title: Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities.
abstract: BACKGROUND
  As one of the most abundant agricultural wastes, sugarcane bagasse is largely under-exploited, but it possesses a great potential for the biofuel, fermentation, and cellulosic biorefinery industries. It also provides a unique ecological niche, as the microbes in this lignocellulose-rich environment thrive in relatively high temperatures (50°C) with varying microenvironments of aerobic surface to anoxic interior. The microbial community in bagasse thus presents a good resource for the discovery and characterization of new biomass-degrading enzymes; however, it remains largely unexplored.
  
  
  RESULTS
  We have constructed a fosmid library of sugarcane bagasse and obtained the largest bagasse metagenome to date. A taxonomic classification of the bagasse metagenome reviews the predominance of Proteobacteria, which are also found in high abundance in other aerobic environments. Based on the functional characterization of biomass-degrading enzymes, we have demonstrated that the bagasse microbial community benefits from a large repertoire of lignocellulolytic enzymes, which allows them to digest different components of lignocelluoses into single molecule sugars. Comparative genomic analyses with other lignocellulolytic and non-lignocellulolytic metagenomes show that microbial communities are taxonomically separable by their aerobic "open" or anoxic "closed" environments. Importantly, a functional analysis of lignocellulose-active genes (based on the CAZy classifications) reveals core enzymes highly conserved within the lignocellulolytic group, regardless of their taxonomic compositions. Cellulases, in particular, are markedly more pronounced compared to the non-lignocellulolytic group. In addition to the core enzymes, the bagasse fosmid library also contains some uniquely enriched glycoside hydrolases, as well as a large repertoire of the newly defined auxiliary activity proteins.
  
  
  CONCLUSIONS
  Our study demonstrates a conservation and diversification of carbohydrate-active genes among diverse microbial species in different biomass-degrading niches, and signifies the importance of taking a global approach to functionally investigate a microbial community as a whole, as compared to focusing on individual organisms.
authors.affiliation: Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand.
authors.forename: Wuttichai
authors.initials: W
authors.lastname: Mhuantong
authors.affiliation: Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand ; Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, 73170 Thailand.
authors.forename: Varodom
authors.initials: V
authors.lastname: Charoensawan
authors.affiliation: Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand.
authors.forename: Pattanop
authors.initials: P
authors.lastname: Kanokratana
authors.affiliation: Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
authors.affiliation: Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand.
authors.forename: Verawat
authors.initials: V
authors.lastname: Champreda
keywords: Biofuels; Biorefinery; Comparative genomics; Lignocellulose degradation; Metagenomics