Deconstructing Microbes

A metagenome data management and analysis system developed and managed by CRD researchers contributed to a breakthrough research recently published in Nature that probed the genetic materials of microbes in a termite’s gut.

Understanding how these microbes convert wood to energy for sustaining a termite’s life would help researchers figure out better ways to convert biomass to biofuels in factories. The microbes exude enzymes that efficiently break down the wood’s cellular structure, but scientists so far have little understanding of how the process works.

The research, led by the DOE Joint Genome Institute (JGI), relied on IMG/M, a system developed for managing and analyzing metagnome data. Metagenomics is a study of genetic material collected directly from organisms in their natural environment, a relatively new and alternative approach to extracting genetic information from specimens cultured in labs.

IMG/M provides tools for conducting comparative analysis of metagenome datasets integrated with a comprehensive collection of reference-isolated microbial genome datasets. For the research on microbes residing in termite guts, Ernest Szeto from CRD’s Biological Data Management and Technology Center (BDMTC) provided critical support for maintaining multiple versions of the dataset in IMG/M and for extending data analysis tools in response to the study’s needs.

“IMG/M has proven to be an extremely useful resource and tool for analyzing our metagenomic data,” said Jared R. Leadbetter, associate professor of environmental microbiology at the California Institute of Technology, and collaborator on the termite hindgut microbial community for bioenergy project. “Such datasets are large, complex and potentially unwieldy. Importantly, IMG/M is more than just an excellent tool to analyze data. The manner in which the results of that analysis are organized and made accessible through a user-friendly interface allows the researcher to rapidly move in a number of different intellectual directions. As a result, the user becomes better educated with and gets a real ‘feel’ for the data in a manner that would not otherwise be possible on such short timescales.”

The research, “Metagenomic and Functional Analysis of Hindgut Microbiota of a Wood-Feeding Higher Termite,” appeared in the Nov. 22 issue of Nature. Lead author Falk Warnecke and members of the research team traveled to Costa Rica in search of termites and the microbes that hold the secret to efficient energy conversion. From a colony of termites in the genus Nasutitermes, the researchers extracted the stomach content of 165 specimens and purified the genetic materials for sequencing at the JGI.

The sequencing work yielded 71 million letters of fragmented genetic code, which provides valuable information on the identities of the microbes and the enzymes that they produce. After assembling and analyzing them using the IMG/M, the scientists identified two major bacterial lineages, treponemes and fibrobacters. Researchers have long known the existence of treponemes. But fibrobacters, as it turned out, was a new find.

“The dataset provided by Warnecke et al. is a treasure trove for researchers,” wrote Andrea Brune, a researcher in the Department of Biochemistry at the Max Planck Institute for Terrestrial Microbiology in Germany, in a separate article in the same issue of Nature.

The researchers identified more than 500 genes related to the enzymatic deconstruction of cellulose and hemicellulose, building blocks of wood.

“Termites can efficiently convert milligrams of lignocellulose into fermentable sugars in their tiny bioreactor hindguts. Scaling up this process so that biomass factories can produce biofuels more efficiently and economically is another story,” said Eddy Rubin, JGI Director. “To get there, we must define the set of genes with key functional attributes for the breakdown, and this study represents an essential step along this path.”

The termite gut metagenome data will become publicly available in IMG/M in January 2008.

The paper in Nature can be found at http://www.nature.com/nature/journal/v450/n7169/full/nature06269.html.