Updated project metadata. In this study, we analyzed the microbial communities from a methane-based bio-reactor with selenate as an electron accepter. Four biological replicates were analyzed by metagenomics, of which data can be found in the SRA database (Accession number: SRP136677, SRP136696, SRP136790 and SRP136859). Based on the metagenomic data, we detected the expressed proteins using metaproteomics. This data is also included in this submission.