Evolution of the gut microbiome in infancy: recent advances

The early-life gut microbiome is a dynamic ecosystem that alongside other niches, such as the oral and skin microbiomes, undergoes rapid assembly and genetic evolution from birth through to adulthood. Although it was originally considered to be a passive colonisation process, recent findings suggest that early microbial development is a co-evolving, host-modulated process influenced by multiple factors, including maternal microbiota, mode of delivery, human milk, feeding practices, environmental exposure, and genetics, highlighting the timeliness of this review.

In recent years, high-resolution sequencing and longitudinal multiomics have enabled the detailed observation of the early stages of microbial adaptation, assembly, strain transmission, diversification, and horizontal gene transfer in the early stages of life. New data also reveal maternal-foetal microbial signalling via metabolites and extracellular vesicles, as well as the evolutionary role of human milk oligosaccharides, and the involvement of phages, plasmids, and mobile genetic elements in infant gut microbial evolution.

This review provides a summary of advances during gestation, birth, breastfeeding and infancy. However, further research is required into microbial evolution, and predicting its clinical significance, as well as  the role of artificial intelligence tools. Understanding early microbial adaptation processes could transform nutrition, precision medicine, and paediatric care.