Energy demand and climate change have demanded the development of renewable energy source such as bioenergy. One key challenge in bioenergy is the low efficiency of the direct or indirect (via lignocellulose) conversion of solar energy and carbon dioxide to biofuels. Research in our group centers on “Consolidated BioProcessing” (CBP), where the integration and ultimate reduction of processing steps into a single cell or cellular system maximizes the energy and cost efficiency. To achieve these goals, the group develops both experimental and computational genomics approaches, with particular emphasis on the dissection, design and engineering of genomes, metagenomes and their regulatory networks.

(1) CBP-Cellulose. In CBP of cellulose, we have been dissecting and engineering Clostridia and Thermoanaerobacter (Gram-positive thermophilic bacteria that grow optimally at over 55℃) that directly degrade cellulose and co-utilize pentose and hexose to produce ethanol (Lin, et al, PLoS Genetics, 2011; Xu C, et al, Bioresource Technology, 2010; Lin, et al, PLoS One, 2010). We have previously discovered glycosylhydrolase genes and their regulatory mechanisms in the intestinal microbial community (Xu, et al, Science, 2003; Xu, et al, Trends Microbiol, 2004), modeled the inter-species interactions underlying polysaccharides utilization (Xu & Gordon, PNAS, 2003), and elucidated the evolution of polysaccharide-degrading apparatus (Xu, et al, PLoS Biology, 2007).

(2) CBP-SE. In CBP of solar energy (CBP-SE), we have been discovering, characterizing and genetically manipulating Nannochloropsis, a group of single-cell microalgae of sigificant industrial interest due to their capability of rapid autotrophic growth, synthesis of large amounts of TAG and polyunsaturated fatty acids (e.g. eicosapentaenoic acid, EPA) that can be readily converted into advanced biofuels and robust outdoor growth with flue gases. Using Nannochloropsis as a model, we have revealed the diversity, divergence and evolution of microalgal genomes, and in particular, their genetic foundation of robust TAG production (Wang, Ning, et al, under review).

(3). Metagenomics and Single-cell Genomics. In the adventures into nature hunting superior cells and cellular communities for CBP, we have established a metagenomics platform (based on our second-generation sequencing facility that includes both 454 and Solexa) and have been supporting collaborative research with over 30 research groups across the globe (Yang, et al, ISME J, 2011; Xia, et al, ISME J, 2011; Wang, et al, under review). Our platform has also moved into the frontier of single-cell functional genomics (Li, et al,, Curr. Opin Biotech., in press).  To support these high-throughput data production, quality control and in-depth analysis, we have been developing both hardware and software solutions (You, et al, Bioinformatics, accepted; Su, et al, IEEE ISB, 2011; Su, et al, IEEE E-Science, 2011). We have previously developed software for sequence alignment (Ning, et al, PLoS ONE, 2010; Ning, et al, Journal of Combinatorial Optimization, 2010; Ning, et al, Nucleic Acids Research, 2005), genome sequencing (Xu & Gordon, Bioinformatics, 2005), metabolic reconstruction from genomes and transcriptomes (Sonnenburg, Xu, et al, Science, 2005; Ippolito, Xu, et al, PNAS, 2005), analysis of proteome data (Ning, et al, BMC Bioinformatics, 2010, 11: 505; Ning, et al, BMC Bioinformatics, 2010, Suppl 11:S14; Ning, et al, Proteomics, 2010), etc.

We gratefully acknowledge the research supports from Ministry of Science and Technology of China (MoST), National Natural Science Foundation of China (NNSFC), Chinese Academy of Sciences (CAS), Department of Science and Technology of Shandong province (SDSTC), as well as our academic and industrial partners.