Bacteroides novel strain WH2
Gut Isolate
Habitat
Co-evolved symbiotic relationships between Bacteria and multi-cellular organisms are a prominent feature of life on Earth. The ecosystem of distal small intestine of humans provides an experimental opportunity to address general questions about symbiosis and ecogenomics. According to the most comprehensive 16S rDNA survey to-date [Science 308:1635 (2005)], this complex ecosystem is composed of ~400 phylotypes, with the vast majority of which belong to two divisions of Bacteria: the Bacteroidetes (48%) and the Firmicutes (51%). Members of the Bacteroides Genus in the Bacteroidetes Division are one of the most populous groups of bacteria found in human digestive tracts.
Biology
Bacteroides thetaiotaomicron type strain ATCC 29148 (BT) has been used as a model to examine symbiotic host-bacterial interactions from the perspective of the host (through functional genomic studies in gnotobiotic mouse models) and microbe (by sequencing its 6.3 Mbp genome) [e.g., Science, 292 :1115(2001); Proc. Natl. Acad. Sci. USA 99 : 15451 (2003) Nature Immunol 4 : 269 (2003);. Science 299 : 2074 (2003); Proc. Natl. Acad. Sci. USA 101, 4596 (2004)]. The 4779-member BT proteome contains an unprecedented expansion (among sequenced prokaryotes) of paralogous groups involved in acquisition and degradation of dietary polysaccharides, an associated highly evolved environmental-sensing system, and a complex armamentarium of genes for refashioning its genome.
Bacteroides novel strain WH2 is a community isolate and was originally classified as a B. thetaiotaomicron strain. However its 16S rDNA sequence reveals that it is a novel Bacteroides species. A complete genome of this species should yield additional insights about the capacity of Bacteroides to evolve its genome, plus better molecular definition of a Bacteroides species and of its metabolic capacities/functional versatility.
Sequencing Plan
The goal is to produce a finished and annotated genome sequence from this strain. The Genome Institute has collected 5.4X WGS coverage (38 Mb Q20 bases, est. genome size 7Mb), including both plasmid and fosmid end reads. In addition, 6 runs of 454 reads (~24X sequence coverage) were collected. Automated sequence improvement is currently ongoing. This project is funded by the National Science Foundation (NSF).
Contacts
| Name | Affiliation |
|---|---|
| Patrick Minx | The Genome Institute, Washington University School of Medicine |
Sequences & Maps
Assemblies
| Name | Date | Description | Blast DBs |
| Bacteroids_novel_WH2-2.0 | Nov 13, 2005 | 7.9X | contigs |
| Bacteroids_novel_WH2-5.0 | May 30, 2006 | 8.6X | contigs supercontigs |
| Bacteroids_novel_WH2-6.0 | Jul 18, 2006 | 8.6X | contigs |
