Strain identifier

BacDive ID: 14671

Type strain: Yes

Species: Staphylococcus pettenkoferi

Strain Designation: B3117

Strain history: CIP <- 2002, K. Trülzsch, Max von Pettenkofer Inst., Munich Univ., Munich, Germany: strain B3117

NCBI tax ID(s): 170573 (species)

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General

@ref: 8171

BacDive-ID: 14671

DSM-Number: 19554

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

description: Staphylococcus pettenkoferi B3117 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from human blood culture.

NCBI tax id

  • NCBI tax id: 170573
  • Matching level: species

strain history

@refhistory
8171<- K. Trülzsch; B3117 {2007}
364182002, K. Trülzsch, M. von Pettenkofer, Munich, Germany: strain B3117
121790CIP <- 2002, K. Trülzsch, Max von Pettenkofer Inst., Munich Univ., Munich, Germany: strain B3117

doi: 10.13145/bacdive14671.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Staphylococcus
  • species: Staphylococcus pettenkoferi
  • full scientific name: Staphylococcus pettenkoferi Trülzsch et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Staphylococcus pettenkoferi

@ref: 8171

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus pettenkoferi

full scientific name: Staphylococcus pettenkoferi Trülzsch et al. 2007

strain designation: B3117

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31818positivecoccus-shapedno
121790positivecoccus-shapedno

colony morphology

@reftype of hemolysisincubation period
8171gamma1-2 days
121790

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8171TRYPTICASE 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
8171COLUMBIA 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
36418MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121790CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
8171positivegrowth37
36418positivegrowth37
59126positivegrowth37
121790positivegrowth22-45
121790nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31818facultative anaerobe
59126aerobe
121790facultative anaerobe

spore formation

@refspore formationconfidence
31818no
125439no94

observation

  • @ref: 31818
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3181828757fructose+carbon source
3181817992sucrose+carbon source
3181817632nitrate+reduction
6837522599arabinose-fermentation
6837559640N-acetylglucosamine-fermentation
6837517632nitrate+reduction
6837516634raffinose-fermentation
6837516899D-mannitol-fermentation
6837527082trehalose-fermentation
6837517716lactose-fermentation
6837516024D-mannose-fermentation
6837518257ornithine-degradation
6837529016arginine-hydrolysis
121790606565hippurate+hydrolysis
12179017632nitrate+reduction
12179016301nitrite-reduction
6837532528turanose-fermentation
6837517057cellobiose-fermentation
6837516988D-ribose-fermentation
6837517306maltose-fermentation
683754853esculin-hydrolysis

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is sensitive: yes
  • sensitivity conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12179035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
6837515688acetoin-
12179015688acetoin-
12179017234glucose-

enzymes

@refvalueactivityec
8171catalase+1.11.1.6
8171cytochrome-c oxidase-1.9.3.1
31818alkaline phosphatase+3.1.3.1
31818catalase+1.11.1.6
31818urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121790oxidase-
121790beta-galactosidase-3.2.1.23
121790alcohol dehydrogenase-1.1.1.1
121790gelatinase-
121790amylase-
121790DNase-
121790caseinase-3.4.21.50
121790catalase+1.11.1.6
121790tween esterase-
121790gamma-glutamyltransferase-2.3.2.2
121790lecithinase-
121790lipase-
121790lysine decarboxylase-4.1.1.18
121790ornithine decarboxylase-4.1.1.17
121790protease-
121790tryptophan deaminase-
121790urease+3.5.1.5
68375beta-glucuronidase-3.2.1.31
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68375pyrrolidonyl arylamidase+3.4.19.3
68375alkaline phosphatase+3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59126C16:00.516
    59126C18:01.118
    59126C20:00.520
    59126C15:0 ANTEISO34.214.711
    59126C15:0 ISO20.214.621
    59126C16:0 iso115.626
    59126C17:0 anteiso22.216.722
    59126C17:0 iso13.116.629
    59126C18:0 ISO0.417.632
    59126C18:1 ω9c0.417.769
    59126C18:2 ω6,9c/C18:0 ANTE0.517.724
    59126C19:0 ANTEISO5.818.729
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121790-+++------++--------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8171----+/-+/---------+---++-+/-----
8171+---++--------+---++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121790++-----------------------------+-------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
8171human blood cultureGermanyDEUEurope
59126Human bloodGermanyDEUEurope1999München
121790Human, BloodGermanyDEUEuropeMünchen2000

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Blood culture
#Host#Human
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_2102.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_1644;99_2102&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AF322002
  • Sequence Identity:
  • Total samples: 7977
  • soil counts: 456
  • aquatic counts: 511
  • animal counts: 6801
  • plant counts: 209

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81712Risk group (German classification)
1217901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8171
  • description: Staphylococcus pettenkoferi strain B3117 16S ribosomal RNA gene, partial sequence
  • accession: AF322002
  • length: 1547
  • database: nuccore
  • NCBI tax ID: 170573

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus pettenkoferi CCUG 51270GCA_002902685scaffoldncbi170573
66792Staphylococcus pettenkoferi strain CCUG 51270170573.8wgspatric170573
66792Staphylococcus pettenkoferi strain FDAARGOS_1071170573.30completepatric170573
66792Staphylococcus pettenkoferi CCUG 512702917437079draftimg170573

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.295yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.923no
125438spore-formingspore-formingAbility to form endo- or exosporesno75.021yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes65.233no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.192yes
125438motile2+flagellatedAbility to perform flagellated movementno81.833yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94
125439BacteriaNetmotilityAbility to perform movementno79
125439BacteriaNetgram_stainReaction to gram-stainingpositive74.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile88.4

External links

@ref: 8171

culture collection no.: DSM 19554, CCUG 51270, CIP 107711, CCM 7495

straininfo link

  • @ref: 83797
  • straininfo: 215038

literature

  • topic: Phylogeny
  • Pubmed-ID: 17625191
  • title: Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens.
  • authors: Trulzsch K, Grabein B, Schumann P, Mellmann A, Antonenka U, Heesemann J, Becker K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64381-0
  • year: 2007
  • mesh: Anti-Bacterial Agents/pharmacology, Bacteremia/*microbiology, Bacterial Typing Techniques, Belgium, Cluster Analysis, Coagulase/*analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Germany, Humans, Locomotion, Microbial Sensitivity Tests, Molecular Sequence Data, Novobiocin/pharmacology, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Staphylococcal Infections/*microbiology, Staphylococcus/chemistry/*classification/*isolation & purification/physiology, Vitamin K 2
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8171Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19554)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19554
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
31818Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2808528776041
36418Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5177
59126Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51270)https://www.ccug.se/strain?id=51270
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)
68375Automatically annotated from API ID32STA
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
83797Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215038.1StrainInfo: A central database for resolving microbial strain identifiers
121790Curators of the CIPCollection of Institut Pasteur (CIP 107711)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107711
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1