Dietary plant diversity and the human gut microbiome

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ABSTRACT: Food shapes gut microbial communities and their impact on human health. Thus, rationally designed diets based on gut microbial ecology could provide a cost-effective intervention that significantly improves public health. Still, there are hundreds of edible food species and thousands of unique gut bacterial taxa. Do basic dietary rules govern microbial systems of this complexity? One intriguing observation has been that the diversity of ingested plant species is linked to gut microbiome structure. However, it remains unknown if and how relationships between dietary diversity and the gut microbiome generalize across diverse human populations. Moreover, we do not know how diets designed to promote plant species diversity could affect existing guidelines that promote intake of nutrients like fiber. This renewal application will address these research gaps. Our project will build on our prior findings that: nutrients from plants can be an effective tool for stimulating the growth and activity of human gut bacteria; and that both habitual diet and intake of diverse nutrients influence microbiome responses to nutritional intervention. Based on our previous results, we will examine the hypothesis that promoting species diversity provides an important complement, and in some cases alternative, to current dietary recommendations involving plants, which focus on fiber intake. In Aim 1, we will test whether relationships between dietary plant diversity and microbiome composition generalize across diverse human settings. To do so, we will refine a novel technique for genomic dietary assessment of plant intake. We will then use our optimized platform to measure plant species consumption across 1,500 individuals who vary by age, sex, race, wealth, and nationality. Next, in Aim 2, we will model tradeoffs between plant species diversity and fiber intake. Current dietary guidelines involving plants have focused on achieving sufficient intake of fiber. Yet, since plants differ in their fiber content, policies that promote plant species diversity could diminish fiber intake. Do diets that optimize fiber consumption or plant dietary diversity tend to benefit the gut microbiome more? Here, we will address this question by creating computational models and using them to predict optimal patterns of plant intake. Last, in Aim 3, we will evaluate ecological theories for how nutritional complexity affects gut microbial ecology. Carbohydrates have typically been considered the key limiting resource for gut microbes. Still, modern ecological thought suggests that multiple nutrients shape the activity of human gut bacteria. We will therefore test three distinct ecological models for the number and identity of dietary nutrients that regulate the gut microbiome. In concert, we expect these three Aims to lead to guidance as to whether there exists a specific set of plant species individuals should consume in a balanced manner; or, if they should instead focus on eating a smaller number of fiber-rich plant-based foods. We also expect our work to identify plant-based nutrients, besides fiber, that could serve as new leads for microbiome-targeting dietary interventions; and to inform ecological theories as to the number and relative importance of limiting nutrients for bacteria in the mammalian gut.