Invited

Abstract

The gastrointestinal tract is host to a diverse microbial ecosystem that can vary depending on both host genetic and environmental factors. Studies have shown that even minor shifts in these populations can have significant impacts on livestock nutrition and productivity. Recent work has reported that the microbiome structures that are naturally occurring in the rumen are highly correlated with, and predictive of the feed efficiency phenotype of an animal (Ben Shabat et al., 2016). The potential for a host-specific microbiological uniqueness of the ruminant was first noted in the protozoal community (Eadie, 1962), and much later in the fibrolytic bacterial community (Weimer et al., 1999), prior to the development of advanced molecular tools to characterize the gut community. The concept of host microbiome individuality has now achieved substantial attention, primarily as a result of recent studies of the human gut microbiome. Such studies have revealed that the human gut contains a "core microbiome" (i.e., a set of taxa present in all subjects in the study), but also a large number of taxa whose presence or abundance varies among hosts.If the microbial community within each rumen is unique to its host, then two main questions arise: i) What are the host-associated factors that drive the uniqueness of such microbial ecosystem? ii)At what stage of life is this community assembled to the point where it can be regarded as compositionally and functionally unique?This review will present the main findings with regards to the above questions: i) A recent work conducted as part of the Rumen Global Census project (Henderson et al., 2015), determined the foregut microbial community composition in ruminants (742 samples from 32 animal species and 35 countries). Although the diet was the main driver, some patterns were associated to the animal species. For example, Fibrobacter abundances presented significantly higher levels in bovines compared to deer, sheep, or camelids. Under recent FP7-RuminOmics project an experiment involving the exchange of ruminal digesta from cows into reindeer was performed. Comparison of the microbial communities in the rumen of reindeer and cows before digesta exchange revealed that both species share a core microbiome. About 80% of identified bacterial taxa did not differ between species, with 10% being more closely associated with either the reindeer or cow host. Following the transfer of digesta from the cow into reindeer, a gradual time dependent increase in bacterial communities specific to this species was detected. Such findings indicate a clear host effect influencing bacterial communities specific to reindeer. In another experiment (a twin cow-cow rumen exchange) no clear evidence was found confirming that the rumen microbiome is consistently more similar in genetically related animals than between unrelated cows. It appears that while there are some indications of host effects on the composition of certain taxonomic groups, there is a stochastic component that can lead to even bigger ...