Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease

Abstract

Background & Aims:

The intestinal microbiome might affect development and severity of nonalcoholic fatty liver disease (NAFLD). We analyzed microbiomes of children with and without NAFLD.

Methods:

We performed a prospective, observational, cross-sectional study of 87 children (8–17 years old) with biopsy-proven NAFLD and 37 children with obesity without NAFLD (controls). Fecal samples were collected and microbiome composition and functions were assessed using 16S rRNA amplicon sequencing and metagenomic shotgun sequencing. Microbial taxa were identified using zero-inflated negative binomial modeling. Genes contributing to bacterial pathways were identified using gene set enrichment analysis.

Results:

Fecal microbiomes of children with NAFLD had lower α-diversity than controls (3.32 vs 3.52; P=.016). Fecal microbiomes from children with nonalcoholic steatohepatitis (NASH) had lowest α-diversity (controls, 3.52; NAFLD, 3.36; borderline NASH, 3.37; NASH 2.97; P=.001). High abundance of Prevotella copri was associated with more severe fibrosis (P=.036). Genes for lipopolysaccharide biosynthesis were enriched in microbiomes from children NASH ( P<.001). Classification and regression tree model with level of alanine aminotransferase and relative abundance of the lipopolysaccharide pathway gene encoding 3-deoxy-D-manno-octulosonate 8-phosphate-phosphatase identified patients with NASH with an area under the receiver operating characteristic curve value of 0.92. Genes involved in flagellar assembly were enriched in fecal microbiomes of patients with moderate to severe fibrosis ( P<.001). Classification and regression tree models based on level of alanine aminotransferase and abundance of genes encoding flagellar biosynthesis protein had good accuracy for identifying cases with moderate to severe fibrosis (area under the receiver operating characteristic curve, 0.87).

Conclusions:

In an analysis of fecal microbiomes of children with NAFLD, we associated NAFLD and NASH with intestinal dysbiosis. NAFLD and its severity were associated with greater abundance of genes encoding inflammatory bacterial products. Alterations to the intestinal microbiome might contribute to pathogenesis of NAFLD and be used as markers of disease or severity.

Lay summary:

The intestinal microbiota of children with nonalcoholic liver disease is altered compared to that of children without this chronic liver disease, with increased levels of bacterial proteins that promote inflammation. These microbial features were associated with liver disease severity.