AVINA grant for CeMESS group leader Shaul Pollak


Swiss independent AVINA Stiftung has awarded one of its sought-after grants to Shaul Pollak, a group leader at the Division for Microbial Ecology at CeMESS. The funding will support Pollak’s research in developing machine learning methods to predict microbial community activity from genomic data.

Without microbes, our world would rapidly descend into lifelessness and desolation. They are the silent architects of our planet's ecosystems, driving essential processes from nutrient cycling to carbon sequestration. But despite their critical importance for our planet’s wellbeing, our understanding of how microbial communities function is still at its infancy.

Analysing environmental sequence data has transformed our understanding of life in the soil. This method provides a genomic snapshot of entire ‘societies’ of microbes, providing a detailed picture of microbial community composition. Despite the recent influx of environmental sequence data, we are still far from grasping the factors shaping community composition, and importantly, the functional significance of those communities. Pollak’s research, now backed by AVINA, aims to address two fundamental questions: how much can genomic data tell us about what microbes ‘do’ in their native habitats, and how do the activities of individual microbes collectively give rise to ecosystem functions?

Pollak zeroes in on bacterial decomposers of complex sugars – like cellulose and starch. “Microbes that decompose complex sugars are key players in virtually all ecosystems and regulate climate, human, and soil health” explains Pollak. “If we want to intervene in these processes effectively, we first need to understand the different ecological functions of the billions of microscopic creatures that together make a single microbial community.”

Leveraging high-throughput lab experiments, Pollak plans to use advanced machine learning approaches to connect specific genes within microbial communities to the specific ecological functions they perform. To understand the consequences of community composition, Pollak will build mathematical models that predict how diverse functions within a community converge to shape its overall role. These insights could set the stage for crafting probiotic communities in agriculture, optimizing composting, and forecasting climate change impacts on soil carbon reserves.


About AVINA funding

The independent Swiss AVINA Stiftung supports forward-thinking projects with high potential to transform food systems. They foster innovation and research that emphasizes a harmonious coexistence between humans and our planet. The project proposed by Pollak is the first Austria-based initiative to receive funding through AVINA.

About Shaul Pollak

Shaul Pollak is a group leader at the Division for Microbiology at CeMESS. He became interested in biological interactions during his Ph.D. while studying the evolution of bacterial communication systems called “Quorum-Sensing” systems in Avigdor Eldar’s lab at Tel Aviv University (TAU, Israel).

During his PostDocs at the Massachusetts Institute of Technology (MIT, USA), Pollak developed machine-learning and experimental methods to study how biological interactions shape marine bacterial communities that degrade complex sugars in Otto Cordero’s group, and studied in Sallie Chisholm’s group how biological and abiotic factors influenced the evolution of the most common photosynthetic organism on earth – the cyanobacterium Prochlorococcus.

“My new research ideas that are now materializing due to this funding would not have been possible without all of the unique individuals, minds, equipment, and opportunities CeMESS offers” says Pollak. “Receiving this support from the AVINA Stiftung will at this early career stage reinforces the value of our interdisciplinary research, and will allow our lab to pursue the questions that excite us at the highest standards of excellence”.