Consumption of only wild foods induces alterations to the gut microbiome

The bacterial composition of the gut microbiome (GM) is implicated in human health, and is known to vary among lifestyles. Some have proposed that adopting more “traditional” diets could lead to substantive changes in the GM, in the direction of more health-associated taxa. However, most studies so far have focused only on diets including domesticated foods. During the fast majority of our evolutionary history, humans consumed only wild foods, which might have unique implications for the GM composition. We explored the impact of a wild-food-only diet on GM, particularly whether this diet increases the presence of health-associated and/or “old friend” taxa, and if the alterations to GM are persistent or transient. One participant collected daily fecal samples and recorded daily food consumption over an eight-week period, the middle four weeks of which he consumed only wild foods (nuts, fruits and leafy greens, wild deer, and fish). Samples were profiled through 16S rRNA amplicon sequencing and the species identified for each sample by applying oligotyping. A wild-food-only diet considerably alters the composition of the GM, and the magnitude of the changes is larger than that observed in other diet interventions. However, no new GM taxa, including “old friends” appeared; instead, the relative proportions of already-present taxa shifted. There is a clear successional shift from the pre-, during- and post-wild-food-only diet. The GM is very sensitive to the change from a “Western” diet to a wild-food-only diet, likely reflecting the different macro- and micronutrient properties of the consumed foods. Some of the alterations remain even after returning to a “Western” diet, though overall the GM quickly regains many aspects of its original configuration.