This study investigates the impact of early-life antibiotic exposure, cesarean section, and infant diet on the development of the gut microbiome in the first two years of life. The researchers followed 43 US infants and found that antibiotic use delayed microbiome development, suppressed *Clostridiales* and *Ruminococcus*, and altered the trajectory of α-diversity changes. Cesarean section led to depleted *Bacteroidetes* populations, altering the establishment of maternal bacteria. Formula feeding was associated with age-dependent diversity deviations. These findings highlight the complexity of early-life microbiome development and suggest that disturbances in early life, such as those caused by antibiotics, cesarean section, and formula feeding, may contribute to health issues like obesity, asthma, and allergies later in life.This study investigates the impact of early-life antibiotic exposure, cesarean section, and infant diet on the development of the gut microbiome in the first two years of life. The researchers followed 43 US infants and found that antibiotic use delayed microbiome development, suppressed *Clostridiales* and *Ruminococcus*, and altered the trajectory of α-diversity changes. Cesarean section led to depleted *Bacteroidetes* populations, altering the establishment of maternal bacteria. Formula feeding was associated with age-dependent diversity deviations. These findings highlight the complexity of early-life microbiome development and suggest that disturbances in early life, such as those caused by antibiotics, cesarean section, and formula feeding, may contribute to health issues like obesity, asthma, and allergies later in life.