The microbiome of the Baltic Sea

Geneticist Petri Auvinen and his research team are using DNA samples to find out what has been happening in the Baltic ecosystem during the past 10,000 years.

“Our aim is to collect sediments samples as far down as possible in the Baltic Sea bed in order to study the history of the Baltic Sea basin. We also take samples deep in marshland, providing us with information about the history of the soil,” says Auvinen.

Petri Auvinen is a research director at the Institute of Biotechnology, University of Helsinki. His research focuses on genomics and metagenomics. While genomics looks at the entire genome of an organism, metagenomics can study and sequence a number of organisms, such as microbes, from a single sample at the same time. The study of micro-organisms has advanced in leaps and bounds. A sequence sample can be taken from any environment, soil or gut to determine the microbiota composition. The term used is microbiome, denoting the microbiota of a specific habitat and its genome, that is, the metagenome.

Some of the data is analysed using the CSC – IT Center for Science’s ePouta hardware, but some must be done with the team’s own.

“The software can be so complex that it cannot be run on the CSC system. We use some virtual computers, but they have their limitations, too. We also have runs that may continue uninterrupted for months. CSC has thousands of users, and the CSC environment obviously has some maintenance outages. For example, when we were working on the genome of the Saimaa ringed seal, the first major assemblies took a thousand hours.”

“Currently we are able to work on large genomes a hundred times better than a few years ago. But there is more and more data all the time, and we must be able to store it efficiently and in a way that it is comparable to other data. We will continue to work with CSC in data storage, transfer and calculation.”

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