If you're pregnant, having an elective caesarean and live in the Auckland region, talk to us about joining the ECOBABe study exploring babies' gut microbiome after birth.

The ECOBABe Study (Early Colonisation with Bacteria After Birth) is investigating whether babies born by caesarean section can be protected from a greater risk of some conditions, including childhood obesity and asthma, by being given their mothers' bacteria soon after birth.

Babies born by caesarean (c-section) miss out on the normal process of exposure to these bacteria, which happens during a vaginal birth. The bacteria may be an important part of developing babies’ digestive and immune systems. The study is trying to see if mimicking the normal process can help babies born by c-section. Even though it sounds helpful, there is still no evidence that it works, which is why we are doing the study.

We need women living in the Auckland region who are having an elective c-section so we can study the gut bacteria of c-section babies.

Why is this study important?

There is growing evidence linking c-section to an increased risk of babies later developing obesity and immune disorders, like asthma and diabetes. A recent very large study in the USA found children born by c-section were nearly 25 percent more likely to have childhood obesity than those born vaginally (even after other differences are taken into account). It is possible that the disruption to the normal process of bacterial colonisation is affecting the development of the immune system during this short, but potentially very important, time of transition. Currently, we know there is an association between c-section birth and obesity, but we are still trying to identify what links them. The ECOBABe study is an important step in the journey.

What is this study trying to find out?

The study is trying to find out whether giving c-section babies their mothers’ vaginal bacteria will result in them having similar gut bacteria to those they'd have if they were born vaginally. We will find out whether the bacteria colonise the babies’ gut, if taken orally when mixed in a small volume of sterile water.

The study will measure the range and number of different types of gut bacteria of all the babies by analysing their stools (poo). This will show us whether there are differences in the gut bacteria of c-section born babies given their mother’s bacteria compared to those which get a placebo. We will also see how the c-section babies gut bacteria differ from vaginally born babies. The study will also measure the babies’ weight, height and body fat composition.

Who can take part?

We are recruiting women who are having an elective caesarean section at Auckland City, Middlemore, North Shore or Waitakere hospital.

What does the study involve?

If you take part, you'll need to complete background health, diet and exercise questionnaires before your baby is born.

Caesarean births

If you are having a planned (elective) c-section, we'll need to take blood and swabs one week before the birth. The tests will check for any infections that could be passed on to the baby. Some of these are repeats of tests you have already had earlier in pregnancy. We do extra tests because this research involves a different way of doing things, requiring extra care to be taken. These tests are done at the Liggins Insitute (central Auckland) but if you live in north or south Auckland, we be may be able to offer tests closer to home.


On the day of your caesarean, after you’ve been admitted to hospital, we’ll meet you and give you a small gauze for you to put into your vagina, and remove after about 30 minutes, before going to theatre. We will then put the gauze into a small amount of sterile water. Soon after birth we will put some of this mixture into some babies mouths via a small syringe. Other babies will be given only sterile water (placebo). This is decided randomly, and you can find out if your baby received bacteria or just placebo at the end of the study.

Vaginal births

We have already recruited a reference group of women planning a vaginal birth for the study. 

Postnatal follow-up for all babies

Once your baby is born, you'll need to collect a small sample of their poo, and another sample at one and three months after the birth (a kit is provided).

At one and three months you'll bring your baby to the Liggins Institute to be weighed and measured. At the three month visit, the babies will also have a scan to measure their muscle, bones and fat. We will pay your transport costs for each visit.

Are there any benefits or risks in taking part?

This study has some potential benefits. Participating in this project could lead to a new method to transfer healthy gut bacteria to babies born by c-section.

All women in the c-section group will be screened one week in advance of their c-section to minimise the risk of transmission of infections.

The body composition machine scans have extremely low radiation dose exposure that is comparable to one day outside in the sun, and do not constitute a safety concern to babies.

How can I find out more?

Please get in touch if you'd like to find out more about the study or to discuss your potential involvement. Email the research team on or call/text 027 606 5140.