The study investigates the assembly of neonatal gut microbiota, focusing on the role of primary colonizers and their impact on pathogen resistance. Using longitudinal fecal metagenomics, researchers analyzed the microbiota of 1,288 UK neonates, identifying three distinct community states dominated by *Enterococcus faecalis*, *Bifidobacterium longum*, and *Bifidobacterium breve*. The community state dominated by *E. faecalis* showed high pathogen loads, while those dominated by *B. longum* and *B. breve* exhibited stable assembly trajectories and long-term resistance to pathogen colonization. *B. breve* demonstrated priority effects in a germ-free mouse model, conferring pathogen colonization resistance. Factors such as maternal age, ethnicity, and parity influenced the acquisition of these community states. The study highlights the crucial role of *Bifidobacterium* species in shaping early-life microbiota assembly and functions, emphasizing the importance of maternal transmission and the neonatal diet in determining the stability and composition of the gut microbiota.The study investigates the assembly of neonatal gut microbiota, focusing on the role of primary colonizers and their impact on pathogen resistance. Using longitudinal fecal metagenomics, researchers analyzed the microbiota of 1,288 UK neonates, identifying three distinct community states dominated by *Enterococcus faecalis*, *Bifidobacterium longum*, and *Bifidobacterium breve*. The community state dominated by *E. faecalis* showed high pathogen loads, while those dominated by *B. longum* and *B. breve* exhibited stable assembly trajectories and long-term resistance to pathogen colonization. *B. breve* demonstrated priority effects in a germ-free mouse model, conferring pathogen colonization resistance. Factors such as maternal age, ethnicity, and parity influenced the acquisition of these community states. The study highlights the crucial role of *Bifidobacterium* species in shaping early-life microbiota assembly and functions, emphasizing the importance of maternal transmission and the neonatal diet in determining the stability and composition of the gut microbiota.