Strain identifier
BacDive ID: 17997
Type strain: 
Species: Peptoniphilus indolicus
Strain Designation: R13
Strain history: <- ATCC <- G.H. Sorensen, R13
NCBI tax ID(s): 997350 (strain), 33030 (species)
version 8.1 (current version)
General
@ref: 8835
BacDive-ID: 17997
DSM-Number: 20464
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, animal pathogen
description: Peptoniphilus indolicus R13 is an anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from summer mastitis secretion of heifer.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 997350 | strain |
| 33030 | species |
strain history
- @ref: 8835
- history: <- ATCC <- G.H. Sorensen, R13
doi: 10.13145/bacdive17997.20230509.8.1
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 indolicus
- full scientific name: Peptoniphilus indolicus (Christiansen 1934) Ezaki et al. 2001
synonyms
@ref synonym 20215 Micrococcus indolicus 20215 Schleiferella indolica 20215 Peptococcus indolicus 20215 Peptostreptococcus indolicus
@ref: 8835
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptoniphilaceae
genus: Peptoniphilus
species: Peptoniphilus indolicus
full scientific name: Peptoniphilus indolicus (Christiansen 1934) Ezaki et al. 2001
strain designation: R13
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.719
Culture and growth conditions
culture medium
- @ref: 8835
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: Name: 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
- @ref: 8835
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 8835 | anaerobe | |
| 69480 | anaerobe | 98.651 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.975
murein
- @ref: 8835
- murein short key: A21.05
- type: A4ß L-Orn-D-Glu
Isolation, sampling and environmental information
isolation
- @ref: 8835
- sample type: summer mastitis secretion of heifer
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Disease | |
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body Product | #Fluids |
taxonmaps
- @ref: 69479
- File name: preview.99_28218.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_38;96_3367;97_4135;98_5291;99_28218&stattab=map
- Last taxonomy: Peptoniphilus indolicus
- 16S sequence: GU993268
- Sequence Identity:
- Total samples: 2083
- soil counts: 203
- aquatic counts: 94
- animal counts: 1754
- plant counts: 32
Safety information
risk assessment
- @ref: 8835
- 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 | Peptoniphilus indolicus strain ATCC 29427 16S ribosomal RNA gene, partial sequence | GU993268 | 1287 | ena | 997350 |
| 8835 | Peptoniphilus indolicus gene for 16S ribosomal RNA, partial sequence | D14147 | 1372 | ena | 997350 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Peptoniphilus indolicus ATCC 29427 | GCA_000227315 | scaffold | ncbi | 997350 |
| 66792 | Peptoniphilus indolicus ATCC 29427 | 997350.3 | wgs | patric | 997350 |
GC content
- @ref: 8835
- GC-content: 34.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 78 | no |
| motile | no | 90.323 | no |
| flagellated | no | 97.645 | no |
| gram-positive | yes | 86.8 | no |
| anaerobic | yes | 98.749 | yes |
| aerobic | no | 98.195 | no |
| halophile | no | 67.699 | no |
| spore-forming | no | 83.686 | no |
| thermophile | no | 98.413 | yes |
| glucose-util | yes | 85.053 | no |
| glucose-ferment | yes | 50.647 | no |
External links
@ref: 8835
culture collection no.: DSM 20464, ATCC 29427, CCM 5987
straininfo link
- @ref: 86984
- straininfo: 45858
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19643871 | Anaerosphaera aminiphila gen. nov., sp. nov., a glutamate-degrading, Gram-positive anaerobic coccus isolated from a methanogenic reactor treating cattle waste. | Ueki A, Abe K, Suzuki D, Kaku N, Watanabe K, Ueki K | Int J Syst Evol Microbiol | 10.1099/ijs.0.011858-0 | 2009 | Anaerobiosis, Animals, Biodegradation, Environmental, Bioreactors/*microbiology, Cattle, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Feces/microbiology, Glutamic Acid/*metabolism, Methanol/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Veillonellaceae/*classification/genetics/*isolation & purification/metabolism, Waste Products/*analysis | Metabolism |
| Phylogeny | 28595834 | The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor. | Tomazetto G, Hahnke S, Langer T, Wibberg D, Blom J, Maus I, Puhler A, Klocke M, Schluter A | J Biotechnol | 10.1016/j.jbiotec.2017.05.027 | 2017 | Animals, Bacterial Typing Techniques, Base Sequence, Biofuels/*microbiology, Bioreactors/*microbiology, Cattle, Clostridiales/*classification/*genetics/*isolation & purification/physiology, DNA, Bacterial, Fatty Acids/metabolism, Fermentation, Genes, Bacterial/genetics, *Genome, Bacterial, Manure/microbiology, Metabolic Networks and Pathways, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/microbiology, Swine, Zea mays | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8835 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20464) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20464 | |||
| 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 | |
| 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) | |||
| 86984 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45858.1 | StrainInfo: A central database for resolving microbial strain identifiers |