Strain identifier
BacDive ID: 11782
Type strain:
Species: Peptococcus niger
Strain history: Y. Benno <-- T. Mitsuoka <-- ATCC 27731 <-- VPI 7953.
NCBI tax ID(s): 2741 (species)
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
@ref | history |
---|---|
8844 | <- ATCC <- T. Wilkins, VPI 7953 |
67770 | Y. 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
@ref | name | growth | link | composition |
---|---|---|---|---|
8844 | RCM MEDIUM (DSMZ Medium 634) | yes | https://mediadive.dsmz.de/medium/634 | Name: RCM MEDIUM (DSMZ Medium 634) Composition: Sodium resazurin 0.0005 g/l dehydrated RCM medium |
8844 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
8844 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8844 | anaerobe | |
69480 | anaerobe | 99.491 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.826 |
murein
- @ref: 8844
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8844 | umbilicus |
67770 | Navel 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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Peptococcus niger DNA for 16S ribosomal RNA | X55797 | 1410 | ena | 2741 |
20218 | Peptococcus niger gene for 16S ribosomal RNA, partial sequence, strain: JCM 6506 | AB644260 | 1528 | ena | 2741 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Peptococcus niger strain DSM 20475 | 2741.7 | wgs | patric | 2741 |
66792 | Peptococcus niger DSM 20475 | 2634166305 | draft | img | 2741 |
67770 | Peptococcus niger DSM 20475 | GCA_900101835 | scaffold | ncbi | 2741 |
GC content
@ref | GC-content | method |
---|---|---|
8844 | 51.0 | |
67770 | 50 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.945 | no |
gram-positive | yes | 77.458 | no |
anaerobic | yes | 98.057 | yes |
halophile | no | 80.425 | no |
spore-forming | no | 68.999 | no |
glucose-util | yes | 57.18 | no |
aerobic | no | 94.628 | yes |
flagellated | no | 98.563 | no |
thermophile | no | 98.374 | yes |
glucose-ferment | no | 68.307 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8844 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20475) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20475 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
81000 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44778.1 | StrainInfo: A central database for resolving microbial strain identifiers |