January 28, 2021

Brianna Petrone (Duke University)

Phylogenetic signatures of food-microbe relationships in the human GI tract

Fall 2020 Graduate Student Award in Pathogenic and Commensal Organisms


The microbes that live in the human digestive system (often called the “gut microbiota” or “gut microbiome”) directly impact health. As a result, they are increasingly the focus of medical interventions like fecal transplants and supplements like prebiotics and probiotics. However, by far the simplest way to shape gut microbial communities is with the food we eat. Diet applies a powerful selective pressure to gut microbes and is a primary driver of gut microbiome structure, more so than factors like host genetics, sanitation, or geography. However, we lack a clear overall set of “rules” for how food groups, foods, or nutrients act together to impact gut microbes, in part because it is challenging to measure food intake in freely-eating people.

We have developed a method that allows us to derive diet information from human stool samples already collected for microbiome analysis by sequencing degraded food DNA that has survived digestion. Rather than labeling foods with their common names (e.g. “apple,” “pear,” or “bean”) like diet surveys do, sequencing allows us to label foods by their species of origin (e.g. Malus pumila, Pyrus communis, or Phaseolus vulgaris) and importantly, gives us information about their evolutionary relatedness (e.g. does a person eat closely related foods on the phylogenetic tree like apple and pear, or distant ones like apple and bean?). In this proposal, we apply our method to study the relationship between diet and gut microbiome composition in a large group of 2,500 subjects from 5 different countries.