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J Bacteriol. Dec 2010; 192(24): 6494–6496.
Published online Oct 1, 2010. doi:  10.1128/JB.01064-10
PMCID: PMC3008519

Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production [down-pointing small open triangle]

Abstract

Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.

Clostridial genomes were sequenced using a combination of Sanger (3× coverage, 8 kb, pMCL200), 454 (20× coverage), and Solexa methods. Standard sequencing protocols are listed on the Joint Genome Institute (JGI) website (http://www.jgi.doe.gov/sequencing/protocols/prots_production.html). Sanger and 454 reads were assembled as previously described (5). Automatic annotations were conducted for all draft genomes using the JGI-Oak Ridge National Laboratory (ORNL) annotation pipeline, and all draft genomes and annotations were loaded into the JGI Integrated Microbial Resource (IMG) for analysis (11). Due to difficulties in assembling and finishing low-GC, high-repeat genomes, many of the genomes targeted for sequencing could not be finished and are presented as a highquality permanent draft. Sequences available at the time of this analysis are listed in Table Table11 and are categorized based on the latest Bergey's taxonomy (9).

TABLE 1.
Clostridium genome sequencing projects related to biomass conversion and biofuels production

Acknowledgments

The biomass-converting clostridium sequencing project was initiated by the Clostridium Sequencing Consortium (see author list) through the Joint Genome Institute. The genome sequencing work was performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory, under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory, under contract no. DE-AC52-07NA27344, Los Alamos National Laboratory, under contract no. DE-AC02-06NA25396, and Oak Ridge National Laboratory, under contract no. DE-AC05-00OR22725. This work was supported by NSF-EPSC.R grant 105118300.

Footnotes

[down-pointing small open triangle]Published ahead of print on 1 October 2010.

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