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Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

Felix G Eikmeyer1, Antje Rademacher2, Angelika Hanreich2, Magdalena Hennig1, Sebastian Jaenicke3, Irena Maus1, Daniel Wibberg1, Martha Zakrzewski3, Alfred Pühler1, Michael Klocke2 and Andreas Schlüter1*

Author Affiliations

1 Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld D-33594, Germany

2 Department Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim, Potsdam, D-14469, Germany

3 Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, D-33594, Germany

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Biotechnology for Biofuels 2013, 6:49  doi:10.1186/1754-6834-6-49

Published: 4 April 2013



In recent years biogas plants in Germany have been supposed to be involved in amplification and dissemination of pathogenic bacteria causing severe infections in humans and animals. In particular, biogas plants are discussed to contribute to the spreading of Escherichia coli infections in humans or chronic botulism in cattle caused by Clostridium botulinum. Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches.


All datasets featured a low abundance of reads that were taxonomically assigned to the genus Escherichia or further selected genera comprising pathogenic species. Higher numbers of reads were taxonomically assigned to the genus Clostridium. However, only very few sequences were predicted to originate from pathogenic clostridial species. Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. Likewise, known virulence determinants could hardly be detected. Only a marginal number of reads showed similarity to sequences described in the Microbial Virulence Database MvirDB such as those encoding protein toxins, virulence proteins or antibiotic resistance determinants.


Findings of this first study of metagenomic sequence reads of biogas producing microbial communities suggest that the risk of dissemination of pathogenic bacteria by application of digestates from biogas fermentations as fertilizers is low, because obtained results do not indicate the presence of putative pathogenic microorganisms in the samples analyzed.

Metagenome analysis; Anaerobic digester; Bacterial pathogens; Virulence determinants; High throughput sequencing; Antibiotic resistance; Biogas