Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial

Abstract

Background: Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention.

Methods: This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected 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 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues.

Findings: Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01).

Interpretation: These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients.

Funding: This study was funded by the American Cancer Society.

Keywords: Colorectal cancer; Dry beans; Gut microbiota; Inflammation; Metabolites; Obesity; Prebiotic; Proteomic biomarkers.

Fig. 1

CONSORT. Of the 240 individuals initially contacted or approached for study recruitment, 71 provided informed consent. Of the 240, 123 did not meet inclusion criteria, 13 declined to participate, 25 were lost to follow-up and 8 withdrew for other stated reasons during the screening process. Immediately post-consent and before completing any study procedures, 1 individual experienced a change in eligibility and 1 decided not to continue; thus, 69 eligible patients began the run-in/equilibration period. Of these, 11 withdrew for various stated reasons and 3 individuals were lost to follow-up resulting in 80% (n = 55) of those initially eligible being randomized. Five participants withdrew post-randomization for various stated reasons, including 1 who withdrew in order to join another program. Two did not attend their final visit due to unrelated illness and were lost to follow-up, resulting in 48 patients (87%) who completed the study for intent-to-treat analysis.

Fig. 2

The BE GONE Trial tested the effect of cooked dry bean addition and depletion within the participant's usual diet. a. Study design, Left to Right: To establish the basal diet and microbiome and introduce study procedures prior to randomization, eligible and consented individuals began the equilibration/run-in. Participants who completed the run-in were randomized to begin the dry bean intervention or to continue the usual diet control for 8 weeks. The intervention diet consisted of adding ½ cup (1 serving) of cooked, canned navy beans to their usual diet over a 2-week ramp-up period followed by 1 cup (2 servings) per day for an additional 6 weeks. At week 8, participants who completed the intervention diet immediately crossed over to the control (usual diet without beans) and vice versa for a total of 5 in-person visits every 4 weeks with stool and fasting blood collection. The primary outcome focused on changes in stool 16S rRNA gene profiles and blood metabolites/markers. Trends in pipecolic acid, a specific marker of dry bean intake and microbiome-derived metabolite of lysine, paralleled the addition and the depletion of cooked navy beans within the usual diet, providing an objective measure of compliance. b. Total dietary fiber intake within the usual diet from multiple 24-h recalls collected across the intervention sequence showed that majority of participants remained below the adequate intake threshold for U.S. adults of 14 g per 1000 kcal [means, medians, interquartile range and outliers presented with p-values comparing intervention (orange) and control (gray) periods]. Within person change in total dietary fiber intake for the 8-week on-intervention period for both groups combined, linear mixed effect (LME) estimate and 95% CI: 0.22 (0.10, 0.35) interpreted as slope above 0 by generalized linear mixed models (proc glimmix, SAS 9.4) with random intercept in natural log scale. c. Beta diversity by weighted Jaccard similarity/distance across randomization groups visualized as PCoA biplots with the most abundant phylum-level taxa at baseline and 8 weeks post-intervention in the full trial cohort (n = 48).

Fig. 3

Parallel effects of cooked dry beans on the gut microbiome, circulating metabolome and protein markers of immune and inflammatory response in obese surveillance patients with a history of colorectal neoplasia otherwise following their usual diet. a. Within 8 weeks, the bean intervention significantly increased the inverse Simpson index [LME and 95% CI: 0.16 (0.02, 0.30), two-sided p = 0.02; n = 48] and the relative abundance of Faecalibacterium [LME and 95% CI: 0.40 (0.02, 0.78), two-sided p = 0.04; n = 42 (88%) carried the genus at baseline]. Across the study sequence no change was observed among participants randomized to remain on the control for the first 8 weeks (n = 20), while among patients randomized to the intervention first, Faecalibacterium dropped significantly [LME and 95% CI: −0.69 (−1.30, −0.08), two-sided p = 0.03, n = 25] within 8 weeks of returning to their usual diet without beans. Forest plot of effect estimates (LME) and 95% confidence intervals by generalized linear mixed models (proc glimmix, SAS 9.4) with random intercept in the natural log scale. b. Heatmap of effects (β) observed by randomization group across the trial sequence by Multivariable Association Discovery in Population-scale Meta-omics Studies (MaAsLin2), a linear mixed model with random intercept of normalized relative abundance (natural log scale; half the minimum relative abundance as pseudo count) for use in sparse, compositional microbial communities. Analysis restricted to min prevalence = 0.1 (total n = 48; n = 28 among the intervention first; 20 among the intervention second). Selected taxa shown met an unadjusted p < 0.05 for the on-intervention effect at either 4- or 8-weeks across the full trial cohort (n = 48; Supplementary Table S10). ∗further indicates the effect within randomization group also met p < 0.05. c. Volcano plot visualizing the results of MaAsLin2 analysis applied to the metagenomic subset (140 stool samples in 48 patients) characterizing the slope across the three on-intervention time points. Maximum estimated false discovery rate when calling all p-values (one-sided) ≤ 0.05 is 0.30. d. Volcano plot visualizing the circulating metabolome results of LME analysis across the three on-intervention time points. Maximum estimated false discovery rate when calling all p-values (one-sided) ≤ 0.05 is 0.48. e. Plot of effect estimates demonstrating significant and consistent increases and decreases within 4 weeks in selected dry bean metabolites, PA and SAM. f. Heatmap of effects (β) observed by randomization group across the trial sequence for plasma metabolites meeting q < 0.2 in d. g. Volcano plot visualizing 8-week on-intervention change in plasma proteins associated with intestinal and systemic inflammatory and immune response (Olink). Maximum estimated false discovery rate when calling all p-values (one-sided) ≤ 0.05 is 0.47.

Fig. 4

Differential co-expression of the gut microbiome, circulating metabolome and protein markers of immune and inflammatory response induced by the 8-week intervention. Differentially correlated module pairs between baseline usual diet (left column) and 8-weeks post intervention (middle column). Heatmaps depict Fisher's z-transformation of Pearson correlation coefficients between paired features that significantly increased or decreased pre-and post-intervention (FDR adjusted p-value <0.25).