9 Out of 10 Infants Experience Gut Microbiome Deficiency, Study Reveals

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Key Takeaways

  • A new study suggests nine out of 10 infants are missing a type of gut bacteria critical to their health and development.
  • Parents can prioritize a healthy gut by implementing probiotics, prebiotics, and healthy food choices in their child's diet.

Gut health has gotten more attention over the years as we become increasingly aware of the important role the gut microbiome plays in our overall health.

The trillions of bacteria, fungi and viruses that make up the human microbiome evolve throughout our lives, and research suggests we first come into contact with those microbes inside our mother's womb. As we're born and growing, the gut microbiome continues to diversify, and this diversity is highly beneficial to our health.

"The gut microbiota is closely linked to the body’s immune and nervous systems and influences many aspects of health and well-being," says Whitney Casares, MD, pediatrician and Gerber medical consultant. "A healthy gut improves the digestion and absorption of nutrients from the food babies eat, which influences the responses of the immune system and brain function communication."

But new research published in Scientific Reports suggests nine out of 10 infants are deficient in a type of bacteria, B. infantis, that's critical to infant health and development.

The Study

The results show that a majority (nine out of 10) of infants are suffering a substantial deficiency of B. infantis. And researchers claim this loss puts infants at greater risk of inability to access the full nutritional value of breast milk, negative impact on the intestinal wall, increased exposure to harmful pathogens, and compromised immune system development.

"A majority of infants are deficient in this key gut bacterium from the earliest weeks of life, and although quite common, this is completely off the radar for most parents and pediatricians," says Rebecca Duar, PhD, study co-author and principal scientist at Evolve Biosystems, Inc. "Our findings highlight the need for expecting and new parents to prevent or address newborn gut deficiency right from the start."

Whitney Casares, MD

A healthy gut improves the digestion and absorption of nutrients from the food babies eat, which influences the responses of the immune system and brain function communication.

— Whitney Casares, MD

In addition to the deficiency, the study found, on average, 26% of all bacteria in the infant gut microbiome could potentially cause disease. Larger amounts of these bacteria species were also connected to higher levels of antibiotic resistance. Duar points out that the lack of B. infantis could be linked to the presence of dangerous bacteria, as it typically protects the infant intestinal tract.

This is especially concerning because, when bad bacteria is able to thrive in the infant gut, babies can have increased risk of colic, diaper rash, eczema, allergies, and Type 1 diabetes.

Prioritizing a Healthy Gut

These study findings of this common deficiency raise awareness for parents and physicians alike. And with this knowledge they can work together to prioritize holistic health.

This new study is the largest to date of its kind. Researchers collected fecal samples from 227 infants under 6 months of age in five different states. The samples were analyzed for bacterial type and amount present.

"Every day I get parents asking me how they can take a proactive approach to their child’s health, and I immediately think about their gut health," says pediatrician Tanya Altmann, MD.


Many experts point to breastfeeding as the best way to feed your baby for the first six months.

"Breast milk has components that can promote the development of a balanced microbiota, rich in bifidobacteria, including probiotic bacteria and oligosaccharides," Casares says.

However, each mother and child are different, so there is no "best" approach to the practice of breastfeeding, and there can be many challenges. In fact, for some new mothers, breastfeeding is not always a safe or healthy option for a number of reasons.

"Though we encourage mothers to breastfeed knowing that there should be an advantage of gaining more immune-boosting Bifidobacterium in their babies’ guts, sometimes a mother’s work, stress, milk production, or desire get in the way," says Rashmi Jain, MD, pediatrician and founder of online pediatric urgent care BabiesMD.

Prebiotics and Probiotics

Probiotics are live microorganisms that support gut health and a strong immune system, and prebiotics are what feeds the microorganisms in the digestive tract. Breast milk is a natural source of both, and infant formulas often include probiotics and prebiotics to optimize gut health.

"Many parents turn to probiotics to increase the abundance of good bacteria in baby’s gut," Altmann says. "However, not all probiotics are created equal."

Tanya Altmann, MD

Many parents turn to probiotics to increase the abundance of good bacteria in baby’s gut. However, not all probiotics are created equal.

— Tanya Altmann, MD

While the American Academy of Pediatrics affirms probiotics to be an effective avenue for promoting gut health, it's always best to consult with a physician or healthcare provider to determine whether a probiotic is necessary in your child's diet.

Setting a Healthy Example

Once solid foods are introduced, it's important to maintain a balanced diet of whole grains, fruits, vegetables, and beans. This will contribute to the development of balanced microbiota. Avoid foods with added sugars, as well as processed and packaged foods.

Children will pick up their parents' habits, so it's important to keep in mind your diet choices don't solely affect you.

"Oftentimes, I think it is more difficult for parents to set the example and lead the way," Jain says. "However, if they're able to incorporate a healthy balanced lifestyle for themselves and the household, children easily fall in line. They learn by the examples they see. Children forget old habits much easier than us adults do."

What This Means For You

Infant gut deficiency is common. Prioritize a health gut microbiome with breast milk or infant formula that contains both probiotics and prebiotics and introducing healthy foods into your child's diet when it comes time.

6 Sources
Verywell Family uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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