Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods

Abstract

Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.

Distinct Gut Microbial Signature and Host Genetic Variants in Association with Liver Fibrosis Severity in Patients with MASLD

“…For instance, the bacterium is enriched in the colonic tissue of patients with colorectal cancer (CRC) and has been strongly implicated in the multi-step processes of CRC development [ 26 ]. Fusobacterium was also reported to be predominant in patients with steatohepatitis when compared to individuals with simple steatosis, suggesting its contributing role in the progression of MASLD [ 27 , 28 ]. Regarding Escherichia_Shigella , this genus is an ethanol-producing bacterium that can lead to de novo lipogenesis and decrease fatty acid oxidation, both of which could induce the occurrence of liver steatosis [ 29 ].…”

Lactobacillus rhamnosus GG triggers intestinal epithelium injury in zebrafish revealing host dependent beneficial effects

“…Data analysis was performed using BMKCloud ( www.biocloud.net ). Primers that are set for universal bacteria or specific bacterial groups have been described in the scientific literature [ 89 , 90 , 91 ] and listed in Table S6 . Results were expressed as Log 10 copy numbers of bacterial 16S ribosomal deoxyribonucleic acid per milligram of intestinal contents.…”