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BioMed Research International
Volume 2015 (2015), Article ID 167249, 5 pages
Research Article

mmnet: An R Package for Metagenomics Systems Biology Analysis

1Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China
2Department of Biochemistry and Molecular Biology, Beijing Institute of Radical Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China

Received 8 October 2014; Revised 8 March 2015; Accepted 17 April 2015

Academic Editor: Yunlong Liu

Copyright © 2015 Yang Cao et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The human microbiome plays important roles in human health and disease. Previous microbiome studies focused mainly on single pure species function and overlooked the interactions in the complex communities on system-level. A metagenomic approach introduced recently integrates metagenomic data with community-level metabolic network modeling, but no comprehensive tool was available for such kind of approaches. To facilitate these kinds of studies, we developed an R package, mmnet, to implement community-level metabolic network reconstruction. The package also implements a set of functions for automatic analysis pipeline construction including functional annotation of metagenomic reads, abundance estimation of enzymatic genes, community-level metabolic network reconstruction, and integrated network analysis. The result can be represented in an intuitive way and sent to Cytoscape for further exploration. The package has substantial potentials in metagenomic studies that focus on identifying system-level variations of human microbiome associated with disease.