Strain identifier

BacDive ID: 18004

Type strain: Yes

Species: Peptoniphilus gorbachii

Strain history: <- CCUG <- Y Song, VAMC, Los Angeles, USA

NCBI tax ID(s): 411567 (species)

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General

@ref: 15720

BacDive-ID: 18004

DSM-Number: 21461

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, coccus-shaped

description: Peptoniphilus gorbachii JCM 15634 is an anaerobe, coccus-shaped bacterium that was isolated from human abscess, groin.

NCBI tax id

  • NCBI tax id: 411567
  • Matching level: species

strain history

@refhistory
15720<- CCUG <- Y. Song, VAMC Los Angeles, USA
67770CCUG 53341 <-- Y. Song WAL 10418.
67771<- CCUG <- Y Song, VAMC, Los Angeles, USA

doi: 10.13145/bacdive18004.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptoniphilaceae
  • genus: Peptoniphilus
  • species: Peptoniphilus gorbachii
  • full scientific name: Peptoniphilus gorbachii Song et al. 2010

@ref: 15720

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptoniphilaceae

genus: Peptoniphilus

species: Peptoniphilus gorbachii

full scientific name: Peptoniphilus gorbachii Song et al. 2010

type strain: yes

Morphology

cell morphology

@refcell shapegram stain
67771coccus-shaped
67771positive

colony morphology

  • @ref: 59871
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15720COLUMBIA 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
15720PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperature
15720positivegrowth37
59871positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15720anaerobe
59871anaerobe
67771anaerobe
69480anaerobe95.28

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838017632nitrate-reduction

enzymes

@refvalueactivityec
68380serine arylamidase+
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alpha-fucosidase-3.2.1.51
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
15720---------------++/-+--++-+-++++
15720------------+---++---+/--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15720human abscess, groinLos Angeles, CaliforniaUSAUSANorth America
59871Human abscess,groinCalifornia,Los AngelesUSAUSANorth America1992-11-01
67770Human clinical specimens
67771From human abscess, groinCalifornia, Los AngelesUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site
#Host Body-Site#Other#Abscess

Safety information

risk assessment

  • @ref: 15720
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15720
  • description: Peptoniphilus sp. WAL 10418 16S ribosomal RNA gene, partial sequence
  • accession: DQ911241
  • length: 1404
  • database: nuccore
  • NCBI tax ID: 411567

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peptoniphilus gorbachii DSM 21461GCA_016908115contigncbi411567
66792Peptoniphilus gorbachii strain DSM 21461411567.4wgspatric411567
66792Peptoniphilus gorbachii DSM 214612901072628draftimg411567

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes82.301no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes95.28yes
69480spore-formingspore-formingAbility to form endo- or exosporesno69.29no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.817yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.096yes
69480flagellatedmotile2+Ability to perform flagellated movementno87.78no

External links

@ref: 15720

culture collection no.: JCM 15634, KCTC 5947, DSM 21461, ATCC BAA-1383, CCUG 53341, WAL 10418

straininfo link

  • @ref: 86991
  • straininfo: 400460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17428937Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin.Song Y, Liu C, Finegold SMJ Clin Microbiol10.1128/JCM.00213-072007Anaerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Genotype, Gram-Positive Bacterial Infections/*microbiology, Gram-Positive Cocci/*classification/drug effects/genetics/isolation & purification, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny34125664Peptoniphilus faecalis sp. nov., isolated from swine faeces.Ryu SW, Kim JS, Oh BS, Yu SY, Lee JS, Park SH, Kang SW, Lee J, Lee MK, Rhee MS, Jung H, Hur TY, Kim HB, Kim JK, Lee JH, Lee JHInt J Syst Evol Microbiol10.1099/ijsem.0.0048362021Animals, Bacteria, Anaerobic/classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Gram-Positive Cocci/classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine/*microbiologyEnzymology

Reference

@idauthorscataloguedoi/urltitle
15720Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21461)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21461
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
59871Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53341)https://www.ccug.se/strain?id=53341
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
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
86991Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400460.1StrainInfo: A central database for resolving microbial strain identifiers