Gut microbial colonization during early life influences human physiology, including the maturation of the immune system, nutrient absorption and metabolism, and the prevention of pathogen colonization. Although extensive microbial colonization of neonates begins postpartum, the source and transmission routes by which an infant acquires maternal microbes is poorly understood.

Two recent studies published in Cell Host Microbe have provided a longitudinal characterization of the microbiome’s transmission from mother to infant over the first few months of life, highlighting the relevance of vertical microbiome transmission in the acquisition and maturation of the infant microbiome. By using high-resolution strain-level metagenomic sequencing the researchers tracked mother-to-infant microbial strain transfer.

Both studies (here; here) have found a high inter-subject diversity and strain heterogeneity in infant gut microbiomes, which was more apparent the first day after birth and recover afterwards.

Although microbial strains from multiple maternal body sites were transferred to the infant microbiome, the maternal gut microbiome provided the largest contribution of transmitted strains. It was also found that maternal gut strains were more likely to adapt and persist in the infant gut compared with those acquired from other sources.

Among the species that were lost in the infants between 24 hours after delivery and subsequent time points up to 4 months, 80% were shared with at least one of the respective mother’s body sites, thus indicating their maternal origin.

The study from Yassour et al. has suggested two mother-to-child transmission patterns, in which not only the mother’s dominant strains (often Bacteroides vulgatus and Bifidobacterium adolescentis) were inherited, but also that the mother’s less dominant or secondary strains (often Bacteroides dorei) colonized the infants successfully. In addition, the transmission patterns vary by family, with some families exhibiting either transmission of a dominant strain, or a secondary strain, or none at all.

Microbial functional analysis showed that inherited maternal secondary strains may have a selective advantage when colonizing infant guts. Specifically, in cases where a secondary strain of B. uniformis was transmitted, a starch utilization gene cluster that was absent in the mother’s dominant strain was identified in her secondary B. uniformis strains that colonized the infant’s gut. The authors suggest that this strain provides a selective advantage in metabolizing specific glycans found in a mother’s breast milk.

The researchers also found the transmission of antibiotic-resistant genes conferring penicillin, macrolide, and tetracycline resistance and showing family-specific patterns, thus suggesting their inheritance.

Both studies allow a better characterization of how the microbiome is transmitted from mother to infant during the first months of life. Follow-up studies that include functional characterization of the gut microbiota are needed for elucidating how gut microbiome acquisition and development during early life affects children health later in life.




Ferretti P, Pasolli E, Tett A, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018; 24(1):133-45. doi: 10.1016/j.chom.2018.06.005.

Yassour M, Jason E, Hogstrom LJ, et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe. 2018; 24(1):146-54. doi: 10.1016/j.chom.2018.06.007.