Strain identifier
BacDive ID: 159445
Type strain: 
Species: Pyramidobacter porci
Strain Designation: SM-530-WT-4B
Strain history: B. Abt; DSMZ, Germany; DSM 105193 (=SM-530-WT-4B) <-- T. Clavel; RWTH Aachen, Germany.
NCBI tax ID(s): 2605789 (species)
version 9.1 (current version)
General
@ref: 66268
BacDive-ID: 159445
DSM-Number: 105193
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Pyramidobacter porci SM-530-WT-4B is an anaerobe, Gram-negative bacterium that was isolated from pig, WT, 37 weeks old, feces.
NCBI tax id
- NCBI tax id: 2605789
- Matching level: species
strain history
| @ref | history |
|---|---|
| 66268 | <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; |
| 67770 | B. Abt; DSMZ, Germany; DSM 105193 (=SM-530-WT-4B) <-- T. Clavel; RWTH Aachen, Germany. |
doi: 10.13145/bacdive159445.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/synergistota
- domain: Bacteria
- phylum: Synergistota
- class: Synergistia
- order: Synergistales
- family: Synergistaceae
- genus: Pyramidobacter
- species: Pyramidobacter porci
- full scientific name: Pyramidobacter porci Wylensek et al. 2021
@ref: 66268
domain: Bacteria
phylum: Synergistetes
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Pyramidobacter
species: Pyramidobacter porci
full scientific name: Pyramidobacter porci
strain designation: SM-530-WT-4B
type strain: yes
Culture and growth conditions
culture medium
- @ref: 66268
- name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339
- composition: 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
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 66268 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 90.604
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 66268 | pig, WT, 37 weeks old, feces | Kranzberg (Bavaria) | Germany | DEU | Europe |
| 67770 | Feces of a German Landrace pig (minipig breed) | Freising | Germany | DEU | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_113791.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_438;96_12713;97_58081;98_77044;99_113791&stattab=map
- Last taxonomy: Pyramidobacter porci subclade
- 16S sequence: MN537479
- Sequence Identity:
- Total samples: 2636
- soil counts: 90
- aquatic counts: 29
- animal counts: 2500
- plant counts: 17
Sequence information
16S sequences
- @ref: 66268
- description: Pyramidobacter porci strain SM-530-WT-4B 16S ribosomal RNA gene, partial sequence
- accession: MN537479
- length: 1481
- database: nuccore
- NCBI tax ID: 2652283
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pyramidobacter porci SM-530-WT-4B | GCA_009695745 | contig | ncbi | 2605789 |
| 66792 | Pyramidobacter sp. SM-530-WT-4B | 2605789.3 | wgs | patric | 2605789 |
| 66792 | Pyramidobacter porci SM-530-WT-4B | 2890187157 | draft | img | 2605789 |
GC content
- @ref: 67770
- GC-content: 59.6
- 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 | no | 71 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 80.028 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 90.604 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 80.853 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 95.612 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 85.142 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86 | no |
External links
@ref: 66268
culture collection no.: DSM 105193, JCM 34368
straininfo link
- @ref: 111939
- straininfo: 400131
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 | |
| 66268 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105193 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105193) | |
| 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/ | ||
| 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/ | |
| 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 | |
| 111939 | 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-ID400131.1 |