Feature: Metagenomics and beyond

Life doesn’t exist in isolation. Yet in the lab, many microbiologists work with pure, or axenic, cultures, which contain only a single species of microorganism in isolation. This is useful for investigating the mores of that particular critter uninterrupted by the activity of other organisms.

But when it comes to gaining a deeper understanding of how that creature interacts with its environment – of the interdependencies it has with other organisms, and the evolutionary path that got it to where it is – pure cultures are of limited utility.

There are also many microorganisms that cannot be grown as a pure culture, meaning we can only explore a fraction of the microbial world in the lab and thus risk underestimating the vast diversity of organisms that exist in the real world.

Enter metagenomics. Instead of separating an organism from its environment and sequencing it in isolation, metagenomics seeks to scoop up and sequence an entire environment, and the full gamut of species therein.

It effectively gives a big picture snapshot of the life within a particular environment, lending an insight not only into which organisms live there, but how they interact in the complex web of life.

Metagenomics has been growing as a discipline for nearly a decade, but it’s with the explosion in throughput and dramatic reduction in price brought by next generation sequencing technologies that have enabled it to truly come into its own.

However, metagenomics is but one tool in the modern biologist’s toolkit. By taking metagenomics and extending it out to also include a systems biology approach, adding in the transcriptome and the proteome, and coupling it to single-cell genomics, we now have a new meta-meta discipline, one Hugenholtz refers to as ‘ecogenomics.’

Through this approach, biological systems can be comprehensively mapped, teasing out the activities of individual organisms, and particular cells or regions within those organisms, and discovering the interdependencies therein.

This approach will be the focus of the new Australian Centre for Ecogenomics at the University of Queensland, headed by Phil Hugenholtz and Gene Tyson, both pioneers in the metagenomics world.

Together, they’ll be exploring some intriguing environments, such as looking at how the humble termite is able to digest stubborn lignocellulosic material with the help of other microorganisms, and will be working to advance the field by looking at more localised environments rather than relying only on the less discriminating approach of traditional metagenomics.

Read part II: Metagenomics goes full circle

Read part III: From metagenomics to ecogenomics