Is Picky Eating Caused by Gut Bacteria?

Picky eating may be caused by gut bacteria

Feeding his gut bugs

Preface:  Much of this article on the connection between picky eating and gut bacteria is based on observation by health practitioners rather than hard scientific research. So far. Perhaps this is because many of the other healthy conditions related to gut bugs are diagnosable medical conditions (such as allergies, asthma, eczema, diaharrea, obesity etc.), while picky eating is widely considered a vague complaint.  However, for those of us living with a pathologically picky eater, the distress feels as great as plenty of other diagnosable medical conditions.  I will continue to follow the news in this area and update this article with as scientific developments in the field emerge.

How do Bacteria Colonize the Gut of a Young Child? 

We all have bacteria living in our bodies – up to 100 trillion microorganisms (including bacteria, fungi and viruses) in any one of us (while we only have an estimated 10 trillion  human cells in our bodies).  The bacteria, fungi and molds living in our guts are called the gut microflora or the microbiome and it is estimated that we all have between 3 and 6 pounds (1.3 – 2.7 kg.) living in our intestines at any time!

Many of these bacteria provide health benefits to their hosts and are called probiotics (which means “for life” in Greek) or as we like to call the good ones that live in our guts, healthy gut bugs.  The microbiome  and humans have actually evolved together, as scientists are starting to find out.   Some bacteria that live in our bodies actually perform functions necessary for human life that the human body cannot do itself.  For example, the gut bacteria living in the large intestine produce Vitamin K, a vitamin essential for clotting.

Babies, who are bacteria-free in utero, get their first exposure to healthy bacteria from their mothers.  They pick up helpful bacteria as they pass through the birth canal. Additionally, beneficial (probiotic) bacteria are passed from mother to child through breast milk.

The intestinal colonization of bacteria is normally stable by about two months of age.  Once established in infants, the mix of bacteria in the gut tend to be relatively stable in that person throughout life.

Events in Infancy Impact Colonization

Disclaimer: I must preface this section.  I am fearful about even writing about the topics in this section as I don’t want to be the cause of a single iota of increased maternal guilt (we all have more than enough of this already, and I for one suffer greatly from it).  Being a new parent is a minefield of self-doubt and paternal guilt over decisions we made or didn’t make.  My goal in this discussion is instead to provide possible explanations for parents looking for answers to gut bacteria related issues that their child may be suffering.  Many a mother and child would have died absent prompt administration of antibiotics, C Sections, admittance to the Neonatal Intensive Care Unit (NICU) and infant formula.  This group includes both of my children and myself.  Protecting the life of a baby or mother is much more important than concerns around gut bugs! 

Factors related to the method of birth and early feeding can impact the mix of gut bacteria that a newborn is exposed to and which bacteria, fungi and molds eventually colonize themselves in a baby’s gut.  Studies have confirmed that delivering babies by Cesarean Section and feeding them formula exclusively, influences their gut microbiomes.  A few studies have found that babies delivered by C. Section had a lower diversity of beneficial bacteria, such as Escherichia-Shigella and Bacteroides species.  Exclusive breastfeeding during the first week of life promotes Bifidobacteria, which are good bacteria that can reduce gut colonization by harmful bacteria.

Other research concluded that exclusively formula fed infants (no breastmilk) had a higher incidence of harmful bacteria such as Clostridium difficile in their stool than breastfed infants.  The researchers wrote, “”Breast milk, rich in prebiotics, selects for persistence of beneficial bacteria and limits colonization of harmful ones,” they wrote.  “The strong selective pressure of breast milk is demonstrated by the lower diversity of microbes in the gut of breastfed infants than in the gut of formula-fed infants.”  If a nursing mother takes antibiotics, this also can impact healthy colonization by probiotics early in a baby’s life.  Delivering a baby by C Section or feeding a baby exclusively with infant formula may reduce baby’s first exposure to friendly bacteria and is now believed to affect the mix of bacteria that eventually get established in a child, potentially increasing the number of harmful bacteria and reducing the number of beneficial bacteria that would otherwise be found there.

Studies of the intestinal flora of babies who were in the NICU after birth have shown that the bacteria colonization reflects exposure to unhealthy bacteria in the NICU and not healthy bacteria normally acquired from the mother after the birth.  Admittance to the NICU can impede healthy colonization of the gut.


