The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota

Abstract

Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism.

Conclusion: NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies.

Figure 1. Taxonomic composition of the gut microbiota as a function of NAFLD severity

No significant difference was observed at the phylum level (Figure 1a). Significant differences appeared from the family level (Figure 1b).

Figure 1. Taxonomic composition of the gut microbiota as a function of NAFLD severity

No significant difference was observed at the phylum level (Figure 1a). Significant differences appeared from the family level (Figure 1b).

Figure 2. Relationship between NASH at liver biopsy and Bacteroides or Prevotella abundance in the gut

Figures 2a/2b: NASH patients had higher abundance of gut Bacteroides (p=0.013) and lower abundance of Prevotella (p=0.053). Figure 2c: As these bacteria act as competitors, Bacteroides and Prevotella abundance had an inverse relationship. Figure 2d: Rate of NASH patients as a function of the tertiles of Bacteroides relative count. The rate of NASH was significantly lower in patients with low abundance of Bacteroides (1^st tertile). * p≤0.02 vs 1^st tertile.

Figure 3. Relationship between significant F≥2 fibrosis at liver biopsy and Bacteroides, Prevotella, or Ruminococcus abundance in the gut

Figures 3a-c: Patients with fibrosis F≥2 had higher abundance of gut Bacteroides (p=0.018) and Ruminococcus (p=0.037), and lower abundance of Prevotella (p=0.017). Figure 3d: Rate of F≥2 patients as a function of the tertiles of Ruminococcus relative count. The rate of F≥2 fibrosis was significantly higher in patients with a high abundance of Ruminococcus (3^rd tertile). * p≤0.01 vs 3^rd tertile.

Figure 4. Severity of NAFLD lesions according to Bacteroides and Ruminococcus abundance

Figure 4a: Rate of patients with NASH or fibrosis F≥2 according to Bacteroides and Ruminoccocus abundance (* p<0.04 vs 1^st subgroup, § p=0,013 vs 3^rd subgroup, & p=0,043 vs 3^rd subgroup). Figure 4b: Severity of NAFLD lesions according to the metabolic syndrome status alone or stratified according to the abundance of Bacteroides and Ruminococcus.