Microbiome: Focus on Causation and Mechanism

Abstract

There is tremendous enthusiasm for the microbiome in academia and industry. This Perspective argues that in order to realize its potential, the field needs to focus on establishing causation and molecular mechanism with an emphasis on phenotypes that are large in magnitude, easy to measure, and unambiguously driven by the microbiota.

Figure 1:

Challenges and approaches to decipher mechanism in microbiome research. (A) In classical genetics, the phenotype and genotype are in the same organism. Genetic studies in the microbiome have two important distinctions: the phenotype and genotype are in different organisms (host and microbe, respectively), and the process of determining which microbial species in a complex mixture are responsible for a phenotype is a formidable challenge. (B) Two areas in which studies of causality and mechanism have gained momentum are small molecule consumption/production and immune modulation. Communities with outlier phenotypes are an important vista for understanding and translating gut microbiome function.