Strain identifier

BacDive ID: 14034

Type strain: Yes

Species: Rikenella microfusus

Strain Designation: Q-1

Strain history: C. Kaneuchi Q-1.

NCBI tax ID(s): 880526 (strain), 28139 (species)

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General

@ref: 6185

BacDive-ID: 14034

DSM-Number: 15922

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

description: Rikenella microfusus Q-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Quail cecum.

NCBI tax id

NCBI tax idMatching level
28139species
880526strain

strain history

@refhistory
6185<- S. Kudo, JCM <- C. Kaneuchi; Q-1
67770C. Kaneuchi Q-1.

doi: 10.13145/bacdive14034.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Rikenellaceae
  • genus: Rikenella
  • species: Rikenella microfusus
  • full scientific name: Rikenella microfusus (Kaneuchi and Mitsuoka 1978) Collins et al. 1985

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides microfusus

@ref: 6185

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Rikenellaceae

genus: Rikenella

species: Rikenella microfusus

full scientific name: Rikenella microfusus (Kaneuchi and Mitsuoka 1978) Collins et al. 1985 emend. Hahnke et al. 2016

strain designation: Q-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
125438negative95.318
125439negative92

colony morphology

  • @ref: 60322
  • incubation period: 2-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_15922_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6185COLUMBIA 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
6185CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
6185PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
6185positivegrowth37
60322positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6185anaerobe
60322anaerobe
125439anaerobe91.9

spore formation

@refspore formationconfidence
125438no93.952
125439no94.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6185Quail cecumJapanJPNAsia
60322Quail caecumJapanJPNAsia
67770Quail cecum

isolation source categories

Cat1Cat2
#Host#Birds
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_4340.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_354;96_2177;97_2634;98_3264;99_4340&stattab=map
  • Last taxonomy: Rikenella microfusus subclade
  • 16S sequence: AB971798
  • Sequence Identity:
  • Total samples: 11109
  • soil counts: 269
  • aquatic counts: 710
  • animal counts: 10054
  • plant counts: 76

Safety information

risk assessment

  • @ref: 6185
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6185Rikenella microfusus ATCC 29728 16S ribosomal RNA gene, complete sequenceL164981472nuccore28139
67770Rikenella microfusus gene for 16S ribosomal RNA, partial sequence, strain: JCM 2053AB9717981490nuccore880526

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rikenella microfusus DSM 15922880526.4wgspatric880526
66792Rikenella microfusus strain NCTC1119028139.3wgspatric28139
66792Rikenella microfusus Q-1, DSM 159222509601020draftimg880526
66792Rikenella microfusus NCTC 111902832823480draftimg28139
67770Rikenella microfusus DSM 15922GCA_000427365scaffoldncbi880526
67770Rikenella microfusus NCTC11190GCA_900455755contigncbi28139

GC content

@refGC-contentmethod
618560.3
618557.0sequence analysis
6777060.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno95.318no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes89.216no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.295no
125438spore-formingspore-formingAbility to form endo- or exosporesno93.952no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.27yes
125438motile2+flagellatedAbility to perform flagellated movementno87.666no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.6
125439BacteriaNetmotilityAbility to perform movementno65.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative92
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe91.9

External links

@ref: 6185

culture collection no.: DSM 15922, ATCC 29728, JCM 2053, NCTC 11190, CCUG 54772, CCM 6143, CCUG 25930

straininfo link

  • @ref: 83201
  • straininfo: 39683

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24899658Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YLInt J Syst Evol Microbiol10.1099/ijs.0.063917-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogen/metabolism, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *WetlandsGenetics
Phylogeny25563920Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana.Nelson MC, Bomar L, Maltz M, Graf JInt J Syst Evol Microbiol10.1099/ijs.0.0000522015Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Hirudo medicinalis/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6185Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15922)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15922
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
60322Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54772)https://www.ccug.se/strain?id=54772
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83201Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39683.1StrainInfo: 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