Paired microbiome samples reveal that milk-feeding patterns and the transition to solid foods coincide with surprisingly early changes in microbial functions developing in the infant gut.
Study: Functional maturation of the infant gut microbiome during dietary transition in the first year of life. Image Credit: Natalia Deriabina / Shutterstock
In a recent study published in the journal Scientific Reports, researchers utilized high-resolution shotgun metagenomic sequencing data to evaluate how dietary transitions during the first year of life are associated with changes in the infant gut microbiome.
The study’s sample cohort comprised 125 mother-infant pairs from the Cork Nutrition and Development Maternal-Infant Cohort Study (COMBINE) in Ireland, with 125 pairs of stool samples (250 samples total) collected before and after the introduction of solid foods into the infant participants’ diets.
Study findings revealed that feeding practices were associated with significant differences in microbial development and microbiome composition. Breastfeeding was observed to exhibit a distinct “pacing effect,” in which the duration of breastmilk intake (rather than the exact infant age at which solid foods are introduced) was associated with patterns of microbial community assembly.
The researchers also found that the transition to complementary feeding, including among infants sampled at 4 months of age, was accompanied by a marked functional shift in microbial pathways, from simple milk sugar fermentation toward complex polysaccharide degradation and pathways involved in short-chain fatty acid (SCFA) fermentation.
Background
The World Health Organization (WHO) recommends exclusive breastfeeding for the first 6 months of life, followed by nutritionally adequate complementary foods alongside continued breastfeeding.
Studies of the infant gut microbiome have consistently documented bacterial succession following the introduction of solid foods into infant diets. The functional changes associated with these shifting microbial communities and the influence of different milk types remain poorly characterized.
Scientists also remain poorly informed about how different milk diets (e.g., infant formula versus human breastmilk) interact with various solid foods during the weaning phase of infant development.
About the study
The present study aimed to address these knowledge gaps by using high-throughput shotgun metagenomic sequencing to elucidate taxonomic and functional microbial adaptations during early-life feeding transitions. The study sample was obtained from the Cork Nutrition and Development Maternal-Infant Cohort Study (COMBINE) participant list and included 125 pairs of stool samples (250 samples total) collected from 125 COMBINE cohort infants before and after complementary feeding began.
The first stool sample was collected during each participant’s milk-feeding stage (mean age = 86.47 days), while the second was collected after complementary feeding began (mean age = 222.35 days). Shotgun metagenomic sequencing of these 250 stool samples yielded more than 2.1 billion read pairs (mean = 8.4 million read pairs per sample).
The resultant dataset was classified at each sampling point into three milk regimens: 1. Exclusively breastfed, 2. Exclusively formula-fed, and 3. Mixed-fed. Around one-third of mothers changed feeding practice between the two sampling points. Subsequent statistical analyses primarily evaluated predictors of breastfeeding duration and solid food timing, alongside changes in microbial diversity (including core species abundances) and estimates of differential abundance in functional metabolic pathways.
Study findings
Summary statistics revealed that infants transitioned from exclusively milk-based diets to solid foods at a median age of 147 days, with formula-fed infants introduced to solids about 17 days earlier than their breastfed counterparts. These findings show that milk-feeding practice was associated with the timing of complementary feeding.
Cross-referencing breastfeeding duration data with metagenomic sequencing results revealed that breastfeeding duration was significantly associated with species diversity and richness, while the age at solid-food introduction was not. The observed patterns were consistent with the authors’ proposed “pacing effect” of breastfeeding on microbial community assembly.
Formula-fed infants exhibited higher initial species richness than breastfed infants. After solids were introduced, formula-fed infants showed a much larger number of differentially abundant functional pathways, with the data identifying 162 altered metabolic pathways in formula-fed infants compared to only 7 in their breastfed counterparts, about 23 times as many. The magnitude of individual pathway changes was relatively small.
Functional metabolic analyses further revealed that the introduction of solids was accompanied by changes in the abundance of microbial genes and pathways involved in carbohydrate metabolism, away from simple milk sugar degradation toward complex starch and mannan metabolism, with higher abundances of pathways involved in butyrate and acetate metabolism and fermentation across the cohort.
At the cohort level, abundances of pathways involved in the biosynthesis of thiamine (vitamin B1), biotin (vitamin B7), and folate (vitamin B9) increased after complementary feeding began. Pathways involved in the biosynthesis of vitamin K2 and vitamin B6 declined.
Finally, statistical analyses found that, after complementary feeding began, daily stool frequency was significantly associated with microbial composition.
Conclusions
The present study found that functional changes associated with microbial succession were detectable in complementary-fed samples from infants as young as four months. The results support the authors’ proposed pacing relationship for breastfeeding, as breastmilk cessation was more closely associated with changes in the microbial community than with the timing of solid-food introduction itself.
Because sampling age and feeding status were strongly correlated, the study could not fully disentangle age-related microbiome maturation from changes associated with complementary feeding. The metagenomic analysis also assessed microbial functional potential by measuring gene and pathway abundance rather than the direct production of SCFAs, vitamins, or other metabolites. The authors also noted that substantial portions of microbial functional potential could not be assigned using existing databases.
The authors said the findings may inform public health strategies and evidence-based infant-feeding guidance. The study did not test clinical outcomes or establish that one feeding-associated microbiome pattern is healthier than another.
