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
691816species
1236512strain

strain history

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

doi: 10.13145/bacdive22935.20250331.9.3

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

@refgram stainconfidence
125438negative92.145
125439negative99

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

@refgrowthtypetemperature
19114positivegrowth37
61917positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19114anaerobe
61917anaerobe
125438anaerobe91.656
125439obligate anaerobe99.1

spore formation

@refspore formationconfidence
125438no90.178
125439no99.8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838029985L-glutamate+degradation
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6838027897tryptophan+energy source
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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleyes
6836735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380alpha-fucosidase+3.2.1.51
68380glutamate decarboxylase+4.1.1.15
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380leucine arylamidase-3.4.11.1
68380leucyl glycin arylamidase+3.4.11.1
68380tryptophan deaminase+4.1.99.1
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
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 16496AB5314891488nuccore1236512
67770Bacteroides rodentium gene for 16S ribosomal RNA, partial sequenceAB5476461488nuccore1236512

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno92.145no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes91.656yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.178no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.905yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.666yes
125438motile2+flagellatedAbility to perform flagellated movementno87.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.8
125439BacteriaNetmotilityAbility to perform movementno65.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe99.1

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1