Antibiotics are a wonder of the modern world.  They have greatly increased human survival and many of us, including me, would not be alive today without them.  They are very effective at killing harmful bacteria, but the antibiotics are a crude weapon against disease – not only do they kill the disease causing bacteria, they also kill many beneficial bacteria living in the person who takes them.   They are indiscriminate bacteria killers!

Since the probiotics living in our bodies, outnumber even our own cells, taking antibiotics that will kill many of the healthy bacteria, which are vulnerable to that antibiotic, can have unintended consequences.  Taking a course of antibiotics can cause other unhealthy bacteria, such as C. diffiicile, which can cause life-threating diaharrea, to proliferate when the healthy bacteria that normally compete with it in the gut are eradicated.  Common wisdom always held that eventually the healthy bacteria would return and that the gut would return to its pre-antibiotic bacterial mix over time.  Current research has shed doubt on this however.

In an article published in Nature, Martin Blaser of New York University’s medical school writes that the friendly gut bacteria never fully return and that antibiotic resistant gut flora can proliferate with permanent, serious health consequences.  He recommends that for this reason, antibiotics should be used sparingly in pregnant women and young children.  A dose of antibiotics may permanently reduce the number and variety of healthy gut bugs in a young child that takes them.


What do Gut Bugs have to do with Picky Eating?

Gut Bacteria Influence Appetite

There is a well-documented connection between the gut and the brain.  Each of us has a Vagus Nerve that transmits signals between the gut and the brain.  A study in the Journal of Bacteriology proposes that gut bacteria actually influence or even control the foods that a person craves. We all have bacteria living in our digestive systems and the bacteria living in our guts eat what we eat.  They may even “eat” before we do.

Researchers writing in the Journal of Bacteriology theorize that that certain bacteria “crave” particular kinds of food and the gut bugs can communicate, perhaps through the compounds they produce, with the brain via the vagus nerve and actually influence the kinds of food that a person chooses to eat.

It seems to follow that if someone has an imbalance or overgrowth of certain unhealthy gut flora, those unwelcome gut bugs might lead him to crave particular types of food that is also “craved” by those types of flora (either bacteria or fungi).

By way of example, Candida albicans (“Candida”), a yeast that commonly occurs in food and in the human gut, is not a bacteria, but a fungus. Hence antibiotics do not kill it.  When the bacteria that it normally competes with it for space and nutrients in the gut are wiped out by antibiotics, Candida can proliferate and become an overgrowth in the gut.

As those of us who bake bread or pastry already know, yeasts need sugars and carbohydrates.  If an adult has a yeast-heavy gut biome, that person may be able to override gut-influenced cravings and still eat a healthy mix of foods.  But when young child has a Candida overgrowth, it may cause him to have unhealthy cravings.  We think this may have been the case with our own son, who pretty much exclusively craved simple carbohydrates (pasta, rice, tortillas) and dairy (butter, milk, cheese).

It can be very difficult, if not impossible, to convince a child experiencing such Candida influenced cravings to eat a healthy range of foods. Other gut flora can influence appetite as well, it is believed.  Thus an unhealthy mix of gut bugs might be one cause of extremely picky eaters who crave only limited types of foods.

How to Help an Appetite Influenced by Unhealthy Gut Bugs

Probiotics Stimulate Appetite and Increase Healthy Gut Bugs

Extremely picky eaters often also have weak appetites.  A groundswell of belief is arising among practitioners in the medical and nutritional fields, that has yet to be extensively scientifically tested in humans (but has been in animals such as rats), that supplementation with certain probiotics can increase appetite in extremely picky eaters, and consequently improve some of the fussiness.  This makes sense as probiotics can aid in food digestion.  Interestingly enough, there is some very exciting recent research on the link between gut bugs and obesity.

Additionally, taking probiotics can increase the numbers of beneficial bacteria living in the gut microbiome – which can crowd out some of the bad gut bugs.  Increasing the number of healthy gut bugs can also potentially influence and expand the types of foods that are craved by the picky eater (by means of the brain gut connection discussed above where gut bugs influence food cravings).

Supplementation with high quality probiotics is the advice that our pediatrician gave to us.  The consensus seems to be that at least 20 billion Colony Forming Units (CFUs) are required to affect appetite.  A probiotic containing a mix of some bacteria that are often recommended for appetite stimulate would be a good choice.    Often mentioned are: bacteria from the Lactobaccilus family (such as: L. acidophilius, L. casei, L. fermentum L. rhamnosus, L. reuteri) and Bifidobacteria.  But, be reminded that little is truly known about this subject, so more research and sharing of knowledge is needed (hint: please comment below or post in our forums).

