PROJECT INFORMATION
GOLD Project ID
Gp0016183  
Project Name
Caldicoprobacter oshimai DSM 21659  
Other Names
  
Legacy ER Project ID
21405  
Legacy GOLD ID
Gi13781  
NCBI BioProject Name Caldicoprobacter oshimai DSM 21659
NCBI BioProject Accession PRJNA195830
NCBI Locus Tag
K363  
NCBI BioSample Accession SAMN02584936
Source Sample ID
PI Jonathan Eisen
Added By JGI automated process on 2012-01-27
Last Modified By JGI automated process on 2022-09-05
Project Comments
  
Project Status
Permanent Draft  
Project Relevance
  
Sequencing Center DOE Joint Genome Institute (JGI) (USA)
Collaborating Institute
  
Funding Agency U.S. Department of Energy (DOE) (USA)
Project Description
This organism is part of the GEBA (Genomic Encyclopedia of Bacteria and Archaea) initiative to sequence genomes that fill phylogenetic gaps.  
Is JGI Project
Yes  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
JGI Data Utilization Status
Unrestricted  
JGI Award DOI 10.46936/10.25585/60007347
JGI Portal Download Raw Sequence Data
Genome Publications Nature biotechnology: 35(7):676-683 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
PubMed: 28604660 DOI: 10.1038/nbt.3886
Other Publications
  
Ignored Publications
  
Unassigned Publications
  
SRA Experiment
 
SRA Experiment Id SRX875116  (Link to NCBI )
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NOBS
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
 
SRA Experiment Id SRX875117  (Link to NCBI )
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection size fractionation
Library Name NHZC
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
PROJECT COMPOSITION
Study Continuation of the Genomic Encyclopedia of Bacteria and Archaea pilot project (GEBA)
Organism Caldicoprobacter oshimai DSM 21659
Analysis Projects Caldicoprobacter oshimai DSM 21659
Number of Analysis Projects (AP) 1
Number of Derived Analyis Projects (DAP)
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 3: Improved-High-Quality Draft
Finishing Goal Level 3: Improved-High-Quality Draft
Contamination Screening Input
  
DNA Amplification Method
  
Single Cell Lysis Protocol
  
Single Cell Lysis Approach
  
Sequencing Comments
  
DNA Amplification Kit
  
Sequencing Technology (MIGS-29) Illumina HiSeq 2500
Library Method (MIGS-28)
  
Library Layout
  
Library Screening Method
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
45  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0016183
Organism Name
Caldicoprobacter oshimai DSM 21659  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
BACILLOTA  
Genus
Caldicoprobacter  
Genus Synonyms
  
Species
Caldicoprobacter oshimai  
Subspecies
  
Species Synonyms
  
Strain
DSM 21659  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
DSM 21659  
Type Strain
Yes  
Exemplar DOI
10.1601/ex.15036  
Exemplar Name
Caldicoprobacter oshimai  
Taxon DOI
10.1601/tx.15036  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 1304880
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Bacillota  
NCBI Class
Clostridia  
NCBI Order
Eubacteriales  
NCBI Family
Caldicoprobacteraceae  
NCBI Genus
Caldicoprobacter  
NCBI Species
Caldicoprobacter oshimai  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Mammals  
Ecosystem Type
Digestive system  
Ecosystem Subtype
Large intestine  
Specific Ecosystem
Fecal  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID AB450762
GENERAL PROPERTIES
Oxygen Requirement
Anaerobe  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
Thermophile  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram+  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats Host
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

  You are going to add the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  You are going to remove permissions for the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  Changing the SP visibility will also change visibility on the following items:

 

Do you want to continue with this visibility change?

 

 

  Checking that this Sequencing Project can be made private:

 

Do you want to continue with this visibility change?

 

 

 

 

 

  Changing the SP Sequencing Strategy will also effect these items:

 

Do you want to continue with this Sequencing Strategy change?