Strain identifier
BacDive ID: 23863
Type strain: 
Species: Youngiibacter fragilis
Strain Designation: 232.1
Strain history: <- T. Allen, Dept. Botany and Microbiol., Univ. Oklahoma, USA; strain 232.1 <- B. Wawrik {2010}
NCBI tax ID(s): 1408819 (species)
version 8.1 (current version)
General
@ref: 21300
BacDive-ID: 23863
DSM-Number: 24749
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Youngiibacter fragilis 232.1 is an anaerobe, mesophilic bacterium that was isolated from natural gas production water.
NCBI tax id
- NCBI tax id: 1408819
- Matching level: species
strain history
- @ref: 21300
- history: <- T. Allen, Dept. Botany and Microbiol., Univ. Oklahoma, USA; strain 232.1 <- B. Wawrik {2010}
doi: 10.13145/bacdive23863.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Youngiibacter
- species: Youngiibacter fragilis
- full scientific name: Youngiibacter fragilis Lawson et al. 2014
@ref: 21300
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Youngiibacter
species: Youngiibacter fragilis
full scientific name: Youngiibacter fragilis Lawson et al. 2014
strain designation: 232.1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 21300
- name: PY + X MEDIUM (DSMZ Medium 104b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104b
- composition: Name: PY + X MEDIUM (DSMZ Medium 104b; with strain-specific modifications) Composition: NaCl 10.0 g/l Yeast extract 10.0 g/l D-Fructose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 21300
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 21300
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 21300
- sample type: natural gas production water
- geographic location: Alaska, Cook Inlet, Beluga River field
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Environmental | |
| #Environmental | #Aquatic |
taxonmaps
- @ref: 69479
- File name: preview.99_1875.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_428;97_1230;98_1477;99_1875&stattab=map
- Last taxonomy: Youngiibacter fragilis
- 16S sequence: JF262039
- Sequence Identity:
- Total samples: 97
- soil counts: 23
- aquatic counts: 52
- animal counts: 17
- plant counts: 5
Safety information
risk assessment
- @ref: 21300
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21300
- description: Youngiibacter fragilis 232.1 16S ribosomal RNA gene, partial sequence
- accession: JF262039
- length: 1442
- database: ena
- NCBI tax ID: 994573
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Youngiibacter fragilis 232.1 | GCA_000495435 | scaffold | ncbi | 994573 |
| 66792 | Youngiibacter fragilis 232.1 | 2582580929 | draft | img | 994573 |
GC content
- @ref: 21300
- GC-content: 45.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 86.808 | no |
| motile | no | 86.808 | no |
| flagellated | no | 91.39 | no |
| flagellated | no | 91.39 | no |
| gram-positive | yes | 79.196 | no |
| gram-positive | yes | 79.196 | no |
| anaerobic | yes | 98.413 | yes |
| anaerobic | yes | 98.413 | yes |
| aerobic | no | 97.767 | yes |
| aerobic | no | 97.767 | yes |
| halophile | no | 82.338 | no |
| halophile | no | 82.338 | no |
| spore-forming | no | 65.963 | no |
| spore-forming | no | 65.963 | no |
| thermophile | no | 87.926 | yes |
| thermophile | no | 87.926 | yes |
| glucose-util | yes | 87.892 | no |
| glucose-util | yes | 87.892 | no |
| glucose-ferment | yes | 61.082 | no |
| glucose-ferment | yes | 61.082 | no |
External links
@ref: 21300
culture collection no.: DSM 24749, ATCC BAA 2257
straininfo link
- @ref: 87876
- straininfo: 405930
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24048874 | Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov. | Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR, Tanner RS, Harriman BH, Strapoc D, Callaghan AV | Int J Syst Evol Microbiol | 10.1099/ijs.0.053728-0 | 2013 | Alaska, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification, Molecular Sequence Data, Natural Gas/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water/*analysis, Water Microbiology | Genetics |
| Phylogeny | 35394905 | Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis. | Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005275 | 2022 | Bacteria, Anaerobic/genetics, Bacterial Typing Techniques, Base Composition, Clostridiaceae, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Seawater/microbiology, Sequence Analysis, DNA | Transcriptome |
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 | |
| 21300 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24749 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24749) | |
| 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 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 87876 | 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-ID405930.1 |