In recent years, new formula milk (FM) products based on milk from farms that strictly adhere to the “organic farming” practices became available. However, little is known about the differences in nutritional profile of these organic formulae with respect to traditional ones. We comprehensively evaluated the metabolite profiles of FM with nuclear magnetic resonance (NMR)-based metabolomic analysis. Five commercial brands of organic and nonorganic formula liquid milk for infants (0–12 months) and toddlers (1–3 years) were analyzed, together with human milk (HM) samples. Proton NMR (1H NMR) spectroscopy mapped molecular characteristics of FM linked to different production techniques, and identified differences between FM and HM samples. We performed a metabolic fingerprint analysis using multivariate and univariate statistical techniques. A clear distinction is found among different commercial brands of the FM samples. In addition, several differences in metabolomic profiles of FM have been found in comparison with HM for the first time. Notably, it was possible to identify, both in the formulations for toddlers and for infants, metabolites that vary in concentration between the formulae produced with milk obtained according to organic farming techniques, and those produced using nonorganic milk. In particular, organic and nonorganic formulations are differentiated by the levels of glucose, methionine, o-phosphocholine, butyrate, hippurate, creatine, and dimethyl sulfone. Importantly, the HM appeared to differ from both organic and nonorganic brands in a context of metabolites. These findings inform efforts to design FM in ways that closely mimic HM, and guide research to differentiate organic and traditional FM.
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