One of the more frequent lab requests that I make in my practice is for stool testing. Why? Because it tells me a lot about what is going on in a child’s gut, without drawing blood or going under anesthesia for endoscopy or colonoscopy. In fact, you may be able to get more action and traction from the findings of this type of test, than from having your child scoped – an invasive, expensive, and challenging procedure. In that sense, it’s a lot of bang for the buck, and easy to do. You don’t even have to tell your child the test is being done (see how below), or leave home.
Often parents tell me, “This test was already done. Everything was normal.”
Here’s the thing: If this was done by your gastroenterologist or pediatrician, chances are that only the most serious bad actors were screened. These are things like Giardia, Salmonella, Shigella, certain types of E. coli, microscopic parasites (or bigger ones), or Campylobacter. These are super nasty microbes that usually trigger obvious symptoms like diarrhea or fever. They can be present with chronic, non-specific symptoms too. Among kids in my practice with this work up already done, finding one of these is somewhat rare.
Does that mean there is no problem? No. The old adage “if you don’t look, it isn’t there” fits here. Stool analysis is no exception. There is much more to assess than whether or not your child has an egregious infection. FPIES, constipation, diarrhea, difficulty potty training, food allergies, growth and feeding problems and more are conditions that are responsive to and dependent on gut microbes, digestive capacity, inflammation, and more. Detailed stool testing can look at all this. Why doesn’t your doctor use it? Mostly, because insurance doesn’t always cover the more detailed testing.
I’ve relied on this often to explore why a child is belly-bloated, has hiccups or reflux, won’t grow well, won’t each much, has unbeatable sugar cravings, or is painfully constipated. Stool testing in this realm includes assessing the profile of beneficial bacteria too, which can guide the use of probiotic supplements as well as foods to support healthier gut terrain.
This isn’t just for kids with active GI symptoms, pain, bloating and so on. It’s also a critical path tool for kids struggling with behavior.
Kids who have conduct disorders, anxiety, OCD, perseveration, volatility or even depression may have a gut biome that drives all of these problems. This is not new, or fringe theory; more and more evidence is piling up to support the gut-brain link. I have witnessed countless cases of this, and seen “psychiatric” features evaporate, with assessment of the gut biome environment followed by a targeted intervention to redirect it. Diet, probiotics, herbs and other supplements can help do this; in some cases, prescriptions for antibiotics, parasites, or antifungals might be needed.
Testing is available to include Candida screening (aka yeast or fungal species in the gut) in detail. Several labs specialize in not only characterizing how much fungal material is in a stool sample, but exactly what types are there (there are at least thirty different types of fungal species that my end up in a human gut) and what will kill them (prescription meds and herbal tools). Conventional tests may simply say yeast is present or not in a stool sample, or not even look for it at all. “It’s normal for a human gut to harbor some yeast”, your doctor might say. “It’s of no consequence, until it’s visible thrush, the white stuff coming out your child’s anus, or coating your child’s tongue.” But there’s more to it than that: How much yeast is normal? As it turns out, there isn’t clear consensus on this in the “standard of care” universe (that is, what insurance companies will pay for). Some kids also have antibody reactions to ordinary yeast strains, meaning that even small amounts in the gut will be quite irritating, behaviorally and for stooling or appetite.
Why does this matter? A healthy gut and immune system control yeast, keeping it to low levels. But many circumstances can leave the gut dominated by yeast – at the expense of healthier, friendlier microbes that we need for good digestion, absorption, and immune function. Symptoms of this scenario can include a chronically bloated belly, or large, hard to pass stools. It can trigger constipation so severe and digestion so sluggish that hospitalization is needed to remove fecal impactions. Others may experience fatigue, mood swings, behavior spikes, or diarrhea with yeast overgrowth in the gut. Yeasty guts also drive rigid appetites that keep kids eating starchy, sugary, empty foods and away from nourishing foods rich in minerals, healthy fats, and protein. All of this can be going on with no particularly notable changes on usual lab tests. Can it really be that bad? I have encountered one case in which a child needed hearing aids by age 10, due to an unertreated, chronic fungal overload. As his mom explained, serious intervention wasn’t offered until “the white stuff was coming out of his ears.”
It gets worse: Once well settled in a human gut, yeast microbes can shift to a mycelial form that behaves like ivy growing up a chimney: It roots into the intestinal wall, making micro-perforations, akin to how ivy anchors itself in the mortar between bricks. This makes the gut too permeable, too permissive. Larger molecules than are normally allowed can pass into circulation, triggering reactions to foods. Voila: You’ve just created a food allergy or sensitivity, thanks to a “leaky gut”. Other gut infections and conditions can create leaky gut, but for sure, yeast is a player that must go if you want better feeding, growth, digestion, and absorption for your kids.
Besides seeing the fungal burden in your child’s gut, many markers for digestion and inflammation can be included, along with extremely sensitive DNA screening for microscopic helminths and parasites. Your doc may say these don’t matter, and we all carry them. But what I have observed time and again is that for underweight small children, they do matter, and can mean the difference between only tolerating three or four foods without reactions and growing poorly, to digesting many foods well and gaining and thriving. Every kid is different.
