Gut Isolate

Habitat

Co-evolved symbiotic relationships between Bacteria and multi-cellular organisms are a prominent feature of life on Earth. The ecosystem of human distal small intestine provides an opportunity to experimentally 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, the vast majority of which belong to two divisions of Bacteria: the Bacteroidetes (48%) and the Firmicutes (51%). Members of Eubacterium Genus are a predominant group among human intestinal Firmicutes.

Biology

Eubacterium spp. are a group of anaerobic Gram-positive nonspore-forming rods. They have been poorly studied in terms of both physiology and genetics. No complete or partial genomes for members of this Genus are available. A complete, annotated genome sequence of a Eubacterium spp., whose predominance is comparable to Gram-negative gut inhabitants such as B. thetaiotaomicron, B. vulgatus and B. distasonis, should help reveal the extent to which abundantly represented Gram-negative and Gram-positive members of two distant Genera have evolved common and/or distinctive strategies to achieve symbiotic relationships with their human hosts. A16S rDNA-based enumeration study of bacteria in the feces of normal adult humans identified E. eligens and E. rectale as the centers of two clades [Operational Taxonomic Unit (OTU)]. E. rectale represents 6% of total sequenced amplicons [Appl Environ Microbiol. 65:4799 (1999)]. Therefore, it has been selected for complete genome sequencing.

Sequencing Plan

The goal is to produce finished and annotated genome sequence from Eubacterium rectale type strain ATCC 33656. The Genome Institute has collected 9X WGS coverage of plasmid end reads (32Mb Q20 bases, est. genome size 3.4Mb). In addition, three runs of 454 reads were collected, representing 36X of sequence coverage. Automated sequence improvement is currently ongoing. This project is funded by the National Science Foundation (NSF).

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Contacts

Name	Affiliation
Patrick Minx	The Genome Institute, Washington University School of Medicine

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Sequences & Maps

Assemblies

Name	Date	Description	Blast DBs
Eubacterium_rectale-2.0	Nov 29, 2005	11.8X	contigs supercontigs
Eubacterium_rectale-5.0	Jul 18, 2006	11.9X	contigs
Eubacterium_rectale-8.0	Jul 18, 2006	13.2X	contigs

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