RESEARCH Open Access Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing Roland Wirth 1 , Etelka Kovács 1 , Gergely Maróti 2,3 , Zoltán Bagi 1 , Gábor Rákhely 1,4 and Kornél L Kovács 1,4* Abstract Background: Renewable energy production is currently a major issue worldwide. Biogas is a promising renewable energy carrier as the technology of its production combines the elimination of organic waste with the formation of a versatile energy carrier, methane. In consequence of the complexity of the microbial communities and metabolic pathways involved the biotechnology of the microbiological process leading to biogas production is poorly understood. Metagenomic approaches are suitable means of addressing related questions. In the present work a novel high-throughput technique was tested for its benefits in resolving the functional and taxonomical complexity of such microbial consortia. Results: It was demonstrated that the extremely parallel SOLiD™ short-read DNA sequencing platform is capable of providing sufficient useful information to decipher the systematic and functional contexts within a biogas- producing community. Although this technology has not been employed to address such problems previously, the data obtained compare well with those from similar high-throughput approaches such as 454-pyrosequencing GS FLX or Titanium. The predominant microbes contributing to the decomposition of organic matter include members of the Eubacteria, class Clostridia, order Clostridiales, family Clostridiaceae. Bacteria belonging in other systematic groups contribute to the diversity of the microbial consortium. Archaea comprise a remarkably small minority in this community, given their crucial role in biogas production. Among the Archaea, the predominant order is the Methanomicrobiales and the most abundant species is Methanoculleus marisnigri. The Methanomicrobiales are hydrogenotrophic methanogens. Besides corroborating earlier findings on the significance of the contribution of the Clostridia to organic substrate decomposition, the results demonstrate the importance of the metabolism of hydrogen within the biogas producing microbial community. Conclusions: Both microbiological diversity and the regulatory role of the hydrogen metabolism appear to be the driving forces optimizing biogas-producing microbial communities. The findings may allow a rational design of these communities to promote greater efficacy in large-scale practical systems. The composition of an optimal biogas-producing consortium can be determined through the use of this approach, and this systematic methodology allows the design of the optimal microbial community structure for any biogas plant. In this way, metagenomic studies can contribute to significant progress in the efficacy and economic improvement of biogas production. Keywords: Biogas, Next-generation sequencing, DNA, Microbial community structure, Bacteria, Methanogens, SOLiD™, Metagenomics, Hydrogen metabolism * Correspondence: kornel@brc.hu 1 Department of Biotechnology, University of Szeged, Középfasor 52 Szeged H-6726, Hungary 4 Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged H-6726, Hungary Full list of author information is available at the end of the article © 2012 Wirth et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Wirth et al. Biotechnology for Biofuels 2012, 5:41 http://www.biotechnologyforbiofuels.com/content/5/1/41