Strain identifier

BacDive ID: 14410

Type strain: Yes

Species: Jeotgalicoccus pinnipedialis

Strain Designation: A/G14/99/10

Strain history: CIP <- 2003, CCUG <- M.D. Collins, Reading, UK <- L. Hoyles, Reading, UK <- G. Foster, Inverness, UK, strain A/G14/99/10

NCBI tax ID(s): 110845 (species)

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General

@ref: 6694

BacDive-ID: 14410

DSM-Number: 17030

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Jeotgalicoccus pinnipedialis A/G14/99/10 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Seal mouth, female southern elephant seal.

NCBI tax id

  • NCBI tax id: 110845
  • Matching level: species

strain history

@refhistory
6694<- CCUG <- M.D.Collins, Reading, <- L. Hoyles, Reading, UK <- G.Foster, A/G14/99/10
121837CIP <- 2003, CCUG <- M.D. Collins, Reading, UK <- L. Hoyles, Reading, UK <- G. Foster, Inverness, UK, strain A/G14/99/10

doi: 10.13145/bacdive14410.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Jeotgalicoccus
  • species: Jeotgalicoccus pinnipedialis
  • full scientific name: Jeotgalicoccus pinnipedialis Hoyles et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Phocicoccus pinnipedialis

@ref: 6694

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Jeotgalicoccus

species: Jeotgalicoccus pinnipedialis

full scientific name: Jeotgalicoccus pinnipedialis Hoyles et al. 2004

strain designation: A/G14/99/10

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30016positivecoccus-shapedno
69480positive100
121837positivecoccus-shapedno

colony morphology

  • @ref: 121837

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6694COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
6694TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
34311MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
121837CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
6694positivegrowth37mesophilic
30016positivegrowth25-42
30016positiveoptimum33.5mesophilic
34311positivegrowth37mesophilic
55531positivegrowth37mesophilic
121837positivegrowth25-41
121837nogrowth10psychrophilic
121837nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6694microaerophile
6694aerobe
30016facultative anaerobe
55531aerobe
121837obligate aerobe

spore formation

@refspore formationconfidence
30016no
69480no99.96

halophily

@refsaltgrowthtested relationconcentration
30016NaClpositivegrowth02-06 %
30016NaClpositiveoptimum4 %
121837NaClpositivegrowth6.5 %

observation

  • @ref: 30016
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
300165291gelatin+carbon source
1218374853esculin+hydrolysis
121837606565hippurate+hydrolysis
12183717632nitrate-reduction
12183716301nitrite-reduction

antibiotic resistance

  • @ref: 121837
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 121837
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
30016acid phosphatase+3.1.3.2
30016catalase+1.11.1.6
30016gelatinase+
30016cytochrome oxidase+1.9.3.1
121837oxidase-
121837beta-galactosidase-3.2.1.23
121837alcohol dehydrogenase-1.1.1.1
121837catalase+1.11.1.6
121837gamma-glutamyltransferase+2.3.2.2
121837lysine decarboxylase-4.1.1.18
121837ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121837--+-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121837+++++-+--++++++--+++++-++------+-+--+-+----+-----++-++++-+-++--------------+---++-+--++--++++-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6694Seal mouth, female southern elephant sealSouth OrkneysAntarcticaATAAustralia and Oceania
55531Seal mouth,female southern elephant sealSouth OrkneysAntarcticaATAAustralia and Oceania1993
121837Swab from the mouth of a female southern elephant sealSouth Orkneys, ScotlandUnited KingdomGBREurope1993

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Mammals
#Host Body-Site#Oral cavity and airways#Mouth
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_124253.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_15623;97_19140;98_23885;99_124253&stattab=map
  • Last taxonomy: Jeotgalicoccus pinnipedialis
  • 16S sequence: AJ251530
  • Sequence Identity:
  • Total samples: 602
  • soil counts: 142
  • aquatic counts: 14
  • animal counts: 441
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66941Risk group (German classification)
1218371Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6694
  • description: Jeotgalicoccus pinnipedialis partial 16S rRNA gene, type strain CCUG 42722T
  • accession: AJ251530
  • length: 1419
  • database: ena
  • NCBI tax ID: 110845

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jeotgalicoccus pinnipedialis CIP 107946GCA_903994035contigncbi110845
66792Jeotgalicoccus pinnipedialis DSM 17030GCA_017873645contigncbi110845
66792Jeotgalicoccus pinnipedialis strain CIP107946110845.3wgspatric110845
66792Jeotgalicoccus pinnipedialis strain DSM 17030110845.4wgspatric110845
66792Jeotgalicoccus pinnipedialis DSM 170302913376348draftimg110845

GC content

  • @ref: 6694
  • GC-content: 38.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileno90.551yes
flagellatedno97.998yes
gram-positiveyes91.145yes
anaerobicno98.268no
aerobicyes88.44no
halophileyes93.355no
spore-formingno91.69no
thermophileno99.593yes
glucose-utilyes81.031no
glucose-fermentno68.314no

External links

@ref: 6694

culture collection no.: DSM 17030, CCUG 42722, CIP 107946

straininfo link

  • @ref: 83554
  • straininfo: 87820

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143018Jeotgalicoccus pinnipedialis sp. nov., from a southern elephant seal (Mirounga leonina).Hoyles L, Collins MD, Foster G, Falsen E, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.02833-02004Animals, Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Female, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seals, Earless/*microbiology, Staphylococcaceae/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny27282768Jeotgalicoccus schoeneichii sp. nov. isolated from exhaust air of a pig barn.Glaeser SP, Kleinhagauer T, Jackel U, Klug K, Kampfer PInt J Syst Evol Microbiol10.1099/ijsem.0.0012302016Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, *Housing, Animal, Nucleic Acid Hybridization, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcaceae/*classification/genetics/isolation & purification, *Sus scrofa, Swine, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6694Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17030)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17030
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
30016Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2638028776041
34311Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5513
55531Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42722)https://www.ccug.se/strain?id=42722
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)
68382Automatically annotated from API zym
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)
83554Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87820.1StrainInfo: A central database for resolving microbial strain identifiers
121837Curators of the CIPCollection of Institut Pasteur (CIP 107946)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107946