Abstract

As the human population expands towards 10 billion, pressure is
being applied to food production systems to develop nutritious,
efficient and sustainable practices, such as optimizing health
benefits from food, improving feed conversion and animal welfare
and mitigating harmful byproducts such as greenhouse gases
(GHG). One promising route to achieve this, is combining the use of
functional dietary components with a deeper understanding of the
intimate genetic and physiological connection between animals
and their microbiomes. However, first we must unlock critical and
poorly understood microbiota and their biological pathways that
control digestion as well as identify exploitable interactions that
exist within the complexity of gut microbiomes. Our research seeks
to combine high-resolution genome-guided meta-omics
technologies with enzymology, bacteriology, bioinformatics and
phenotyping of relevant digestive eco-systems from human and
production animals (pigs, fish and ruminants). Herein we highlight
how such an integrated approach can visualizes how distinctive
dietary fibres stimulate known model microorganisms within a
complex endogenous microbiome. We further reveal the
metabolic influence of uncharacterized bacterial and eukaryotic
populations that are surprisingly conserved across diverse dietary
conditions and host species. Importantly, as we develop with the
technological advancements, we are actively expanding our
analyses further across the “holobiont”, with the long-term
objective being: to understand, monitor and ultimately manipulate
host-microbiome interactions.