Strain identifier
BacDive ID: 130920
Type strain:
Species: Clostridium cochlearium
Strain Designation: G7K4R3-PYG-96
Strain history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; G7K4R3-PYG-96
NCBI tax ID(s): 1494 (species)
General
@ref: 22212
BacDive-ID: 130920
DSM-Number: 29358
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen
description: Clostridium cochlearium G7K4R3-PYG-96 is an anaerobe, mesophilic human pathogen that was isolated from caecal content; wildtype C57BL/6 mouse.
NCBI tax id
- NCBI tax id: 1494
- Matching level: species
strain history
- @ref: 22212
- history: <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; G7K4R3-PYG-96
doi: 10.13145/bacdive130920.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium cochlearium
- full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923 (Approved Lists 1980)
synonyms
@ref synonym 20215 Clostridium lentoputrescens 20215 Bacillus cochlearius
@ref: 22212
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium cochlearium
full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923
strain designation: G7K4R3-PYG-96
type strain: no
Morphology
colony morphology
- @ref: 22212
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
22212 | FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) | yes | https://mediadive.dsmz.de/medium/1203 | Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water |
22212 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | 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: 22212
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 22212
- oxygen tolerance: anaerobe
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | - | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | - | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | - | builds acid from |
68367 | 17057 | cellobiose | - | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 5291 | gelatin | - | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 65327 | D-xylose | - | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | - | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | - | builds acid from |
68367 | 16899 | D-mannitol | - | builds acid from |
68367 | 17634 | D-glucose | - | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | - | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | catalase | - | 1.11.1.6 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | gelatinase | - | |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22212 | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22212 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 22212
- sample type: caecal content; wildtype C57BL/6 mouse
- geographic location: Freising
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body-Site | #Gastrointestinal tract | #Large intestine |
#Host Body Product | #Gastrointestinal tract | #Caecal content |
taxonmaps
- @ref: 69479
- File name: preview.99_16844.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_643;97_746;98_865;99_16844&stattab=map
- Last taxonomy: Clostridium cochlearium
- 16S sequence: KR364756
- Sequence Identity:
- Total samples: 3721
- soil counts: 855
- aquatic counts: 733
- animal counts: 1929
- plant counts: 204
Safety information
risk assessment
- @ref: 22212
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22212
- description: Clostridium sp. G7K4R3-PYG-96 16S ribosomal RNA gene, partial sequence
- accession: KR364756
- length: 1415
- database: ena
- NCBI tax ID: 1796625
Genome sequences
- @ref: 66792
- description: Clostridium cochlearium DSM 29358
- accession: GCA_024622865
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1494
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 55.23 | no |
gram-positive | yes | 72.426 | no |
anaerobic | yes | 99.394 | yes |
aerobic | no | 97 | yes |
halophile | no | 82.022 | no |
spore-forming | yes | 95.736 | no |
glucose-ferment | yes | 61.344 | no |
thermophile | no | 84.92 | yes |
glucose-util | yes | 85.02 | no |
motile | yes | 81.056 | no |
External links
@ref: 22212
culture collection no.: DSM 29358
straininfo link
- @ref: 89400
- straininfo: 398831
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
22212 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29358 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29358) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68367 | Automatically annotated from API 20A | |||
68380 | Automatically annotated from API rID32A | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
89400 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398831.1 |