Parenthood is a wild ride. No matter how much formal education you have, no matter how many “what to expect” books you read, nothing can truly prepare you for this journey. Nobody can “tell” you how amazing it is, and nobody can tell you how dark the dark days truly are.

Luckily, in our case, there was a light at the end of this dark tunnel.

This is my son’s gut healing story. This is NOT his birth story, but rather, what happened in the aftermath of that trauma. (You can read the full birth story here.)

To be perfectly clear, you do not need to have a traumatic birth to have a baby with gut health issues — in fact, you could have the most beautiful, perfect experience with a stellar, healthy baby and STILL stumble upon these problems in his or her growth. It’s a part of being human — being animals, interacting with nature, teetering on the fence with modern comforts and technology.

Rather than give you a boring “how-to” article, I wanted to show you just how significant functional testing and natural approaches can be for pediatric health issues, especially those in babies — a population we’re told can’t be helped and to whom everything negative that’s happening (like colic, vomiting, constipation…) is normal.

Just because something is common does NOT make it normal. Once we accept this truth, we can take the appropriate steps toward resolving the issue.

Here’s the story and the context.

Microbiome Development, Hospital-Style

Like I said before, Anthony’s birth story can be found in another blog post. His NICU journey is not documented there, but I will summarize the pertinent pieces here as it relates to his gut health.

Babies are not necessarily born “sterile” like we once thought, however their microbiomes are still very immature and require colonization immediately upon birth to build their immune system. This colonization occurs from how they’re physically handled, the environment they’re born into, and the food they consume. As their internal systems are exposed to more and more things — AKA more and more flora in the environment — the immune system can build antibodies, other immune cells, and help the GI tract function properly. Gut health and immune health are intimately connected all throughout life and the critical moments begin at birth.

The perfect immune system birth setting: the baby would be delivered vaginally without antibiotics, where he/she can be inoculated orally, nasally, and in the eyes with the mother’s vaginal flora on the way out of the birth canal. Once that initial large inoculation process occurs, the baby would be brought directly to the mother’s chest where her skin-to-skin contact adds more flora to the baby’s various orifices and would also assist in helping the baby regulate his/her own body temperature. Bonus if the umbilical cord clamping is delayed so baby can get the rest of his/her final blood supply from the placenta, which contains added nutrients that prevent blood sugar dysregulation and anemia.

After this immediate skin-to-skin contact, the baby would find its way to mom’s nipples and latch for colostrum intake. This initial milk is HIGH in antibodies and nutrients specifically designed to colonize the baby’s very primitive microbiome and immune system. This suction also helps send the signal to the breasts to begin bringing the long-term milk in, which changes over time to meet the immune system demands of the newborn. The human body truly is amazing.

Of course, being premature, this was not even close to our experience.

Let’s line up the multiple factors that affected Anthony’s initial microbiome colonization, both good and bad.

The Factors at Play

— He was born surgically via C-section in a sterile environment and had exposure to antibiotics. Both of these procedures already set him up for struggle, microbiome-wise. Nothing helpful was there to colonize him, so it leaves room for pathogenic species to take over. Combine that with the fact that hospitals are overrun with antibiotic-resistant superbugs on every surface and you can imagine what that does to the gut!

— His first nutrition postpartum was an IV fluid of similar macronutrients he’d be getting in the cord blood if he were still in utero. He was too small and unstable yet for his digestive system to be able to handle breastmilk (plus mine had not come in yet, obviously).

— He also, as many preemies do, had some breathing difficulty at birth. As you might recall from his birth story, he was resuscitated multiple times in the OR prior to stabilization for transport to the NICU. This series of events and procedures changed the way his body was receiving inoculation of flora as well, because any entryway into the body — especially at birth — is going to introduce new microorganisms into the system, including what goes in your mouth and nose, such as breathing equipment and tubing.

— After a few days, his digestive tract was deemed stable and he was given donor breastmilk via nasogastric (NG) tube. Most people don’t know this, but beautiful blessed angelic mamas out there who have an oversupply of breastmilk often donate a ton to hospitals for premature babies to consume. How freaking absolutely amazing is that? This helped to colonize his gut with the flora of these other mamas while my milk sloooooowly came in. Unfortunately, however, this donor milk was likely pasteurized by the hospital for legal reasons, in which case it provided way less immune system support than fresh breastmilk would have. But still… it was such a blessing to receive this gift.

