Carolyn Weiss has a very peculiar birth plan.

An hour before Weiss, who is 37 and lives in Brooklyn, gives birth this January via C-section, she will insert a piece of saline-soaked gauze into her vagina. Right before the surgery, she’ll remove the gauze and place it in a sealed container. Seconds after the birth, Carolyn’s husband will take the gauze and swab it inside the baby’s mouth, around her eyes, and on her skin. The practice, called “seeding”, is beginning to attract some attention.

Why? First, a little science. The human body is home to an estimated 100tn microorganisms that form a complex ecosystem known as the microbiome. Scientists are just beginning to understand the tremendously vital role the microbiome plays in human health, but emerging research shows that these trillions of little guys (which collectively weigh about 2.5lb [1kg]) keep very busy.

They train our immune system, help us deal with infection and process our food. In fact, given the wide range of metabolic activities regulated by the microbiome, researchers are beginning to think of it as a newly recognized organ. While the intestines and colon have the densest population of microbes, distinct microbial populations live on every surface of our body: skin, mouth, vagina, lungs, bladder, etc.

To date, western medicine has often considered microbes foreign invaders, leading to the prevailing view that eliminating pathogens – through everything from antibiotics to hand sanitizers – will prevent disease. But that idea is under serious reconsideration as scientists begin to understand the level to which humans and their microbes share a mutually beneficial relationship, beginning at birth.

In the womb, a baby’s gut is most likely a sterile environment until the membranes rupture and the water breaks. At this point, researchers believe, the microbiome is first colonized by mom’s bacteria. It continues to be planted during the trip through the birth canal, where a child is coated with its mother’s microbes. Right after birth, a baby’s microbiome closely resembles the bacteria of the mom’s vagina.

But what happens when a baby is born via C-section, deprived of contact with its mother’s vaginal bacteria? Its bacterial community resembles the bacterial communities found on skin. And not just mom’s skin, but that of doctors, nurses, other patients in the hospital, the person who cleaned the operating room floor. This is a cause for concern, as a pioneer colonization by these types of bacteria may make a baby more susceptible to harmful pathogens and eventual illness.

Compared to vaginally born babies, those born via C-section are more likely to suffer from a host of health problems: asthma, allergies, eczema, type 1 diabetes and celiac disease. They are more likely to be hospitalized for gastroenteritis.

Can this be partly explained by their microbiomes? Many researchers now believe so.

What’s more, the difference in the microbiome resulting from the mode of delivery persists over time. Caesarean-born infants have a more slowly diversifying microbiota, even after six months of age – and a 2014 Dutch study found these differences still existed in children at seven years of age.

“What we’re finding is that interaction with microbes very early on in life will lead to a certain immune pathway – a tolerizing one or one that is more disease producing,” says Dr Josef Neu, a professor of pediatrics at the University of Florida.

This begs the question, what’s a mom who is facing a C-section to do?

Enter Dr Maria Gloria Dominguez-Bello.

Dominguez-Bello, a microbiologist from NYU, has been studying the microbiome for several years. For the past three she’s been trying to determine if C-section babies can reap the benefits of a vaginal birth through the process of seeding with gauze that’s been incubated in its mother’s vagina. So far, the results are very promising.

Last year, Dominguez-Bello conducted a study in Puerto Rico on 21 babies. Now under peer review, the results showed that her technique – remove the baby from mom’s uterus; swab its mouth, eyes and skin; place on mom’s chest – does have a positive impact on the diversity of a newborn’s microbiome. “We saw that if you expose a baby to an inoculum, you got the inoculum in the baby,” she says. In other words, babies who were seeded with the gauze had a microbiome closer to a baby born vaginally than those born via C-section – results which were still present after one month. “While it’s not equivalent to a baby born vaginally, there is some important restoration happening,” Bello says.

The ultimate question is whether this very simple process will do what Dominguez-Bello hopes: lower the risk of illness in babies born surgically. She intends to answer this question by expanding her research to include more babies, whom she would follow for at least three years. “Will we see less incidence of asthma?” she says. “Less obesity? Will this have a real impact on babies’ health?”

That’s what Carolyn Weiss is hoping for. Her first daughter, born via C-section, suffered from eczema as a newborn and began to exhibit signs of food allergies. It was Weiss’s research into the possible causes of this that led her to Dominguez-Bello’s study. When she became pregnant again and was told she’d likely have to have another C-section, Weiss and her husband decided they’d give this a try. “As a parent, you want to give your baby the strongest possible armor,” says Weiss. “If there’s even a small chance this will help, we’re going to do it.”

Dominguez-Bello, who receives frequent emails from expectant mothers asking for advice on the procedure, emphasizes the point that it’s still under study. And because it’s such a new idea, it may be difficult to find a doctor willing to perform the procedure, forcing interested parents to take matters into their own hands.

“Our doctor is generally supportive of the idea, but he won’t do it himself,” says Weiss. “That task will fall to my husband.” There’s some risk in spreading infection to the baby, so it’s imperative that a mom has a healthy microbial ecology, checking, for example, they have an acid lactobacillus-dominated vagina, are HIV- and strep-B negative, and showing no signs of an STD.

With the rate of C-section births on the rise in the US and globally, Dominguez-Bello believes this idea could have an enormous impact on human health. “I gave birth to a daughter via C-section 24 years ago,” she says. “If I had known then what I know now from my research, I would have considered doing this myself.”