Strain identifier
BacDive ID: 2251
Type strain: 
Species: Atopostipes suicloacalis
Strain Designation: PPC79
Strain history: <- T. R. Whitehead, National Center for Agricultural Utilization Research, USDA, Peoria, USA; PPC79 <- T. R. Whitehead {1998}
NCBI tax ID(s): 1121025 (strain), 180295 (species)
version 8.1 (current version)
General
@ref: 6059
BacDive-ID: 2251
DSM-Number: 15692
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Atopostipes suicloacalis PPC79 is an anaerobe, mesophilic bacterium that was isolated from stored swine manure.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 180295 | species |
| 1121025 | strain |
strain history
- @ref: 6059
- history: <- T. R. Whitehead, National Center for Agricultural Utilization Research, USDA, Peoria, USA; PPC79 <- T. R. Whitehead {1998}
doi: 10.13145/bacdive2251.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Carnobacteriaceae
- genus: Atopostipes
- species: Atopostipes suicloacalis
- full scientific name: Atopostipes suicloacalis corrig. Cotta et al. 2004
synonyms
- @ref: 20215
- synonym: Atopostipes suicloacale
@ref: 6059
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Atopostipes
species: Atopostipes suicloacalis
full scientific name: Atopostipes suicloacalis Cotta et al. 2004
strain designation: PPC79
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 92.681 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 6059
- name: WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339a
- composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l D-Glucose 5.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 6059
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 6059
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 6059
- sample type: stored swine manure
- geographic location: Illinois, Eureka
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Suidae (Pig,Swine) |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_31864.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16069;96_15493;97_18963;98_23652;99_31864&stattab=map
- Last taxonomy: Atopostipes suicloacalis subclade
- 16S sequence: AF445248
- Sequence Identity:
- Total samples: 1956
- soil counts: 317
- aquatic counts: 176
- animal counts: 1381
- plant counts: 82
Safety information
risk assessment
- @ref: 6059
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6059
- description: Atopostipes suicloacalis strain PPC79 16S ribosomal RNA gene, partial sequence
- accession: AF445248
- length: 1546
- database: ena
- NCBI tax ID: 180295
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Atopostipes suicloacalis DSM 15692 | GCA_900129085 | scaffold | ncbi | 1121025 |
| 66792 | Atopostipes suicloacalis DSM 15692 | 1121025.4 | wgs | patric | 1121025 |
| 66792 | Atopostipes suicloacalis DSM 15692 | 2582581273 | draft | img | 1121025 |
GC content
- @ref: 6059
- GC-content: 43.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 97 | no |
| motile | no | 96.265 | no |
| flagellated | no | 97.839 | no |
| gram-positive | yes | 91.135 | no |
| anaerobic | no | 95.733 | no |
| aerobic | no | 92.528 | yes |
| halophile | yes | 89.02 | no |
| spore-forming | no | 95.992 | no |
| thermophile | no | 95.119 | yes |
| glucose-util | yes | 89.477 | no |
| glucose-ferment | yes | 79.158 | no |
External links
@ref: 6059
culture collection no.: DSM 15692, NRRL 23929
straininfo link
- @ref: 71810
- straininfo: 134277
literature
- topic: Phylogeny
- Pubmed-ID: 16701518
- title: Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit.
- authors: Cotta MA, Whitehead TR, Collins MD, Lawson PA
- journal: Anaerobe
- DOI: 10.1016/j.anaerobe.2004.04.001
- year: 2004
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6059 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15692) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15692 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 71810 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134277.1 | StrainInfo: A central database for resolving microbial strain identifiers |