You’ve had the dietary fiber discussion countless times in the clinic, educating your pediatric patients and parents. Teaching families about dietary modifications comes second nature to you when treating constipation or diarrhea.
But have you ever shared about the magical microbiotic world with your kids and parents? When they can conceptualize the role of a healthy gut microbiome on digestion and overall health, they are more likely to implement dietary changes. This can help to shift the narrative at home.
A child should understand that when they eat healthy food, they are feeding and supporting their gut microbiota.

You already know the child’s typical negative narrative, “Mom is making me eat my vegetables.” This becomes a struggle or battle. Instead, the child can shift to a positive narrative, “I get to feed the tiny pets inside my belly!” This empowers the child.
With further research delving into the gut microbiome, the scientific community continues to gain greater understanding. The public is becoming more privy to this knowledge now. It’s time we begin to share this fascinating knowledge with our children as well!
In addition to improving patient compliance, having a better understanding of the pediatric gut microbiome can further help you in the treatment of pelvic floor dysfunction.
In this blog, you will learn how the pediatric gut microbiome is unique, what factors influence early life gut flora, and how this impacts your work as a pelvic floor therapist.

Significance Of The Early Life Intestinal Microbiome
The early microbiome plays a crucial role in the maturation and overall health of a child. Babies and children have a different physiology than adults, therefore their dietary needs and microbiomes are different.
Microbes are responsible for digesting nutrients, which produce metabolites and signaling molecules that influence the gut lining and digestive health. The early presence or absence of certain bacteria also influences immune system health and even the development of the nervous system!
The first 1,000 days of life are key in establishing a healthy gut flora. Each child’s microbiome is unique– akin to a personalized fingerprint, shaped by genetics, environment, and diet.
Establishing a healthy microbiome early is paramount, as disruptions may lead to long-term health complications, including allergies, autoimmune diseases, and metabolic disorders.
Many factors influence the development of the early gut microbiome. A baby born via vaginal delivery has a very different flora than one born via C-section. A baby who is fed breast milk versus formula will also have very different microbiomes.
We will delve further into understanding these factors in the next section, looking at the nutritional and functional requirements of a child’s first 1,000 days of life.

Factors That Influence The Pediatric Gut Microbiome
The first 1,000 days of life are broken down into 4 phases. Each phase reflects the nutritional requirements of the baby’s function during development. Within this, certain bacteria dominate the baby’s microbiome and play specific roles.
Phase 1: Milk Lover
The first phase is called the milk lover phase, and lasts from 0-6 months of age. This reflects the baby’s job — to eat! This phase is dominated by Bifidobacteria. These good bacteria are responsible for digesting breast milk and producing nutrients to be absorbed by the baby’s gut lining. While the baby’s immune system is not yet developed, Bifidobacteria keep opportunistic bacteria in check.
Ideally, only a small percentage of Enterobacteriaceae are present in the gut to help stimulate the baby’s immune system and help it learn how to respond properly to opportunistic bacteria. This percentage is usually higher in babies born via C-section or given antibiotics at birth. However, vaginal delivery and breastfeeding do not guarantee the majority of Bifidobacteria will be present.
Phase 2: Baby on the Move
The second phase is named baby on the move, and occurs from 6-12 months of age. During this phase, Bifidobacteria are still the majority (about 50%) within the gut and Enterobacteriaceae are still present. The microbiome diversity is increasing because the baby is now moving around more, exploring, and putting things in their mouth.

Phase 3: Solid Adventurer
The third phase is called solid adventurer, from 1-2 years old. At this point, some Bifidobacteria is still present (about 15%). Food is no longer just for fun and exposure, but now the baby is getting most nutrients from different foods instead of just milk. The microbiome needs more diversity to help digest a variety of foods.
As the child integrates with family eating, optimizing a healthy diet for everyone in the household is important. Family members who live together have similar gut flora, so this is a good opportunity to maximize family health.
Phase 4: Confident Eater
The fourth phase is named confident eater, from 2-3 years old. This is when the child’s microbiome becomes greatly diverse. Bifidobacteria make up 3% of the flora and Enterobacteriaceae is 2%. The microbiome should now be digesting fibers and complex sugars, and producing short-chain fatty acids (SCFAs).
In the next section, you will learn why fiber and SCFAs are so important for the baby’s gut!
Why Is Gut Health Important to Consider With Pelvic Floor Therapy?
There are 3 functions of the gastrointestinal system that are important to consider when drawing connections between the pediatric gut microbiome and bowel function.
First, the microbiome influences intestinal motility, or transit time. When a child ingests fibrous foods, the bacteria digest the fiber and create SCFAs as metabolites. Mainly butyrate, these compounds stimulate colonic contraction and assist in stimulating peristalsis.
This is why having a healthy microbiome with good bacteria that support SCFA production is so important for kids with constipation. They need methods that naturally and regularly induce peristalsis.
Second, the microbiome controls gut permeability. “Leaky” gut in adults is frowned upon, but infants necessarily have greater permeability. The tight junctions in babies have a higher degree of permeability to allow for immunoglobulins to easily cross the barrier during breastfeeding. This influences immune development and protection.
As a child ages, the tight junctions should close and create more of a barrier with less permeability. Establishing a strong microbiome early in life sets the stage for a resilient gut lining. Maintenance of a strong gut flora throughout life is also important to consider when treating a child with diarrhea or constipation.

Third, the microbiome influences the gut-brain axis, which is bidirectional communication between the enteric nervous system and the brain. The vagus nerve is responsible for this communication. The microbiome is involved in the production of neurotransmitters in the gut.
Neurotransmitters are communicated via the vagus nerve, which has implications for anxiety, neurodivergence, and psychological conditions. Children with interoception differences and gastrointestinal pain are affected functionally by vagal tone as well.
Bowel and Bladder Disorders Directly Influenced By The Intestinal Microbiome
The mode of delivery (vaginal versus C-section) and type of feeding (breastfed long, short, or nil) both influence the prevalence of constipation, colic, and urinary tract infections.
The mode of delivery initially sets the stage for a child’s microbiome. When a baby naturally moves through the birth canal, he ingests better flora as opposed to a baby entering through an artificial opening through the skin. Higher levels of pathogenic bacteria such as Enterobacteriaceae, E. coli, and Klebsiella have been found in children born via C-section.
Constipation is more common in babies who were delivered via C-section. Consumption of human breast milk in infants is important because it contains human milk oligosaccharides (HMOs), which act as an osmotic to increase water content in the GI tract. HMOs also act as a prebiotic for Bifidobacteria, thereby indirectly supporting the production of SCFAs and increasing gut motility.
Colic, gassiness, and gastrointestinal discomfort are associated with higher levels of pathogenic bacteria and decreased protective bacteria with C-section delivery. These distinct microbiomes are not related to feeding methods, which suggests that early pioneering microbes can set a child up for colic. Reducing inflammation in the gut will reduce colic symptoms. Interestingly, the presence of Lactobacillus reuteri is associated with a reduction in daily crying time.
Recurrent urinary tract infections are commonly associated with disrupted gut microbiomes, such as an increased presence of E. coli and other pathogenic bacteria. When you are a child with UTIs, having good communication with the child’s physician is key to addressing underlying dysbiosis and immune function.

The nuances of growth and development in the baby’s gut microbiome are quite fascinating! We are just scratching the surface here. If you are interested in learning more particulars and in greater depth about pediatric gut health, sign up to view the entire Pediatric Pelvic Health Summit!
Although nutritional interventions are not within your scope of practice, having this solid foundation of knowledge will help you in treating children who are dealing with bowel and bladder dysfunction.
When working with children who have any disorders associated with the gut-brain axis, remember to consider the pediatric microbiome. You can find a local naturopathic physician in your area to become part of your team.
In the Summit, we have a guest lecturer who discusses how the Tiny Health microbiome test is paving the way to help parents and physicians improve their child’s gut health.
For additional resources, here is a list of children’s books about the microbiome that your pediatric patients will find to be both entertaining and insightful:
- A Garden in Your Belly: Meet the Microbes in Your Gut
- By D’yans, Masha
- Gut Garden: A journey into the wonderful world of your microbiome
- By Brosnan, Katie
- Are you What You Eat?
- By DK
- The Army Inside You: A Children’s Guide to the Microbiome
- By Garvin, Lindsey
