Bedtime story to foster your infant’s brain development? Check. Warm bath to clean her? Check. Lullaby to soothe her? Check. Probiotics to improve her gut health for the rest of her life? Probably worth looking into.

The researchers looked at changes in mice’s digestive systems during infancy. Within the digestive system, the gut microbiome contains an ecosystem of bacteria influenced by diet that helps the body break down food and fight off infections. Intestinal epithelial cells that line the small intestine absorb nutrients and produce a mucus layer that protects them from the caustic, bacteria laden environment inside.

Bacterial exposure during infancy may affect gut health into adulthood, according to researchers at Baylor College of Medicine. “Many, many diseases appear to be influenced by various environmental exposures during critical periods of early development,” said Dr. Robert Waterland, who collaborated with lead author Dr. Lanlan Shen and a team of researchers.

In the United States, one in five people struggle with digestive issues, including incurable chronic diseases such as inflammatory bowel disease (IBD) that can require removal of the colon or small intestine. However, a recent study in Genome Biology suggests that the best approach might be to fix things before they are broken.

Intestinal epithelial cells turn over every four days and are continually replaced by intestinal stem cells that are tucked away tiny pocket-like glands of the small intestine called crypts. These stem cells are the only cells in the digestive system that are maintained from infancy to adulthood, Dr. Waterland said.

The DNA of intestinal stem cells is a blueprint for new intestinal epithelial cells. It can be changed through a process called DNA methylation, where methyl (CH 3 ) groups are tacked onto the DNA in different patterns that alter gene expression. The researchers focused on changes in DNA methylation patterns during the suckling period that lasts from birth until mice transition to solid food, equivalent to the breastfeeding period in humans. “This is a beautiful period where mice are undergoing dramatic environmental changes,” Dr. Shen said.

The researchers compared “germ-free” mice that lacked a gut microbiome to regular mice with a normal gut microbiome and found that the intestinal stem cells of the germ-free mice had less DNA methylation, which resulted in slow production of new intestinal epithelial cells and a thinner mucus layer. However, when they reintroduced gut bacteria during infancy, DNA methylation in those stem cells increased, which restored proper functioning and improved intestinal health. The key to their finding is that bacteria in the gut microbiome only influence methylation patterns in intestinal stem cells during the suckling period early in development. Once that critical period is over, the DNA in intestinal stem cells is set for life.

So what does all of this this mean for your infant? Dr. Shen and Dr. Waterland are hoping to use dietary bacteria to adjust the gut microbiome during infancy to improve long term gut health. In the system they are developing, you could test your infant’s feces, which contain DNA from old epithelial cells that have sloughed off, and compare the methylation patterns to an index of infant gut maturity. If something looks off in the DNA methylation patterns, you could give your infant probiotics to correct the issue, potentially sidestepping intestinal problems down the line. The next step in their research is to identify the specific bacteria strains that restore DNA methylation patterns in intestinal stem cells and pinpoint the period when restoration is most successful.

Dr. Pia Pannaraj, a pediatric infectious disease specialist at Los Angeles Children’s Hospital, conducts related research on the role of breast milk in establishing the infant gut microbiome. She points to the gut microbiome as a factor in certain allergic and autoimmune diseases as well as IBD and obesity. She agrees that probiotics are a viable strategy for correcting imbalances in intestinal bacteria early in life and that early development should be the focus of infant gut microbiome research.

“It’s important to know the changes over the first year of life, particularly during infancy, because that is when the immune system is learning how to be an immune system,” she said.