Strain identifier
BacDive ID: 2755
Type strain: 
Species: Clostridium intestinale
Strain Designation: Catt39
Strain history: W.-K. Lee strain Catt 39.
NCBI tax ID(s): 1121320 (strain), 36845 (species)
version 9.3 (current version)
General
@ref: 2519
BacDive-ID: 2755
DSM-Number: 6191
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium intestinale Catt39 is an anaerobe, mesophilic bacterium that was isolated from faeces of cattle.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121320 | strain |
| 36845 | species |
strain history
| @ref | history |
|---|---|
| 2519 | <- ATCC <- T. Mitsuoka, Catt39 |
| 67770 | W.-K. Lee strain Catt 39. |
doi: 10.13145/bacdive2755.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium intestinale
- full scientific name: Clostridium intestinale corrig. Lee et al. 1989
synonyms
- @ref: 20215
- synonym: Clostridium intestinalis
@ref: 2519
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium intestinale
full scientific name: Clostridium intestinale Lee et al. 1989
strain designation: Catt39
type strain: yes
Culture and growth conditions
culture medium
- @ref: 2519
- name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339
- composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 2519 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2519 | anaerobe | |
| 125439 | anaerobe | 99.2 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 2519 | faeces of cattle | Japan | JPN | Asia |
| 67770 | Cat feces |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_7089.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_3322;97_4075;98_5212;99_7089&stattab=map
- Last taxonomy: Clostridium intestinale subclade
- 16S sequence: X76740
- Sequence Identity:
- Total samples: 5947
- soil counts: 990
- aquatic counts: 625
- animal counts: 4023
- plant counts: 309
Safety information
risk assessment
- @ref: 2519
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 2519 | Clostridium intestinale 16S rRNA gene., type strain DSM 6191T | X76740 | 1385 | nuccore | 36845 |
| 67770 | Clostridium intestinale gene for 16S ribosomal RNA, partial sequence, strain: JCM 7506 | LC037210 | 1482 | nuccore | 36845 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium intestinale DSM 6191 | GCA_900130055 | scaffold | ncbi | 1121320 |
| 66792 | Clostridium intestinale DSM 6191 | 1121320.3 | wgs | patric | 1121320 |
| 66792 | Clostridium intestinale DSM 6191 | 2585428084 | draft | img | 1121320 |
GC content
| @ref | GC-content |
|---|---|
| 2519 | 27.0 |
| 67770 | 27 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 60.605 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 83.246 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 94.467 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 79.028 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 91.745 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 86.711 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 79.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 77.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 69.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.2 |
External links
@ref: 2519
culture collection no.: DSM 6191, ATCC 49213, JCM 7506, VTT E-032440
straininfo link
- @ref: 72285
- straininfo: 42355
literature
- topic: Phylogeny
- Pubmed-ID: 21358765
- title: Isolation and characterization of a hydrogen- and ethanol-producing Clostridium sp. strain URNW.
- authors: Ramachandran U, Wrana N, Cicek N, Sparling R, Levin DB
- journal: Can J Microbiol
- DOI: 10.1139/W11-005
- year: 2011
- mesh: Carbon Dioxide/metabolism, Cellobiose/metabolism, Clostridium/genetics/*isolation & purification/metabolism, Culture Media, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Ethanol/*metabolism, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 2519 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6191) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6191 | |
| 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 | |
| 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) | |
| 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 | |
| 72285 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42355.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |