Beneficial bacteria lay the groundwork for future health in kids. And the earliest moments of life shape the microbiome for years to come.


At first glance, the process of microbial colonization in newborns appears to be somewhat random. But with a closer look it becomes apparent that that there is a step-wise succession of microbiota change over the days, weeks, and months following birth.


Today, I’m highlighting some of the biggest players in infant gut microbial ecology. These three genera of beneficial bacteria pack a powerhouse of health benefits for newborns, infants, and children.


1. Bacteroides 


Bacterioides colonies typically appear about 10 days after birth.  These anaerobic (i.e. organisms that thrive in the absence of oxygen) bacteria occur at relatively low numbers in the early days of an infants life and breast feeding appears to keep those numbers small. However, after weaning Bacteroides numbers increase dramatically and they play a number of important roles in the gut microbiome.


Numerous studies have shown that they produce beneficial molecules like polysaccharide A and short-chain fatty acids. These post-biotics (i.e. metabolites produced by beneficial microbes) serve as an energy source for human metabolism. Bacteroides also appear to affect the maturation of humoral immunity in early infancy and balance Th1 & Th2 cell immunity in children.


2. Bifidobacterium


Infant guts are loaded with Bifidiobacterium – or at least they should be! These baby friendly bacteria are passed along from mom during birth (except in the case of cesarean section, which is a topic all to itself).

Interestingly, the species composition changes over time, with the two most common infant species being B. longum and B. bifidum. By the time a child is 6 years of age though, B. adolescentis replaces B. bifidum as the second most common Bifidobacterium species, and each serves a different role.


An added perk is that Bifidobacterium are stimulated by HMO’s (human oligosaccharides) in breast milk and can out-compete harmful microbes, including Clostridium difficile and E. coli.  The latest research also suggests that Bifidobacterium are protective against atopic dermatitis and childhood obesity.


 3. Lactobacillus


Lactobacillus are lactic acid producing bacteria. They literally alter the pH of the gut microenvironment favoring their own proliferation and that of other beneficial microbes. Lactobacillus are super common in over the counter probiotic supplements.


One of the most common strains in children is L. reuteri.  A recent study found that administering Lactobacillus reuteri to both third trimester mothers and to infants throughout the first year of life decreased the occurrence of allergies in children at 2 years of age.





Johnson, C. L., & Versalovic, J. (2012). The human microbiome and its potential importance to pediatrics. Pediatrics129(5), 950-960.


Mueller, N. T., Bakacs, E., Combellick, J., Grigoryan, Z., & Dominguez-Bello, M. G. (2015). The infant microbiome development: mom matters. Trends in molecular medicine21(2), 109-117.


Tiihonen, K., Ouwehand, A. C., & Rautonen, N. (2010). Human intestinal microbiota and healthy ageing. Ageing research reviews9(2), 107-116.


Vael, C., & Desager, K. (2009). The importance of the development of the intestinal microbiota in infancy. Current opinion in pediatrics21(6), 794-800.