— I also had beautiful lactating friends who pumped extra breastmilk and dropped it off to me to bring to the NICU when my own personal supply struggled to come in. This gave plenty of unpasteurized immunoglobulins from different environments to diversify his microbiome, which is very important. They were diverse for a few reasons: different aged mamas, different diets and ethnic backgrounds, not on medications, exposed to different homes and work environments, had other kids at home that strengthened their immune cell production, etc.

— Unfortunately, NICU policy included human milk fortifier (HMF) and Poly-vi-sol additives that were put into my pumped breastmilk. HMF is basically added macronutrients to help premature babies grow faster. Studies show it helps for babies up to a certain weight limit. It’s also known to cause digestive upset for a variety of reasons, and it tastes/smells horrid. Anthony received this in every NICU feed. Toward the end, they also added Poly-vi-sol which is an iron supplement created by Enfamil, with which the hospital had a contract. Any baby that showed signs of anemia was given this, despite asking “why” the signs of anemia were there, or wondering if they served an evolutionary purpose. It also tastes/smells horrid and iron feeds gut pathogens. Keep this in mind for the rest of the blog post.

— Being in the NICU for 50 days, Anthony was treated by many different people and held by many different hands. Unfortunately, this was during the early post-COVID era and our hospital was still requiring facemasks. In some regard, this can be helpful to prevent unnecessary respiratory infections in premature babies whose lungs and immune systems are weak. However, most of these providers did not wear gloves and hands can come with more germs than anything, so removing masks was probably no big deal in comparison. In a normal situation this diversity exposure can be a good thing, but in a premature case, it may not be. We may never truly know.

— We practiced nursing throughout our 50 days in the NICU and beyond. This constant skin-to-skin contact, even outside of strict nursing, helped his immune system and microbiome develop. Once we realized nursing long-term would not work out, I pumped my breastmilk and delivered it to him that way instead. He had received only breastmilk at this point, which was something I was truly proud of.

What Happened Between the NICU and Home

In the hospital, Anthony mostly ate and slept. He really just needed to grow, so his body prioritized that and didn’t expend much additional energy. He had stools at regular intervals as expected. He did have gas and what appeared to be internal discomfort at times, especially toward the end of his stay, but in general no major issues.

The moment we got home, he was a totally different baby.

He’d get alternating constipation and diarrhea. He slept horribly. He seemed to be in pain when laying on his back. He would scream in agony with distended gas bubbles in his abdomen. He also had a massive umbilical hernia from all the straining and pressure.

It was exhausting. Luckily, he drank my milk like a champ and we never had to worry about him gaining enough weight (or losing any), but something wasn’t right. In his second month home, his stools were very infrequent and would come out bright orange and watery. By all available measures with his pediatrician, he was doing okay. We were given a vitamin D3/K2 supplement, probiotics, fish oil, and iron (which we did not use much of).

He seemed to react horribly to the probiotics, so I opted for a brand I knew and trusted for infants. If you can believe it, this lit a fire in his gut even hotter than it was before; I couldn’t believe it was possible for him to feel WORSE. I felt like a terrible mother for not being able to soothe him or make these horrible symptoms go away.

It was time for intervention.

Right around Memorial Day, I collected a stool sample from one of his diapers using the GI-MAP collection kit and sent it in. A week later, we also had his lip and tongue ties revised.

Let’s go over some of the relevant results. First up is the normal or commensal bacteria section. (Disclaimer: this GI-MAP report is an older version and the presentation of the data does look different now, so if you have a report that does not look like this, have no fear!)

He alternated between low and high in this section, and ideally we’d like to see things more balanced and within the lab range. He also had a couple species that were completely undetectable. Overall, the imbalance was high and likely causing a lot of inflammation.

NOW — I want to emphasize the point that this picture would likely be vastly different had we waited a couple months to test him. We tested him early — at 3 months old, actual age (not adjusted for prematurity) — and the infant microbiome undergoes a LOT of change between birth and about 6 months old, especially if they begin solids around that time. That’s not to say there isn’t work that can be done, but rather to note that we’re not overly focused on populating the gut with probiotics in this phase when there’s symptoms of dysbiosis. We want to address those imbalance concerns first before adding in more “good gut bugs.”

On to the next section — the dysbiotic species:

As the title suggests, these are species we want to keep at-bay. He had multiple species come back lab-high, which is not surprising, given his symptoms and how his microbiome was shaped in a hospital setting, where some nasty gut bugs live, such as Staphylococcus aureus, the species involved in MRSA, which was lab-high for Anthony.

