The relationship between rumen microbial ecology and the host is regulated by multiple factors including diet, the microbial inoculum entering the gut, and host genetics. Two hypotheses associated with this statement were developed and tested during this project. The first focused on the relationship between diet, early life microbial inoculum and rumen microbiota and the second concentrated on the association between host genetics and gut microbial ecology. Hypothesis one was that the rumen microbiome of lambs could be altered by post-natal diet and by early-life microbial intervention, to achieve differences in rumen fermentation, development and animal performance that persist beyond weaning. Secondly, it was hypothesized that sheep with different genetic merit for wool growth harbour differences in their rumen microbiome that are associated with differences in gut morphology, physiology, digesta retention time and microbial protein outflow which underpin their wool phenotypes.