Working with a provider experienced with this testing can save time and trouble. No single test can answer all the questions, and all tests have limits. These tests are no exception. A helpful back up is a urine microbial organic acids test, also available to collect at home. This test picks up by-products of toxic microbes, rather than detect the microbes themselves. If the toxins are present in urine, then the microbe is active somewhere in the body, perhaps beyond the gut. Still, viewed in the context of the child’s food intake, growth pattern, and other signs and symptoms, I’ve found detailed stool tests to be one of the most helpful tools in my practice – especially for detecting yeast overgrowth and possible Helicobacter pylori infection that nobody had yet noticed.
Fun fact: Blood-draw antibody tests for H. pylori are a less reliable way to discern active infection, but they are commonly used for that purpose. H. pylori is a disruptive microbe that can trigger ulcers, reflux, and weak digestion; it can handily establish itself in the digestive tract in children with weak nutrition or poor growth status.
How to collect a stool sample without telling your child
Got a nervous kiddo who doesn’t want you messing with his poop (who does?)? Here’s how to capture a sample:
- Drain the water out of the toilet, by shutting off the valve behind the toilet.
- Then flush it, so it empties out its water, and doesn’t refill.
- Secure a generous hammock of plastic wrap loosely across back two-thirds of the toilet bowl, and close the seat (not the lid) over it. The idea is to let the stool sample fall into the plastic, with little or no contact with toilet bowl water.
- If necessary, remind your child not to flush the toilet (some kids don’t anyway).
- Once the sample is in the toilet, lift the plastic with the sample out of the toilet bowl, and follow instructions in your home collection kit from there. Don’t forget to fill your toilet bowl again with water by opening the spigot behind the toilet!
Do kids need to know? Unless your child enjoys this scrutiny and detail (doubtful), which many will not understand anyway, they don’t need to know. Who wants their poop scrutinized and discussed? Nobody, frankly. For older kids or kids who are the more vigilant type, if they must know or are likely to notice, the simplest, plain, and least invasive information is best. Let them ask questions if they need more information. “The doctor is looking for anything that could make your stomach hurt” may suffice for younger ones. Err on the side of less, not more.
Long short, if your child has had GI consults and no results, consider more detailed functional stool analysis. I have a number of tools at my disposal for this and can help you complete this testing. It may yield enough new information to help your child access effective support and treatment, so they can feel better, eat healthier, and thrive.
Hello. Thank you for the useful article. Do you know where and how specifically can I order detailed functional stool analysis for my child? It does not seem like his pediatric office would do it.
Correct, most pediatricians will do a simple stool screen for parasites or bacteria that may cause food poisoning, but that’s about it. To get a detailed analysis, work with a functional medicine provider, integrative dietitian like myself (though my practice is full), or a naturopathic doctor (ND). You might also be able to obtain a test kit at sites such as My Med Labs but you will still need an experienced practitioner to interpret the findings and guide next steps.
9 month old who is breaking out in what looks like a herpetic rash. She is not irritated by it and physician felt it was viral. However I have noticed that her rash reddens with different foods and also it coincided with changing from breast milk to formula. Will a stool test help determine if she may have an imbalance or intolerance to some foods?
This does sound viral. Has your baby had 9 month doses of MMR or Varicella (in the US, we give those earlier than many other countries)? If so then I would suspect she is shedding these viruses from her shots. This should be transient. Switching to formula can be part of this also for sure. If this was the culprit, some GI distress would likely be in the mix, and you haven’t mentioned that. She’s too young to test for food intolerances, but if hives develop, ask your doctor for skin prick testing to foods.
Would a 2 year old consistently (probably 95% of the time he poops for the last year) having green poop be a reason to get a stool test? What specifically should/could be tested for if so?
Hi Allie, unless your child is eating a lot of green or blue foods (blueberries?) then I would run this by your pediatrician and/or GI doc. One possibility with green stools is that food is moving too fast through the gut. In this situation bile isn’t able to do its job very well because motility is too fast. Bile doesn’t get reabsorbed like it should before stool moves in to the colon, leaving stool more green. Another possibility is viral burden. This can turn stools green too. Lastly certain formulas can make for more greenish stool, especially elemental formulas like Neocate, Elecare, or PurAmino. Ask for a stool study to assess fecal fat or steatocrit, pH, and elastase at list. Your child should be gaining and growing well too.
Does a toddlers stool test show the inflammation markers
Any stool test that includes a marker called calprotectin reflects inflammation, regardless of age. Other markers that may suggest inflammation are stool level of IgA (immunoglobulin A), zonulin, mucus visible in stool, or occult (microscopic) blood.
