Reducing rumen complexity to its essential components to understand and modulate ecosystem structure and function

Ruminants represent a paradigmatic case of obligatory host-microbiome relationships. These animals require complex microbial communities to digest plant fibers. Which functions are essential and how the assembly of these functions impacts host physiology remain unknown.

My goal is to understand the underlying aspects that allow the host and its microbes to coexist and to identify the essential requirements of this microbial community to sustain the life of the host. This proposal aims to address this ambitious and fundamental challenge.

These efforts build on a unique research platform involving germ-free ruminant animals, modeling, genomics, metabolomics, as well as animal and microbial physiology, developed over nine years of experience working with animal microbiomes.

To do so, I propose to identify the minimum rumen community (RuMinimum) using top-down and bottom-up approaches that will complement each other.

Once defined, the RuMinimum will serve as a platform for experimenting and understanding how the ecosystem functions and supports the life of the host, and how to modulate it.

We will specifically augment and decrease functional redundancy and richness at different edges of the trophic network and measure their impact on ecosystem function and host physiology.

These endeavors will allow us to learn how to modulate host physiology towards better feed efficiency or lower methane production, which will have an immense environmental and agricultural impact.

The results of this project will be relevant not only to ruminants but also to other gut ecosystems and anaerobic, carbon-degrading communities in general.

Our research efforts will lead to new paradigms and concepts vis-a-vis microbial community assembly, the design of synthetic microbial communities, and host-microbiome interactions, with strong scientific and applicative potential.