Strain identifier

BacDive ID: 132557

Type strain: No

Species: Peptoniphilus pacaensis

Strain Designation: Kh-D5, KHD5

Strain history: <- S. Khelaifia, Timone Hospital, Marseille, France; Kh-D5 <- Unité de Recherche sur les Maladies Infectieuses;

NCBI tax ID(s): 1776390 (species)

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General

@ref: 24346

BacDive-ID: 132557

DSM-Number: 101839

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Peptoniphilus pacaensis Kh-D5 is a mesophilic bacterium that was isolated from human vagina specimen, 33-year-old woman exhibiting a bacterial vaginosis.

NCBI tax id

  • NCBI tax id: 1776390
  • Matching level: species

strain history

  • @ref: 24346
  • history: <- S. Khelaifia, Timone Hospital, Marseille, France; Kh-D5 <- Unité de Recherche sur les Maladies Infectieuses;

doi: 10.13145/bacdive132557.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptoniphilaceae
  • genus: Peptoniphilus
  • species: Peptoniphilus pacaensis
  • full scientific name: Peptoniphilus pacaensis Diop et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Peptoniphilus pacaensis

@ref: 24346

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptoniphilaceae

genus: Peptoniphilus

species: Peptoniphilus pacaensis

full scientific name: Peptoniphilus pacaensis et al. 2016

strain designation: Kh-D5, KHD5

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24346PYG 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
24346COLUMBIA 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

culture temp

  • @ref: 24346
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

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-
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380proline-arylamidase+3.4.11.5
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
24346-----------------+/-++/-----+/-----

Isolation, sampling and environmental information

isolation

  • @ref: 24346
  • sample type: human vagina specimen, 33-year-old woman exhibiting a bacterial vaginosis
  • geographic location: Provence Alpes Cote d'Azur
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient#Specimen
#Host#Human#Female
#Host Body-Site#Urogenital tract#Vagina

taxonmaps

  • @ref: 69479
  • File name: preview.99_6168.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_378;96_1665;97_1993;98_2452;99_6168&stattab=map
  • Last taxonomy: Peptoniphilus pacaensis
  • 16S sequence: LN998072
  • Sequence Identity:
  • Total samples: 10925
  • soil counts: 122
  • aquatic counts: 148
  • animal counts: 10615
  • plant counts: 40

Sequence information

16S sequences

  • @ref: 24346
  • description: Peptoniphilus sp. KHD5 partial 16S rRNA gene, strain KHD5
  • accession: LN998072
  • length: 1491
  • database: ena
  • NCBI tax ID: 1776390

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peptoniphilus pacaensis Kh-D5GCA_900088125contigncbi1776390
66792Peptoniphilus pacaensis KHD52837111862draftimg1776390

External links

@ref: 24346

culture collection no.: DSM 101839, CSUR P2271

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27408739'Peptoniphilus pacaensis' sp. nov., a new species isolated from human female genital tract.Diop K, Bretelle F, Mediannikov O, Fournier PE, Fenollar FNew Microbes New Infect10.1016/j.nmni.2016.06.0072016
Phylogeny29931836Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov.Diop K, Diop A, Michelle C, Richez M, Rathored J, Bretelle F, Fournier PE, Fenollar FMicrobiologyopen10.1002/mbo3.6612018Adult, Anaerobiosis, *Bacterial Typing Techniques, Base Composition, Body Fluids/*microbiology, Cytosol/chemistry, Fatty Acids/analysis, Female, Firmicutes/*classification/genetics/*isolation & purification/physiology, Humans, Phylogeny, Sequence Homology, Nucleic Acid, Vaginosis, Bacterial/*microbiologyPathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24346Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101839Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101839)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/