Figure 2. Gut microbiomes predict extant and ancestral mammalian diets.

(a) Diet-correlated bacterial lineages (squares coloured by phylum) and mammals (black dots) separated by dietary distances are jointly projected in the same ordination space using the OMI⁵⁹ mapping procedure (see Methods). Predicted niche breadth⁵⁹ of a bacterial lineage is depicted with an ellipse. The time period selected to define bacterial lineages is ∼300 Myr ago. Bacterial niche breadths show that many bacterial groups are herbivore or carnivore specific. However, no bacterial lineage has a niche breadth encompassing omnivores only (omnivores are in brown). (b) Workflow for microbiome-based prediction of ancient diet. (c) Inference of ancient mammalian diets. Left: trait-based reconstruction using 1,534 mammals³⁴. Right: Microbiota-based reconstruction with the 33 mammals under study. At each ancestor, the probability vector for each diet category is transformed into a linear variable bound between 0 (carnivorous) and 1 (herbivorous). Between two ancestors, diet is assumed to evolve linearly. Animal images courtesy of Julien Renaud.