Drexel University

Research

In silico simulations of metabolic interactions between bacterial endosymbionts and their hosts.

NetInteract is an end-to-end pipeline for modelling metabolic interactions among bacterial endosymbionts and their hosts, from network reconstruction to exploratory data analytics. This software expands upon three published tools: NetSeed, which infers exogenously acquired metabolites based on network topology; NetCooperate, which calculates a metabolic complementarity index (MCI) score, estimating possible levels of symbiont cross-feeding; and NetCmpt, which calculates an effective metabolic overlap (EMO) score, a potential indicator of symbiont competition. 

NetInteract improves upon these tools by conserving the intrinsic hierarchical structure of metabolic networks, by re-formulating MCI and EMO scores to consider downstream effects of metabolites, and by shifting from a fragmented pair-wise model in favor of a holistic community view. This software thus enables researchers to explore simulated species interactions at varying levels of granularity, from genome-wide trends to more specific pathway-level variations. Combining reverse-ecology theory with bioinformatic techniques, this work contributes to the larger field of microbial evolution.