Study Finds Nine in Ten U.S. Infants May Lack Key Gut Bacterium Tied to Breast Milk Digestion and Immunity

A study published in Scientific Reports reports that about nine out of ten infants in its sample were missing a single gut bacterium: Bifidobacterium longum subsp. infantis, known as B. infantis. The researchers describe it as the largest effort so far to benchmark how widespread that gap is among U.S. infants, and what it does to the way their gut microbiomes function.

The work rests on fecal samples from 227 infants under six months old. The samples were collected during pediatrician office visits in five states: California, Georgia, Oregon, Pennsylvania and South Carolina. The team analyzed which bacteria were present and in what amounts, tested whether the bacteria could fully use human breast milk, and looked for antibiotic resistance genes. They excluded infants with jaundice, infants actively being treated with antibiotics, and infants diagnosed with problems absorbing carbohydrates in the intestine, because those conditions can change how the infant gut works.

B. infantis matters because of what it does with breast milk. Human milk contains carbohydrates called human milk oligosaccharides, or HMOs, which the infant cannot access on its own. B. infantis breaks them down into usable nutrients, and it differs from other Bifidobacteria species in being specifically adapted to human milk for this purpose. It is also increasingly linked to immune system development, to protecting the intestinal tract from dangerous bacteria, and to lower rates of common childhood conditions such as colic and diaper rash. The source describes B. infantis as having been widely considered among the most prevalent bacteria in infant intestines, which makes its absence in so many outwardly healthy babies a surprise.

The second finding concerns what was there instead. Potentially dangerous bacteria made up, on average, 93 percent of all bacteria in the infant gut microbiome. The most common were Escherichia coli, Klebsiella pneumoniae, Salmonella, Streptococcus, Staphylococcus and Clostridium difficile. Many of these are known to carry antibiotic resistance genes, and the researchers found 325 such genes in total, with 54 percent of them conferring resistance to multiple antibiotics.

Karl Sylvester, MD, a co-author, is a professor of surgery and pediatrics and associate dean of maternal child health research at Stanford University. He said the deficiency begins in the earliest weeks of life and is largely off the radar for parents and pediatricians. In his words, the infant gut is essentially a blank slate at birth that quickly picks up bacteria from the mother and environment. He said the team was surprised both by the lack of beneficial bacteria and by the high presence of potentially pathogenic ones and widespread antibiotic resistance. He called the U.S. infant gut microbiome clearly dysfunctional and said he believes this is a critical factor behind many infant and childhood ailments.

The study places this in a longer history. Evidence points to a substantial loss of Bifidobacteria in the infant gut over the past 100 years, with research citing more C-section deliveries, more antibiotic use and more infant formula use as contributing factors. Losing B. infantis, the source says, puts infants at greater risk of not getting the full value of breast milk, compromised immune development, a rise in harmful gut pathogens linked to increased gut pH, and a negative effect on the intestinal wall.

The sample is modest, though: 227 infants from five states, which alone cannot establish national prevalence or explain causes. Further research will be needed to confirm how common the deficiency is and what drives it.