Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome

Publication date: Available online 19 January 2017
Source:Cell Host & Microbe
Author(s): Ohad Manor, Elhanan Borenstein
Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.

Graphical abstract

Teaser

Comparative human microbiome analyses have identified both taxonomic and functional shifts associated with diseases. Manor and Borenstein present an integrative multi-omic framework that identifies the microbial drivers of functional shifts. Its application reveals that shifts in the microbiome's functional capacity can be traced back to function-, site-, and disease-specific taxa.


http://ift.tt/2jEM6VB