Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study

Abstract

Nonalcoholic fatty liver disease (NAFLD) is a risk factor for liver cancer and prevalence varies by ethnicity. Along with genetic and lifestyle factors, the gut microbiome (GM) may contribute to NAFLD and its progression to advanced liver disease. Our cross-sectional analysis assessed the association of the GM with hepatic adiposity among African American, Japanese American, White, Latino, and Native Hawaiian participants in the Multiethnic Cohort. We used MRI to measure liver fat and determine nonalcoholic fatty liver disease (NAFLD) status (n = 511 cases) in 1,544 participants, aged 60-77 years, with 12-53% overall adiposity (BMI of 17.8-46.2 kg/m²). The GM was measured by 16S rRNA gene sequencing and, on a subset, by metagenomic sequencing. Alpha diversity was lower overall with NAFLD and in certain ethnicities (African Americans, Whites, and Latinos). In models regressing genus on NAFLD status, 62 of 149 genera (40%) exhibited a significant interaction between NAFLD and ethnicity stratified analysis found 69 genera significantly associated with NAFLD in at least one ethnic group. No single genus was significantly associated with NAFLD across all ethnicities. In contrast, the same bacterial metabolic pathways were over-represented in participants with NAFLD regardless of ethnicity. Imputed secondary bile acid and carbohydrate pathways were associated with NAFLD, the latter of which was corroborated by metagenomics, although different genera in different ethnicities were associated with these pathways. Overall, we found that NAFLD was associated with altered bacterial composition and metabolism, and that bacterial endotoxin, assessed by plasma lipopolysaccharide binding protein (LBP), may mediate liver fat-associated systemic inflammation in a manner that seems to vary by ethnicity.

Keywords: chronic liver disease; diabetes; ethnic groups; genetics; hepatocellular carcinoma; inflammation; metabolic syndrome; nonalcoholic fatty liver disease (NAFLD).

Figure 1.

Overview of the microbiome in NAFLD in the MEC-APS study. 1A.) Distribution of individuals with and without NAFLD. 1B.) Variation in the microbiome between individuals with and without NAFLD illustrated by a PCOA of weighted Unifrac metric. 1 C.) Vector overlay of the demographic, anthropometric, health, diet, and lifestyle variables. 1D.) Alpha diversity in subjects with and without NAFLD by ethnicity and 1E.) Variation in the microbiome explained by the demographic anthropometric, health, diet, and lifestyle variables using perMANOVA analysis

Figure 2.

Heatmap of regression coefficients for association with NAFLD resulting from beta-binomial regression models of genera counts stratified by self-report ethnicity. Genera significantly enriched or depleted in individuals with NAFLD are shown. Coefficients are adjusted for sex, and total fat mass. Red = positive, blue = negative

Figure 3.

Heatmap of the association between imputed microbial functional pathways with percent liver fat by sex and ethnicity in the MEC-APS (n = 1529). The colors represent the magnitude of the pathway standardized coefficient in the linear model of the natural log of percent liver fat on each pathway, adjusted for sex, ethnicity, total fat mass, and sequencing batch. The gene counts were inferred from piCRUST and pathways summarized by summing all counts in the pathway and then normalized for the total number of sequences per sample, which were then standardized for the model. Asterisks indicate a BH corrected p value less than 0.1. (Also see Supplemental Table 5.)