How early is the gut microbiome prepared to develop toward an adult state?

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Human gut-associated microbial communities change profoundly in structure from birth to adulthood. Their taxonomic composition has been extensively studied, but changes over time in microbial metabolic functions involving bioactive small molecules remain largely unexplored.

To investigate these changes alongside age-related gut microbiome development, researchers collected 6,617 publicly available human fecal shotgun metagenomes and 42 metatranscriptomes from infants and adults. They also selected metagenomic data from 250 breastfed and 217 formula-fed infants to investigate how feeding type might shape the metabolic functionality of the developing gut microbiome.

From the perspective of small-molecule metabolism, the findings suggested that human gut microbial communities are genetically equipped and prepared to evolve metabolically toward an adult state as early as 1 month after birth. At age 4, however, they still appeared functionally underdeveloped compared with those of adults.

Compared with formula-fed newborns, breastfed infants showed enrichment in microbial metabolic functions related to specific amino acids present at low concentrations in human milk. The authors interpreted this as highlighting that the infant gut microbiome has specifically evolved to synthesize bioactive molecules that can complement human milk composition and contribute to a complete nutritional supply for the infant.