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Toward decoding the metabolism of microbiomes

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WASHINGTON, DC – Stilianos Louca has been named the 2017 Grand Prize winner of the Science & SciLifeLab (Science for Life Laboratory) Prize for Young Scientists for work that makes sense of how microbial communities and geophysical processes together influence the Earth's chemistry. The prize recognizes promising early-career scientists who conduct groundbreaking life-science research and includes a grand-prize award of US $30,000. It is supported by SciLifeLab, a coordinated effort among four universities in Sweden and the journal Science, which is published by AAAS, the nonprofit science society.

While microorganisms are known to fuel many of the biochemical changes that occur in ecosystems like the ocean, soil and human gut, researchers' understanding of their specific role has remained a mystery, in part because of their incredible diversity. According to Louca, "Until 15 years ago, it was very hard to even identify most microorganisms in an environment, let alone determine what they may be doing metabolically. The vast majority of bacteria, for example, have never been cultured in the lab. High-throughput sequencing technology is now changing that, by allowing us to not only identify microorganisms, but also to estimate what metabolic processes they may be involved in."

Louca predicted that similar environments would promote the growth and activity of similar energy-consuming cellular pathways, even if the species encoding each pathway were different. To test his hypothesis, he sequenced the DNA of entire microbial communities living in the foliage of bromeliad plants. He estimated the species composition of the microbial communities as well as the abundances of various pathways encoded in the microbial genomes, discovering that each bromeliad hosted a distinct community of microbial species.

Interestingly, these different microbial communities showed a striking similarity in terms of the abundances of genes involved in various pathways, including those with a role in fermentation, oxygen respiration and carbon fixation. This observation suggested that environmental constraints largely determined the growth of these pathways and had much less influence over which species happened to represent each pathway in a bromeliad.

To further validate these findings, Louca analyzed DNA sequencing data from an international ocean microbiome survey in combination with oceanographic data from satellite imaging. He classified over 30,000 marine microorganisms into various metabolic groups based on the pathways that they utilize to gain energy (distinguishing between organisms that consume methane, a potent greenhouse gas, and organisms that eat sulfide, a toxic gas found in parts of the ocean, for example).

Louca pioneered an approach that allowed him to quickly pinpoint the metabolic functions of microorganisms based on their species. He developed a mathematical model that suggests a disconnect between function and taxonomy in microbiomes (such as the ocean's) may stem from biological interactions between organisms. He then used this platform to study how microbial communities change over space or time, resulting from processes that are separate from selection for specific metabolic functions.

He then went on to use computer simulations, mathematical modeling, and statistical methods, to show that environmental conditions strongly predicted the distribution of metabolic groups across the world's ocean. In contrast, environmental conditions poorly predicted which microbial species were associated with each metabolic group in each location – a perplexing finding, because ocean currents can transport microorganisms across large distances, and yet the same pathways were represented by different organisms in different locations of the ocean. Hence, he uncovered that additional mechanisms, based on interactions between species seem to influence which species get to perform these pathways in each location.

In Louca's grand-prize winning essay, "Probing the metabolism of microorganisms," which will appear in the 8 December 2018 issue of Science, he highlights how his team's research efforts have important implications for various microbial-driven industrial processes, such as bioremediation of acid mine drainage, where a stable microbial community is often an objective of operation control.

"Many environmentally relevant processes mediated by microorganisms may remain stable even if the specific microbial taxa involved in them change over time. For example, in biofuel-producing bioreactors it may be nearly impossible to control which microorganisms will be dominant at any moment in time, however the overall performance of the bioreactor may be controlled much more easily," Louca said.

"Tracking how microbes gobble up energy in the ocean and the interplay between environment and species interactions, as Dr. Louca has done in his work, will provide new approaches to bioremediation and a greater understanding of ocean chemistry," said Barbara Jasny, deputy editor of Science.

Louca is interested in pursuing several follow up experiments, noting, "if we want to model biogeochemical processes in an ecosystem, or the chemical transitions over Earth's history, it seems that we can go to great lengths by simply focusing on genes and the metabolic pathways that they encode, rather than considering each microbial species." With this idea in mind, he plans to extend his model to other ecosystems beyond the ocean.

Louca will receive the award for his research in the field of Ecology and Environment in Stockholm, Sweden, on Monday, 11 December, during an award ceremony and dinner with close to 200 guests at the Grand Hôtel in the Hall of Mirrors, which hosted the first Nobel Prize ceremony in 1901.

"SciLifeLab is a proud sponsor and co-organizer of this young scientist award. As a national hub for molecular biosciences in Sweden, we cover both health and environmental applications of biosciences. The innovative science performed and elegantly described by this year's winners provide inspiration to our community of young scientists and we are happy to see Science Magazine propagate this globally," said SciLifeLab Director Olli Kallioniemi.

