Fecal Metagenomics and Metabolomics Identifying Microbial Signatures in Non-Alcoholic Fatty Liver Disease

Abstract

The frequency of non-alcoholic fatty liver disease (NAFLD) has intensified, creating diagnostic challenges and increasing the need for reliable non-invasive diagnostic tools. Due to the importance of the gut-liver axis in the progression of NAFLD, studies attempt to reveal microbial signatures in NAFLD, evaluate them as diagnostic biomarkers, and to predict disease progression. The gut microbiome affects human physiology by processing the ingested food into bioactive metabolites. These molecules can penetrate the portal vein and the liver to promote or prevent hepatic fat accumulation. Here, the findings of human fecal metagenomic and metabolomic studies relating to NAFLD are reviewed. The studies present mostly distinct, and even contradictory, findings regarding microbial metabolites and functional genes in NAFLD. The most abundantly reproducing microbial biomarkers include increased lipopolysaccharides and peptidoglycan biosynthesis, enhanced degradation of lysine, increased levels of branched chain amino acids, as well as altered lipid and carbohydrate metabolism. Among other causes, the discrepancies between the studies may be related to the obesity status of the patients and the severity of NAFLD. In none of the studies, except for one, was diet considered, although it is an important factor driving gut microbiota metabolism. Future studies should consider diet in these analyses.

Keywords: NAFLD; diet; gut microbiota; liver fat; metabolic pathways; metabolomics; metagenomics.

Figure 4

Main findings from studies reporting fecal metagenomics and/or metabolomics in children with NAFLD. FA—fatty acids; CH—carbohydrates; BA—bile acids; AA—amino acids, BCAA—branched chain amino acids; AAA—aromatic amino acids; LPS-lipopolysaccharides. The figure was created using BioRender.

Figure 1

The abundance of many members of the gut microbiota affects the human physiology by processing the ingested food into certain bioactive metabolites. These molecules can act as inter-tissue signaling messengers by penetrating the portal vein and subsequently, the liver, to promote or prevent hepatic fat accumulation. For instance, dietary fiber is metabolized by the gut microbiota into short-chain fatty acids (SCFA, mainly butyrate, acetate, and propionate), and ethanol is produced from dietary carbohydrates. Gut microbiota produce trimethyl amine (TMA) from dietary choline, which is mainly derived from meat, yolk, and dairy products. TMA is further converted into trimethyl amineoxide (TMAO) in the liver. Primary bile acids (BA) are synthesized in the liver, stored in the gallbladder, and then released into the gut, where they are converted into secondary BA by the gut microbiota. In the liver, ethanol can increase fat accumulation by reducing beta-oxidation. TMAO has been shown to induce insulin resistance (IR) and further fat accumulation in the liver. Controversial findings on the role of BA and SCFA in hepatic fat accumulation exist. These will be reviewed in this article. The figure was created using BioRender.

Figure 2

Main findings from two fecal metagenomic studies and one metabolomics study in individuals with hepatic steatosis and without diagnosed NAFLD. CH—carbohydrates; AA—amino acids; BCAA—branched chain amino acids; AAA—aromatic amino acids; LPS—lipopolysaccharides. The figure was created using BioRender.

Figure 3

Main findings from studies reporting fecal metagenomics and/or metabolomics in NAFLD and advanced fibrosis. NAFL—non-alcoholic fatty liver; NASH—non-alcoholic steatohepatosis; CH—carbohydrates; BA—bile acids. The figure was created using BioRender.