Probiotic Supplementation to Reduce Unhealthy Gut Bugs

Depending on the mix of gut bacteria, it might be necessary to not only increase the number of intestinal probiotics, but also to actively attempt to eliminate some of the unhealthy bacteria, fungi or molds.  For picky eaters who crave starchy and sweet foods only who may have an excess of Candida affecting their appetite, Saccharomyces boulardii (S. Boulardii) has been proven effective against yeast overgrowth in the gut. S. Boulardii is available as an over-the-counter probiotic.  Anti-fungal medication have been found to be effective against intestinal Candida infections and can be obtained by prescription from a doctor.

In Conclusion

There can be many causes of picky eating.  Physiological factors, personal temperament, sensory issues, psychological aversions and habit are potential causes.  In certain cases, however, it appears that the mix of flora that have colonized a child’s gut may contribute to extreme picky eating.

Our pediatrician once mentioned to us in an off-hand way that the issue of picky eating seemed to be a first-world problem that wasn’t seen in the third world where there were issues of hunger.  At the time I interpreted that as his implying that indulgent parenting in the first world created this issue.  However, upon further reflection after doing a lot more research, I think that there may be something to what he said.  If it’s true that gut bugs affect appetite and it’s also true that exposure to medical interventions that are widely available in the first world (such as antibiotics, NICU and C sections) can impact the colonization in child’s gut by healthy gut bugs, then it would make sense that picky eating was more commonly seen in first-world children.  It’s an example of the law of unintended consequences.

For our family, I strongly suspect that this is what caused our issue with picky eating.  My two-week-old son had a massive course of antibiotics, which I believed disrupted his gut microbiome, and which was first evidenced by the onset of colic following the antibiotics.  The almost total refusal of breast milk and all food other than starchy or sweet foods after that was our next clue.  The fact that the probiotics seem to have made such an improvement in his eating, adds weight to my suspicions about what caused the problem.

However, even if I knew then what I know now I would still have given him the antibiotics.  He was struggling to breathe and could have died without them.  What I wish I had known then was that I could have given him probiotics during and after the course of antibiotics, which could have replaced the healthy gut bugs being wiped out by the antibiotics before the bad gut bugs took such a strong hold. More and more doctors are recommending this when they prescribe antibiotics.   I wonder if that would have made a difference….

This is a new area of medical inquiry and I will continue to follow it and post any relevant updates.

I hope you post your picky eating story in the comments below.

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  1. Jon says

    Our son with possible data useful to this article is almost 3. Born in July 2012.

    He began to become a picky eater in May 2013. He is totally different now after one week on probiotics in May 2015.

    Probiotic that was prescribed for other issues and accidentally worked is:
    Bacillus clausii (Enterogermina), 2 billion spores per dose.

    He took 2 doses of the probiotic per day for the first four days and has taken 1 per day since (for three days and counting). We will try to stop and see if his interest in food holds after ten days.

    He was born at home. He is still breast feeding. He has never had formula. We made our own baby food for him at home (purees of everything from green beans to beets, small watermelon chunks, et cetera).

    Until this past week, he didn’t want to drink anything except water and his mother’s breast milk. The only caveat is he has had some interest in cereal with milk the last few months, but wouldn’t drink milk otherwise.

    Three things were going on in May through September 2013 that may have impacted his progressive change to being picky:
    1) My wife was pregnant with our second child (from December 2012) and the quality of her milk may have declined during pregnancy.
    2) In May 2013 our older son had bread for the first time and loved it. He became so infatuated with it that we baked him bread at home.
    3) When my wife’s new milk came in after the birth of our second son in September 2013, our older son was highly vested in breast feeding as suddenly there was a new flow of nutrition after he got through a number of “lean months” with lower quality milk.

    We accidentally got the probiotic when he contracted a stomach virus two weeks ago and it was prescribed alongside something else to calm his stomach.

    Since he got the probiotic, his appetite has markedly improved and the diversity of food he is interested in has broadened. Prior to being sick, he was mainly interested in starch and sweets (french fries, pizza, pasta, cookies, ice cream and their like). He is now eating a range of fruits and is showing a greater interest in protein/meats/poultry than we’ve ever seen in him.

    I found this article on a Google search because my wife and I never heard of anyone recommending probiotics as a solution to a child being a picky eater and were curious if there was any data to support the theory.

    Thank you for doing this work.

Your comments are encouraged. Please share your story.