Degradation Network Reconstruction Guided by Metagenomic Data

Methods Mol Biol. 2017:1539:145-157. doi: 10.1007/978-1-4939-6691-2_9.


Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.

Keywords: AromaDeg; Aromatics; Biodegradation; Metagenomics; Network reconstruction; Next-generation sequencing; Pathways; Pollutants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodegradation, Environmental*
  • Computational Biology / methods*
  • High-Throughput Nucleotide Sequencing
  • Metabolic Networks and Pathways / genetics
  • Metagenome*
  • Metagenomics* / methods
  • Software