Strain identifier

BacDive ID: 22935

Type strain: Yes

Species: Bacteroides rodentium

Strain Designation: ST28

Strain history: M. Kitahara ST28.

NCBI tax ID(s): 1236512 (strain), 691816 (species)

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General

@ref: 19114

BacDive-ID: 22935

DSM-Number: 26882

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

description: Bacteroides rodentium ST28 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Chinchilla feces.

NCBI tax id

NCBI tax idMatching level
1236512strain
691816species

strain history

@refhistory
19114<- JCM <- M. Kitahara; ST28
67770M. Kitahara ST28.

doi: 10.13145/bacdive22935.20230509.8.1

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 rodentium
  • full scientific name: Bacteroides rodentium Kitahara et al. 2011

@ref: 19114

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides rodentium

full scientific name: Bacteroides rodentium Kitahara et al. 2011

strain designation: ST28

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.989

colony morphology

@refincubation period
191141-2 days
619171 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19114COLUMBIA 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
19114CHOPPED 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
19114positivegrowth37mesophilic
61917positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19114anaerobe
61917anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.986

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
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
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
19114+-+-++++++++-++-+---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
19114--++-+++-+++++-++--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
19114Chinchilla fecesJapanJPNAsia
61917Chinchilla feces (Chinchilla lanigera)JapanJPNAsia
67770Chinchilla feces

isolation source categories

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

Safety information

risk assessment

  • @ref: 19114
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19114Bacteroides rodentium gene for 16S rRNA, partial sequence, strain: JCM 16496AB5314891488ena1236512
67770Bacteroides rodentium gene for 16S ribosomal RNA, partial sequenceAB5476461488ena1236512

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides rodentium JCM 164961236512.3wgspatric1236512
66792Bacteroides rodentium JCM 164962565956595draftimg1236512
67770Bacteroides rodentium JCM 16496GCA_000614125contigncbi1236512

GC content

@refGC-contentmethod
1911441.0high performance liquid chromatography (HPLC)
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.787no
gram-positiveno96.402no
anaerobicyes98.651yes
aerobicno97.263no
halophileno91.877no
spore-formingno92.585no
glucose-utilyes91.14no
flagellatedno97.205no
thermophileno97.189no
glucose-fermentyes74.708no

External links

@ref: 19114

culture collection no.: DSM 26882, CCUG 59334, JCM 16469, JCM 16496

straininfo link

  • @ref: 87183
  • straininfo: 406101

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20495039Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.024026-02010Anaerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Chinchilla/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny35657444Bacteroides humanifaecis sp. nov., isolated from faeces of healthy Korean.Kim HS, Kim JS, Suh MK, Eom MK, Lee JH, Park SH, Kang SW, Lee DH, Yoon H, Lee JH, Lee JSArch Microbiol10.1007/s00203-022-02967-x2022Bacterial Typing Techniques, *Bacteroides/genetics, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/microbiology, Humans, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitle
19114Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26882)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26882
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
61917Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59334)https://www.ccug.se/strain?id=59334
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/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
87183Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406101.1StrainInfo: A central database for resolving microbial strain identifiers