Strain identifier
BacDive ID: 2603
Type strain: 
Species: Clostridium innocuum
Strain Designation: B-3
Strain history: ATCC 14501 <-- L. DS. Smith B-3 <-- CDC (E. King) <-- Murfreesboro Med. Clinic, TN, USA.
NCBI tax ID(s): 1522 (species)
version 9.3 (current version)
General
@ref: 606
BacDive-ID: 2603
DSM-Number: 1286
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic
description: Clostridium innocuum B-3 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from appendiceal abscess.
NCBI tax id
- NCBI tax id: 1522
- Matching level: species
strain history
| @ref | history |
|---|---|
| 606 | <- ATCC <- L.DS. Smith, B-3 <- E. King, CDC <- Murfreesboro Medical Clinic, Tenn., USA |
| 67770 | ATCC 14501 <-- L. DS. Smith B-3 <-- CDC (E. King) <-- Murfreesboro Med. Clinic, TN, USA. |
doi: 10.13145/bacdive2603.20250331.9.3
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 innocuum
- full scientific name: Clostridium innocuum Smith and King 1962 (Approved Lists 1980)
@ref: 606
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium innocuum
full scientific name: Clostridium innocuum Smith and King 1962
strain designation: B-3
type strain: yes
Culture and growth conditions
culture medium
- @ref: 606
- name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
- growth: yes
- link: https://mediadive.dsmz.de/medium/78
- composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 606 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 606
- oxygen tolerance: anaerobe
spore formation
- @ref: 125439
- spore formation: yes
- confidence: 91.2
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 606 | appendiceal abscess |
| 67770 | Appendiceal abscess |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body-Site | #Gastrointestinal tract | #Large intestine |
| #Host Body-Site | #Other | #Abscess |
taxonmaps
- @ref: 69479
- File name: preview.99_678.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_135;96_419;97_475;98_546;99_678&stattab=map
- Last taxonomy: [Clostridium] innocuum subclade
- 16S sequence: AB971793
- Sequence Identity:
- Total samples: 1575
- soil counts: 1
- aquatic counts: 1
- animal counts: 1573
Safety information
risk assessment
- @ref: 606
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium innocuum strain DSM 1286 16S ribosomal RNA gene, partial sequence | HM245947 | 832 | nuccore | 1522 |
| 606 | [Clostridium] innocuum strain B-3 16S ribosomal RNA gene, partial sequence | M23732 | 1543 | nuccore | 1522 |
| 67770 | [Clostridium] innocuum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1292 | AB971793 | 1501 | nuccore | 1522 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | [Clostridium] innocuum ATCC 14501 | GCA_012317185 | complete | ncbi | 1522 |
| 66792 | [Clostridium] innocuum ATCC 14501 | GCA_018458805 | scaffold | ncbi | 1522 |
| 66792 | [Clostridium] innocuum strain ATCC 14501 | 1522.132 | complete | patric | 1522 |
| 66792 | [Clostridium] innocuum strain ATCC 14501 | 1522.172 | wgs | patric | 1522 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 606 | 44.0 | |
| 67770 | 44 | thermal denaturation, midpoint method (Tm) |
| 67770 | 44.5 | genome sequence analysis |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 77.482 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 83.449 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 96.798 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 52.977 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 92.29 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 78.009 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 91.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 89.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 84.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 73.2 |
External links
@ref: 606
culture collection no.: DSM 1286, ATCC 14501, NCIB 10674, JCM 1292, BCRC 14517, CCUG 24036, CCUG 35868, CCUG 36763, KCTC 5183, NCIMB 10674
straininfo link
- @ref: 72134
- straininfo: 92603
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Pathogenicity | 9620417 | Low-level vancomycin resistance in Clostridium innocuum. | Mory F, Lozniewski A, David V, Carlier JP, Dubreuil L, Leclercq R | J Clin Microbiol | 10.1128/JCM.36.6.1767-1768.1998 | 1998 | Anti-Bacterial Agents/*pharmacology, Clostridium/*drug effects/genetics/isolation & purification, Drug Resistance, Microbial/genetics, Genes, Bacterial, Humans, Microbial Sensitivity Tests, Polymerase Chain Reaction, Teicoplanin/pharmacology, Vancomycin/*pharmacology | Enzymology |
| Genetics | 15150227 | Mechanism of intrinsic resistance to vancomycin in Clostridium innocuum NCIB 10674. | David V, Bozdogan B, Mainardi JL, Legrand R, Gutmann L, Leclercq R | J Bacteriol | 10.1128/JB.186.11.3415-3422.2004 | 2004 | Amino Acid Sequence, Base Sequence, Clostridium/*drug effects, Molecular Sequence Data, Peptidoglycan/biosynthesis, Plasmids, Racemases and Epimerases/genetics, Uridine Diphosphate/metabolism, *Vancomycin Resistance | Pathogenicity |
| Phylogeny | 28754474 | Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov. | Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, Chang YH | Anaerobe | 10.1016/j.anaerobe.2017.07.006 | 2017 | Animals, Bacterial Typing Techniques/*veterinary, Base Composition/genetics, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Dogs, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/analysis, Firmicutes/*classification/genetics/isolation & purification, Intestines/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
| Genetics | 32703829 | Complete Genome Sequence of Clostridium innocuum Strain ATCC 14501. | Cherny KE, Ozer EA, Kochan TJ, Kociolek LK | Microbiol Resour Announc | 10.1128/MRA.00452-20 | 2020 | ||
| Phylogeny | 33083133 | Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces. | Ghimire S, Wongkuna S, Scaria J | PeerJ | 10.7717/peerj.10071 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 606 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1286) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1286 | |||
| 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 | |||
| 72134 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92603.1 | 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 |