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Gut Check looks at health claims made by studies, newsmakers, or conventional wisdom. We ask: Should you believe this?

The claim:

Delivery by caesarean section alters a baby’s microbiome in a way that increases the risk of becoming obese and developing asthma or other allergies.

Tell me more:

The explosion of research on the microbiome — bacteria and other microbes that live in us and on us — has linked these bugs to ills ranging from mental illness to heart attacks. Lately, studies have suggested that how we’re born helps determine the composition of our microbiome, since vaginal birth exposes the baby to bacteria in mom’s birth canal, while caesarean section doesn’t.


Back in 2006, scientists reported that babies born through C-section had lower populations of entire groups of bacteria (bifidobacteria and Bacteroides, for you microbe lovers) and were more likely to harbor dangerous bugs like C. difficile, compared with babies born vaginally (possibly because they had fewer “good” bugs to out-compete C. difficile). A 2016 study reported that C-sections (as well as mom’s use of antibiotics during pregnancy and formula feeding) alter babies’ microbiomes.

The microbiome that a newborn carries into the world may matter for health. Last month, scientists reported that children delivered by C-section were 15 percent more likely to become obese. Although the study didn’t measure microbiomes, it’s been interpreted as supporting the claim that C-sections, by depriving newborns of exposure to the microbiome in mom’s birth canal, put babies at risk for health problems.


But are such problems the fault “of the caesarean or of the company that caesareans keep?” asked Dr. Kjersti Aagaard, a maternal-fetal medicine specialist at Baylor College of Medicine and senior author of a new paper questioning the caesarean-microbiome-health link.


Caesareans do keep lots of unusual company. That is, many factors that raise the risk of C-section are also associated with an altered fetal microbiome.

Although scientists used to think that babies were first exposed to mom’s microbiome during birth, it turns out they’re bathed in it in utero. “The fetal microbiome is established during gestation,” said Aagaard. As a result, factors that drive caesareans — but not the caesarean itself — might also alter a fetus’s microbiome.

For instance, obese women have higher caesarean rates. So do women with diabetes and whose fetuses tip the scales. Factors that can cause obesity, diabetes, and large fetuses, including mom’s calorie-dense diet during pregnancy, can change a fetus’s microbiome from what it would have been if mom ate more healthfully and controlled her weight, according to monkey and human studies. That means C-section babies might have had the microbiomes they did even if they had been delivered vaginally: The factor that led to a caesarean also altered the microbiome.

“A high-calorie maternal diet both disturbs the establishment of the infant’s microbiome and can produce a large baby who cannot safely fit through the birth canal,” said Aagaard.

Gestational age alters the fetal microbiome, too. Bacteria in the placenta vary over the nine months in utero. Preterm delivery is often by C-section. Therefore if a newborn has a skewed microbiome, it may be because she was born too soon, not because she wasn’t exposed to mom’s vaginal bacteria.

Caesareans also “keep company” with microbiome-altering factors after the baby is born. Babies fed only formula are more likely to harbor certain bugs that breastfed infants don’t. If caesarean babies are more likely to be formula-fed than breast-fed, as a 2016 study found, then their altered microbiomes might be due to what they eat and not their route out of the womb.

There’s one more reason to be cautious in blaming a child’s health problems on his microbiome at birth: Differences in the microbiomes of babies born through caesarean or not seem to disappear over time, making it unlikely that the microbiome at birth affects health long-term.

The verdict:

Research to date falls far short of proving that a caesarean birth alters a baby’s microbiome in a way that hurts later health.

  • A thoughtful analysis. Perhaps further studies will better define the best approach.
    Twenty years ago, we didn’t/couldn’t even study the microbiome, so perhaps in another twenty years we will have more supporting evidence that vaginal birth is best for reasons that we don’t fully understand at present. “First do no harm” We should consider the baby’s microbiome also, when deciding whether or not to perform a C-section. The foundational species present in the vagina, right before birth, are there for a reason. Just because we don’t fully understand those reasons yet, we shouldn’t cloud our judgement . It’s been argued that C-sections are playing a role in why the average American is losing beneficial species of bacteria.

    I also would like to recommend the recent book, “Dirt is Good”.

  • And what about C-section babies who are breastfed??
    Did the study compare them to breastfed babies via vaginally deliveries, or to other C-section babies??
    What opening hypotheses did the study use to determine its research factors? Cause or coincidence??

  • C-sections are done for many reasons. To choose the newborns’ possible exposure to beneficial microbes over the definite risks to maternal health in such cases is nuts. But it does sound like something “pro (fetal) life” advocates would insist upon…

    • Thanks for giving a thorough and succinct picture of what all might affect the microbiome that could also correlate with the event of a C-section. I wonder if a focus on the promotion of better pregnancy health in general would both help improve fetus’s microbiomes and decrease the occurrence of C-sections.

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