Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial condition influenced by the gut microbiome (GM). While previous studies have reported inconsistent associations between MASLD and key microbial clades using low-resolution 16S rRNA profiling, we employed high-resolution metagenomic sequencing and multi-marker taxonomic classification across three independent cohorts to identify robust microbial and functional signatures of MASLD. We consistently detected a depletion of Agathobacter rectalis, a known butyrate producer, in MASLD patients. Functionally, MASLD was characterized by a depletion of genes involved in butyrate and methane biosynthesis -particularly within the crotonyl-butyryl-CoA axis- alongside an enrichment of genes driving the production of endogenous alcohols such as ethanol and 1-propanol. Genes encoding these fermentative pathways, often organized in operons like pdu and tor, were more abundant in MASLD samples, indicating a potential shift toward alcohol-producing metabolism. These geno-metabolic changes were accompanied by a broader displacement of beneficial taxa and an increase in accessory gene content across the GM, underscoring the limitations of taxonomy-based disease associations. Many of the differentially abundant genes were also found on plasmids, suggesting that horizontal gene transfer contributes to strain-level metabolic variability relevant to MASLD progression. Our findings support a model in which GM-driven metabolic shifts -rather than taxonomic changes alone- play a central role in MASLD pathogenesis, highlighting the importance of functional and mobile genetic element profiling for uncovering mechanistic links between the microbiome and liver disease.
Competing Interest Statement
The authors have declared no competing interest.