Strain identifier
BacDive ID: 164290
Type strain: 
Species: Pseudoflavonifractor sp.
Strain history: M. Kuroda; Natl. Inst. of Infect. Dis., Japan; Choco116.
NCBI tax ID(s): 1980281 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 164290
keywords: genome sequence, Bacteria, anaerobe, mesophilic
description: Pseudoflavonifractor sp. JCM 32528 is an anaerobe, mesophilic bacterium that was isolated from Fecal sample of a healthy Japanese adult.
NCBI tax id
- NCBI tax id: 1980281
- Matching level: species
strain history
- @ref: 67770
- history: M. Kuroda; Natl. Inst. of Infect. Dis., Japan; Choco116.
doi: 10.13145/bacdive164290.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Pseudoflavonifractor
- species: Pseudoflavonifractor sp.
- full scientific name: Pseudoflavonifractor Carlier et al. 2010
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Pseudoflavonifractor
species: Pseudoflavonifractor sp.
full scientific name: Pseudoflavonifractor sp.
type strain: no
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | anaerobe | 93.081 |
| 125439 | anaerobe | 99.8 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Fecal sample of a healthy Japanese adult
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridiales bacterium Choco116 | 2109689.3 | wgs | patric | 2109689 |
| 67770 | Clostridiales bacterium Choco116 | GCA_003202955 | contig | ncbi | 2109689 |
GC content
- @ref: 67770
- GC-content: 56.6
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 69.178 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 93.081 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 58.873 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 96.224 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 91.795 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 88.821 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 81.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 59.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 87.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.8 |
External links
@ref: 67770
culture collection no.: JCM 32528
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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/ | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |