Untargeted LC–MS Plasma Metabolomics Reveals Altered Amino Acid and Carbohydrate Metabolism in Dairy Calves Supplemented with Direct-Fed Microbials

Background/Objectives: Direct-fed microbials (DFMs) are widely used in dairy calves to improve gut health and mitigate neonatal disorders, yet their systemic metabolic effects remain poorly defined. This study evaluated the impact of DFM supplementation on the plasma metabolome of pre-weaned dairy calves using untargeted liquid chromatography–mass spectrometry (LC–MS). Methods: Eighty-six Holstein bull calves (2 to 5 days old) were assigned to one of four treatments in a 2 × 2 factorial randomized complete block design: Lactobacillus plantarum in starter (CLP), a culture mix of Bifidobacterium animalis and Lactobacillus animalis in milk replacer (BBCM), and a combination of both (CMLP), or no supplementation (CON). Blood samples collected on days 0 and 56 were subjected to metabolomic profiling, and metabolites were annotated using Human Metabolome Database and Kyoto Encyclopedia of Genes and Genomes databases. Results: A total of 231 plasma metabolites were detected. Compared with CON, 24 metabolites were differentially abundant in DFM-treated calves (fold change ≥ 1.2 or ≤ 0.83; p ≤ 0.05). Supplemented calves exhibited increased abundances of ketone functional groups, aldehydes and amino acid-related metabolites. Metabolite set enrichment analysis identified 11 significantly enriched pathways. Branched-chain amino acid degradation pathways (valine, leucine, and isoleucine) were enriched in CLP and CMLP calves, whereas carbohydrate metabolism pathways, including pentose and glucuronate interconversions, were enriched in the CLP and BBCM groups. Conclusions: These findings demonstrate that DFM supplementation modulates systemic metabolism in dairy calves, particularly pathways involved in amino acid and carbohydrate utilization, suggesting enhanced metabolic efficiency during early life.