The Landscape of Metabolic Interactions in Human Gut Ecosystem

The human gut is colonized by different types of microorganisms, which are known to play important roles in the human host by physiological homeostasis. The human host provides a nutrient rich environment and the microbiota provide some beneficial functions that humans cannot perform. A comprehensive analysis of the human gut microbiome is thus important to reveal the mechanisms of these host-microbe interactions. The development of high-throughout sequencing technology and related computational frameworks enables exploration of the metabolic capacity and related metabolic interactions and their roles in human health and diseases. In this study, we present a comprehensive analysis of gut microbiota biosynthesis capacity and their metabolic interaction based on the available gut microbe genomes and corresponding genome-scale metabolic models. With the available gut microbial genomes, we focus on the presence or absence of enzymes involved in different metabolic pathways. With the genome-scale metabolic models, we check the biosynthetic ability involved in more than 100 specific reactions or bioprocesses. Moreover, the metabolic interactions within two-specie pairs are inferred using the topological methods and constraint based modeling approach. Taken together, our results show different biosynthetic capacities and metabolic interactions of gut microbial species, and provide clues for future applications in metabolic modeling of the gut microbial communities.