Strain identifier
BacDive ID: 14034
Type strain: 
Species: Rikenella microfusus
Strain Designation: Q-1
Strain history: C. Kaneuchi Q-1.
NCBI tax ID(s): 880526 (strain), 28139 (species)
version 8.1 (current version)
General
@ref: 6185
BacDive-ID: 14034
DSM-Number: 15922
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Rikenella microfusus Q-1 is an anaerobe, mesophilic bacterium that was isolated from Quail cecum.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 880526 | strain |
| 28139 | species |
strain history
| @ref | history |
|---|---|
| 6185 | <- S. Kudo, JCM <- C. Kaneuchi; Q-1 |
| 67770 | C. Kaneuchi Q-1. |
doi: 10.13145/bacdive14034.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: 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
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 97.2 | |
| 69480 | 99.97 | negative |
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
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6185 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| 6185 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | Name: 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 |
| 6185 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6185 | positive | growth | 37 | mesophilic |
| 60322 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6185 | anaerobe | |
| 60322 | anaerobe | |
| 69480 | anaerobe | 98.158 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 6185 | Quail cecum | Japan | JPN | Asia |
| 60322 | Quail caecum | Japan | JPN | Asia |
| 67770 | Quail cecum |
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #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
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 6185 | Rikenella microfusus ATCC 29728 16S ribosomal RNA gene, complete sequence | L16498 | 1472 | ena | 28139 |
| 67770 | Rikenella microfusus gene for 16S ribosomal RNA, partial sequence, strain: JCM 2053 | AB971798 | 1490 | ena | 880526 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rikenella microfusus DSM 15922 | 880526.4 | wgs | patric | 880526 |
| 66792 | Rikenella microfusus strain NCTC11190 | 28139.3 | wgs | patric | 28139 |
| 66792 | Rikenella microfusus Q-1, DSM 15922 | 2509601020 | draft | img | 880526 |
| 66792 | Rikenella microfusus NCTC 11190 | 2832823480 | draft | img | 28139 |
| 67770 | Rikenella microfusus DSM 15922 | GCA_000427365 | scaffold | ncbi | 880526 |
| 67770 | Rikenella microfusus NCTC11190 | GCA_900455755 | contig | ncbi | 28139 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6185 | 60.3 | |
| 6185 | 57.0 | sequence analysis |
| 67770 | 60.3 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.664 | no |
| flagellated | no | 96.827 | no |
| gram-positive | no | 97.658 | no |
| anaerobic | yes | 98.599 | yes |
| halophile | no | 91.194 | no |
| spore-forming | no | 96.072 | no |
| thermophile | no | 97.485 | no |
| glucose-util | yes | 82.446 | no |
| aerobic | no | 98.067 | yes |
| glucose-ferment | yes | 51.266 | no |
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
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24899658 | Acetobacteroides 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 YL | Int J Syst Evol Microbiol | 10.1099/ijs.0.063917-0 | 2014 | Bacterial 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, *Wetlands | Genetics |
| Phylogeny | 25563920 | Mucinivorans 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 J | Int J Syst Evol Microbiol | 10.1099/ijs.0.000052 | 2015 | Animals, 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, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6185 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15922) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15922 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 60322 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54772) | https://www.ccug.se/strain?id=54772 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69479 | João 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 83201 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39683.1 | StrainInfo: A central database for resolving microbial strain identifiers |