Diet rapidly and reproducibly alters the human gut microbiome

Summary

This study established a foundational point in microbiome research: dietary changes alter gut microbial composition rapidly and reproducibly. Ten participants alternated between an entirely animal-based diet (meat, eggs, cheese) and an entirely plant-based diet (grains, legumes, fruits, vegetables) for five days each. Microbiome composition shifted within 24 hours of dietary change and reverted within 48 hours of returning to baseline diet. The animal-based diet specifically increased the abundance of bile-tolerant microorganisms (Bilophila wadsworthia, Alistipes putredinis, Bacteroides) and decreased the abundance of Firmicutes that metabolize plant polysaccharides. Functional metagenomic analysis confirmed corresponding shifts in microbial gene expression. The paper is the canonical reference for the rapid-response biology of the human gut microbiome to dietary substrate change and for the bidirectional, plastic nature of these shifts.