Deciphering Functional Redundancy in the Human Microbiome

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved. The striking conservation of functional capacity implies an ecological property known as functional redundancy. Although this redundancy is thought to underlie the stability and resilience of the human microbiome, its origin is elusive. Here, we decipher the basis for functional redundancy in the human microbiome by analyzing its genomic content network --- a bipartite graph that links microbes to the genes in their genomes. We show that this network exhibits special topological features that favor high functional redundancy. Moreover, we find that the assemblage of microbes plays a more important role than their abundances in determining the high functional redundancy of the human microbiome. We propose a simple genome evolution model to explain the key topological features observed in the real genomic content network. These observations deepen our understanding of species-function relationships, a critical step for developing function-based diagnostics and therapeutics.