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Background  Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH 4 /kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype.    Methods  Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from  Succinivibrio dextrinosolvens  strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of  S. dextrinosolvens  strain H5 growth on methane formation by rumen methanogens was explored using co-cultures.    Results  Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus  Succinivibrio,  and searches of bacterial genome sequences found that strains of  S. dextrinosolvens  were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments,  S .  dextrinosolvens  strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the  Methanobrevibacter gottschalkii  clade.    Conclusions  This is the first report of bacterial type III secretion system genes being associated with high methane emissions in ruminants, and identifies these secretions systems as potential new targets for methane mitigation research. The effects of  S. dextrinosolvens  on the growth of rumen methanogens in co-cultures indicate that bacteria-methanogen interactions are important modulators of methane production in ruminant animals.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-017-2671-0) contains supplementary material, which is available to authorized users.

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep