Ferretti et al. investigate the early acquisition and development of the infant gut and oral microbiomes, focusing on the role of different maternal sources in this process. They use strain-resolved metagenomics to track mother-to-infant microbiome transfer over the first 4 months of life. Key findings include: 1. **High Initial Diversity and Strain Heterogeneity**: The infant gut microbiome exhibits high microbial diversity and strain heterogeneity even at birth, which decreases rapidly in the first week before recovering and gradually increasing over the next 4 months. 2. **Maternal Microbiome Sources**: Multiple maternal body sites contribute to the infant microbiome, with the maternal gut providing the largest contribution of colonizing microorganisms. 3. **Niche Selection**: The early microbial diversity in the infant gut is rapidly shaped by niche selection, with some species and strains appearing later. 4. **Strain Transmission**: The study identifies microbial strains present in infants with strong evidence of transmission from their mothers, and these strains are more likely to adapt to and persist in the infant gut compared to non-maternally acquired strains. 5. **Methodological Approach**: The authors use a novel combination of reference-based and assembly-based computational profiling to comprehensively describe mother-to-infant strain transmission and strain-level dynamics in the infant microbiome. These findings highlight the importance of vertical mother-to-infant microbial transmission from multiple sources and the role of niche selection in shaping the developing infant microbiome.Ferretti et al. investigate the early acquisition and development of the infant gut and oral microbiomes, focusing on the role of different maternal sources in this process. They use strain-resolved metagenomics to track mother-to-infant microbiome transfer over the first 4 months of life. Key findings include: 1. **High Initial Diversity and Strain Heterogeneity**: The infant gut microbiome exhibits high microbial diversity and strain heterogeneity even at birth, which decreases rapidly in the first week before recovering and gradually increasing over the next 4 months. 2. **Maternal Microbiome Sources**: Multiple maternal body sites contribute to the infant microbiome, with the maternal gut providing the largest contribution of colonizing microorganisms. 3. **Niche Selection**: The early microbial diversity in the infant gut is rapidly shaped by niche selection, with some species and strains appearing later. 4. **Strain Transmission**: The study identifies microbial strains present in infants with strong evidence of transmission from their mothers, and these strains are more likely to adapt to and persist in the infant gut compared to non-maternally acquired strains. 5. **Methodological Approach**: The authors use a novel combination of reference-based and assembly-based computational profiling to comprehensively describe mother-to-infant strain transmission and strain-level dynamics in the infant microbiome. These findings highlight the importance of vertical mother-to-infant microbial transmission from multiple sources and the role of niche selection in shaping the developing infant microbiome.