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Background  Anaerobic digestion is a biological process in which a consortium of microorganisms transforms a complex substrate into methane and carbon dioxide. A good understanding of the interactions between the populations that form this consortium can contribute to a successful anaerobic digestion of the substrate.  In this study we combine the analysis of the biogas production in a laboratory anaerobic digester fed with the microalgae  Spirulina , a protein rich substrate, with the analysis of the metagenome of the consortium responsible for digestion, obtained by high-throughput DNA sequencing. The obtained metagenome was also compared with a metagenome from a full scale biogas plant fed with cellulose rich material.    Results  The optimal organic loading rate for the anaerobic digestion of  Spirulina  was determined to be 4.0 g  Spirulina  L −1  day −1  with a specific biogas production of 350 mL biogas g  Spirulina   −1   with a methane content of 68 %.  Firmicutes dominated the microbial consortium at 38 % abundance followed by Bacteroidetes, Chloroflexi and Thermotogae. Euryarchaeota represented 3.5 % of the total abundance. The most abundant organism (14.9 %) was related to  Tissierella , a bacterium known to use proteinaceous substrates for growth. Methanomicrobiales and Methanosarcinales dominated the archaeal community. Compared to the full scale cellulose-fed digesters, Pfam domains related to protein degradation were more frequently detected and Pfam domains related to cellulose degradation were less frequent in our sample.    Conclusions  The results presented in this study suggest that  Spirulina  is a suitable substrate for the production of biogas. The proteinaceous substrate appeared to have a selective impact on the bacterial community that performed anaerobic digestion. A direct influence of the substrate on the selection of specific methanogenic populations was not observed.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0615-1) contains supplementary material, which is available to authorized users.

Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads