SummaryBackgroundThe reconstruction of metagenome‐assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations.AimTo use this new approach to highlight mechanisms linking gut microbiota to NAFLD severityMethodsStool samples were collected from 96 NAFLD patients on the day of liver biopsy. Shotgun DNA sequencing of the gut microbiota was performed on an Illumina HiSeq3000 system. Contigs were binned into MAGs according to their co‐abundances and tetranucleotide frequencies using Metabat v.0.32.4. Predicted protein‐coding genes were clustered in orthologous groups (OGs) with DIAMOND against the EggNOG v4.5 database. Liver biopsies were read in accordance with the NASH CRN classification.ResultsFifty‐four patients had NASH and 44 had significant fibrosis (F ≥ 2). Sequencing of DNA extracted from stools resulted in 13.8 + 3.2 million paired‐end reads per sample. Of the 4,000 reconstructed MAGs, 220 in NASH patients, 192 in non‐NASH patients, 203 in F ≥ 2 patients and 230 in F0‐1 patients had > 70% completeness and < 5% contamination. Within these MAGs, 28 OGs were associated with NASH, 33 with significant fibrosis, and seven with both NASH and significant fibrosis. The study of MAGs showed associations between NAFLD severity and some gut bacteria with microbiota functions related to hydrogen sulfide production, citrate transport, hemicellulose degradation, aldehyde production and vitamin B12 synthesis.ConclusionUsing new metagenomics methods, our study unveils potential mechanisms by which certain bacteria from the gut microbiota could protect or contribute to the development of NASH and liver fibrosis in NAFLD.