Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production

Author:

Hemme Christopher L.12,Mouttaki Housna123,Lee Yong-Jin12,Zhang Gengxin4,Goodwin Lynne5,Lucas Susan6,Copeland Alex6,Lapidus Alla6,Glavina del Rio Tijana6,Tice Hope6,Saunders Elizabeth5,Brettin Thomas57,Detter John C.5,Han Cliff S.5,Pitluck Sam6,Land Miriam L.7,Hauser Loren J.7,Kyrpides Nikos6,Mikhailova Natalia6,He Zhili12,Wu Liyou12,Van Nostrand Joy D.12,Henrissat Bernard8,He Qiang9,Lawson Paul A.1,Tanner Ralph S.1,Lynd Lee R.10,Wiegel Juergen11,Fields Matthew W.12,Arkin Adam P.13,Schadt Christopher W.14,Stevenson Bradley S.1,McInerney Michael J.1,Yang Yunfeng14,Dong Hailiang4,Xing Defeng15,Ren Nanqi15,Wang Aijie15,Huhnke Raymond L.16,Mielenz Jonathan R.17,Ding Shi-You18,Himmel Michael E.18,Taghavi Safiyh19,van der Lelie Daniël19,Rubin Edward M.6,Zhou Jizhong12

Affiliation:

1. Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma

2. Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma

3. German Research Center for Environment and Health, Neuherberg, Germany

4. Miami University, Oxford, Ohio

5. Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico

6. Joint Genome Institute Production Genomics Facility, Walnut Creek, California

7. Computational Biology and Bioinformatics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee

8. CNRS, Universités Aix-Marseille, 13628 Aix-en-Provence, France

9. Department of Civil and Environmental Engineering, University of Tennessee—Knoxville, Knoxville, Tennessee

10. Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire

11. Department of Microbiology, University of Georgia, Athens, Georgia

12. Department of Microbiology, Montana State University, Bozeman, Montana

13. University of California—Berkeley, Berkeley, California

14. Molecular Microbial Ecology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee

15. State Key Lab of Urban Water Resource and Environment, Harbin 160090, People's Republic of China

16. Oklahoma State University, Stillwater, Oklahoma

17. Bioconversion and Science Technology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee

18. National Renewable Energy Laboratory, Golden, Colorado

19. Brookhaven National Laboratory, Upton, New York

Abstract

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.

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

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