Strain identifier
BacDive ID: 2721
Type strain: 
Species: Clostridium symbiosum
Strain Designation: 2
Strain history: C. Kaneuchi <-- ATCC 14940 <-- R. E. Reeves ("Bacteroides symbiosus") <-- J. Shaffer 2 (M. Sebald strain LSU).
NCBI tax ID(s): 411472 (strain), 1512 (species)
version 8.1 (current version)
General
@ref: 472
BacDive-ID: 2721
DSM-Number: 934
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Clostridium symbiosum 2 is an anaerobe, mesophilic, Gram-positive bacterium of the family Clostridiaceae.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1512 | species |
| 411472 | strain |
strain history
| @ref | history |
|---|---|
| 472 | <- C. Kaneuchi <- ATCC <- R.E. Reeves (Bacteroides symbiosus) <- J. Shaffer, 2 |
| 67770 | C. Kaneuchi <-- ATCC 14940 <-- R. E. Reeves ("Bacteroides symbiosus") <-- J. Shaffer 2 (M. Sebald strain LSU). |
doi: 10.13145/bacdive2721.20230509.8.1
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 symbiosum
- full scientific name: Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacteroides symbiosus
@ref: 472
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium symbiosum
full scientific name: Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976
strain designation: 2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 472
- name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110
- composition: 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 |
|---|---|---|---|---|
| 472 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 472 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 93.364
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_5102.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_2483;97_3033;98_3808;99_5102&stattab=map
- Last taxonomy: [Clostridium] symbiosum subclade
- 16S sequence: LC036311
- Sequence Identity:
- Total samples: 189499
- soil counts: 1377
- aquatic counts: 3039
- animal counts: 184529
- plant counts: 554
Safety information
risk assessment
- @ref: 472
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium symbiosum strain ATCC 14940 16S ribosomal RNA gene, partial sequence | M59112 | 1478 | ena | 1512 |
| 20218 | Bifidobacterium thermophilum gene for 16S rRNA, partial sequence, strain: JCM 1297 | AB116355 | 458 | ena | 33905 |
| 472 | Clostridium symbiosum strain DSM 934 16S ribosomal RNA gene, partial sequence | HM245954 | 845 | ena | 1512 |
| 67770 | [Clostridium] symbiosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1297 | LC036311 | 1492 | ena | 1512 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | [Clostridium] symbiosum strain NCTC13233 | 1512.13 | wgs | patric | 1512 |
| 66792 | Clostridium symbiosum ATCC 14940 | 411472.5 | wgs | patric | 411472 |
| 66792 | Lachnoclostridium symbiosum ATCC 14940 | 2597490298 | draft | img | 411472 |
| 66792 | Lachnoclostridium symbiosum NCTC 13233 | 2814123396 | draft | img | 1512 |
| 67770 | [Clostridium] symbiosum ATCC 14940 | GCA_000466485 | scaffold | ncbi | 411472 |
| 67770 | [Clostridium] symbiosum NCTC13233 | GCA_900461275 | contig | ncbi | 1512 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 472 | 46.1 | |
| 67770 | 46.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 63 | no |
| gram-positive | yes | 81.91 | no |
| anaerobic | yes | 99.628 | yes |
| halophile | no | 92.74 | no |
| spore-forming | yes | 83.555 | no |
| glucose-util | yes | 90.827 | no |
| aerobic | no | 97.934 | yes |
| flagellated | yes | 52.575 | no |
| thermophile | no | 97.38 | yes |
| motile | yes | 83.483 | no |
| glucose-ferment | yes | 65.374 | no |
External links
@ref: 472
culture collection no.: DSM 934, ATCC 14940, LSU (M. Sebald), JCM 1297, BCRC 14487, CCM 6065, NCTC 13233, VTT E-981051
straininfo link
- @ref: 72249
- straininfo: 36207
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 472 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 934) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-934 | |||
| 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) | |||
| 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) | |||
| 72249 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID36207.1 | StrainInfo: A central database for resolving microbial strain identifiers |