The intestinal microbiota is established at birth and develops into a stable community. Early-life exposure to low-dose antibiotics, such as penicillin, can alter host metabolism and adiposity. This study shows that low-dose penicillin (LDP) administered from birth induces metabolic changes and affects ileal gene expression related to immunity. LDP transiently disrupts the microbiota, which is sufficient to cause long-term effects on body composition, indicating that early-life microbiota interactions are critical for long-term metabolic outcomes. LDP enhances the effects of a high-fat diet on obesity. The growth-promoting phenotype is transferable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics, are responsible for the effects. These findings highlight important variables in early-life microbe-host metabolic interactions and identify several taxa consistently linked with metabolic changes. The study also shows that LDP exposure increases the risk of obesity and metabolic syndrome. LDP alters microbial community composition, measured by β-diversity, and affects gene expression related to adipogenesis and lipid metabolism. The altered microbiota alone, not continued LDP exposure, is causal. Transferring microbiota from LDP-exposed mice to germ-free hosts results in metabolic changes, indicating that the altered microbiota drives metabolic effects. The study demonstrates that early-life microbiota disruption can lead to long-term metabolic consequences. LDP exposure affects the ileum, reducing gene expression related to immune responses and increasing adiposity. The altered microbiota is sufficient to induce metabolic changes, and the effects persist even after antibiotic cessation. These findings suggest that early-life microbiota plays a critical role in metabolic development and that microbiota changes can influence long-term metabolic outcomes. The study also highlights the importance of the microbiota in immune function and metabolic health, and the potential for microbiota-based interventions to mitigate metabolic disorders.The intestinal microbiota is established at birth and develops into a stable community. Early-life exposure to low-dose antibiotics, such as penicillin, can alter host metabolism and adiposity. This study shows that low-dose penicillin (LDP) administered from birth induces metabolic changes and affects ileal gene expression related to immunity. LDP transiently disrupts the microbiota, which is sufficient to cause long-term effects on body composition, indicating that early-life microbiota interactions are critical for long-term metabolic outcomes. LDP enhances the effects of a high-fat diet on obesity. The growth-promoting phenotype is transferable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics, are responsible for the effects. These findings highlight important variables in early-life microbe-host metabolic interactions and identify several taxa consistently linked with metabolic changes. The study also shows that LDP exposure increases the risk of obesity and metabolic syndrome. LDP alters microbial community composition, measured by β-diversity, and affects gene expression related to adipogenesis and lipid metabolism. The altered microbiota alone, not continued LDP exposure, is causal. Transferring microbiota from LDP-exposed mice to germ-free hosts results in metabolic changes, indicating that the altered microbiota drives metabolic effects. The study demonstrates that early-life microbiota disruption can lead to long-term metabolic consequences. LDP exposure affects the ileum, reducing gene expression related to immune responses and increasing adiposity. The altered microbiota is sufficient to induce metabolic changes, and the effects persist even after antibiotic cessation. These findings suggest that early-life microbiota plays a critical role in metabolic development and that microbiota changes can influence long-term metabolic outcomes. The study also highlights the importance of the microbiota in immune function and metabolic health, and the potential for microbiota-based interventions to mitigate metabolic disorders.