Important new research from the CHILD Cohort Study (CHILD) has found that a mother’s genes play a role in determining which microbes live in her breastmilk and that this, in turn, can influence whether her breastfed child later develops asthma or allergies.
“We were aware that the microorganisms in human milk influenced the health of breastfed babies,” said lead author Zhi Yi (Sarah) Fang, PhD Candidate in Biomedical and Molecular Sciences at Queen’s University.
“However, we didn’t know exactly how, or why the microorganisms in milk differed so much from mom to mom. This study has given us new insight into both questions: It has identified specific groups of microbes in breastmilk that are linked to a child’s later development of asthma or allergies, and it has identified genetic variations in the moms that are associated with these groups of microbes in her milk.”
The study, published in Cell Host & Microbe, analysed the milk and genetic make-up of 885 mothers participating in CHILD, a Canadian longitudinal birth cohort study, and determined their potential impact on the health outcomes of their breastfed children at five years of age, with a particular focus on the development of asthma or allergic sensitivity.
“Human milk is considered the gold standard in infant feeding because it offers so many health benefits,” commented co-author and CHILD Deputy Director Dr. Meghan Azad, a leading breastmilk researcher and University of Manitoba professor and Canada Research Chair in Early Nutrition and the Developmental Origins of Health and Disease. “Previously, it was thought human milk was sterile, but we now know it is inhabited by many microorganisms and that these contribute importantly to its health-giving properties.”
The human microbiome is the community of microorganisms living on and within us. Research is increasingly revealing the crucial role that these microorganisms play in our health. Everyone’s microbiome is unique and is shaped in early life by many things such as the microbes they are exposed to during birth and through their food, including breastmilk.
For this first-of-its-kind study, human milk researchers at the University of Manitoba, led by Dr. Azad, collaborated with the Computational Genomics Laboratory at Queen’s, led by Dr. Qingling Duan, the Queen’s National Scholar in Bioinformatics.
Dr. Azad’s team spearheaded the collection of microbiome data from breastmilk samples taken from CHILD moms three to four months after they gave birth. Dr. Duan’s group applied a machine learning algorithm to identify groups of correlated—or networked—clusters of bacteria in the breastmilk. They then determined that these bacterial clusters potentially impact the health outcomes of the breastfed children, as documented in CHILD through questionnaires, skin prick tests for allergic sensitization, and parent-reported physician diagnoses.
From this, the researchers discovered that the presence of certain bacterial clusters in a mother’s milk appeared to either increase or decrease the breastfed children’s risk of developing asthma or allergies, and that the clusters were more influential this way than individual microbes. In particular, the researchers found that greater bacterial diversity in breastmilk was associated with a lower risk of allergy; that increased abundance of the bacteria Lawsonella increased allergy risk; and that the presence of certain clusters involving the bacteria Pseudomonas increased asthma risk.
The bioinformatics and computational genomics team led by Dr. Duan then conducted genome-wide association studies (GWASs) that looked at millions of DNA sequence variations in the mothers and how these variations related to the bacterial patterns in their milk—especially the patterns associated with allergy and asthma risk.
“Our GWAS of the human milk microbiome identified maternal genes associated with various microbes implicated in the long-term health of breastfed children,” said Fang. “For example, we identified a gene (NPR1) associated with the overall bacterial diversity of milk, which was linked to lower allergy risk, and another gene (COTL1) associated with the abundance of Lawsonella, which was linked to increased asthma risk.”
“Our study is the first to demonstrate that host genomics regulate the microbial composition of human milk and highlights the importance of including host genomics in microbiome research,” added Dr. Duan. “This nuanced study has improved our understanding of why human milk is such a health-boosting superfood, and our findings may enable the development of new therapies to optimize the health impacts of breastfeeding.”