Metagenomic Analysis Reveals 90% of U.S. Infants Studied Lack of Key Gut Bacteria for Breast Milk Utilization and Immune System Development
The results of a study by researchers at Stanford University, the University of Nebraska and Evolve BioSystems suggest that the vast majority of infants in the United States may have a substantial deficiency in an important gut bacteria that is essential for the use of breast milk and the immune system. development, as well as protection against intestinal pathogens associated with common newborn conditions such as colic and diaper rash. The metagenomics study, published in Scientific reports, found that the gut microbiomes of about nine out of ten infants were missing Bifidobacterium longum subsp. infantis (B. infantis), a type of bacteria that play an essential role in the health and development of infants. This specific gut bacteria has been widely documented to have the most beneficial impact on the gut health of infants and possess the ability to fully unleash the nutritional benefits of breast milk.
The study is considered the most important to date to assess the widespread deficiency of gut bacteria in American infants and the resulting reduced function of their gut microbiomes. “The vast majority of infants are deficient in this key gut bacteria from the first weeks of life, and that is completely off the radar for most parents and pediatricians,” said study co-author Karl Sylvester. , MD, professor of surgery and pediatrics and associate dean of maternal and child health research, Stanford University. “This study provides the clearest picture to date of the magnitude of this problem and highlights the need to tackle B. infantis deficiency in the infant’s intestine early on. Sylvester and colleagues reported on their findings in an article titled “Metagenomic Perspectives of Child Microbiome Community Structure and Function at Multiple Sites in the United States.”
The neonatal period represents a unique stage in life where the “essential foundations of health throughout life” – including the proper development of the immune system – are established, the authors wrote. Key to this foundation of health is the infant’s gut microbiome, which requires the presence of thousands of different bacteria to perform different functions, from biological processes to the development of biological structures and systems.
When present in the gut microbiome of the infant, B. infantis breaks down carbohydrates called human milk oligosaccharides (HMOs) which are present in human breast milk and which would otherwise be inaccessible to the infant. B. infantis differs from others Bifidobacteria species in its unique adaptation to human breast milk and in particular in its ability to break down HMOs into usable nutrients. Perhaps more importantly, B. infantis is increasingly linked to the development of the infant’s immune system, protecting the infant’s intestinal tract against potentially harmful bacteria as well as a lower incidence of common childhood ailments such as colic and diaper rash.
It has also been shown that disruption of the neonatal gut microbiome – dysbiosis – may be relevant to persistent problems, such as an increased risk of immunologic disorders later in life and acute chronic inflammation, the researchers noted. Dysbiosis in newborns is marked by a substantial imbalance between beneficial and potentially pathogenic bacteria in the gastrointestinal tract.
There is strong evidence characterizing a substantial loss of Bifidobacteria in the infant’s gut over the past 100 years, with research indicating many factors including increased cesarean delivery, increased use of antibiotics, and increased use of infant formula. As a result of B. infantis loss, the infant’s gut is at greater risk of negative consequences, including suboptimal access to the full value of human breast milk, compromised immune system development, increase in harmful intestinal pathogens due to the increase intestinal pH and negatively impact the intestinal wall of the infant. “In recent years, reliable evidence has emerged on the state of the infant gut microbiome in the United States, showing a general trend towards dysbiosis and the associated acute and long-term negative health consequences,” commented Researchers.
However, they explained, to date, researchers have based their findings largely on single-site microbiome studies, often limited to a geographic area where samples were collected. Small association studies also demonstrate inherent limitations in terms of method reproducibility, from sample collection to analysis, they continued. “Currently, there is limited data to comprehensively assess the state of the gut microbiome of healthy infants in the United States,” while most studies of the infant microbiome have been conducted in premature infants, who may exhibit intestinal instability. microbiome and dysbiosis more severe than that seen in term infants. .
For their recently published metagenomics study, the team collected stool samples from 227 infants under six months of age, during pediatrician visits, in five different US states (CA, GA, OR, PA, SC). The samples were analyzed for the type and amount of bacteria present, which represents the bacterial composition in the intestines of infants. The fecal samples were evaluated for the bacterial ability to make full use of human breast milk – a hallmark of the presence of beneficial bacteria for health – as well as for the presence of antibiotic resistant genes in the bacteria.
“Specifically, we applied shotgun metagenomics to characterize: (1) intestinal bacterial communities of healthy American infants during the first six months of life; (2) ecosystem functions by determining the metabolic potential of gut microbiomes in different enterotypes to metabolize human milk oligosaccharides (HMO) from breast milk; and (3) the transport of antibiotic resistant genes (ARGs) in infants in different US states, ”they explained. The researchers did not include samples from infants with jaundice, or those who were actively undergoing antibiotic treatment, or who had been diagnosed with problems absorbing carbohydrates in their gut, due to the impact that such conditions may have had on the ability of the infant’s gut to carry out normal processes.
The results showed that potentially dangerous bacteria made up, on average, 93% of all bacteria in the infant’s gut microbiome, with the most prevalent bacteria being Escherichia coli, Klebsiella pneumoniae, Salmonella, Streptococcus, Staphylococcus, and Clostridium difficile. Many of these bacteria are known to harbor genes linked to antibiotic resistance. In fact, a total of 325 antibiotic resistant genes have been found in gut bacteria, with more than half (54%) of these genes being the ones that confer bacterial resistance to multiple antibiotics. The results also indicated that approximately 97% of the infants were “probably missing” B. infantis“, Reported the scientists. Given that B. infantis has been so widely regarded as one of the most prevalent bacteria in the gastrointestinal tract of infants, its absence on such a wide swath of externally healthy infants is surprising.
“This investigation offers a new perspective when you consider infants in the context of a healthy microbiome and the acute and long-term consequences that this entails,” they wrote. “Given recent discoveries linking the early life microbiome to key elements of infant health and that understanding of this community has improved, our results reveal that infants in the United States have microbiomes that may not be not provide the functions necessary early in life, including the formation of the immune system. system, protecting against colonization by pathogens and maximizing nutrition from breast milk (eg, HMOs).
As Sylvester also noted, “The infant gut is basically a blank slate at birth and quickly acquires bacteria from the mother and the environment. We were surprised not only by the significant lack of good bacteria, but also by the incredibly high presence of potentially pathogenic bacteria and by an environment of antibiotic resistance that seems so prevalent. The infant gut microbiome in the United States is clearly dysfunctional, and we believe it is a critical factor underlying many of the infant and childhood illnesses we see today through the country. “