Metabolic dysfunction-associated steatotic liver disease (MASLD) is a complex metabolic disease associated with multiple systemic comorbidities and poses a major public health challenge. Although growing evidence suggests alterations in the gut microbiome and its derived metabolites contribute to MASLD development, the mechanisms underlying microbe-metabolite-host interactions remain incompletely understood. Here, we present an integrative multi-omics workflow for linking gut microbial composition and functional potential with microbial metabolites and disease-related host phenotypes.
We applied this workflow to the FLORINASH cohort, comprising 662 non-diabetic individuals with MASLD from Spain and Italy, spanning a range of obesity levels and liver disease severity. For each participant, matched shotgun metagenomic sequencing, untargeted UHPLC-MS metabolomics, and clinical phenotyping data were available. Metagenomic data were used to generate species-level taxonomic profiles and KEGG Orthology-based functional annotations, while gutSMASH was applied to predict microbial metabolic gene clusters across the identified gut species. These results were then integrated with metabolomic and clinical data to characterise microbe-metabolite-host associations.
Using this workflow, we identified a candidate phenol-associated host-microbiome interaction in MASLD. Phascolarctobacterium was implicated in hydroxybenzoate-to-phenol metabolism, with its abundance positively associated with marker metabolites of phenol metabolism. Mediation analysis further suggested that both Phascolarctobacterium abundance and related KEGG Orthology gene counts were linked to kidney function-related clinical features via phenol-associated metabolites in MASLD.
Together, these findings highlight the utility of our multi-omics workflow for uncovering microbe-metabolite-host interactions and suggest its potential for biomarker discovery and microbiome-targeted therapeutic strategies.

Co-authors: Ulrike Löber, Marc-Emmanuel Dumas, Rémy Burcelin, Jose Manuel Fernández-Real, Massimo Federici, Lesley Hoyles, Miriam Moffatt, Julian Marchesi, Sofia Forslund, Manyi Jia, Zhaojie Wang, Jordi Mayneris-Perxachs, José María Moreno-Navarrete, Rossella Menghini, Marina Cardellini, Fiona Newberry, Kanta Chechi