Microbial colonization of the human gut starts at birth, and disruptions of the gut microbiota over the first few years can impact long-term health. A new study adds to evidence that the development of the infant gut microbiota is influenced by factors such as birth method, diet and antibiotic use. 

The findings, published in Nature Medicine, reveal how the community of gut microbes evolves throughout early life, especially during key transitions phases such as weaning.

While much is known about the overall composition of the infant gut microbiota, it’s still unclear how individual bacterial strains evolve and adapt. For example, recent studies show that some bacterial strains can persist in the rapidly changing infant gut microbiota, but less is understood about how the specific genes that mutate differ across bacterial species and how they respond to changes in the gut environment.

To understand how microbial communities develop and change over time, Sanjam Sawhney at Washington University School of Medicine in St. Louis, Missouri, and his colleagues looked at more than 1,000 stool samples from 26 sets of twins and their mothers.

Evolving communities

The researchers collected stool samples from the infants from birth to age eight. They found that infant microbiotas initially differ from adult microbiotas, with distinct patterns of bacterial composition in the first few years of life. 

Infants had more diverse microbiomes compared to their mothers, with the number of bacterial strains increasing as the infant gut matured from birth to age three. Certain bacteria, including Veillonella parvula and Bifidobacterium longum, were more common in infants, while others, such as Anaerostipes hadrus, were more prevalent in mothers. 

The composition of the infant microbiotas varied by age and was influenced by factors such as birth mode, antibiotic use, and whether the infants were breastfed or formula-fed. Breastfed infants had microbiotas that transitioned more slowly to adult-like forms, while the microbiotas of formula-fed infants shifted faster. The team found nine distinct microbiota types, or enterotypes, that were linked to diet.

Long-lasting effects

Further analyses revealed that the gut microbiotas of infants accumulate mutations faster than those of mothers, especially during the first nine months of life. A key factor driving this rapid mutation accumulation was the weaning process, which marks a major shift in the microbiota’s development. 

Bacterial strains that persisted through weaning showed higher mutation rates and carried more enzymes involved in carbohydrate breakdown, which may be related to dietary changes. After weaning, the gut microbiotas of infants started to resemble those of their mothers more closely, the researchers found.

The findings highlight how early feeding and transitions phases such as weaning can have long-lasting effects on the gut microbiota, with implications for the development of the immune system and metabolism, the authors say.