Strain identifier
BacDive ID: 2284
Type strain: 
Species: Trichococcus patagoniensis
Strain Designation: PmagG1
Strain history: CIP <- 2003, E. Pikuta, NSSTC/NASA, Huntsville, Alabama, USA: strain PmagG1
NCBI tax ID(s): 382641 (species)
version 9.1 (current version)
General
@ref: 7708
BacDive-ID: 2284
DSM-Number: 18806
keywords: genome sequence, 16S sequence, Bacteria, aerobe
description: Trichococcus patagoniensis PmagG1 is an aerobe bacterium that was isolated from Guano of magellanic penguin.
NCBI tax id
- NCBI tax id: 382641
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7708 | <- CIP <- E. Pikuta, NSSTC/NASA, Alabama, USA; PmagG1 |
| 33873 | 2003, E. Pikuta, NSSTC/NASA, Huntsville, Alabama, USA: strain PmagG1 |
| 67770 | E. V. Pikuta PmagG1. |
| 121629 | CIP <- 2003, E. Pikuta, NSSTC/NASA, Huntsville, Alabama, USA: strain PmagG1 |
doi: 10.13145/bacdive2284.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Carnobacteriaceae
- genus: Trichococcus
- species: Trichococcus patagoniensis
- full scientific name: Trichococcus patagoniensis Pikuta et al. 2006
@ref: 7708
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Trichococcus
species: Trichococcus patagoniensis
full scientific name: Trichococcus patagoniensis Pikuta et al. 2006
strain designation: PmagG1
type strain: yes
Morphology
cell morphology
- @ref: 121629
- gram stain: positive
- cell shape: coccus-shaped
- motility: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 7708 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
| 7708 | ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412) | yes | https://mediadive.dsmz.de/medium/412 | Name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412) Composition: NaHCO3 6.0 g/l Na-acetate 5.0 g/l Glucose 4.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.255 g/l (NH4)2SO4 0.255 g/l K2HPO4 0.225 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Distilled water |
| 33873 | MEDIUM 494 - for Trichococcus sp. | yes | Sodium hydrogen carbonate (0.300 g);Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Potassium chloride (0.300 g);Magnesium sulphate heptahydrate(0.100 g);Glucose (5.000 g);Yeast extract (0.500 g);Potassium di-hydrogen phosphate (0.300 g | |
| 121629 | CIP Medium 494 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=494 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 7708 | positive | growth | 30 |
| 33873 | positive | growth | 30 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7708 | aerobe |
| 7708 | anaerobe |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | isolation date |
|---|---|---|---|---|---|---|
| 7708 | Guano of magellanic penguin | Patagonia | Chile | CHL | Middle and South America | |
| 67770 | Guano of Magellanic penguins collected in Chilean Patagonia | |||||
| 121629 | Guano of magellanic penguin | Patagonia | Chile | CHL | Middle and South America | 2000 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Birds | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_24449.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_12252;97_14862;98_18388;99_24449&stattab=map
- Last taxonomy: Trichococcus
- 16S sequence: AF394926
- Sequence Identity:
- Total samples: 38677
- soil counts: 4890
- aquatic counts: 19650
- animal counts: 13208
- plant counts: 929
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 7708 | 1 | Risk group (German classification) |
| 121629 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7708
- description: Trichococcus patagoniensis strain PMagG1 16S ribosomal RNA gene, partial sequence
- accession: AF394926
- length: 1483
- database: nuccore
- NCBI tax ID: 382641
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Trichococcus patagoniensis strain DSM 18806 | 382641.5 | wgs | patric | 382641 |
| 66792 | Trichococcus patagoniensis DSM 18806 | 2737471637 | draft | img | 382641 |
| 67770 | Trichococcus patagoniensis DSM 18806 | GCA_003051085 | scaffold | ncbi | 382641 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7708 | 45.82 | |
| 67770 | 45.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 70 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 82.014 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 60.62 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 71.603 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.577 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 92.627 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 82.954 | no |
External links
@ref: 7708
culture collection no.: DSM 18806, ATCC BAA-756, CIP 108035, JCM 12176
straininfo link
- @ref: 71842
- straininfo: 201778
literature
- topic: Phylogeny
- Pubmed-ID: 16957099
- title: Trichococcus patagoniensis sp. nov., a facultative anaerobe that grows at -5 degrees C, isolated from penguin guano in Chilean Patagonia.
- authors: Pikuta EV, Hoover RB, Bej AK, Marsic D, Whitman WB, Krader PE, Tang J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64225-0
- year: 2006
- mesh: Animals, Bacteria, Anaerobic/classification/genetics/*isolation & purification, Bacterial Typing Techniques, Chile, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Spheniscidae/*microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7708 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18806) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18806 | |
| 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 | |
| 33873 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5613 | ||
| 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) | |
| 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. | 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 | |
| 71842 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID201778.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 121629 | Curators of the CIP | Collection of Institut Pasteur (CIP 108035) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108035 |