A study of 1,288 UK neonates reveals three distinct community states in the neonatal gut microbiota (NGM), each dominated by a single microbial species: Bifidobacterium breve (BB), Bifidobacterium longum (BL), and Enterococcus faecalis (EF). BB, dominated by B. breve, showed stable assembly and long-term pathogen resistance, likely due to strain-specific adaptations to breast milk. EF, dominated by E. faecalis, was unstable and associated with high pathogen loads. BL, dominated by B. longum, had moderate stability. BB was uniquely influenced by host factors, independent of clinical factors. The study found that maternal transmission of B. longum was common, while B. breve and E. faecalis likely originated from environmental or maternal sources. BB's dominance was linked to maternal ethnicity and breastfeeding. EF was associated with cesarean birth and maternal antibiotics. BB showed strong priority effects, outcompeting pathogens like E. faecalis. In a mouse model, BB conferred pathogen resistance. BB's ability to metabolize human milk oligosaccharides (HMOs) enhanced its fitness against pathogens. EF, enriched with antibiotic resistance and virulence genes, was linked to hospital environments. The study highlights the role of Bifidobacteria in shaping early microbiota and pathogen resistance, with BB being a key driver. The findings suggest that early microbiota assembly is influenced by maternal and environmental factors, with BB providing long-term protection against pathogens. The study underscores the importance of Bifidobacteria in neonatal health and the need for targeted interventions to promote beneficial microbial colonization.A study of 1,288 UK neonates reveals three distinct community states in the neonatal gut microbiota (NGM), each dominated by a single microbial species: Bifidobacterium breve (BB), Bifidobacterium longum (BL), and Enterococcus faecalis (EF). BB, dominated by B. breve, showed stable assembly and long-term pathogen resistance, likely due to strain-specific adaptations to breast milk. EF, dominated by E. faecalis, was unstable and associated with high pathogen loads. BL, dominated by B. longum, had moderate stability. BB was uniquely influenced by host factors, independent of clinical factors. The study found that maternal transmission of B. longum was common, while B. breve and E. faecalis likely originated from environmental or maternal sources. BB's dominance was linked to maternal ethnicity and breastfeeding. EF was associated with cesarean birth and maternal antibiotics. BB showed strong priority effects, outcompeting pathogens like E. faecalis. In a mouse model, BB conferred pathogen resistance. BB's ability to metabolize human milk oligosaccharides (HMOs) enhanced its fitness against pathogens. EF, enriched with antibiotic resistance and virulence genes, was linked to hospital environments. The study highlights the role of Bifidobacteria in shaping early microbiota and pathogen resistance, with BB being a key driver. The findings suggest that early microbiota assembly is influenced by maternal and environmental factors, with BB providing long-term protection against pathogens. The study underscores the importance of Bifidobacteria in neonatal health and the need for targeted interventions to promote beneficial microbial colonization.