Research could lead to new microbiome assays that clinical laboratories could use to identify genetic and other health conditions in developing baby

It would seem to be common sense, but now a study conducted by the Broad Institute of MIT and Harvard confirms that a pregnant mother’s microbiome has an effect on the development of her baby’s own gut microbiota. These findings could create opportunities for clinical laboratories to help in diagnosing a broader range of health conditions by testing the gut bacteria of pregnant mothers.

The Broad Institute’s study suggests the mother’s gut microbiome helps form the baby’s gut bacteria not only during pregnancy and birth, but into the baby’s first year of life as well.

“This study helps us better understand how the rich community of microbes in the gut initially forms and how it develops during infancy,” said Tommi Vatanen, PhD, a co-first author on the study who is now a researcher and associate professor at the University of Helsinki, in a Broad Institute news release. “The microbiome is very dynamic and develops along with other systems, so there’s a lot going on in the first years of life.”

The researchers published their findings in the journal Cell titled, “Mobile Genetic Elements from the Maternal Microbiome Shape Infant Gut Microbial Assembly and Metabolism.”

“We’ve shown that the maternal microbiome plays an important role in seeding the infant microbiome, and that it’s not a one-time event, but a continuous process,” said gastroenterologist and senior study author Ramnik Xavier, MD, of the Broad Institute. Clinical laboratories and microbiologists may soon have new tools for testing a mother’s microbiome during pregnancy. (Photo copyright: Maria Nemchuk, Broad Institute.)

Study Highlights Physiological Connection Between Mother and Child

This study, according to the Broad Institute news release, is the “first to uncover large-scale horizontal gene transfer events between different species of maternal and infant gut bacteria.” The researchers also found that the bacteria in the mother’s microbiome “donate” genes that go into the bacteria of her unborn child. The mother’s genes help the baby in other ways as well during pregnancy and after birth.

“Benign bacteria in the maternal gut share genes with the child’s intestinal microbes during early life, potentially contributing to immune and cognitive development,” states the news release, adding, “The microbiomes of the mother and baby change during pregnancy and the first year of life … some bacteria in the mother’s gut donate hundreds of genes to bacteria in the baby’s gut. These genes are involved in the development of the immune and cognitive systems and help the baby to digest a changing diet as it grows.”

The study also sheds light on a baby’s unique metabolites (chemicals produced by bacteria) and how they connect with the mother’s microbiome.

“This is the first study to describe the transfer of mobile genetic elements between maternal and infant microbiomes,” gastroenterologist Ramnik Xavier, MD, Core Institute Member, Director of the Immunology Program, and Co-Director of the Infectious Disease and Microbiome Program at the Broad Institute, told Neuroscience News.

“Our study also, for the first time, integrated gut microbiome and metabolomics profiles from both mothers and infants and discovered links between gut metabolites, bacteria, and breastmilk substrates,” he added.

Researchers Use Multiomics

The human microbiome influences health in many ways. For several years, Broad Institute scientists have been trying to better understand the human microbiome and the role it plays in diseases like type 1 diabetes, cancer, and inflammatory bowel disease.

According to the organization’s website, the scientists recently began using multiomics techniques in their research that include:

Xavier and his colleagues were particularly interested in the development of the microbiome during the first year of the baby’s life.

“The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites,” the researchers wrote in Cell. “Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to one year of age using longitudinal multiomics data.”

The researchers deployed bacterial DNA sequencing from stool samples of 70 mother and child pairs.

They found “hundreds of genes” in the infant gut bacterial genome that originated in the mother. According to the scientists, this suggests a mother does not transfer her genes all at once during childbirth. Instead, it likely occurs in an “ongoing” gene transfer from mother to baby through the baby’s first year of life, the news release explains.

Here are details on the study findings, according to Neuroscience News:

  • Genes associated with diet were involved in the “mother-to-infant interspecies transfer of mobile genetic elements.”
  • Infant gut metabolomes were less diverse than maternal metabolomes.
  • Infants had 2,500 unique metabolites not detected in the mothers.
  • Infants that received baby formula had distinct metabolites and cytokine signatures as compared to those receiving breast milk.
  • A link between pregnancy and an increase in steroid compounds could be due to impaired glucose tolerance in mothers.

“We also found evidence that prophages—dormant bacteriophages (viruses that reside on bacterial genomes)—contribute to the exchange of mobile genetic elements between maternal and infant microbiomes,” Xavier told Neuroscience News.

Research Could Lead to New Clinical Laboratory Assays

Microbiologists and clinical laboratory scientists are gaining a deeper understanding of the role gut bacteria play in many aspects of human life. But how a mother’s microbiome influences a baby’s development during and after birth is particularly intriguing.

“We’ve shown that the maternal microbiome plays an important role in seeding the infant microbiome, and that it’s not a one-time event, but a continuous process,” said Xavier in the Broad Institute news release. “This may be yet another benefit of prolonged bonding between mother and child, providing more chances for these beneficial gene transfer events to occur.”

Pediatricians, microbiologists, and clinical laboratories may one day have new microbiome assays to help identify a broad range of health conditions in mothers and infants and explore gut bacteria’s effects on a baby’s developing health. 

—Donna Marie Pocius

Related Information:

Mobile Genetic Elements from the Maternal Microbiome Shape Infant Gut Microbial Assembly and Metabolism

How a Mother’s Microbiome Helps Shape Her Baby’s Development

Evidence of Horizontal Gene Transfer Between Human Maternal Microbiome and Infant Gut Microbiome

Broad Institute: The Human Microbiome

Harvard T.H. Chan School of Public Health: The Microbiome

NIH: Introduction to the Human Gut Microbiota

Maternal Microbiome Promotes Healthy Development of Baby

Researchers Find Health of Human Microbiome Greatly Influenced by Foods We Eat