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What does a healthy infant gut microbiome look like?

As diet and the microbiome are closely entwined, the first step in understanding a healthy infant gut microbiome is to understand a healthy infant diet. Fortunately, a healthy infant diet is at least superficially simple to define, exclusive breastfeeding for the first six months is the best nutrition for infants according to the World Health Organisation. A common alternative to human breast milk for infants is formula and the microbiomes of breastfed and formula fed infants are known to differ.

Microbially accessible carbohydrates (MACs) are the key to maintaining the diversity of the adult microbiome. However, Western diets have driven the extinction of microbiome community members because they are low in MACs (1). One key difference between human breast milk and infant formula is the presence of high levels of a diverse array of human milk oligosaccharides (HMOs) – and HMOs are MACs. This has provoked natural experiments, in which generations of infants in countries with high rates of formula feeding have been exposed to a low MACs diet, while infants with lower formula adoption rates continued to be exposed to the traditional high MACs breast milk diet.

Instead of considering only how differences in the microbiome of developed and developing nations may contribute to stunting and malnutrition, we should also consider what differences in historical breastfeeding rates might tell us about a healthy infant microbiome. This could shed new light on approaches to studies that compare the gut microbiome of infants from different countries. For instance, a 2012 study found that Finnish infants had lower levels of Bifidobacterium than Malawian infants (2). Finland, like most European nations, experienced a significant drop in breastfeeding rates in favour of formula during the 19th and 20th centuries, but Malawi has experienced consistently high breastfeeding rates, although lower rates of exclusive breastfeeding, which suggests that Bifidobacterium may be among the taxa affected by a formula-feeding induced low-MAC bottle neck.

Early reports on the infant microbiome consistently reported high levels of Bifidobacterium (3, 4). By the 1970s, scientists in the United States were surprised to note that breastfed infants had low levels of Bifidobacterium in their stool (5),an observation that differed from their past experience and co-occurred with a nadir in US breastfeeding rates. Modern studies have found Bifidobacterium levels vary considerably by country and differences in breastfeeding rates are thought to be one reason driving the difference (6).

But do Bifidobacterium truly matter for infant health? Yes, and they matter in many different ways. High Bifidobacterium levels are associated with a wide array of positive health effects. Bifidobacterium can improve infant vaccine response (7), reduce the levels of antimicrobial resistance genes present in the infant gut microbiome (8), reduce the risk of diarrhoea in infants (9), and reduce the chance of obesity later in life (10).

The good news is that at least one strain of Bifidobacterium can dominate the infant gut as a probiotic (11), meaning it is possible to reintroduce infant strains of Bifidobacterium to populations that may have lost them due to low breastfeeding rates. The complication is that not all strains of Bifidobacterium are equal and at this moment there is no clear answer to which strains will be best for infant health.


Diana Hazard Taft, Ph.D., is a post-doctoral research fellow at University of California, Davis in the laboratory of Dr. David A. Mills.


Diana Taft will be presenting on Bifidobacterium, breastfeeding, and infant health at the 6th Microbiome R&D and Business Collaboration Forum: USA. See the agenda to find out more.

See the full list of references here.

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