Meta data of 520 rumen samples collected from 260 selection line sheep (born 2011/12). Corresponding sequence data of bacterial 16S rRNA genes were obtained using 454 pyrosequencing and have been submitted to the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/sra) under the accession number PRJNA294244. These will only be made public upon acceptance of the manuscript “Host genotype controls rumen microbiota composition and consequently methane emissions in sheep" (working title; authors: Kittelmann S, Rowe SJ, Wood GR, Dodds KG, Pinares-Patiño CS, Kirk MR, Ganesh S, McEwan JC, Janssen PH).