Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host

作者：Melanie K. Hess, Hannah E. Hodgkinson, Andrew S. Hess, Larissa Zetouni, Juliana C. C. Budel, Hannah Henry, Alistair Donaldson, Timothy P. Bilton, Tracey C. van Stijn, Michelle R. Kirk, K. G. Dodds, Rüdiger Bräuning, Alan McCulloch, S. M. Hickey, Patricia L. Johnson, Arjan Jonker, Nickolas Morton, Shaun C. Hendy, V. Hutton Oddy, Peter H. Janssen, John C. McEwan, Suzanne J. Rowe · 发表于：BMC Genomics · 年份：2023 · DOI：10.1186/s12864-023-09660-3 · 被引用次数：11 · 研究领域：Ruminant Nutrition and Digestive Physiology、Genetic and phenotypic traits in livestock、Agriculture Sustainability and Environmental Impact

BACKGROUND: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. RESULTS: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet,...