Comparative Analysis of Metabolic Pathways in Metagenomics

Metagenomics is the study of organismal DNA sequences obtained from an environmental sample. Metagenomic studies often compare samples taken from different locations (e.g., the human gut, lakes and oceans, soil) to assess significant differences in taxonomic makeup, genetic makeup, or function. Differences in function can be characterized by measuring the differential abundance of metabolic pathways found among the organisms in a sample. This is typically done by taking reads from the sample (short DNA sequences) and aligning them to genes in a database on the basis of sequence similarity. The genes code for proteins which are known to be catalytic enzymes involved in biochemical reactions in canoncial metabolic pathways. Previous studies have binned sequences into pathways by treating a pathway simply as a set of genes, ignoring its network topology. In this project, we explore techniques for comparing metagenomic samples that take both metabolic pathway structure and enzyme abundance into account