State of the art

Our appreciation of the role of microbiomes for life on Earth has dramatically changed in the last two decades as a consequence of technological advances. Application of methods such as metagenomic sequencing have shown how tremendously diverse and abundant microbial life is, everywhere we look: In our gut, in the gut of animals, in and on plants, in soils and oceans, or in engineered systems such as wastewater treatment plants.

Human microbiomes can differ dramatically in composition between individuals, notably as a function of nutrition. Human microbiomes also differ in diseased individuals or those undergoing antibiotic or pharmaceutical treatment. Soil microbiomes differ from one place to the next at the functional and community level, and even ocean microbiomes are distinct at different locations or depths. This has raised fundamental and still largely unanswered questions: How important is this microbial diversity for the host or for the environment? Can microbial diversity predict host and environmental health? To what extent can it be engineered?

Microbiomes contribute to host and environmental health. Researchers now aspire to positively influence microbiomes, and to restore disordered or poorly performing ones back to a ‘healthy’ state. A better understanding of microbiome functioning and the host or environmental context may permit the building of microbial systems with novel functionalities. In practice, however, we are only at the very beginning of any reasonable attempt to influence or manipulate microbiomes. We need novel enabling technologies for assembling or reconstructing microbial communities, for adding or removing specific species, and for stimulating or creating new functionalities in the microbiome.

Research structure and work packages

The basic premise of the NCCR Microbiomes is that fundamental understanding of the functioning of microbiomes can only be achieved by simultaneous development of engineering and computational approaches across diverse systems. To fulfil its goals, the NCCR Microbiomes will thus use a combination of six interlinked research work packages that will foster parallel advances in understanding and in the development of management and intervention strategies.

Host institutes and principal investigators of the NCCR Microbiomes.
The overall work package structure is shown, with details of the research groups contributing to each WP. Each research group brings specific excellence and complementary expertise to create a strong intertwined and collaborative network between experimental (micro-) biologists, bioinformaticians, clinicians, engineers and computational biologists.