PROJECT INFORMATION
GOLD Project ID
Gp0003993  
Project Name
Atopobium rimae ATCC 49626  
Other Names
  
Legacy ER Project ID
13880  
Legacy GOLD ID
Gi03355  
NCBI BioProject Name Atopobium rimae ATCC 49626
NCBI BioProject Accession PRJNA30999
NCBI Locus Tag
HMPREF0086  
NCBI BioSample Accession SAMN00000717
PI Dodson R.
Added By Heather Creasy on 2008-09-06
Last Modified By Janey Lee on 2020-06-03
Project Comments
  
Project Status
Permanent Draft  
Project Relevance Human Microbiome Project (HMP)
Human Pathogen
Medical
Sequencing Center J. Craig Venter Institute
Collaborating Institute
  
Funding Agency NIH (USA)
Project Description
reference genome for the Human Microbiome Project  
Is JGI Project
No  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Genome Publications
  
Other Publications FEMS microbiology letters 74(2-3):235-40 Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium.

SRA Experiment
 
SRA Experiment Id SRX001334  (Link to NCBI )
Experiment Title 454 sequencing of Atopobium rimae ATCC 49626 HMP017 genomic fragment library
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name HMP017-4F-01-495
Library Layout SINGLE
Library Instrument 454 GS FLX
PROJECT COMPOSITION
Study Human Microbiome Project (HMP) Reference Genomes
Organism Atopobium rimae ATCC 49626
Analysis Projects Atopobium rimae ATCC 49626
Number of Analysis Projects (AP) 1
Number of Derived Analyis Projects (DAP)
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 6: Finished
Finishing Goal Level 6: Finished
Contamination Screening Input
  
DNA Amplification Method
  
Sequencing Comments
  
DNA Amplification Kit
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Library Layout
  
Library Screening Method
  
Number Of Reads
294398  
Read Size
  
Vector
  
GC Percent
49  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0003993
Organism Name
Atopobium rimae ATCC 49626  
Other names (alias, synonyms, short names, common names)
Lactobacillus rimae  
Organism Domain
BACTERIAL  
Phylogeny
ACTINOBACTERIA  
Genus
Atopobium  
Genus Synonyms
  
Species
Atopobium rimae  
Subspecies
  
Species Synonyms
  
Strain
D140H-11A  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
ATCC 49626  
Type Strain
Yes  
Exemplar DOI
10.1601/ex.5425  
Exemplar Name
Lancefieldella rimae  
Taxon DOI
10.1601/tx.32703  
Biosafety Level
1  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 553184
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Actinobacteria  
NCBI Class
Coriobacteriia  
NCBI Order
Coriobacteriales  
NCBI Family
Atopobiaceae  
NCBI Genus
Lancefieldella  
NCBI Species
Lancefieldella rimae  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Mammals: Human  
Ecosystem Type
Digestive system  
Ecosystem Subtype
Oral cavity  
Specific Ecosystem
Gingival crevice/sulcus  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID AF292371
GENERAL PROPERTIES
Oxygen Requirement
Obligate anaerobe  
Cell Shape
Rod-shaped  
Motility
Nonmotile  
Sporulation
Nonsporulating  
Temperature Range
Mesophile  
Salinity
  
pH
3.8  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram+  
Biotic Relationships Free living
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements Singles
Pairs
Chains
Diseases Peritonitis
Known Habitats Host
Human oral cavity
Metabolisms
  
Phenotypes Pathogen
Energy Sources
  
HMP METADATA
HMP ID
86  
Show in DACC?
Yes  
HMP Project Status
Complete  
BEI Status
  
NCBI Submission Status
6. annotation (and sequence) public on NCBI site  
Isolate Suggestion Source
  
HMP Isolation Body Sample Site
Oral  
HMP Isolation Body Sample Subsite
  
HMP Finishing Goal
  
Source, Sample & Medical Relevance Comments
  
Isolate Availability Comments
  
Project Comments
  
DNA Received
Yes  
Date DNA Received
2008-05-28  
Date Sequencing Begins
  
Date Draft Sequencing Completed
2008-08-08  
Cross Reference ID
HOMD: tax_750  

 

 

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