Infant gut microbiota diversity and composition as a potential link between feeding method and atopic dermatitis

Background: Atopic dermatitis (AD) is a chronic inflammatory skin disease with no known cause or cure, often beginning in the first year of life. The gut microbiota, which is proposed to play a role in AD development, is integral in immune system development and regulation. Breastfeeding shapes the gut microbiota and has been observed to lower AD incidence. Thus, it has been viewed as a type of early intervention to prevent AD. Here, we investigate the microbiota as a link between feeding method and AD to contribute to ongoing research on this topic, which may inform future infant diet recommendations. Methods: Stool samples from 325 mother-infant dyads at various time points over a 1 year period, collected by Dr. Kyung Rhee at the University of California San Diego, were analyzed for their microbial composition. A Pearson’s chi-square test was performed to test for correlation between feeding method (breastfeeding and formula feeding) and AD status in infant samples. Alpha and beta diversity analysis and taxonomic classification were then conducted in QIIME2. Infant samples were stratified by feeding method, then differential abundance and relative abundance analysis were conducted using DESeq2. Results: We report a significant correlation between feeding method and AD status, with higher AD incidence observed in the formula-fed group. We found that breastfed infants had greater Faith’s phylogenetic diversity (PD) compared to formula-fed infants. However, there was no difference in alpha diversity based on infant AD status. Furthermore, breastfeeding was found to only favour the abundance of certain genera in healthy infants. In comparison, formula feeding favours the abundance of different genera in both healthy infants and AD infants. Conclusion: Our results support our hypothesis that infant feeding method influences the development of AD by altering gut microbial diversity and structure. The present study validates previous literature that breastfeeding has protective effects against AD development. Furthermore, our work provides evidence that this relationship may be linked through the gut microbiota.