The Science & SciLifeLab Prize for Young Scientists is an annual prize aimed at rewarding young scientists at an early stage of their careers. The categories for this annual award are Cell and Molecular Biology, Ecology and Environment, Genomics and Proteomics, and Translational Medicine.

Applicants for the 2017 Science & SciLifeLab Prize for Young Scientists submitted a 1000-word essay that was judged by an independent editorial team organized by the journal Science. Its content was evaluated on the quality of research and the applicants' ability to articulate how their work would contribute to the scientific field.

The 2017 award also recognizes three category winners, whose essays will be published in the journal Science online at http://www.sciencemag.org/prizes/scilifelab. Each of the category winners will receive $10,000 and be featured in Science online at http://www.sciencemag.org/prizes/SciLifeLab/2017.

After the embargo has lifted, follow #ScienceSciLifeLabPrize or #SciLifeLabPrize on Twitter @ScienceMagazine @SciLifeLabPrize @SciPak and Facebook.

2017 Grand Prize Winner:

Stilianos Louca: For his essay, "Probing the metabolism of microorganisms." As an undergraduate, Stilianos Louca studied physics and mathematics at the Friedrich-Schiller-Universität, Germany, before going on to attain a PhD in applied mathematics at the University of British Columbia, Canada. During his doctoral research, he investigated how microorganisms, in particular their genes, interact with the environment and with each other to drive elemental fluxes at ecosystem scales. Louca is currently a postdoctoral researcher at the Biodiversity Research Centre in Vancouver, where he continues to investigate the ecology and evolution of microbial metabolism using mathematical modeling, molecular sequencing and laboratory experiments.

2017 Category Winners:

Jared Mayers: For his essay on the topic of translational medicine, "Metabolic markers as cancer clues." Jared Mayers is a resident in Internal Medicine at Brigham and Women's Hospital in Boston, MA, working towards a career that balances basic science research with clinical practice. After completing his undergraduate degree at Williams College, he earned his M.D. from Harvard Medical School and his Ph.D. in Biology from the Massachusetts Institute of Technology. His research interests center on identifying and understanding the mechanisms driving whole body metabolic alterations and tissue interactions in early disease states. Outside of the hospital and lab, he enjoys running and spending time with his family.

Kelley Harris: For her essay on the topic of genomics and proteomics, "Reading the genome like a history book." Kelley Harris studied mathematics as an under-graduate at Harvard and transitioned into genomics during a postgraduate year at the Well-come Trust Sanger Institute. She then earned a Ph.D. in Mathematics at UC Berkeley, with a Designated Emphasis in Computational Biology, where she continued building statistical methods that describe how genome sequences evolve. In January 2018, Harris will finish her postdoctoral fellowship at Stanford and become an assistant professor of genome sciences at the University of Washington.

Mijo Simunovic: For his essay on the topic of cell and molecular biology, "Biology and physics rendezvous at the membrane." A native of Europe, Mijo sought higher education in the U.S. and in France; earning his Ph.D. in theoretical chemistry from The University of Chicago, and his Ph.D. in experimental physics from University of Paris. In his scientific work, he pursues com-plex biological problems that are fundamentally driven by physics. Currently, he is at The Rockefeller University where, as a Junior Fellow of the Simons Society, he uses stem cells to build experimental models of the human embryo, aimed at elucidating the earliest events in human development. Simunovic is passionate about teaching, having served as a teaching consultant at the University of Chicago and instructed undergraduate bio-physics courses in Chicago and New York.

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About SciLifeLab

SciLifeLab, Science for Life Laboratory, is a national hub for molecular biosciences in Sweden, with the mission to provide enabling infrastructures for life science research, create a collaborative research community and translate research towards society benefits. SciLifeLab was established in 2010 and today comprises more than 1,200 researchers and personnel. SciLifeLab has over 40 different infrastructure facilities that annually serve over 3,000 users across Sweden and beyond. We offer a cross-disciplinary research setting that addresses the needs of academic research, industry, health care and environment. In addition, SciLifeLab provides education for students and researchers at all levels. SciLifeLab is hosted by four universities; Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The infrastructure is located in Stockholm and Uppsala but there are also SciLifeLab sites at most other major Swedish universities.

About the American Association for the Advancement of Science: AAAS is the world's largest general scientific society and the publisher of Science – which has the highest paid circulation of any peer-reviewed general science journal – as well as Science Translational Medicine, Science Signaling, Science Advances, Science Immunology and Science Robotics. Founded in 1848, the nonprofit AAAS encompasses nearly 250 affiliated societies and academies of science, serving 10 million individuals. It is open to all and fulfills its mission to "advance science and serve society" through initiatives in science policy, international programs, science education, public engagement and more. For the latest research news, log on to EurekAlert!, a service of AAAS.

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