Experts: Fecal Swabbing Could Rescue the Microbiomes of C-Section Infants

Sam Westreich, PhD

The healthy, doctor-advised move may be to give babies a taste of their own medicine, the little shits
If a baby is ever suspiciously happy, it's time to check the diaper.Filip Mroz/Unsplash

Babies are well known for being great at three things: crying, pooping, and turning their parents’ lives upside down.

But while babies are totally fine to cause lots of stress to their parents, they don’t happen to be great at handling stress, themselves. Babies are fragile, with a weak and barely developed immune system, and there are lots of diseases that can take advantage of a baby’s vulnerability.

What if we could make babies stronger, more resilient, by applying a salve to them? What if this salve could:

  • Improve their immune system
  • Lower their chances of developing allergies
  • Reduce their chances of developing auto-immune diseases in later years
  • Help prevent juvenile arthritis (yeah, it’s a thing)
  • Lower chances of developing type II diabetes or obesity, for years to come
  • Potentially help improve brain development and avoid neurodevelopmental disorders

Wow, that’s some pretty amazing salve. What’s in it?

Oh, shit?

Literally shit?

Gosh, this sounds like a joke, the sort of thing that would be published in The Onion. But there’s a large body of evidence, many peer-reviewed studies, that suggest that one of the best things we could be doing for newborns is to wipe them down and fill them up with a bit o’ poop.

Before you write your angry comments, check out the science behind it. It all comes down to one word:


Here’s where it comes into play.

Baby’s first bacteria

No matter how many times you wash your hands, you aren’t sterile — and neither is your baby.

In fact, babies have bacteria and fungi co-existing with them even before they’re born. Evidence strongly indicates that the human fetus, before birth, still has bacteria living in the womb alongside it.

But the first big batch of bacteria that stick around on the baby for a significant amount of time are seeded at birth — literally. When a baby is born, as it travels out the birth canal, it’s exposed to a mixture of vaginal and fecal-associated bacteria, seeding its own microbiome and adding bacteria to both its skin and its gut.

By the time a baby has its very first poop, it’s got bacteria living in its gut.

But not all babies make the journey down the birth canal. C-section babies are not exposed to the same bacterial seeding sources as vaginally born infants — and it shows in their microbiome.

And this effect sticks around. For months to years afterward, examination of an infant’s microbiome can reveal whether that child is consuming breast milk or formula, and whether that child was born vaginally or via C-section.

Certain bacteria, such as Lactobacillus crispatus, Atopobium vaginae, and Gardnerella vaginalis, are found in the vaginas of mothers — and then show up in the infant’s first stools, hours later. Other bacterial species that are in the infant originate in the mother’s bowel, as there’s a noticeable overlap in bacterial species present in the vagina versus the rectum/lower bowel.

Evolution has created a great two-part system for ensuring that infants have a healthy, balanced gut microbiome:

  1. Expose infants to the right bacteria at birth through exposure during the birthing process;
  2. Provide a complex nutrition source in breastmilk that contains complex sugars to further encourage the growth of those selected bacteria.

How can we make sure that, in our modern world, we preserve both components of this system?

Expose them early — the window closes fast!

One of the challenges of seeding an infant’s microbiome is that, from the moment the contractions begin, a clock is ticking.

Microbiome researchers know that no surface remains sterile for long. Bacteria are everywhere, and they can take advantage of nearly any environment to not only survive, but thrive.

When a fresh baby is born, it’s a gold mine, prime real estate. Bacteria will rush to colonize that brand new virgin gut, and once they claim a foothold, they will be much harder to supplant or replace.

This is why, for C-section babies, a number of experts recommend that the newborn infant be immediately exposed to vaginal and fecal bacteria. Ideally, we’d know the best bacteria to seed onto a newborn and would only provide those specific bacteria — but it’s still an area of debate and study, and we haven’t yet narrowed down which species in a microbiome are the critical capstones that need to be present.

(It is, funnily enough, the same reason why we don’t have synthetic blood for transfusions. We can’t yet create synthetic blood that measures up to the real stuff, so we keep asking for blood donations.)

Transplantation of the microbiome may be especially important for two well-known genera of probiotic bacteria, Bifidobacterium and Bacteroides. These microbes are known for being busy little consumers of the complex sugars in breastmilk, and providing a protective effect on the infant’s gut. They are not good at surviving outside the gut, however, which means that they are unlikely to settle in the infant by chance. They need to be explicitly introduced.

The mother may also seek to introduce these bacteria into infants through breast milk, but there’s no reason why we can’t consider microbiome seeding as one of the normal, everyday hospital steps after a baby is born.

Even some experts are now doing it, and preliminary studies suggest that this process can help alter the microbiome of infants born during a C-section to more closely align with those that are born vaginally. Rob Knight, a prominent microbiome researcher, performed this same swabbing procedure with his own child when they were born via emergency C-section.

Of course, there are other concerns to keep in mind.

The biggest one is suitability. Not all mothers will have microbiomes that are deemed healthy enough to transfer over to an infant. (If a mother is a chronic sufferer of bowel disease, she probably won’t want to pass that on!)

Instead, in the near future, there’s likely to be a screening process during pregnancy, when the mother’s microbiome is sampled and evaluated. If it is up to snuff, a fecal sample may be given to the infant shortly after birth. If she has any potential pathogenic bacteria that could cause trouble, doctors could elect to give the infant a sample from another mother instead, one who donated a “good” microbiome.

Soon to come: the most expensive poop a baby will ever be given

Right now, this is not a standard offering in hospitals. There is some effort to expose babies to the mother’s microbiome if possible, but it’s not at the point of providing full fecal transplants.

The more we learn about the two-step mechanism of birth-associated microbiome exposure and the specialized sugars in breast milk that support these microbes, the more we can plan to give our children the best chance in life — to have a healthy development, and to be at lower risk of a wide range of metabolic and bowel-related diseases.

If you or your partner is pregnant, there’s no shame in still choosing a C-section — but definitely inquire as to whether there is a method to help expose the child to the best microbes at birth, no matter what approach you choose.

Many hospitals are not opposed to the idea, but may not be permitted to perform the operation themselves. There's nothing stopping new parents from taking this action on their own. It may not be the most pleasant after-birth activity, but it could lead to lasting microbial benefits for a newborn.


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A microbiome scientist working at a tech startup in Silicon Valley, Sam Westreich provides insights into science and technology, exploring the strangest areas of biology, science, and biotechnology.

Mountain View, CA

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