The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks

Comput Struct Biotechnol J. 2019 Jul 29;17:1040-1046. doi: 10.1016/j.csbj.2019.07.011. eCollection 2019.


Microbiome studies estimate the functions of bacterial flora in situ on the basis of species composition and gene function; however, estimation of interspecies interaction networks is challenging. This study aimed to develop a method to predict the interaction networks among bacterial species from human gut metagenome data using bioinformatics methods. Our proposed method revealed that adjacent gene pairs involved in bacterial interspecies interactions are localized at boundary regions and encode membrane proteins mediating interactions between the intracellular and extracellular environments, e.g., transporters and channel proteins, and those mediating interactions between metabolic pathways. Actual human gut metagenome data displayed numerous such highly reliable interspecies interaction gene pairs in comparison with random simulated metagenome data sets, suggesting that the species composition of the actual microbiome facilitated more robust interspecific interactions. The present results indicate that molecular interaction networks in human gut flora are organized by a combination of interaction networks common to all individuals and group-specific interaction networks.

Keywords: Human gut; IGC, Integrated reference catalog of the human gut microbiome; Interspecific interaction; KO, KEGG Orthology; Metagenomics; Microbiome; Molecular interaction networks.