R+D CSIC

SINGEK trains a new generation of Single Cell Genomics experts

The SINGEK project is now finished. It was a project coordinated by the Institut de Ciències del Mar (ICM, by its Spanish acronym) of the CSIC, and it had as a main goal the training of young researchers in the application of single cell genomics for the study of microbial eukaryotes’ ecology and evolution. This emerging methodology also has applications in biotechnology and biomedicine.

There is a great diversity in marine microbes, but the vast majority continue to be great mysteries, since their ecological and evolutionary patterns are not known. This information can be decoded from its gene content, but until now, obtaining marine microbes’ genomes was hindered by the difficulty to grow most species in the lab.

With the recent appearance of the single cell genomics, the situation has now changed, as this new methodology allows us to isolate cells individually and to decode their genome. It lets us answer questions that before were even impossible to contemplate due to a lack of technology to address them.

Aware of the possibilities of this methodology, the ICM researcher Ramon Massana started building more than four years ago SINGEK, a Marie-Skłodowska-Curie Training Network, to explore this new field. This network, under the H2020 Framework Program, was awarded with 3.9 million Euros with the goal of training a new generation of researchers. 

Training and applications in ecology, biotechnology and biomedicine

Researchers in charge of SINGEK explain that “genomic information obtained by single cells is key for future research in several disciplines. In the fields of ecology and evolution it will help to complete the tree of eukaryote life, to reveal interactions and to investigate the ecological potential of unknown species”.

Moreover, in biotechnology it will allow to decode promising genes in uncultured species and link the extracted compounds from natural samples with microbes responsible of their synthesis. Finally, in biomedicine it will enable a better understanding of the function of single cells and detect the cells that start a cancer.

They have gathered a group of ESR at the start of their career to make them single cell genomics specialists.

However, this is a recent methodology, which does not count with many trained specialists. That is precisely what SINGEK wanted to solve. They have gathered a group of ESR at the start of their career to make them single cell genomics specialists.

"Coordinating the SINGEK network was arduous at some times, but we successfully implemented the project’s proposal as originally envisaged. After more than 4 intense years, I feel very happy that I managed to assure the overall project progress and success", celebrates Massana, the network’s coordinator.

Elena Torrecilla, a researcher at the ICM and project manager at SINGEK claims that “participating in the project has been a very enriching opportunity”. Torrecilla has coordinated the international consortium of SINGEK, formed up by fifteen research teams of four universities, seven research institutions and one company.

According to Torrecilla, “the key to success has been the regular contact established with researchers through project meetings, research visits, outreach activities and training courses. These activities were key to create a successful collaborative network and also to see the improvements of the ESR as science communicators in different formats and in front of different audiences”.

In this regard, a total of 5 researchers have already obtained their PhD degree and 8 are graduating next year. Moreover, more than 25 peer-reviewed articles co-authored by these ESR have already been published and 25 more will be released soon. This list of publications includes a special issue entitled “Single Cell Ecology”, that brings together all the presentations that took place at the international congress organized by the SINGEK consortium and has been published by the prestigious journal Philosophical Transaction of the Royal Society B.

 “This training program was a great opportunity to work in a multidisciplinary environment. It definitely provided an educational, as well as challenging and rewarding experience”, explains Aurelie Labarre, one of the ESRs that has participated in the project. “The eclectic nature of this experience has helped me to develop my own research project with a large degree of autonomy”.

Overall, the SINGEK project covered a number of aspects which will for sure have a long-term impact. "Now I look back and see what SINGEK has accomplished: a whole generation of young scientists well trained to fully exploit single cell genomics potential”, highlights Massana.

“Inside this project, innovative results have been published that will give us the possibility of getting to know better the diversity, evolution and functional insights of uncultured microbial eukaryotes, and thus we will be able to study them in detail in the lab. This will help us in better understanding their role in the ecosystem as well as in refining the eukaryotic tree of life”, concludes the SINGEK’s coordinator.

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