Strain identifier
BacDive ID: 18080
Type strain:
Species: Proteocatella sphenisci
Strain Designation: PPP2
Strain history: E. V. Pikuta PPP2.
NCBI tax ID(s): 1123009 (strain), 181070 (species)
General
@ref: 16721
BacDive-ID: 18080
DSM-Number: 23131
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Proteocatella sphenisci PPP2 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from guano of Magellanic penguins Spheniscus magellanicus.
NCBI tax id
NCBI tax id | Matching level |
---|---|
181070 | species |
1123009 | strain |
strain history
@ref | history |
---|---|
16721 | <- JCM/RIKEN <- E. V. Pikuta, NASA/NSSTC, Huntsville, USA; PPP2 |
67770 | E. V. Pikuta PPP2. |
doi: 10.13145/bacdive18080.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptostreptococcaceae
- genus: Proteocatella
- species: Proteocatella sphenisci
- full scientific name: Proteocatella sphenisci Pikuta et al. 2009
@ref: 16721
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptostreptococcaceae
genus: Proteocatella
species: Proteocatella sphenisci
full scientific name: Proteocatella sphenisci Pikuta et al. 2009
strain designation: PPP2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
28967 | positive | 4 µm | 0.75 µm | rod-shaped | yes | |
69480 | positive | 99.72 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_23131_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_23131_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_23131_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_23131_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_23131_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 16721
- name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412)
- growth: yes
- link: https://mediadive.dsmz.de/medium/412
- composition: Name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412; with strain-specific modifications) Composition: NaHCO3 6.0 g/l Na-acetate 5.0 g/l Glucose 4.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l (NH4)2SO4 0.255 g/l KH2PO4 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 CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Riboflavin 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16721 | positive | growth | 30 | mesophilic |
28967 | positive | growth | 02-37 | |
28967 | positive | optimum | 29 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
28967 | positive | growth | 6.7-9.7 | alkaliphile |
28967 | positive | optimum | 8.3 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
28967 | anaerobe | |
69480 | anaerobe | 99.005 |
spore formation
@ref | spore formation | confidence |
---|---|---|
28967 | yes | |
69481 | yes | 96 |
69480 | no | 99.846 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
28967 | NaCl | positive | growth | 0-4 % |
28967 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 28967
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16721 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
16721 | guano of Magellanic penguins Spheniscus magellanicus | Spheniscus magellanicus | coast of Chilean Patagonia | Chile | CHL | Middle and South America |
67770 | Guano of the Magellanic penguin in Chilean Patagonia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Birds | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_86546.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_757;96_28159;97_35469;98_45813;99_86546&stattab=map
- Last taxonomy: Proteocatella sphenisci subclade
- 16S sequence: AF450134
- Sequence Identity:
- Total samples: 1134
- soil counts: 37
- aquatic counts: 1029
- animal counts: 59
- plant counts: 9
Safety information
risk assessment
- @ref: 16721
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16721
- description: Proteocatella sphenisci strain PPP2 16S ribosomal RNA gene, partial sequence
- accession: AF450134
- length: 1450
- database: ena
- NCBI tax ID: 181070
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Proteocatella sphenisci DSM 23131 | 1123009.3 | wgs | patric | 1123009 |
66792 | Proteocatella sphenisci DSM 23131 | 2523533562 | draft | img | 1123009 |
67770 | Proteocatella sphenisci DSM 23131 | GCA_000423525 | scaffold | ncbi | 1123009 |
GC content
@ref | GC-content | method |
---|---|---|
16721 | 39.5 | high performance liquid chromatography (HPLC) |
28967 | 39.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 96 | no |
motile | yes | 89.185 | yes |
flagellated | no | 67.68 | no |
gram-positive | yes | 84.954 | yes |
anaerobic | yes | 99.611 | no |
aerobic | no | 96.68 | yes |
halophile | no | 90.81 | yes |
spore-forming | yes | 69.708 | yes |
glucose-util | yes | 87.296 | no |
thermophile | no | 83.801 | yes |
glucose-ferment | yes | 56.815 | no |
External links
@ref: 16721
culture collection no.: DSM 23131, CIP 108034, JCM 12175, ATCC BAA 755
straininfo link
- @ref: 87068
- straininfo: 403712
literature
- topic: Phylogeny
- Pubmed-ID: 19620379
- title: Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano.
- authors: Pikuta EV, Hoover RB, Marsic D, Whitman WB, Lupa B, Tang J, Krader P
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.002816-0
- year: 2009
- mesh: Amino Acids/metabolism, Anaerobiosis, Animals, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Catalase/metabolism, Chile, Cluster Analysis, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Fermentation, Gram-Positive Endospore-Forming Bacteria/*classification/genetics/*isolation & purification/physiology, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spheniscidae/*microbiology, Spores, Bacterial/*cytology
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16721 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23131) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23131 | ||||
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 | ||||
28967 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25404 | 28776041 | ||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68380 | Automatically annotated from API rID32A | ||||||
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 | ||||
87068 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403712.1 | StrainInfo: A central database for resolving microbial strain identifiers |