The goal of this study was to obtain causative information about beta-diversity (differentiation between microbiomes) by comparing sequencing information between studies rather than just knowledge about alpha-diversity (microbiorne richness). Here, published sequencing data were merged representing 78 anaerobic digester samples originating from 28 different studies for an overall comparison of beta-diversity (measured using unweighted UniFrac). It was found that digester microbiomes based on bacterial sequences clustered by substrate type, independent of the study of origin, and that this clustering could be attributed to distinct bacterial lineages. (C) 2013 Elsevier Ltd. All rights reserved.