BE GONE Trial: Dietary Bean Intervention Enhances Gut Microbiome

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Adding navy beans to one’s usual diet may be a viable dietary strategy for modulating the gut microbiome and regulating host markers associated with metabolic obesity and colorectal cancer.

Findings from a single-center dietary intervention study are underscoring the prebiotic and potential therapeutic role of navy beans in enhancing the gut microbiome and regulating host markers associated with metabolic obesity and colorectal cancer.

Results of the Beans to Enrich the Gut Microbiome vs Obesity's Negative Effects (BE GONE) trial suggest consistent and sustainable dietary adjustments among high-risk patients may be viable for targeting the composition and metabolic function of the microbiome.1

“Preclinical studies demonstrate that navy bean supplementation within a high-fat diet is sufficient to improve intestinal health and mitigate the severity of the obese, inflammatory phenotype, a finding further supported by clinical and follow-up studies linking bean consumption to improvements in cardiovascular health and reduced risk of advanced colorectal adenoma recurrence,” wrote investigators.1 “Previous clinical studies have not addressed whether simply increasing or adding beans to the usual diet is sufficient and effective in high-risk patients with known or expected challenges in cooperatively managing both gut and metabolic health.”

Diet, chemical exposures, disease-causing organisms, and bowel movement regularity impact the health of the gut microbiome, which interacts with various body systems to assist with bodily functions.2 Prebiotics are non-digestible fibers that promote the growth of beneficial bacteria in the gut microbiome to aid digestive and overall health. Dry beans are among the most beneficial prebiotics, although they are not popular in the standard US diet and little research has explored the impact of adding beans on managing both gut and metabolic health.3

To assess the effect of an increase in navy bean consumption on gut microbiota, circulating marker, and metabolite profiles, Xiaotao Zhang, MD, PhD, postdoctoral associate at Baylor College of Medicine, and colleagues conducted a low risk, noninvasive dietary intervention trial at MD Anderson Cancer Center in Houston, Texas, with clinic-based recruitment targeting patients at the major specialty centers. For inclusion, patients were required to be > 30 years of age, be classified as obese, and have either a history of pathology-confirmed precancerous polyps of the colon or rectum or classified as a colorectal cancer survivor that had completed treatment with adequate maintenance of bowel length and reached normalized bowel habits.1

In total, 69 patients were enrolled in the study and subject to a 4-week run-in and equilibration period where they followed their usual diet without dry beans. Then, 55 participants were block randomized based on the use of statins and/or metformin to 1 of 2 sequences, either continuing their usual diet without dry beans or beginning the intervention of adding study beans to their usual diet. After the first 8-week cycle, patients immediately crossed over to the other sequence.1

Throughout the study, patients were able to choose and prepare their own meals with close follow-up and counseling support from the study dietitian. The intervention diet consisted of adding ½ cup of cooked, canned navy beans to their usual diet over a 2-week ramp-up period followed by 1 cup per day for an additional 6 weeks. Beyond the addition of study beans, participants were asked to not change their usual diet, physical activity, and lifestyle habits during the study period.1

Participants provided stool and fasting blood samples every 4 weeks to assess the primary outcome of intra- and inter-individual changes in the gut microbiome and in circulating markers and metabolites within the 8-week intervention.1

In total, 48 (87%) participants completed the full 16-week trial, although 2 of these patients did not provide sufficient information to accurately estimate adherence. Of those who did, 95% met the 28 cup target for total amount of study beans consumed across the on-intervention period and 74% consumed the prescribed bean dose on all or most days within a week for each of the 8 weeks.1

Results showed an increase on-intervention in diversity (linear mixed effect, 0.16; 95% Confidence interval [CI], 0.02-0.30; P = .02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all P < .05). Investigators noted parallel shifts in nutrient and microbiome-derived metabolites in the circulating metabolome, including increased pipecolic acid and decreased indole (all P < .002) that regressed upon returning to the usual diet.1

In the absence of other lifestyle changes, circulating lipoprotein profiles did not change within 8 weeks of consuming 1 daily cup of beans (P > .05) and chronic disease medication use or basal diet did not appear to modulate the effect of the intervention on low-density lipoprotein (P > .05). Investigators pointed out proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (P = .01).1

“Advancing our understanding of the metabolites and biological markers paralleling interactions of the microbiota with prebiotic foods is critical to effectively design and monitor extended trials with clinically relevant outcomes,” investigators concluded.1


  1. Zhang X, Irajizad E, Hoffman KL, et al. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. The Lancet.
  2. Cleveland Clinic. Gut Microbiome. Body Systems & Organs. August 18, 2023. Accessed December 12, 2023.
  3. Miller, S. Prebiotics versus Probiotics for Gut Health: What’s the Difference? Jefferson Health. May 22, 2023. Accessed December 12, 2023.