Microbes fulfill a crucial role as a symbiotic partner in many biological systems - especially in the gastrointestinal tract of herbivores where they perform anaerobic digestion and act as an interface between the nutrients in the feed and the metabolism of the host animal. Despite the rapid advancement of biotechnological tools, knowledge still is limited on these complex host-microbiome ecosystems, commonly referred to as the holobiont. To combat this, we seek to create and analyze high resolution datasets from the molecular data i.e. DNA, RNA and proteins that constitute the rumen holobiont as a whole, and thereby disentangle metabolic interactions that exist within.
Our experimental design has utilized beef cattle with additional explorable perturbations in our data, including using different breeds, progeny groups as well as diet, which incorporated anti-methanogenic red seaweed (Asparagopsis taxiformis) into selected feeds. With the use of holo-omics, an integrative application of genomics, transcriptomics, proteomics and metabolomics, from both host tissue and microbiome samples we are attempting to track the intricacies of the metabolic cascade that occurs across different cattle individuals over time when fermentation pathways are shifted away from methane and towards alternative metabolites.
Our initial data suggests a dependence from the microbiome on the parental genotype of our sampled individuals, which indicates that selected host-microbiome interactions may be influenced directly by the host. It is envisaged that disentangling the intimate connection between the host cow and its microbiome will ultimately yield valuable contributions towards ongoing efforts to improve the sustainability of ruminant production.