We need to address infant gut deficiency now, researchers warn

By Danielle Masterson

- Last updated on GMT

Getty Images / gsader
Getty Images / gsader

Related tags b. infantis Gut microbiome dysbiosis

Initially thought to play a limited role, evidence shows the gut microbiome performs essential duties related to digestion and metabolism, immune system development and neurotransmitter production that affect behavior and cognitive function—from the moment a baby is born. However, infants in the US may have diminished function of their gut microbiome, according to a new study.

A new peer-reviewed study, published in Scientific Reports​, found that 90% of US infants may be suffering from a substantial deficiency in an important bacterium key to breast milk digestion and immune system development.

Study details 

Researchers at Stanford University, the University of Nebraska, and Evolve BioSystems collected fecal samples from 227 infants under six months of age during pediatrician office visits in five different states: California, Georgia, Oregon, Pennsylvania, and South Carolina. 

The research team applied shotgun metagenomics to characterize: (1) gut bacterial communities of healthy US infants in the first 6 months of life; (2) ecosystem functions by determining the metabolic potential of gut microbiomes in different enterotypes to metabolize human milk oligosaccharides (HMOs) from breast milk; and (3) the carriage of antibiotic resistant genes (ARGs) in infants across different US states. 

The above criteria was used to classify microbiomes as dysbiotic or not, based on the concept of ecosystem services adapted to evaluate the benefits infants receive from functions provided by their gut microbiomes.

The samples were analyzed for bacterial type and amount present. They were also tested for bacterial ability to fully use human breast milk—a hallmark of the presence of health-promoting bacteria, as well as for the presence of antibiotic resistant genes in the bacteria. 

The researchers did not include samples from infants with jaundice, those who were actively undergoing antibiotic treatment, or those diagnosed with problems with absorbing carbohydrates in their intestine, due to the impact such conditions may have on the ability of the infant gut to carry out normal processes.


The study revealed that about nine out of 10 infants are missing Bifidobacterium longum subsp. infantis (B. infantis)​ in their gut microbiome —a type of bacteria that plays a critical role in infant health and development. This specific type of gut bacteria has been widely documented​ as providing the most beneficial impact to infant gut health and possessing the ability to fully unlock the nutritional benefits of breast milk which includes some oligosaccharide fractions that are not digestible by other means.

"The vast majority of infants are deficient in this key gut bacterium from the earliest weeks of life, and this is completely off the radar for most parents and pediatricians alike,"​ said study co-author Karl Sylvester, MD, professor of surgery and pediatrics and associate dean of Maternal Child Health Research, Stanford University.

What is ‘healthy’?

According to the authors, “This survey offers a new perspective when considering infants in the context of a healthy microbiome and the acute and long-term consequences it implies”​—which begs the question: Can babies be considered healthy when they lack good bacteria and have a high presence of potentially pathogenic bacteria?

“That’s exactly right. We tend to consider health as the absence of disease, but in this case, babies may look healthy and reach their developmental milestones, but their gut microbiomes are not healthy on the inside. We have to remember the early months of life set the trajectory for many aspects of our immune, metabolic and cognitive health, and this is all connected to the proper development of our gut microbiome. And that’s why B. infantis is so important. When B infantis digest HMO in the baby’s gut, it nourishes the baby’s intestinal cells, helps seal up the lining of the gut wall and reduces inflammation. Babies lacking B. infantis in their gut microbiome are missing out on these benefits and we believe that’s one main reason why we’re seeing increases in allergy, asthma eczema and other diseases like type 1 diabetes,”​ explained Dr. Rebbeca Duar, Principal Scientist at Evolve Biosystems and co-author of the study. 

Antibiotic resistance: the next global pandemic

Duar said the most surprising revelation to come out of the study was that diet appeared to have no effect.

“We tend to associate breastfeeding with higher bifidobacteria, but this was not what we found. Both formula fed and human milk fed infantis were dysbiotic. This finding likely means the absence of B. infantis is a generational problem and we disrupted the natural transfer of B. infantis from mom to baby,”​ said Duar. 

She added that another surprising and rather grim finding was the detection of antibiotic resistance genes that were state-specific. “These genes allow pathogens to survive antibiotic treatment, sometimes referred to as ‘superbugs.’  In California, we found 20 antibiotic resistant genes that were not found in infants at any other site we tested, and another 17 were unique to infants from South Carolina. This could mean that resistance to antibiotics is developing independently in different regions and infants are picking up these bacteria where they live. Antibiotic resistance is widely considered to be the next global pandemic. If we learned our lesson from this study, we really must take a proactive approach to solving infant dysbiosis now.”

Looking ahead

"This study provides the clearest picture to date of just how widespread this issue is and highlights the need to address B. infantis deficiency in the infant gut right from the start,”​ suggested Sylvester.

While the report acknowledges that this B. Infantis deficiency is completely off the radar for most parents and pediatricians alike, so what can they do? 

Duar suggests parents take it upon themselves to conduct microbiome testing through companies such as LabCorp, which can provide a window into the infant gut microbiome. 

“Elevated fecal pH, defined as 5.5 or higher, not only has an irritating effect on the skin which can present as diaper rash, but is also a sign that B. infantis is missing and baby is suffering from gut dysbiosis, or what is also called Newborn Gut Deficiency. Evivo (activated B. infantis EVC001) is the only infant probiotic clinically proven to restore B. infantis to the infant gut, reduce pathogenic bacteria by 80%, bring fecal pH down to recommended levels and create a protective environment in the infant gut. Bifidobacterium (including B. infantis) is the 'friendly' strain of bacteria found in many types of probiotics marketed for babies, but Evivo (B. infantis EVC001) is the only strain clinically proven to limit the growth of bad bacteria in baby’s gut, helping guide immune system development as a foundation for lifelong health,”​ explained Duar. 

“Our hope is that the focus does not stay with the problem, but that we begin to focus on the available solutions,” ​said Duar. “We have previously shown in clinical studies that B. infantis can be restored and infant gut dysbiosis can be solved. The goal now needs to be making sure all babies have B. infantis in their microbiomes.​”

Microbiome science: a burgeoning field 

Monumental advances in next-generation sequencing and omics technologies have taken off in recent years, pushing microbiome science into an exciting new frontier in personalized nutrition.

Given the tremendous advances, Duar said she does see microbiome testing on infants a standard of care in the future. 

“The cost of sequencing, the method used to read the microbiome, has dramatically decreased in the last decade. As technologies advance and we continue to learn about how much our microbiomes are interconnected with our health, microbiome analysis is very likely to become standard of care. The key here is having the expertise to interpret the results,” ​said Duar. “The microbiome is incredibly complex and we’re constantly learning more about what functions it provides, and progress is being made at a tremendous pace.”

Source: Scientific Reports 
11, 1472 (2021) doi.org/10.1038/s41598-020-80583-9
“Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States”
Authors: G. Casaburi et al.

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