High fiber, whole foods dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids

Abstract

Dietary shifts can have a direct impact on the gut microbiome by preferentially selecting for microbes capable of utilizing the various dietary nutrients. Intake of dietary fiber has decreased precipitously in the last century, while consumption of processed foods has increased. Fiber, or microbiota-accessible carbohydrates (MACs), persist in the digestive tract and can be metabolized by specific bacteria encoding fiber degrading enzymes. Digestion of MACs results in the accumulation of short-chain fatty acids (SCFAs) and other metabolic byproducts that are critical to human health. Here, we implemented a two-week dietary fiber intervention aiming for 40-50 grams of fiber per day within the context of a course-based undergraduate research experience (CURE) (n = 20). By coupling shotgun metagenomic sequencing and targeted gas-chromatography mass spectrometry (GC/MS), we found that the dietary intervention significantly altered the composition of individual gut microbiomes, accounting for 8.3% of the longitudinal variability within subjects. Notably, microbial taxa that increased in relative abundance as a result of the diet change included known MAC degraders (i.e., Bifidobacterium and Lactobacillus). We further assessed the genetic diversity within Bifidobacterium, assayed by amplification of the groEL gene. Concomitant with microbial composition changes, we show an increase in the abundance of genes involved in inositol degradation. Despite these changes in gut microbiome composition, we did not detect a consistent shift in SCFA abundance. Collectively, our results demonstrate that on a short-term timescale of two weeks, increased fiber intake can induce compositional changes of the gut microbiome, including an increase in MAC degrading bacteria. IMPORTANCEA profound decrease in the consumption of dietary fiber in many parts of the world in the last century may be associated with the increasing prevalence of Type II diabetes, colon cancer, and other health problems. A typical U.S. diet includes about [~]15 grams of fiber per day, far less fiber than daily recommended allowance. Changes in dietary fiber intake affect human health not only through the uptake of nutrients directly, but also indirectly through changes in the microbial community and their associated metabolism. Here we conducted a two-week diet intervention in healthy young adults to investigate the impact of fiber consumption on the gut microbiome. Participants increased their average fiber consumption by 25 grams/day on average for two weeks. The high fiber diet intervention altered the gut microbiome of the study participants, including increases in known fiber degrading microbes such as Bifidobacterium and Lactobacillus.