Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items

Food supply is one of the major drivers of animal behaviour and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of six male and six female macaques was monitored in each the four seasons (total 120 days observations). For each individual we found significant variation in the microbiome between all four seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of six ecological guilds - sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds. This article is protected by copyright. All rights reserved.