Few studies on humans have comprehensively evaluated the intake composition of methyl-donor nutrients (MDNs: choline, betaine, and folate) in relation to visceral obesity (VOB)-related hepatic steatosis (HS), the hallmark of non-alcoholic fatty liver diseases. In this case–control study, we recruited 105 patients with HS and 104 without HS (controls). HS was diagnosed through ultrasound examination. VOB was measured using a whole-body analyzer. MDN intake was assessed using a validated quantitative food frequency questionnaire. After adjustment for multiple HS risk factors, total choline intake was the most significant dietary determinant of HS in patients with VOB (Beta: −0.41, p = 0.01). Low intake of choline (<6.9 mg/kg body weight), betaine (<3.1 mg/kg body weight), and folate (<8.8 μg/kg body weight) predicted increased odds ratios (ORs) of VOB-related HS (choline: OR: 22, 95% confidence interval [CI]: 6.5–80; betaine: OR: 14, 95% CI: 4.4–50; and folate: OR: 19, 95% CI: 5.2–74). Combined high intake of choline and betaine, but not folate, was associated with an 81% reduction in VOB-related HS (OR: 0.19, 95% CI: 0.05–0.69). Our data suggest that the optimal intake of choline and betaine can minimize the risk of VOB-related HS in a threshold-dependent manner.

Inadequate choline intake-induced choline metabolic stress (CMS) has been divergently linked to metabolic dysfunction-associated steatotic liver disease (MASLD), yet underlying mechanisms remain unclear. We hypothesized that CMS modifies plasma-free amino acid (PFAA) signatures to influence MASLD risk. In a nested case–control study of 125 participants, dietary choline intake and blood choline metabolites were assessed together with targeted metabolomics and transcriptomic profiling. MASLD was characterized by low choline intake, reduced plasma betaine/choline ratio (Pbcr), elevated homocysteine, increased branched-chain amino acids (BCAAs), and depleted serine/glycine, achieving strong predictive accuracy (AUC = 0.90). CMS was associated with reduced lymphocytic transcripts involved in BCAA catabolism and altered mTORC1/Akt/IRS1 signaling. Nonlinear Pbcr- and intake-dependent MASLD risk patterns were attenuated after adjustment for genetic–metabolite networks. These findings identify CMS-responsive metabolic mediators supporting precision choline interventions.