Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studies

Abstract

Objective: Tryptophan can be catabolised to various metabolites through host kynurenine and microbial indole pathways. We aimed to examine relationships of host and microbial tryptophan metabolites with incident type 2 diabetes (T2D), host genetics, diet and gut microbiota.

Method: We analysed associations between circulating levels of 11 tryptophan metabolites and incident T2D in 9180 participants of diverse racial/ethnic backgrounds from five cohorts. We examined host genome-wide variants, dietary intake and gut microbiome associated with these metabolites.

Results: Tryptophan, four kynurenine-pathway metabolites (kynurenine, kynurenate, xanthurenate and quinolinate) and indolelactate were positively associated with T2D risk, while indolepropionate was inversely associated with T2D risk. We identified multiple host genetic variants, dietary factors, gut bacteria and their potential interplay associated with these T2D-relaetd metabolites. Intakes of fibre-rich foods, but not protein/tryptophan-rich foods, were the dietary factors most strongly associated with tryptophan metabolites. The fibre-indolepropionate association was partially explained by indolepropionate-associated gut bacteria, mostly fibre-using Firmicutes. We identified a novel association between a host functional LCT variant (determining lactase persistence) and serum indolepropionate, which might be related to a host gene-diet interaction on gut Bifidobacterium, a probiotic bacterium significantly associated with indolepropionate independent of other fibre-related bacteria. Higher milk intake was associated with higher levels of gut Bifidobacterium and serum indolepropionate only among genetically lactase non-persistent individuals.

Conclusion: Higher milk intake among lactase non-persistent individuals, and higher fibre intake were associated with a favourable profile of circulating tryptophan metabolites for T2D, potentially through the host-microbial cross-talk shifting tryptophan metabolism toward gut microbial indolepropionate production.

Keywords: diabetes mellitus; dietary factors; genetics.

Figure 1. Overview of the workflow integrating host genetics, diet, gut microbiota and circulating metabolites in relation to type 2 diabetes

Eleven tryptophan (TRP) metabolites included TRP, serotonin, five kynurenine-pathway metabolites (kynurenine, kynurenate, xanthurenate, quinolinate, and picolinate), and four indole derivatives (indoleacetate, indolelactate, indolepropionate [IPA] and indoxyl sulfate). T2D, type 2 diabetes; GWAS, genome-wide association study; HCHS/SOL, Hispanic Community Health Study/Study of Latinos; ARIC, Atherosclerosis Risk in Communities Study; DIAGRAM, Diabetes Genetics Replication and Meta-analysis Consortium; LCT-rs498823, a function variant related to lactase persistence.

Figure 2. Associations between circulating tryptophan metabolite levels and incident type 2 diabetes

Data are Hazard ratios and 95% confidence intervals of incident type 2 diabetes per standard deviation increment in metabolite levels, adjusted for age, sex, smoking, alcohol consumption, education, family income, family history of diabetes, self-reported hypertension and/or antihypertensive medication use, self-reported dyslipidemia and/or lipid-lowering medication us, and other study-specific covariates (Model1); and further adjusted for body mass index and waist-to-hip ratio (Model 2). Results across 5 studies were combined by fixed-effect meta-analysis.

Figure 3. Manhattan plot for GWAS of circulating tryptophan metabolite levels

Meta-analyses of GWAS in up to 9,290 individuals from HCHS/SOL, ARIC, and FHS identified 13 loci for 9 tryptophan metabolites (color indicated in inset). The significant P-value threshold is 4.5×10–9 (indicated by a dash line).

Figure 4. Dietary intake and serum tryptophan metabolite levels

(A) Polar plot for associations of 10 major food groups with serum tryptophan metabolites in the HCHS/SOL. Red: positive associations (FDR<0.05); Blue, inverse associations (FDR<0.05). (B) Differences (95% CI) in serum tryptophan metabolite levels (inverse normal transformed) associated with 1g/1000Kcal per day of dietary fiber intake in the HCHS/SOL.

Figure 5. Dietary fiber intake, gut microbiota and serum indolepropionate

(A) Phylogenetic tree of taxonomic features in association with host serum indolepropionate levels in the HCHS/SOL. A total of 21 gut microbial genera significantly associated with serum indolepropionate (FDR<0.05) are indicated by solid circles. Data showing in the outer ring are effect sizes (positive, red; inverse, blue) of gut microbiota genera on serum indolepropionate. (B) Associations of 21 indolepropionate-assocaited gut microbial genera with dietary fiber intake in the HCHS/SOL. To show comparable estimates for the associations of gut microbial genera with indolepropionate and fiber intake, data are presented as Z-scores (regression coefficients/standard errors). *FDR<0.05 for the associations between dietary fiber intake and gut microbial genera. (C) Associations between dietary fiber intake and serum indolepropionate levels with and without adjustment for gut microbiota (20 indolepropionate-associated gut microbial genera) in the HCHS/SOL. Bifidobacterium, which showed opposite associations with indolepropionate and fiber intake, was not included.

Figure 6. Host LCT genotype, milk intake, gut Bifidobacterium and serum indolepropionate

(A) Adjusted means and 95% confidence intervals (CIs) of milk intake (servings/day) according to LCT-rs49883235 genotypes in the HCHS/SOL. (B) Adjusted means and 95% CIs of gut Bifidobacterium abundance (center log-ratio transformed) according to LCT-rs49883235 genotypes in the HCHS/SOL. (C) Adjusted means and 95% CIs of serum indolepropnate levels (inverse normal transformed) according to LCT-rs49883235 genotypes in the HCHS/SOL. (D) Adjusted means and 95% CIs of gut Bifidobacterium abundance (center log-ratio transformed) according to milk intake stratified by the LCT-rs49883235 genotype in the HCHS/SOL. (E) Adjusted means and 95% CIs of serum indolepropnate levels (inverse normal transformed) according to milk intake stratified by the LCT-rs49883235 genotype in the HCHS/SOL. (F) Differences and 95% CIs in serum indolepropnate levels (inverse normal transformed) associated with one serving per day of milk intake according to the LCT-rs49883235 genotype in the HCHS/SOL and ARIC separately, and combined by meta-analysis.