High-Fiber, Whole-Food 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. The 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. The digestion of MACs results in the accumulation of short-chain fatty acids (SCFAs) and other metabolic by-products that are critical to human health. Here, we implemented a 2-week dietary fiber intervention aiming for 40 to 50 g 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 2 weeks, increased fiber intake can induce compositional changes of the gut microbiome, including an increase in MAC-degrading bacteria. IMPORTANCE A 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 g of fiber per day, far less fiber than the 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 2-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 g/day on average for 2 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.

Dietary spinach reshapes the gut microbiome in an Apc-mutant genetic background: mechanistic insights from integrated multi-omics

“…[9][10][11] There are many types of dietary fiber in commonly consumed foods, exerting differential impacts on the gut microbiota, short-chain fatty acid production, and metabolic regulation. [62][63][64] Future studies should seek to corroborate the relative contributions of the fiber and phytochemical content, given the promising anticancer efficacy outcomes identified here. Clinical translation of freeze-dried whole foods, such as SPI, to at-risk patients might provide valuable quality-of-life benefits by delaying colectomy and drug intervention.…”

Resistant Starches and Non-Communicable Disease: A Focus on Mediterranean Diet

“…At the end of the study, in the RS group, anthropometric parameters, such as body weight, body mass index (BMI) and waist circumference, were slightly more decreased, and a negative correlation was found between RS intake and adiponectin level, along with a negative correlation between RS intake and blood level of resistin, a possible pro-inflammatory mediator of insulin resistance. Furthermore, leptin and apelin levels were significantly decreased only in the RS group [ 71 , 72 ]. As already discussed above, RS exists in different types, having different chemical structures.…”

“…Shelf life also increases RS content in some foods, such as durum wheat pasta. RS food claims were based on clinical trials [ 12 , 16 , 39 , 40 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ].…”

Are all dietary fibers equal for patients with inflammatory bowel disease? A systematic review of randomized controlled trials

“…This intake has dropped, in recent times, with the increasing intake of processed foods -nowadays only an average of 10-20 g/day is consumed. 13 Dietary fibers can be divided into two basic groups: insoluble fibers -including cellulose, hemicellulose, and lignin, and soluble fibers -such as pectins, gums, and mucilages, which become gummy when added to water. 12 Furthermore, these fibers can be classified based on function.…”