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ASM's Stefano Bertuzzi on the Kavli Ideas Challenge

Tim Donohue, Ph.D., on the Kavli Ideas Challenge

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Over the past decade, scientists have learned that the majority of life on our planet is microbial. Bacteria, viruses, and fungi carpet our bodies, both inside and out, and populate our oceans and soils. Low-cost, high-throughput DNA sequencing has provided the means to detect and identify microbes and led to recognition of their ubiquity and central importance.

Still missing, however, is a detailed understanding of how microbes interact with each other and their environments, and of the causal roles that particular organisms play in critical ecosystem environments. Microbes in the human gut, for instance, have been implicated in regulating immune function, obesity, mood and cognitive function – but the complex chemical and neural signals that mediate these effects are largely unknown.

See also:

Alivisatos et al. (2015) A unified initiative to harness Earth’s microbiomes. Science, 350 (6260), 507-508.

Biteen et al. (2015) Tools for the microbiome: Nano and beyond. ACS Nano, 10(1), 6-37

Blaser et al. (2016) Toward a predictive understanding of Earth’s microbiomes to address 21st century challenges. mBio7(3):e00714-16.

Scientific Needs 

Sensors that enable detection of microbially-derived chemical signals, in real-time and in situ, would enable a new understanding of the chemical language through which microbes communicate with each other and their hosts. New imaging technologies for probing the spatial structure and composition of complex microbial communities would similarly advance our knowledge of how community structure and function are intertwined.

Few experimental tools are available to precisely and selectively manipulate microbes in situ in a way that would enable rigorous hypothesis testing. In the field of molecular genetics, techniques for ablating or manipulating specific genes (i.e., knockout and transgenic mice) have played a central role in driving understanding of the functional roles of specific genes and their protein products. Analogous methods for targeted manipulation of microbial species in an ecosystem could play a similarly transformative role in dissecting microbial function.

Call for Ideas

This Ideas Challenge invites the broad scientific community – including microbiologists, nanoscientists, neuroscientists, engineers, chemists, materials scientists, physicists and others – to submit innovative, blue-sky, and aspirational ideas for novel experimental tools and methods for understanding microbial function. The Challenge will be managed and judged through a collaboration of three leading scientific societies – led by the American Society for Microbiology, in partnership with the American Chemical Society and the American Physical Society. The Kavli Foundation will award $1M for recipients to launch their innovate research ideas. 

The focus of the Microbiome Ideas Challenge is the development of new tools and methods that will help transition the field of microbiome research from correlative studies – i.e., genomics-driven microbial censusing efforts – to causal understanding of microbial function. Ideally, ideas for novel tools and methods will be broadly applicable across the many environments studied in microbiome research – the Earth’s soils, ocean and freshwater environments, and atmosphere; as well as animal hosts’ gut and skin ecosystems.  

Awards and Use of Funds

Funds provided to the recipients of the Ideas Challenge are intended to launch nascent research efforts, rather than to support ongoing, well-established research programs.

Applications are invited from individual scientists as well as collaborative teams, but emphasis will be placed on Ideas that are cross-disciplinary and leverage the expertise of different research disciplines in generating tools and methods that address compelling microbiome research needs using innovative technical approaches. Support from this Ideas Challenge cannot be used for institutional indirect costs.

Recipients’ use of funds awarded through the Ideas Challenge is largely unconstrained, so long as funds are directed toward enabling the research described in the winning Idea. Funds may be used for salary support of personnel directly involved in conducting research, equipment and supply purchases, and for travel related to collaborative efforts.


For more information, contact Connie Herndon at

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