The authors gratefully acknowledge Doctoral Training Partnership funding from the BBSRC (M.J.D.) and funding from the Scottish Government (P.J.M., A.W.R., and A.W.W.). We also thank the Centre for Genome-Enabled Biology and Medicine for help with next-generation sequencing and Karen Garden and the Rowett’s Analytical Services for SCFA analysis. SUPPLEMENTAL INFORMATION Supplemental Information includes four figures and two tables and can be found with this article online at https://doi.org/10.1016/j.celrep.2017.10.056.Peer reviewedPublisher PD