Strain identifier

BacDive ID: 133840

Type strain: Yes

Species: Bacteroides reticulotermitis

Strain Designation: Rs-03

Strain history: M. Ohkuma Rs-03.

NCBI tax ID(s): 1445607 (strain), 1133319 (species)

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General

@ref: 42660

BacDive-ID: 133840

DSM-Number: 105720

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

description: Bacteroides reticulotermitis Rs-03 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of a subterranean termite.

NCBI tax id

NCBI tax idMatching level
1133319species
1445607strain

strain history

@refhistory
42660<- JCM RIKEN BioResource Center, Tsukuba, Japan; JCM 10512 <- M. Ohkuma; Rs-03
67770M. Ohkuma Rs-03.

doi: 10.13145/bacdive133840.20250331.9.3

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 reticulotermitis
  • full scientific name: Bacteroides reticulotermitis Sakamoto and Ohkuma 2013

@ref: 42660

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides reticulotermitis

full scientific name: Bacteroides reticulotermitis Sakamoto and Ohkuma 2013

strain designation: Rs-03

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30643negative2.1 µm0.8 µmrod-shapedno
125438negative93.815
125439negative99.8

pigmentation

  • @ref: 30643
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 42660
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperature
42660positivegrowth37
30643positivegrowth25-40
30643positiveoptimum37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 30643
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
30643no
125439no99.7

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3064322599arabinose+carbon source
3064317057cellobiose+carbon source
3064317234glucose+carbon source
3064317716lactose+carbon source
3064317306maltose+carbon source
3064337684mannose+carbon source
3064316634raffinose+carbon source
3064326546rhamnose+carbon source
3064317814salicin+carbon source
3064317992sucrose+carbon source
3064318222xylose+carbon source
306434853esculin+hydrolysis

enzymes

@refvalueactivityec
30643alkaline phosphatase+3.1.3.1
30643alpha-galactosidase+3.2.1.22

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
30643gut of a subterranean termite
42660termite gut Reticulitermes speratusReticulitermes speratusSaitama PrefectureJapanJPNAsia
67770Gut of the subterranean termite Reticulitermes speratusReticulitermes speratus

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_6766.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_3195;97_3920;98_4990;99_6766&stattab=map
  • Last taxonomy: Bacteroides reticulotermitis subclade
  • 16S sequence: AB692943
  • Sequence Identity:
  • Total samples: 16994
  • soil counts: 518
  • aquatic counts: 1807
  • animal counts: 14462
  • plant counts: 207

Safety information

risk assessment

  • @ref: 42660
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 30643
  • description: Bacteroides reticulotermitis gene for 16S ribosomal RNA, partial sequence
  • accession: AB692943
  • length: 1419
  • database: nuccore
  • NCBI tax ID: 1445607

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides reticulotermitis DSM 105720GCA_014196955scaffoldncbi1133319
66792Bacteroides reticulotermitis JCM 105121445607.3wgspatric1445607
66792Bacteroides reticulotermitis strain DSM 1057201133319.4wgspatric1133319
66792Bacteroides reticulotermitis DSM 1057202830041218draftimg1133319
66792Bacteroides reticulotermitis JCM 105122609459943draftimg1445607
67770Bacteroides reticulotermitis JCM 10512GCA_000517545contigncbi1445607

GC content

@refGC-contentmethod
3064344.9
6777044.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno93.815yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes81.326yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.96no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no89.493no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.474yes
125438motile2+flagellatedAbility to perform flagellated movementno87.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.7
125439BacteriaNetmotilityAbility to perform movementno68.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe75.7

External links

@ref: 42660

culture collection no.: JCM 10512, CCUG 62153, DSM 105720

straininfo link

  • @ref: 91616
  • straininfo: 400491

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22544795Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus).Sakamoto M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.040931-02012Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Genetics24526645Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite.Yuki M, Oshima K, Suda W, Sakamoto M, Iida T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.00072-142014Phylogeny

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcataloguejournal
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
30643Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172697428776041
42660Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105720Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105720)
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/
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/
91616Reimer, 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-ID400491.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG