The performances of dairy cattle have traditionally been viewed as the combination of their genes and the environment they are raised in. More recently, it has become apparent that the number of microbial cells on and in the dairy cow far outnumbers the actual cow’s cells. The microbes within the rumen are known to play a vital role in the digestion and metabolism of the cow. Interestingly, studies have shown that for some of these microbes the cow has an influence on their presence and abundance, whilst other microbes are only found in animals raised in certain parts of the world or fed particular diets. This then begs the question “How does the cow’s genes and macro-environment effect the microbial composition and abundance and how do these microbes in turn affect the host’s performance?” The objective of this study was to identify production traits under varying levels of genetic and microbial influence and evaluate the changes in predictive accuracy of said traits associated with inclusion of information from bacterial and archaeal diversity and abundance. To this end rumen samples were collected from~ 1000 lactating Holstein cows on commercial farms in Denmark and the 16s rRNA gene sequenced and assembled to obtain ruminal diversity and abundance estimates. Additive genetic (heritability) and microbial variances (microbiability) were estimated simultaneously using univariate animal models and the most contrasting traits selected. Bayesian variable selection models were fitted for genetic information and microbial information independently and jointly and evaluated for predicted ability through cross validation. Results showed clear interactions between variance captured by additive cow genetics and microbial diversity and abundance. The increase in predictive ability of traits varied from 0–40%, with the largest increases associated with lowly heritable traits. Results of this study show some cow performance traits are influenced by ruminal microbial diversity and abundance outside of the host but more research is needed to fully understand the mechanisms driving cow, environment, microbial abundance and diversity dynamics.