininfo: 401567

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23563230Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces.Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.050146-02013Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Chaperonin 60/genetics, Chinchilla/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/microbiology, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny32071723Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota.Benabdelkader S, Naud S, Lo CI, Fadlane A, Traore SI, Aboudharam G, La Scola BNew Microbes New Infect10.1016/j.nmni.2019.1006422020

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20719Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29073Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29073)
31031Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172736128776041
62787Curators of the CCUGhttps://www.ccug.se/strain?id=62154Culture Collection University of Gothenburg (CCUG) (CCUG 62154)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88262Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401567.1