Assembling Individual Genomes from Complex Metagenomics Sequencing Samples

A major objective of metagenomic studies is to recover the genome sequence, complete or draft, of a genotype or species from a sample.

The Science

Microbes in nature often live in communities containing many different species. Identifying the mix of species is necessary for many studies of microbes for energy and environmental missions. Genome sequencing of an entire community (determining the metagenome) is often the best means of discovering which species are in a given community. However, it is a major challenge to pull out and assemble the whole genomes of the individual microbes comprising the community. Although many of the species are difficult to culture in a laboratory, they often contain a wealth of novel capabilities that must be characterized to enable understanding of the processes that take place in a community. Researchers at the DOE Joint Genome Institute have shown, through simulations and analysis of reference microbial communities, that extracting and assembling single genotypes requires 20X sequencing coverage. Their results also suggest that a higher coverage of sequencing will not enhance the assembly of individual organism. This result will help researchers plan metagenomic sequencing experiments for a wide range of DOE-relevant microbial communities.


Luo, C., D. Tsementzi, N. Kyrpides, and K. Konstantinidis. 2012. “Individual Genome Assembly from Complex Community Short Read Metagenomic Datasets,” ISME Journal 6, 898–901. DOI:10.1038/ismej.2011.147.