A C-section and early antibiotics shaped this child's IBS

1DemographicsStop 1 of 8

Who Johnny is

Johnny was 5 years old when his mother, Helen, brought him to the clinic where I work as a scientific collaborator. He had been born by a planned caesarean section and was breastfed for two weeks.

• 5 years old
• Boy
• Born by C-section
• Breastfed for 2 weeks
• 10 antibiotic courses by age 5

His main complaints were frequent diarrhea, tummy pain, bloating and allergic rashes. The full case is described in the book IBSyncrasy.

2IntroductionStop 2 of 8

Why the first years matter for the gut

From birth until about the age of three, a child's gut bacteria, gut immunity and future risk of disease are still taking shape. The way a baby is born, how long and how it is fed and how many antibiotics it receives all leave a mark on this process.

The start differs with the mode of birth. Babies born vaginally pick up bacteria that resemble their mother's vaginal bacteria, while babies born by C-section pick up bacteria that resemble skin bacteria.² In a large UK study, babies born by C-section received fewer of their mother's Bacteroides strains and were more often colonized by hospital-associated bacteria, including Enterococcus, Enterobacter and Klebsiella.³

Feeding matters as well. In mice, the secretory IgA antibodies in breast milk shaped the gut bacteria and the gut lining well into adulthood.⁴ Antibiotics are the third factor. In Finnish children aged 2 to 7, macrolide antibiotics were linked with a long-lasting shift in the gut bacteria.⁵ More on these early influences is in C-section, allergies and asthma and in breast milk, formula and the microbiome.

IBS itself is not rare in childhood. A review of 58 studies with almost 200,000 children found functional abdominal pain disorders in 13.5% of children, and IBS was the most common of them (8.8%).¹

3MeetingStop 3 of 8

Meeting Johnny

Johnny was born in December 2011 by a planned caesarean section. His birth assessment was very good, with a perfect APGAR score and no jaundice, and he was breastfed directly. His newborn screening for 45 metabolic diseases was clear, and he left the maternity ward three days later.

Helen stopped breastfeeding two weeks after his birth and moved him to a cow's milk formula. Two weeks later, Johnny developed rashes on his legs and tummy. The pediatrician considered a milk allergy and changed the formula brand, and when the rashes continued, suggested a soy formula. The rashes cleared, and until six months of age all went well.

At six months, Johnny started solid food and, at the same time, caught a viral infection that led to a 7-day course of antibiotics. After that course, Helen noticed that he was passing stools more than three times a day. This is how it started: diarrhea, tummy pain, blood in the stool, poor weight gain, many tests and many more antibiotics, until they came to see me.

Looking back, four factors had built on each other.

C-section birth

His gut bacteria started from a different template than those of a vaginally born baby.²

Two weeks of breastfeeding

He missed months of the antibodies and nourishment for gut bacteria that breast milk provides.⁴

Repeated antibiotics

Ten courses by the age of 5 kept disturbing a gut community that was still forming.⁵

Diet and sleep

His daily routine left little room for the gut lining and its bacteria to recover.

4DiagnosticsStop 4 of 8

Diagnostics: ruling out the serious first

Finding the cause of tummy pain in a child is not easy. At the age of five, stool and urine samples are simple to collect, but a blood draw needs preparation, so children are best prepared for it days ahead. The first task was to rule out anything serious. Johnny had a full blood count, thyroid tests and celiac antibodies, among others, while a molecular stool test of his gut bacteria formed the core of the assessment.

Other details completed his picture:

• Frequent gastroenteritis
• C-section birth
• Breastfed for only 2 weeks
• 10 antibiotic courses by age 5

5ResultsStop 5 of 8

Results: what the stool test showed

Johnny's tests showed no serious metabolic or hormonal problem. His gut bacteria, however, were far from healthy. Beneficial populations were almost absent, while Bacteroides vulgatus, Klebsiella pneumoniae and E. coli were very high, and many other bacteria were at moderate levels. Candida was 100 times higher than normal. Neutrophil inflammation markers were normal, but eosinophil protein X was very high, which fitted both his diarrhea and his allergies. Fat in his stool was high, vitamin levels in his blood were low, and secretory IgA was below normal in both stool and saliva.

Of the 9 results we reviewed, four guided the care plan.

High eosinophil activation in stool

Ongoing eosinophil activation drives allergic-type reactions in the gut and elsewhere in the body.

Low vitamin levels

His body was not using vitamins and nutrients well, and his gut bacteria were making fewer of the cofactors they normally provide.

Low secretory IgA

Secretory IgA is the gut's first line of defense, and low levels fit his frequent gastroenteritis and other infections.⁶

Low levels of beneficial bacteria

Few beneficial bacteria (what I call probiotic sterility) had settled in his gut from the start.

6Care planStop 6 of 8

Care plan: gradual change

Johnny had already received many antibiotics, so his plan used a plant-based antimicrobial blend instead. Restoring a gut that has been different from the start is a slow process. To avoid strong side effects, the harmful bacteria were reduced gradually, while beneficial bacteria were brought in step by step to take their place. At the same time, the vitamins found at very low levels were replenished, since he was in a fast phase of growth.

Every case is different, so Johnny's plan describes his care and is not a plan for any other child. Any treatment for a child is best decided with the child's pediatrician.

7Follow-upStop 7 of 8

Follow-up: sleeping well again

The family had done a good job with his diet, and Johnny had gained 1.5 kg. A repeat test of eosinophil inflammation was clearly encouraging, as the value was now within normal limits.

What pleased Helen most was that Johnny now slept well at night and seemed rested and happy during the day. Over the next two months, our appointments were short, as he kept improving. At the six-month visit, his bowel function was very good, and his diarrhea had stopped the month before. I encouraged Helen to keep up the good work and, for as long as possible, to keep dairy, ice cream and soft drinks to a minimum.

8ConclusionStop 8 of 8

Conclusion: a critical window

Cases in children are always demanding. Both children and parents need to learn early how to eat and how to protect a gut that is still developing. The first six months, before solid food, are especially important, which is why mode of birth, breastfeeding and antibiotic use matter so much for later gut health. After solid food starts, the differences between well-nourished and predisposed babies shrink, but this early window still sets the course for years.

What Johnny's case shows

• The mode of birth sets the starting template for the gut bacteria.^{2, 3}
• In my practice, diarrhea and allergies are a common pattern in children born by C-section who were not breastfed, while constipation is less common.
• Breast milk feeds the gut bacteria and supplies antibodies that help shape them.⁴
• Antibiotics in early childhood can shift the gut bacteria for a long time.⁵