Strain identifier
BacDive ID: 159030
Type strain: 
Species: Oliverpabstia intestinalis
Strain Designation: BSU-380-WT-5A, BSM-380-WT-5A
Strain history: B. Abt; DSMZ, Germany; DSM 106162 (=BSM-380-WT-5A) <-- T. Clavel; RWTH Aachen, Germany.
NCBI tax ID(s): 2606633 (species)
version 9.1 (current version)
General
@ref: 65853
BacDive-ID: 159030
DSM-Number: 106162
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive
description: Oliverpabstia intestinalis BSU-380-WT-5A is an anaerobe, Gram-positive bacterium that was isolated from feces; pig, 5 month old, wild type.
NCBI tax id
- NCBI tax id: 2606633
- Matching level: species
strain history
| @ref | history |
|---|---|
| 65853 | <- T. Clavel, TU Munich; |
| 67770 | B. Abt; DSMZ, Germany; DSM 106162 (=BSM-380-WT-5A) <-- T. Clavel; RWTH Aachen, Germany. |
doi: 10.13145/bacdive159030.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Oliverpabstia
- species: Oliverpabstia intestinalis
- full scientific name: Oliverpabstia intestinalis Wylensek et al. 2021
@ref: 65853
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Lachnospiraceae
genus: Oliverpabstia
species: Oliverpabstia intestinalis
full scientific name: Oliverpabstia intestinalis
strain designation: BSU-380-WT-5A, BSM-380-WT-5A
type strain: yes
Morphology
cell morphology
- @ref: 69645
- gram stain: positive
- cell shape: coccus-shaped
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 65853 | WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) | yes | https://mediadive.dsmz.de/medium/339 | Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water |
| 69645 | Wilkins-Chalgren Anaerobe broth | yes | supplemented with L-cysteine and DTT (0.05% and 0.02% (w/v), respectively) | |
| 69645 | Bifidus Selective Medium | yes | ||
| 69645 | Brain Heart Infusion (BHI) agar | yes |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 65853 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
| 69645 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 69480 | anaerobe | 92.935 |
| 69645 | obligate anaerobe |
observation
| @ref | observation |
|---|---|
| 69645 | Cells often grow in pairs |
| 69645 | Deconjugates primary bile acids |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature | isolation procedure |
|---|---|---|---|---|---|---|---|---|---|
| 65853 | feces; pig, 5 month old, wild type | Kranzberg (Bavaria) | Germany | DEU | Europe | ||||
| 67770 | Feces of a German Landrace pig | Freising | Germany | DEU | Europe | ||||
| 69645 | Pig feces | Thalhausen, Bavaria | Germany | DEU | Europe | Bifidus Selective Medium | 1-3 days | 37 | anaerobic |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Mammals | #Suidae (Pig,Swine) |
Sequence information
16S sequences
- @ref: 65853
- description: Oliverpabstia intestinalis strain BSM-380-WT-5A 16S ribosomal RNA gene, partial sequence
- accession: MN537507
- length: 1487
- database: nuccore
- NCBI tax ID: 2652302
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oliverpabstia intestinalis BSM-380-WT-5A | GCA_009696065 | contig | ncbi | 2606633 |
| 66792 | Lachnospiraceae bacterium BSM-380-WT-5A | 2606633.3 | wgs | patric | 2606633 |
| 69645 | Whole genome shotgun | VUMS00000000 | ncbi | 2606633 |
GC content
- @ref: 69645
- GC-content: 44.1
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 82 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 81.603 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 92.935 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 51.268 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 96.61 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.523 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 80.943 | no |
External links
@ref: 65853
culture collection no.: DSM 106162, JCM 34394
straininfo link
- @ref: 111544
- straininfo: 396938
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 | |
| 65853 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-106162 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106162) | |
| 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 | |
| 69645 | David Wylensek, Thomas C. A. Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R. Lesker, Sara B. Hernández, Viktoria Heine, Eva M. Buhl, Paul M. D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J. Taverne-Thiele, Marcel Giesbers, Jerry M. Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M. Ridlon, Tobias A. M. Gulder, Jörg Overmann, Thomas Clavel | A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity | 10.1038/s41467-020-19929-w | |
| 111544 | 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-ID396938.1 |