Good gut health begins at birth. From the first moment a child meets the environment, her gut microbes are taking shape.


One of the most common misconceptions about gut microflora is that the only way to heal gut dysbiosis (i.e. a harmful imbalance of gut microbes) is through probiotic supplementation. Although probiotics are profoundly therapeutic, they are merely a piece of the picture.


There are 5 key environmental factors that affect the composition and integrity of the pediatric microbiome. Here they are:


 1. Birth Beginnings


Early colonization of the gut begins at birth. One of the first differences we see in the development of the microbial community is between vaginally-born and cesarean-born children. Those children born naturally represent the mother’s vaginal and intestinal microbiota, while those born via c-section portray the mother’s skin environment.

In particular, cesarean births appear to result in fewer beneficial Bifidobacterium and Bacteroides spp. colonizing the guts of newborns.


Take Home: When possible, encourage your patients to advocate for a vaginal birth. Help them understand their rights as a patient, the health benefits of natural childbirth, and the role of a birth doula in increasing their chances of having a successful vaginal birth.  If a cesarean section is deemed medically necessary, then perhaps encourage your patients to inquire with their obstetrician or midwife about vaginal swabbing after birth.


2. First Foods


Breast milk has been described as “liquid gold”. It contains immunoglobulins, cytokines, growth factors, and human milk oligosaccharides (HMO) to name a few. Numerous beneficial bacteria species are well adapted to HMO’s, and exclusively breast-fed babies have been found to have a greater abundance of Bifidobacterium and Lactobacillus in their microbial community.


Interestingly, formula-fed babies have been found to be at greater risk of Clostridium difficile colonization. This greater presence of C. difficile in the intestinal microbiome of infants has been associated with an increased occurrence of neonatal diarrhea and eczema.

Meanwhile, the abundance of beneficial microbes supported by breastfeeding may be protective against allergies, obesity, and type 2 diabetes.


Take Home: Breast milk really is best! Feel free to urge your new mom patients to exclusively breast feed, when possible. If they are having latch complications or difficulties breast feeding, advise them to seek the help of a lactation counselor. In those patients who have difficulty producing milk, consider breast milk banks.


3. Out of Home Births


Hospital births have become the norm in industrialized countries. However, for most of human history babies have been born at home. Recent research has found that extended hospital stays and increased pharmaceutical interventions following delivery are associated with delays in the colonization and development of the infant microbiome.


Since the establishment of a healthy and robust microbiome occurs in infancy, any disruption or delay of microbial functions could result in a wide range of disease later in life.


Take Home: Encourage your patients to explore all the options available to them for prenatal care. Remember that child birth is a natural process, and that low risk patients may benefit greatly from the midwifery model of care. If home birth or birth center options exist in their area, it could help their baby get a jump start on establishing a healthy gut microbial environment.


 4. Curious Cuisine


Just as first foods have a dramatic impact on microbial diversity, so does the transition from weaning to solid foods. In fact, research now suggests that changes in the fiber, fat, and protein content of solid foods can produce sustained changes in the pediatric gut microbiome within a mere 24 hours after ingestion. For example, the consumption of animal protein and saturated fat favors the growth of Bacteroides, while a carbohydrate rich diet proliferates Prevotella.


These different genera of health promoting bacteria have been found to help maintain gut epithelium integrity, provide energy for human metabolism, and regulate Th1 and Th2 cell immunity.


Take Home: Food choices in childhood matter! Children’s microbes and their health are determined by what they eat. Reminding parents to introduce whole, organic, and local foods (rather than processed rice cereal) during the initial stages of weaning will help set the stage for their child’s future microbiome integrity.


 5. Antibiotic Overload


We’ve all heard about the antibiotic epidemic in pediatric care. Antimicrobial agents have been found to drastically alter the composition and diversity of the intestinal microbiota within days of administration. Worse yet, a complete recovery of the initial bacterial community is “rarely achieved”.


This impact is greatest in infants younger than one year of age, with significant reductions in health promoting Bacteroides and Bifidobacterium following antibiotic use. These findings are now being linked to disease later in childhood, namely childhood obesity and asthma.


Take Home: Avoid antibiotic use in children unless absolutely necessary, especially in children under one year of age. Feel free to trust in and rely on herbal medicine and immune boosting nutrients to prevent and fight infections.






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