National screening programs use dried blood specimens to detect abnormal metabolism or aberrant protein function in infants shortly after birth, thus identifying disorders that are not clinically evident in the newborn period. Gut microbiota metabolites and immunological acute phase proteins are capable of revealing potential immune aberrations. Microbial metabolites interact with xenobiotic receptors (i.e., aryl hydrocarbon and pregnane-X) and maintain gastrointestinal tissue health, supported by acute-phase proteins, functioning as sensors of microbial immunomodulation and homeostasis. The delivery mode (vaginal or cesarean section) shapes the microbial colonization, which substantially modulates both the immune system's response and mucosal homeostasis. This study profiled microbial metabolites of the kynurenine and tryptophan pathway and acute phase proteins in 134 neonatal dried blood specimens. We newly established neonatal blood levels of the aryl hydrocarbon receptor microbial ligands (indole-3-aldehyde, indole-3-butyric acid, and indole-3-acetamide) on the second day of life. Furthermore, we observed divergent microbial metabolic profiles in neonates born vaginally or via cesarean section, hypothesizing potential microbial immunomodulatory influence. In summary, these findings suggest the supportive role of human gut microbiota in developing and maintaining immune system homeostasis.