Association of distinct microbial signatures with premalignant colorectal adenomas

Abstract

Environmental exposures are a major risk factor for developing colorectal cancer, and the gut microbiome may serve as an integrator of such environmental risk. To study the microbiome associated with premalignant colon lesions, such as tubular adenomas (TAs) and sessile serrated adenomas (SSAs), we profiled stool samples from 971 participants undergoing colonoscopy and paired these data with dietary and medication history. The microbial signatures associated with either SSA or TA are distinct. SSA associates with multiple microbial antioxidant defense systems, whereas TA associates with a depletion of microbial methanogenesis and mevalonate metabolism. Environmental factors, such as diet and medications, link with the majority of identified microbial species. Mediation analyses found that Flavonifractor plautii and Bacteroides stercoris transmit the protective or carcinogenic effects of these factors to early carcinogenesis. Our findings suggest that the unique dependencies of each premalignant lesion may be exploited therapeutically or through dietary intervention.

Keywords: colonic adenoma; colorectal cancer; fecal microbiome; metagenomics; microbial communities.

Figure 1:. Descriptive demographics, environmental exposures and adenoma characteristics within the GIDER cohort.

(A) Pie chart of the 917 participants within GIDER, grouped by their adenoma histological subtypes (i.e., no adenoma, serrated adenomas, tubular adenomas). (B, C) Number of patients with TA or SSA risk stratified as mid- or high-clinical risk depending on the total number of adenomas and size. (D) Significant demographic factors and environmental exposure differences between SSA and TA - participants with TA were of older age, more likely to be male, more likely to use aspirin, and self-reported higher daily servings of vegetables and lower daily servings of processed meat.

Figure 2:. Summary of GIDER community microbiome sub-communities.

(A) Principal coordinate analysis (PCoA) plot coloured by five microbial clusters (meta-communities) identified by Dirichlet multinomial distribution. (B) The five clusters are determined by 137 significant (qval <0.05) differential abundant microbial species, as shown in this heatmap, whereby each cell represents the normalized average relative abundances. (C) The most abundant microbial species of each cluster is plotted on this density dot plot, to highlight that the five microbial clusters correspond predominant with Faecalibacterium prausnitzii (DMM1), Bacteroides uniformis (DMM3), Eubacterium rectale (DMM2), Bacteroides vulgatus (DMM4) and Prevotella copri (DMM5). (D) The significant (pval <0.05) host and environmental variables (yellow - demographics, green - diet, blue - medical history, purple - medications) explaining the microbiome variance determined by PERMANOVA on Bray-Curtis dissimilarity distances are shown in the barplot.

Figure 3:. Association of gut microbiome taxonomic features associated with adenoma subtypes.

(A) Dotplot with both axes indicating the respective TA and SSA linear discriminant analysis (LDA) scores, demonstrating the segregation of the subjects by the presence of TA (blue), SSA(orange) or neither (gray). Boxplot of the Adenoma Microbial Dysbiosis Index (ADMI), a function of both LDA scores, which is significantly higher in cases with TA and lower in cases with SSA, whereby subjects are coloured as green, brown or pink, respectively, if they are predicted by LDA score to either be TA, SSA or both TA and SSA. The ADMI cut-offs to determine if subjects’ microbiome were TA-like or SSA-like are the green and brown dashed lines. (B) Phylogenetic tree (generated using the software GraPhlAn) constructed on 170 bacterial species detected in at least >10% of the GIDER cohort. Colored tree leaves indicate the species belong to the same phylum, and the outer rings indicate adenoma subgroup specific results with those microbial species enriched in the subgroup colored as red, and those diminished coloured as blue (C) Heatmap of microbial species significantly associated with TA, SSA, proximal TA, distsal TA, low and high risk adenomas, whereby each cell represents the average relative abundance of the microbial species, specific to the subgroup of interest, and * depicting those p<0.05, FDR <0.2.

Figure 4:. Association of gut microbiome functional features associated with adenoma subtypes.

(A) Barplot of 363 significant microbial EC functional features (FDR <0.2), agglomerated to their parent metabolic pathway function, associated with either SSAs or TAs. (B) Patients with tubular adenomas also have significant negative associations with microbial features associated with methanogen metabolism, with (C) corresponding lower abundance of methanogenic microbial species - Methanobrevibacter smithii. (D) Participants with either SSAs or TAs have the most numbers of positive associations with amino acid metabolism, whereas amino-acid related pathways include both essential and non-essential amino-acids (E) Volcano plots highlighting predicted metabolites with increased or decreased abundance in either TA or SSA.

Figure 5:. Interplay of environmental factors and gut microbiome features associated with adenoma subtypes.

(A) Significant dietary-microbe and medication-microbe correlations associations limited to significant microbial species identified to be associated with either TAs (A) or SSAs (B) in GIDER, are plotted in this network correlation plot. Network shows all significant correlations (FDR < 0.05) between each pair of measurement types. Nodes coloured by class of environmental factor and sized by number of associations, lines by sign and strength of association (red for positive correlation, blue for negative correlation). (B) Mediation plots demonstrating statistically significant environmental exposure and microbe effects on tubular adenomas.