Population analysis of sheep rumen metagenome profiles captured by restriction enzyme reduced representation sequencing

The rumen microbiome may serve as a proxy for many environmental and production livestock traits due to the role it plays in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling; however, the systematic and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on country, diet, age and time off feed at the time of sample collection. Systematic and biological effects in the RB and RF profiles were examined.