Introduction of solid foods triggers early functional changes in the infant gut microbiome

The transition from milk to solid foods is associated with early changes in the functional activity of the infant gut microbiome, according to a new study published in Scientific Reports.

Researchers analyzed high-resolution shotgun metagenomic data from 125 mother-infant pairs participating in the Cork Nutrition and Development Maternal-Infant Cohort Study (COMBINE) in Ireland. A total of 250 stool samples were collected before and after infants began eating solid foods.

The findings indicate that feeding patterns influence the development and composition of the infant gut microbiome. In particular, the duration of breastfeeding appeared to have a stronger association with microbial community development than the exact age at which solid foods were introduced.

Shift from milk sugar metabolism to complex carbohydrates

The researchers found that the introduction of complementary foods was accompanied by a pronounced functional shift in the gut microbiome. Microbial pathways involved in the breakdown of simple milk sugars became less prominent, while pathways involved in the degradation of complex carbohydrates, including starch and mannan, increased.

The transition was also associated with greater activity of pathways involved in short-chain fatty acid metabolism, including butyrate and acetate fermentation.

These changes were detectable even in some infants who were sampled at four months of age, suggesting that functional maturation of the gut microbiome can begin relatively early during dietary transition.

The World Health Organization recommends exclusive breastfeeding during the first six months of life, followed by nutritionally adequate complementary foods while breastfeeding continues. However, the way different feeding practices influence the functional development of the infant microbiome has remained incompletely understood.

Breastfeeding duration may influence microbiome development

Infants in the study began eating solid foods at a median age of 147 days. Formula-fed infants started complementary feeding approximately 17 days earlier than breastfed infants.

When the researchers compared feeding information with metagenomic data, they found that the duration of breastfeeding was significantly associated with microbial species richness and diversity. The age at which solid foods were introduced, by contrast, was not significantly associated with these measures.

The researchers described this pattern as a possible “pacing effect” of breastfeeding, in which continued exposure to breast milk may influence the rate at which the infant gut microbial community develops.

Formula-fed infants initially had greater microbial species richness than breastfed infants. After solid foods were introduced, however, the number of significantly altered functional pathways was much higher among formula-fed infants: 162 pathways changed compared with seven among breastfed infants.

The researchers noted that the differences in individual pathway abundances were generally relatively small.

Changes in vitamin-related pathways

The introduction of complementary foods was also associated with changes in pathways involved in vitamin metabolism.

At the overall cohort level, pathways involved in the production of thiamine (vitamin B1), biotin (vitamin B7) and folate (vitamin B9) became more abundant after complementary feeding began. In contrast, pathways associated with the production of vitamin K2 and vitamin B6 decreased.

The study also found that, after the introduction of solid foods, the frequency of daily bowel movements was significantly associated with differences in the composition of the gut microbiome.

Study limitations

The researchers caution that the findings do not establish that one type of feeding or microbiome profile is healthier than another. The study examined associations between feeding practices and microbial composition and function rather than clinical health outcomes.

Because the infants' age and feeding status were closely linked at the time of sampling, the researchers could not completely separate normal age-related microbiome maturation from changes specifically associated with the introduction of complementary foods.

In addition, the metagenomic analysis measured the abundance of microbial genes and metabolic pathways rather than directly measuring the production of short-chain fatty acids, vitamins or other metabolites. Some microbial functions also could not be identified using currently available databases.

The authors say that a better understanding of how early dietary changes shape the gut microbiome could contribute to future evidence-based recommendations on infant feeding.

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