Many of these can cause AND be strengthened by constipation, reduced gastrointestinal function, poor digestive capacity, a weakened immune system, exposure to antibiotics, chronic stress, etc. — many of these we can infer were players in his life at the time, due to his symptom presentation and traumatic entrance into this world.

He had nothing show up for yeast, viruses, or parasites — but this does not mean they weren’t playing a role. Oftentimes these species can remain undetected in stool samples because they’re excellent at hiding within biofilms. More on that another time. For our purpose here, it’s sufficient enough to know that none of these things resulted.

Now this is where things get interesting. This is my favorite section of the GI-MAP because it tells us so much about the internal, invisible state of the gut. It’s important to take this with a grain of salt, because he was a very tiny baby at this point and their guts are CONSTANTLY changing in the first six months of life. Here’s the overall picture of what this was telling me:

• His body was digesting fats appropriately.

• His body was making enough of its own pancreatic enzymes.

• His liver detox function was working well.

• There was no microscopic bleeding in his colon.

• His immune system was in FULL-ON OVERDRIVE — I’ve never seen a result this high, to this day. His body and gut were going absolutely haywire, so it was obvious something had to change.

• His reactivity to gluten was also off the lab scale — which told me I needed to gut gluten from my diet IMMEDIATELY. Which is so frustrating, because I had been essentially gluten-free for a decade before getting pregnant. Then, during pregnancy and postpartum, I was almost compelled to include it simply for survival foods like sandwiches, cereal, etc. I was kicking myself at this point too, because the 400 ounces of breastmilk I had saved in our chest freezer was no longer suitable food for him due to the gluten transfer, and I had to donate it.

• He had considerable colonic inflammation.

What We Did With the Test Results

Obviously my first step was to remove gluten from my diet, since the transfer into my breastmilk was his only source of exposure. That one was 100% on me. Luckily, a few days before submitting his stool test, I had a sneaking suspicion gluten was playing a role and I already removed it, so by the time this suspicion was confirmed, he was already drinking “clean” milk. I also know dairy intolerance was not playing a role here because I had been strictly dairy-free for multiple years leading up to his birth, due to my own intolerance issues. So we were able to nail down this gluten-specific sensitivity nicely.

Next, I addressed his overall gut imbalance and immune system dysfunction first. I put him on three key supplements, one at a time: a binder, silver drops, and herbal antimicrobial drops. This was in addition to vitamins D3/K2 and cod liver oil.

Note: these supplements and the dosing (not mentioned for a reason) were specifically chosen for his presentation, age, symptoms, etc. This is NOT a regimen that would work well for all kids or people in general. In fact, this regimen would often be insufficient to address most of the pediatric GI-MAPs I see in my practice and my recommendations often look different than this. His age and history were big factors in these choices.

The binder was introduced first, before any eradication supports, in a quarter ounce of breastmilk before bed. This is because binders are the mops — they come in and make sure whatever toxins or pathogens are circulating in the body get eliminated properly. If we began killing off the bad gut bugs first, they have the risk of NOT being properly removed by the body and therefore recirculate in the bloodstream, wreaking havoc everywhere they go and making the symptoms worse. This also puts the body at risk for organ damage. No bueno. Binder first, always, regardless of the person’s age.

Then we introduced the silver drops (not going into specific products or type of silver for a reason), directly into his mouth while laying on his back, away from milk intake. These have antimicrobial properties but also help support the immune system, which was necessary, given his overactive state. This helped serve a dual-purpose.

Finally, once the first two were confirmed to be tolerated, we introduced the herbal antimicrobial drops at the same time as the silver. This kind of product is very potent but effective. It also helps to break up those biofilms I mentioned earlier, so that any species trying to hide out from the immune system gets exposed and vulnerable to being killed by the herbs.

He was on this regimen for about six weeks. It took us some time to slowly work our way up to therapeutic dosage, but we saw changes within the first week — every complaint he had going on before was resolving. His umbilical hernia even resolved by the end of the six weeks — a hernia that our pediatrician told us would likely not resolve until he was walking and able to utilize his core muscles more functionally.

It was extremely validating to be the one responsible for change that nobody thought was possible.

The “After” Time

After the six weeks, we debated trying to assess for parasites, since these are common and my husband and I knew we both had them as well, but my son’s symptoms had completely resolved. Even after introducing solids around eight months, he was doing just fine — no changes in stool, no developing skin issues like eczema, nothing. No major signs that parasites needed addressing. So we decided against it.

We began repopulating his gut with the same safe infant probiotics I mentioned before and he tolerated it just fine this time — further proving that the work we did helped to eliminate the imbalance in his gut and make room for the right species to flourish.

