Strain identifier

BacDive ID: 11782

Type strain: Yes

Species: Peptococcus niger

Strain history: Y. Benno <-- T. Mitsuoka <-- ATCC 27731 <-- VPI 7953.

NCBI tax ID(s): 2741 (species)

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General

@ref: 8844

BacDive-ID: 11782

DSM-Number: 20475

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, human pathogen

description: Peptococcus niger DSM 20475 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from umbilicus.

NCBI tax id

  • NCBI tax id: 2741
  • Matching level: species

strain history

@refhistory
8844<- ATCC <- T. Wilkins, VPI 7953
67770Y. Benno <-- T. Mitsuoka <-- ATCC 27731 <-- VPI 7953.

doi: 10.13145/bacdive11782.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptococcaceae
  • genus: Peptococcus
  • species: Peptococcus niger
  • full scientific name: Peptococcus niger (Hall 1930) Kluyver and van Niel 1936 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Micrococcus niger

@ref: 8844

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptococcaceae

genus: Peptococcus

species: Peptococcus niger

full scientific name: Peptococcus niger (Hall 1930) Kluyver and van Niel 1936

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 97.781

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8844RCM MEDIUM (DSMZ Medium 634)yeshttps://mediadive.dsmz.de/medium/634Name: RCM MEDIUM (DSMZ Medium 634) Composition: Sodium resazurin 0.0005 g/l dehydrated RCM medium
8844CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8844positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8844anaerobe
69480anaerobe99.491

spore formation

@refspore formationconfidence
69481no100
69480no99.826

murein

  • @ref: 8844
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

Isolation, sampling and environmental information

isolation

@refsample type
8844umbilicus
67770Navel swab

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_21996.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1904;96_8221;97_13471;98_16590;99_21996&stattab=map
  • Last taxonomy: Peptococcus niger subclade
  • 16S sequence: AB644260
  • Sequence Identity:
  • Total samples: 10925
  • soil counts: 79
  • aquatic counts: 185
  • animal counts: 10638
  • plant counts: 23

Safety information

risk assessment

  • @ref: 8844
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Peptococcus niger DNA for 16S ribosomal RNAX557971410ena2741
20218Peptococcus niger gene for 16S ribosomal RNA, partial sequence, strain: JCM 6506AB6442601528ena2741

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peptococcus niger strain DSM 204752741.7wgspatric2741
66792Peptococcus niger DSM 204752634166305draftimg2741
67770Peptococcus niger DSM 20475GCA_900101835scaffoldncbi2741

GC content

@refGC-contentmethod
884451.0
6777050thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.945no
gram-positiveyes77.458no
anaerobicyes98.057yes
halophileno80.425no
spore-formingno68.999no
glucose-utilyes57.18no
aerobicno94.628yes
flagellatedno98.563no
thermophileno98.374yes
glucose-fermentno68.307no

External links

@ref: 8844

culture collection no.: DSM 20475, ATCC 27731, VPI 7953, JCM 6506, CCM 6019, CIP 105947, NCTC 11805

straininfo link

  • @ref: 81000
  • straininfo: 44778

literature

  • topic: Phylogeny
  • Pubmed-ID: 8123556
  • title: 16S ribosomal DNA sequences of anaerobic cocci and proposal of Ruminococcus hansenii comb. nov. and Ruminococcus productus comb. nov.
  • authors: Ezaki T, Li N, Hashimoto Y, Miura H, Yamamoto H
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-44-1-130
  • year: 1994
  • mesh: Anaerobiosis, Base Sequence, DNA, Bacterial/*chemistry, DNA, Ribosomal/*chemistry, Molecular Sequence Data, Peptococcaceae/*classification/*genetics, RNA, Ribosomal, 16S/*genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8844Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20475)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20475
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
81000Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44778.1StrainInfo: A central database for resolving microbial strain identifiers