Predicting microbial interactions through computational approaches

• It is challenging to infer microbial interactions from metagenomic survey data.
• Predicted interactions from genomic data reveals insights into microbial crosstalk.
• Verified microbial interaction from scientific literature has been overlooked.

Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions – a largely overlooked data source for experimentally validated interactions.