Strain identifier

BacDive ID: 18080

Type strain: Yes

Species: Proteocatella sphenisci

Strain Designation: PPP2

Strain history: E. V. Pikuta PPP2.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
181070species
1123009strain

strain history

@refhistory
16721<- JCM/RIKEN <- E. V. Pikuta, NASA/NSSTC, Huntsville, USA; PPP2
67770E. 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
28967positive4 µm0.75 µmrod-shapedyes
69480positive99.72

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_23131_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23131_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23131_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23131_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23131_5.jpgelectron 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

@refgrowthtypetemperaturerange
16721positivegrowth30mesophilic
28967positivegrowth02-37
28967positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
28967positivegrowth6.7-9.7alkaliphile
28967positiveoptimum8.3

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
28967anaerobe
69480anaerobe99.005

spore formation

@refspore formationconfidence
28967yes
69481yes96
69480no99.846

halophily

@refsaltgrowthtested relationconcentration
28967NaClpositivegrowth0-4 %
28967NaClpositiveoptimum0.5 %

observation

  • @ref: 28967
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-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

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16721------------------+/-----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16721guano of Magellanic penguins Spheniscus magellanicusSpheniscus magellanicuscoast of Chilean PatagoniaChileCHLMiddle and South America
67770Guano of the Magellanic penguin in Chilean Patagonia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Proteocatella sphenisci DSM 231311123009.3wgspatric1123009
66792Proteocatella sphenisci DSM 231312523533562draftimg1123009
67770Proteocatella sphenisci DSM 23131GCA_000423525scaffoldncbi1123009

GC content

@refGC-contentmethod
1672139.5high performance liquid chromatography (HPLC)
2896739.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
motileyes89.185yes
flagellatedno67.68no
gram-positiveyes84.954yes
anaerobicyes99.611no
aerobicno96.68yes
halophileno90.81yes
spore-formingyes69.708yes
glucose-utilyes87.296no
thermophileno83.801yes
glucose-fermentyes56.815no

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16721Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23131)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23131
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
28967Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2540428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87068Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403712.1StrainInfo: A central database for resolving microbial strain identifiers