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 a 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 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.

B. vulgatus and B. distasonis are two other Bacteroides with varied phylogenetic relationships to BT. Their genome sequences should provide testable hypotheses about the role of various paralogous groups in determining the representation of Bacteroides within, and its functional contributions to the gut microbial community. The polysaccharide utilization systems of B. distasonis and B. vulgatus are less well characterized than that of B. thetaiotaomicron. Nonetheless, ex vivo studies have established that B. distasonis is less capable of degrading plant-derived polysaccharides than B. thetaiotaomicron. For example, unlike B. thetaiotaomicron, it is not able to ferment amylose, amylopectin, dextran, polygalacturonate, pectin, or larch arabinogalactan. The substrate range of B. vulgatus is intermediate between that of B. distasonis and B. thetaiotaomicron. In addition, unlike B. thetaiotaomicron, neither of these two Bacteroides spp. appears to be able to degrade mucopolysaccharides. Together, these observations provide one important rationale for choosing these species to sequence: their genomes should not only provide key insights about the role polysaccharide utilization plays in the human-Bacteroides symbioses, but may also disclose distinct strategies that underlie their predominance in the distal intestinal ecosystem.

Sequencing Plan

The goal is to produce a finished and annotated genome sequence from B. distasonis type strain ATCC 8503. The Genome Institute has collected 13.2X WGS sequence coverage, including both plasmid and fosmid end reads. Automated sequence improvement and manual finishing have been conducted to finish the genome. The size of the circular chromosome is 4,811,369 bp. This work 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
Bacteroides_distasonis-1.0	Aug 04, 2004	13.2X	contigs

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