Strain identifier
BacDive ID: 140074
Type strain: 
Species: Butyricimonas paravirosa
Strain Designation: 214-4
Strain history: Y. Tanaka 214-4.
NCBI tax ID(s): 1472417 (species)
version 8.1 (current version)
General
@ref: 42681
BacDive-ID: 140074
DSM-Number: 105722
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Butyricimonas paravirosa 214-4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.
NCBI tax id
- NCBI tax id: 1472417
- Matching level: species
strain history
| @ref | history |
|---|---|
| 42681 | <- JCM RIKEN BioResource Center, Tsukuba; JCM 18677 <- Y. Tanaka; 214-4 |
| 67770 | Y. Tanaka 214-4. |
doi: 10.13145/bacdive140074.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Odoribacteraceae
- genus: Butyricimonas
- species: Butyricimonas paravirosa
- full scientific name: Butyricimonas paravirosa Sakamoto et al. 2014
@ref: 42681
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Odoribacteraceae
genus: Butyricimonas
species: Butyricimonas paravirosa
full scientific name: Butyricimonas paravirosa Sakamoto et al. 2014 emend. Le Roy et al. 2019
strain designation: 214-4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.994
colony morphology
- @ref: 63242
- incubation period: 2 days
Culture and growth conditions
culture medium
- @ref: 42681
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 42681 | positive | growth | 37 | mesophilic |
| 63242 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 63242 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.992 |
observation
- @ref: 67770
- observation: quinones: MK-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|
| 42681 | human faeces | Japan | JPN | Asia | |
| 63242 | Human feces | Japan | JPN | Asia | 2010-07-08 |
| 67770 | Human feces |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
Safety information
risk assessment
- @ref: 42681
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42681
- description: Butyricimonas paravirosa gene for 16S ribosomal RNA, partial sequence, strain: 214-4
- accession: AB916502
- length: 1486
- database: ena
- NCBI tax ID: 1472417
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Butyricimonas paravirosa JCM 18677 | GCA_014647355 | contig | ncbi | 1472417 |
| 66792 | Butyricimonas paravirosa strain DSM 105722 | 1472417.6 | wgs | patric | 1472417 |
| 66792 | Butyricimonas paravirosa strain JCM 18677 | 1472417.7 | wgs | patric | 1472417 |
| 66792 | Butyricimonas paravirosa DSM 105722 | 2830049664 | draft | img | 1472417 |
| 67770 | Butyricimonas paravirosa DSM 105722 | GCA_011927845 | scaffold | ncbi | 1472417 |
GC content
- @ref: 67770
- GC-content: 44.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.398 | no |
| gram-positive | no | 95.434 | no |
| anaerobic | yes | 99.055 | no |
| aerobic | no | 97.079 | yes |
| halophile | no | 87.974 | no |
| spore-forming | no | 91.88 | no |
| thermophile | no | 99.015 | yes |
| glucose-util | yes | 88.027 | no |
| flagellated | no | 96.939 | no |
| glucose-ferment | no | 54.875 | no |
External links
@ref: 42681
culture collection no.: DSM 105722, CCUG 65563, JCM 18677
straininfo link
- @ref: 96488
- straininfo: 401232
literature
- topic: Phylogeny
- Pubmed-ID: 24903545
- title: Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas.
- authors: Sakamoto M, Tanaka Y, Benno Y, Ohkuma M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.065318-0
- year: 2014
- mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
- topic2: Pathogenicity
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 42681 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105722 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105722) | |
| 63242 | Curators of the CCUG | https://www.ccug.se/strain?id=65563 | Culture Collection University of Gothenburg (CCUG) (CCUG 65563) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 96488 | Reimer, 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 identifiers | 10.60712/SI-ID401232.1 |