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.

Modulating the Human Gut Microbiome and Health Markers through Kombucha Consumption: A Controlled Clinical Study

“…Several studies have indicated that dietary interventions may cause profound changes in microbiota structure (David et al, 2014;Oliver et al, 2021;von Schwartzenberg et al, 2021;Wastyk et al, 2021). While in this study, a four week-daily kombucha consumption resulted in a minimal decrease in microbiota diversity, a finding which contrasts with the increased microbial diversity frequently associated with individuals consuming fermented foods (Galena et al, 2022;Wastyk et al, 2021).…”

Consumption of a Recommended Serving of Wheat Bran Cereals Significantly Increases Human Faecal Butyrate Levels in Healthy Volunteers and Reduces Markers of Inflammation Ex Vivo

“…In this case 40 g of wheat bran cereals, equivalent to 11 g of dietary fibre (one third of the daily recommended amount) in one meal would deliver potential benefits associated with SCFA production by allowing the fibre to be properly fermented and for the SCFAs (especially butyrate) to be produced and increased in the colon. Other studies have also reported on the impact of increasing dietary fibre intakes and found no significant increase in faecal SCFAs concentrations [21,22]. The main difference between these studies and the present study is that in the present study the samples were collected following chronic consumption of a cereal fibre whilst in other studies the specific type of fibre (which was often mixed fibres present in fruits and vegetables, therefore likely to be rich in pectin) and source is not specified.…”