Study shows effects of breast milk on the microbiome and respiratory health of infants

Breast milk regulates a baby's microbial composition, known as the microbiome, during the first year of life. This in turn reduces the child's risk of developing asthma, a new study shows.

Led by researchers at NYU Langone Health and the University of Manitoba, the study's findings showed that breastfeeding beyond three months supports the gradual maturation of the microbiome in the infant's digestive system and nasal cavity, the upper part of the respiratory tract. Conversely, weaning before three months disrupts the even development of the microbiome and is associated with a higher risk of preschool asthma.

Some components of breast milk, such as complex sugars, the so-called human milk oligosaccharides, can only are broken down with the help of certain microbes. This gives microbes that can digest these sugars a competitive advantage. In contrast, infants who are weaned from breast milk earlier than three months and then fed exclusively with formula are inhabited by a different group of microbes – namely, those that help the infant digest the components of the formula. Although many of these microbes that thrive in formula ultimately end up in all babies, the researchers showed that their early arrival is associated with an increased risk of asthma.

Just as a pacemaker regulates the heart rhythm, breastfeeding and breast milk dictate the pace and sequence of microbial colonization of the infant's gut and nasal cavity, ensuring that this process occurs in an orderly and timely manner.”

Liat Shenhav, PhD, co-lead researcher of the study and computational biologist

“Healthy microbiome development is not just about having the right microbes. They also have to arrive in the right order at the right time,” said Shenhav, an assistant professor in the NYU Grossman School of Medicine, its Institute for Systems Genetics and the school's Department of Microbiology.

For the study, Shenhav, who is also an assistant professor at NYU's Courant Institute of Mathematical Sciences, collaborated with the study's co-lead investigator, Dr. Meghan Azad, who is director of the Manitoba Interdisciplinary Lactation Center and professor of pediatrics and child health at the University of Manitoba.

Another important finding of the study was that the bacterial species Ruminococcus gnavus occurred much earlier in the guts of children weaned from breast milk early than in those of children who were exclusively breastfed. The bacterium is known to be involved in the production of molecules called short-chain fatty acids, as well as the formation and breakdown of the amino acid tryptophan. Both tryptophan and its metabolites have been linked in previous studies to immune system regulation and disruption, including increased asthma risk. The study authors noted that an infant's microbiome not only helps with digestion, but also plays a crucial role in immune system development.

Publication in the journal cell The study, published online Sept. 19, tracked the ebb and flow of microbes in infants' guts and noses during the first year of life and also examined details about breastfeeding and the composition of breast milk. All of the children and their mothers participated in the CHILD cohort study, a long-term research project that follows the same 3,500 Canadian children at different stages of life, from the womb through adolescence.

Using data from the CHILD cohort study, researchers were able to separate the effects of breastfeeding on an infant's microbiome from a number of other environmental factors, including prenatal smoke exposure, antibiotics, and the mother's asthma history.

Even when these factors were taken into account, they found that breastfeeding duration remained an important factor in the infant's microbial composition over time. They also used these microbial dynamics and data on milk components to train a machine learning model that accurately predicted asthma years in advance. Finally, they built a statistical model to learn causal relationships that showed that breastfeeding reduces asthma risk primarily by shaping the infant's microbiome.

“The algorithms we developed provide valuable insights into the microbial dynamics during an infant's first year of life and how these microbes interacted with the infant,” Shenhav said. “These insights allowed us to go beyond simply identifying associations and improve our ability to make predictions and examine causal relationships.”

“Our research highlights the profound impact of breastfeeding on the infant microbiome and the essential role of breastfeeding in supporting respiratory health. By uncovering the mechanisms behind the protective effects of breast milk as shown in this study, we aim to create national guidelines on breastfeeding and weaning from breast milk in a data-driven manner.

“With further research, our findings could also help develop strategies to prevent asthma in children who cannot be breastfed for at least three months,” she added.

The study was funded by National Institutes of Health grant DP2AI185753. Additional funding was provided by Genome British Columbia (274CHI), the University of British Columbia, CIHR CGS-D, the Humans and the Microbiome program of the Canadian Institute for Advanced Research, and the Canada Research Chair Program. Study participants were all volunteers from families involved in the CHILD cohort study, which was originally funded by the Canadian Institute of Health Research (CIHR) and AllerGen NCE.

In addition to Shenhav and Azad, other lead researchers on the study include Padmaja Subbarao of the University of Toronto and Michael Surrette of McMaster University in Hamilton.

Other co-investigators on the study include co-first author Kelsey Fehr and co-author Elinor Simons, both at the University of Manitoba; and co-authors Myrtha Reyna, Ruixue Dai, Theo Moraes and Vanessa Breton at the University of Toronto; Charisse Petersen, Darlene Dai and Stuart Turvey at the University of British Columbia; Laura Rossi and Marek Smieja at McMaster University; Michael A. Silverman and Maayan Levy at the University of Pennsylvania in Philadelphia; Lars Bode at the University of California, San Diego; Catherine Field and Piush Mandhane at the University of Alberta; and Jean S. Marshall of Dalhousie University in Halifax.