This repository contains the code used in the manuscript accepted for publication in Communications Biology described below: Manuscript title: Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome Manuscript authors: Boris J. SepulvedaABH, Oscar González-RecioC, Amanda J. ChamberlainAB, Ruidong XiangAB, Benjamin G. CocksB, Jianghui WangA, Claire P. Prowse-WilkinsAD, Leah C. MarettE, S. Richard O. WilliamsE, Joe L JacobsBE, Aser García-RodríguezF, Jose A. Jiménez-MonteroG, Jennie E. PryceAB A Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia B School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia C Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CSIC), Madrid, 28040, Spain D Department of Animal Science, University of California, Davis, 95616, USA E Agriculture Victoria Research, Ellinbank, VIC, 3821, Australia F Department of Animal Production, NEIKER-BRTA, Granja Modelo de Arkaute, Apdo. 46, 01080 Vitoria-Gasteiz, Spain G Spanish Holstein Association (CONAFE). Ctra. Andalucía km 23600 Valdemoro, 28340 Madrid, Spain H Corresponding author. Email: boris.sepulveda@agriculture.vic.gov.au CODE DESCRIPTION Supplementary Code 1 has the code to generate descriptive figures, estimate variance components and prediction accuracy of EME with BLUP models, and estimation of reference population size. Please notice that due to commercial restrictions, the input data for Supplementary Code 1 has the animal and sample IDs masked, and the genotypes, EME, metadata and fixed effects simulated, and therefore the results are not the same as those reported in the manuscript. However, the metagenome data is real. Supplementary Code 2 is the code to identify KOs that could be from Bos taurus. Supplementary Code 3 is an example of the parameter file used as input in BayesR3. All other files are dependencies.