He’s now over 20 months old and thriving, and we still have yet to need to address any other gut health struggles. There may (and likely will) come a day where he needs this kind of care, but I know how to handle it seamlessly now and do so on a daily basis with the kids in my practice.

How This Story Applies to Other Babies and Kids

Babies Before Six Months

These days, I prefer not to work with babies on this functional of a level — especially as it relates to eradication — until they’re at least six months old (unless absolutely necessary). Like I mentioned before, we were in dire straits and I knew Anthony’s rough start did not set him up to function well. I’m glad I did the testing and the protocol, because he may have suffered with nutrient deficiencies and autoimmune development if I didn’t.

If you’re looking for support for a baby this young, have no fear. There’s still plenty of work we can do. If mom is breastfeeding, we can look into food sensitivity testing for her and remove any foods or additives that come back as highly reactive. I did this as well during this time! The reason being is that even if you don’t experience outright symptoms to a food you result as reactive to, your body is still producing mediators and having an immune response to it. These inflammatory cells can also transfer via breastmilk and lead to added inflammation in baby. So this is a great place to start. The test I run tests for over 170 different foods, chemicals, additives, beverages, etc.

We can also work on mom’s digestion and immune system capacity to boost her ability to provide this to her child. Even if the child is not being breastfed or consumes some formula in addition to breastmilk, there are lots of things we can try. There are functional ways to support the liver, adjunct therapies to bring in, and low-tox holistic remedies that can be added. It could mean trialing and erroring different formulas for sensitivity issues as well. There are definitely possibilities!

Babies and Older Kids

Stool testing is my preferred modality for kids. (Food sensitivity testing is done via a 7-vial blood draw, so this is not a reasonable test for a child.) Especially for the yet-to-be potty-trained, the stool sample is easy to collect and you can have it shipped directly from your porch. Even for potty-trained kids, I have tips and tricks for helping them get a good sample collection — and the bonus is you never have to leave your home. They don’t have to have practitioner oversight, they don’t have to poop at a healthcare office, none of that. It’s non-invasive and done from the comfort of their own home with the help of their parent.

The insight that the test results provide for how to build an appropriate gut healing protocol is unmatched. It’s great because it helps us get a picture of what’s going on inside YOUR unique child, who will then receive a fully unique protocol to address those findings. I don’t do cookie-cutter recommendations here. The work needs to be tailored to the child, otherwise we’d see a mixed bag of results.

What Conditions Can Functional Nutrition Support Help With?

Anthony’s story is about GI troubles — gas, bloating, alternating constipation and diarrhea, fiery stools, umbilical hernia. It’s also about sleep troubles, tension, and difficulty with co-regulation. But the list does not stop here.

This work, whether done through mom or done directly for the child, can help with all of the following (and more):

• Gut issues of any kind — constipation, diarrhea, gas, bloating, belching, bottomless OR lack of appetite, straining, abdominal pain, reflux, colic

• Skin issues of any kind — eczema, hives, rashes, rosacea, dermatitis, molloscum, psoriasis, itchiness

• Picky eating

• Immune system struggles — allergies, frequent or prolonged illnesses, post-nasal drip, sore or swollen throat/adenoids, asthma, mouth-breathing

• Behavioral challenges — outbursts, ADD/ADHD

• Sensory issues

• Sleep troubles — difficulty falling asleep, multiple wakes, itchiness at night, night sweats

Pretty much all dysfunctional symptoms have roots in the gut and immune system.

The beauty about kids, too, is that they respond SO fast! As you saw, Anthony’s protocol was only six weeks long — whereas my own protocol has now been over three months long at the time of this published post. They are SO much more resilient. I like to emphasize this because it’s important for the empowerment of mom and/or dad — your child can heal. His/her body knows what to do, we just have to test for the right inputs.

I also help the parents along every step of this journey. I provide all the details about what the test results mean, we discuss each line item thoroughly, and I also discuss the protocol I’ve built from those results, line by line as well. I want you fully informed and comfortable because you, as the parent, will be administering supplements, helping your child through dietary transitions, and overall executing the entire protocol with and alongside them. I’m simply here to provide the information. Making it a success is alllllllllll you — and that’s a GOOD thing.

You want the person in charge of your child’s health to be the one who knows them best.

I can tell you from personal experience: it’s liberating, humbling, and so worthwhile.

If you have additional questions or concerns, feel free to comment on this post. You can also reach me on the Contact page, linked above in the header of my website.