The hunt for rainforest’s secret recipes

The temperature is boiling hot. The air humidity is close to the 100 per cent and we are wearing long trousers and big chunky boots to protect us from aggressive mosquitoes and creepy-crawlies as we move through the jungle. We are on the outskirts of the world’s largest expanse of tropical rainforest—the Amazonas.

Despite the presence of huge, hairy, spectacularly coloured spiders and ants the size of matchboxes, we are here to study the plants. For within the mass of interweaving green vegetation there are very likely substances that can treat incurable diseases—substances which the pharmaceutical industry can scarcely dream of.

The local guide leads us through the jungle, stopping at each growth, explaining at length precisely the plant’s unique gastronomic qualities or medical properties. We are in Brazil with a team of researchers from DTU Bioinformatics to initiate an extremely ambitious project—the genome sequencing of the rainforest’s plant life.

“The aim is to utilize all the latest technologies we have at our disposal (next-generation sequencing, proteome, metagenome and metabolomics analysis as well as fluorescence spectroscopy) to explore and preserve the rainforest’s incredible biodiversity and genetic wealth before it’s too late,” explains Professor Thomas Sicheritz-Pontén, who is leading the project.

For the rainforest is undeniably under threat. Every year, the Amazonas is shrinking by about 25,000 square kilometres (an area the size of Jutland) due to deforestation intended to make way for farming land. Unfortunately, the very discovery of the medical applications of the rainforest’s valuable plants, for example, has led to certain plant species being endangered. However, this is where this project is decisively different, says Thomas Sicheritz-Pontén:

“We only need a single leaf or a spoonful of soil for our analyses in order to map which substances the plants produce and how they do it. We will also examine the micro-organisms present, as they contribute to the overall gene pool. You might say we are trying to ‘trick’ the plants into giving up their secret recipes so that we can start producing valuable substances by means of synthetic biology—thereby helping to maintain the forest ecosystem rather than interfering with it.”

Chemical warfare

Professor Birger Lindberg Møller from the University of Copenhagen is an expert in the bioactive natural substances of plants and a member of the team in Brazil. He explains how the many interesting substances produced by the plants form part of an advanced chemical warfare, enabling the plants to defend themselves against attacks from microorganisms and insects, for example.

“At the Center for Synthetic Biology, we are in the process of developing methods to produce complex substances in algae—e.g. using sunlight. The challenge is mapping the biochemical synthesis and developing the system in the algae. But once this has been done, the production process is relatively simple, and our plan with this project is to initiate a production in Brazil which will benefit the country in the form of revenue and jobs—and hopefully provide a viable alternative to deforestation for the purposes of livestock farming,” explains Birger Lindberg Møller.

The plan is to begin mapping the genes of some of the plants which we already know offer a specific medical or biotechnological potential—e.g. plants such as Jaborandi, Açaí, and Jambu (see fact boxes). That said, the project must also identify plants which are currently undiscovered.

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“Together with highly skilled Brazilian researchers, we’ve already started to sequence the group of plants called Jaborandi, which are currently under threat due to their medical properties,” explains Associate Professor Bent Petersen from DTU Bioinformatics.

“We would never be able to complete a project such as this without a really great research partner in Brazil, and in fact it was our meeting with Guilherme de Oliveira from Vale Institute of Technology (ITV) in Belém that actually crystallized the whole project in our minds.”

Supercomputer at DTU

It was none other than Guilherme de Oliveira who hosted the event throughout the week the team was in Brazil. Immediately after landing, the team was shown around the ITV campus. The Danish researchers visited the laboratories with plants and sequencing machines for genetic analyses—and the basement—so Peter Løngren, Head of Supercomputing at DTU Bioinformatics, could inspect the department's server capacity.

The Brazilian server is not overly impressive—nor does it need to be. Even though the project will generate huge volumes of data, all the complex calculations will be processed by the Computerome supercomputer at DTU, which will be set up to handle the pan-continental cooperation with the help of cloud technology.

The project is not just about generating large volumes of data, but also about processing and applying these data in a smart way—among other things using artificial intelligence. And this is why a group of bioinformaticians who normally sit behind a computer screen at DTU are now relocating to the jungle.

The goal is to train computers to recognize interesting plants or substances—either based on their appearance or their genetic profile— in order to create an intelligent workflow that makes the almost insurmountable task of sequencing the Amazonas a little more manageable.