Son is 2 years old has had alternating constipation to diarrhea. For over a year. 6 months ago had thrush and ear infection has speech delay. Has random giggle fits want to test for candidia overgrowth but dr won’t
My son is 2 he has had constipation/ diarrhea since he was 11 months old. The stool always have strong smell. He has an ear infection and thrush 6 months ago. He has eczema He is developmental delayed in speech. He has giggling fits for no reason. He has problem sleeping. I’m wondering about yeast overgrowth dr won’t test his stool
Your doctor may not know how to test for yeast, and/or, may have been trained that this is not an issue unless white fluffy stuff is coming out of anus and coating tongue. What you describe is consistent with intestinal candidiasis. You can try some antifungal herbs if you like, as probiotics alone don’t usually impact this when symptoms are as active and entrenched as you describe. Usual tools are grapefruit seed extract (not to be used if your son is using any medications), goldenseal (berberine), caprylic acid (also known as C8 oil), houttuynia cordata, and many others. Ideally speak with a naturopathic doctor who is trained in using these in young children. These are pungent and don’t do well administered directly into mouth, so get help with how to give them to your son.
My son is 2 he has had constipation/ diarrhea since he was 11 months old. The stool always have strong smell. He has an ear infection and thrush 6 months ago. He has eczema He is developmental delayed in speech. He has giggling fits for no reason. He has problem sleeping. I’m wondering about yeast overgrowth
My son is going to be six next month. He is very active energetic kid. Sometimes I feel like may be he has ADHD. He is very intelligent but he doesn’t like to stick with one thing for long time. I feel like he never gets tired although he is playing outdoor every single day.
Can I get his stool examined so if I could find if there is something I need to work on.
Hi Linta, I don’t offer lab tests to families who are not working with me as clients, but follow me on Facebook for updates on click-to-learn material I will be building for parents. You can possibly obtain a stool study from sites like AnyLabTestNow.com or MyMedLabs.com.
Hi Judy, My daughter is 4.5 years old and we have been struggling her whole like with her gaining weight and not being able to go to the bathroom. her doctor just sums it up to her being small because i am small myself. Also she’s a great eating isn’t very picky at all. We changed her diet to dairy free 8 months ago, and that helped she has gained 3 lbs she is up to 24lbs now, but her ora still consists of her being very agitated, horrible stomach pains and extremely constipated and excessive amount of gas.
Hi Jana, glad you’re seeing some growth/gain. Contact me if you’d like more help through my contact form here, and my assistant will get back to you to set up an appointment.
My pediatrician requested a stool sample from our infant and I’m a little concerned.
Is this common?
My daughter is 17 weeks old. She has been refusing to eat while she’s awake for the most part since early October at about 8 weeks old. Since then we have been scrambling to figure out what is going on with her and why she won’t eat. From about 2 weeks of age she started showing signs of reflux. Arching her back after feeds, crying (not always but usually in the afternoon), making a grunting noise after feeds, not sleeping well etc. We tried to go med free until she stopped eating at 8 weeks old. She went from drinking 5oz or more of breastmilk at a time to barely able to take 2 oz at one feeding. If we tried to get her to take more she would projectile vomit everything back up as if all the sudden her stomach was too small to tolerate what she had been taking before. At the point we knew we had to address her symptoms more aggressively with medication to get her out of pain and able to take food. She was prescribed 10mg of omeprazole which seemed to help her reflux symptoms around day 4 on them. However, she then started showing signs of digestive distress. Grunting and straining to poop, going red in the face and becoming very frustrated and then when she would finally poop, it was soft. Her poop went from being normal seedy yellow and sweet smelling to orange, very loose and mucousy with a very foul smell. Her straining wakes her up every night usually at the same time. After being hospitalized for a week for observation, her doctor has her on 10mg of nexium 2x daily. She has only had an upper GI done and the doctor refuses to do any other kind of testing saying he thinks it isn’t necessary. So basically she’s on one of the strongest medications at a pretty substantial dose, having awful, painful poops and she is still not eating. I don’t know what more he needs to see that further testing is absolutely necessary. Do you have any recommendations? Is there a way to order the stool analysis without the doctor requesting it? A few facts: she has been on breastmilk only (we tried other formulas very briefly to rule out an aversion to taste but she refused to take any formulas we tried even more than the breastmilk), I have been on a total elimination diet for a little over a month with no improvement in her diapers, she is also taking Klaire Labs Infant Ther-Biotics although she has only been on them for a few days. Any guidance would be so much appreciated! Thanks.
Hi Jennifer, you’ve given me a lot of history and asked for professional guidance – unfortunately I can’t do that in this forum. I’m happy to help if you’d like to make an appointment, you are welcome to schedule that any time via my calendar here.
Thanks for sharing Kristi, good to rule this out indeed. Pyloric stenosis is not normal either. Common perhaps, but not normal, and it’s always worthwhile to resolve less invasive triggers that may exacerbate this, such as hepatitis B vaccine dose or Rotavirus vaccine dose, antibiotics prior to, during, or after delivery, milk protein intolerance, FPIES or other gut inflammation sources.
I know this was posted a while ago however, my son, age 3, tested positive for yeast in his stool. He has been having issues with weight gain and recently has been identified as failure to thrive. He is only 25 lbs. Have u seen a correlation between failure to thrive and yeast in stool?
Yup. And I have seen many, many who children flopped on usual interventions for failure to thrive – because their care teams did not include optimization of gut environment (flora and metabolome) with the right foods and supplements.