The community of microorganisms colonizing the gut changes during the first postnatal years of life. This ecosystem, henceforth described as the microbiome, modulates infant physiology and health, but uncertainty remains about the significance of variation in microbiome composition and function. Some may be tolerable, yet some microbiomes may be less healthy than others. Most efforts to identify parameters of microbiome health focus on adults, and derived concepts may not directly translate to early life that is characterized by dynamic and sequential changes. Data suggest that an orderly progression from an immature neonatal microbiome to a mature adult state is preferable to delayed or over-rapid development. This can be parameterized as a "microbiome development trajectory". Diet modifies early life microbiome development and is the principal modifiable factor to this end. Infants fed with infant formulas show different microbiome development trajectories from breastfed infants. Early data suggest that formulas containing a specific blend of human milk oligosaccharides partially mitigate this difference. Introduction of a complementary diet complexifies the identification of diet-microbiome development interactions. A better understanding will only be achievable through detailed, longitudinal characterization of large cohorts.