Cesarean babies have high levels of hospital bugs in their guts, unlike vaginally-born babies who get their bacteria from mothers

The study is the largest to show that babies born by cesarean section have a very different gut bacteria than those born vaginally; The differences mostly even out by the time children are one-year-old


                            Cesarean babies have high levels of hospital bugs in their guts, unlike vaginally-born babies who get their bacteria from mothers

Babies born by cesarean section largely miss out on their mother's healthy bacteria, and their guts are instead colonized by bugs typically found in hospitals. Vaginally born babies, on the other hand, get most of their gut bacteria from their mothers. These are the findings of the largest-ever study of neonatal microbiomes, which has provided the most substantial evidence yet that babies born by cesarean section have a very different gut bacteria than those born vaginally.

Currently, not much is known about the role of the baby's gut bacteria. Similarly, the health implications of these differences at birth and whether they will have any effect on later health also remain unclear. 

What is worrying is that the harmful microbes that babies born via cesarean acquire from the hospitals are more likely to be antibiotic-resistant, says the team from the Wellcome Sanger Institute, UCL, the University of Birmingham, and other collaborators. The guts of cesarean section babies had "high-level colonization by opportunistic pathogens" associated with the hospital environment, including Enterococcus, Enterobacter and Klebsiella. The findings have been published in Nature.

"This is the largest genomic investigation of newborn babies' microbiomes to date. We discovered that the mode of delivery had a great impact on the gut bacteria of newborn babies, with the transmission of bacteria from mother to baby occurring during vaginal birth. Further understanding of which species of bacteria help create a healthy baby microbiome could enable us to create bacterial therapies," says Dr. Trevor Lawley, a senior author on the paper from the Wellcome Sanger Institute.

The study - part of the Baby Biome Study - also shows that the microbiome of vaginally delivered newborns did not come from the mother's vaginal bacteria, but from the mother's gut. This calls into question the controversial practice of swabbing infants born via cesarean with mother's vaginal bacteria. 

The practice is known as vaginal seeding, and scientists are yet to prove whether it is safe and effective. The technique involves using cotton gauze or a cotton swab to transfer vaginal fluids to the mouth, nose or skin of a newborn, and the aim is to transfer a mother's vaginal bacteria to her baby, in case of cesarean section. Experts have warned that this practice can increase the risk of infection. The American College of Obstetricians and Gynecologists currently does not recommend or encourage vaginal seeding outside of a research setting. Understanding how the birth process impacts the baby's microbiome will enable future research into bacterial therapies, says the team.

The study also shows that the microbiome of vaginally delivered newborns did not come from the mother's vaginal bacteria, but from the mother's gut. This calls into question the controversial practice of swabbing infants born via cesarean with mother's vaginal bacteria. (Getty Images)

The researchers also found that the differences in gut bacteria between vaginally born and cesarean delivered babies largely evened out by the time they turn 1. 

"Our study showed that as the babies grow and take in bacteria when they feed and from everything around them, their gut microbiomes become more similar to each other. After they have been weaned, the microbiome differences between babies born via cesarean and delivered vaginally have mainly evened out. We don't yet know whether the initial differences we found will have any health implications," says Dr. Nigel Field, a senior author on the paper from UCL. 

Professor Peter Brocklehurstm of the University of Birmingham, who is the principal investigator of the Baby Biome Study, says that the first weeks of life are a critical window of development of the baby's immune system, but little is known about it. "We urgently need to follow up this study, looking at these babies as they grow to see if early differences in the microbiome lead to any health issues. Further studies will help us understand the role of gut bacteria in early life and could help us develop therapeutics to create a healthy microbiome," says Prof. Brocklehurst.

Why the study?

The gut microbiome is a complex ecosystem of millions of microbes and is thought to be important for the development of the immune system. The researchers say that lack of exposure to the right bacteria in early childhood has been implicated in autoimmune diseases such as asthma, allergies, and diabetes. 

"However, it is not fully understood how important the initial gut microbiome is to the baby's immune system development and health, how a baby's microbiome develops, or what happens to it with different modes of birth," says the study.

Accordingly, to understand more about the development of the microbiome, and if the delivery method affected this, researchers studied 1,679 samples of gut bacteria (taken at several time points during the neonatal period, and in infancy) from 596 full-term babies (282 were cesarean and 314 vaginal births) born in UK hospitals and 175 mothers. Fecal samples were taken from babies aged four, seven, or 21 days old, who had been born in UK hospitals by vaginal delivery or cesarean. Some babies were also followed up later, up to one year of age.

The findings show stark differences

During birth, a baby comes into contact with bacteria from the mother's gut. For their study, the research team used DNA sequencing and genomics analysis to understand which bacteria were present. They found there was a significant difference between the two delivery methods. 

The analysis shows that it was the mother's gut bacteria that made up much of the microbiome in the vaginally delivered babies. Babies born via cesarean had many fewer of these bacteria. "Vaginally delivered babies had many more health-associated (commensal) bacteria from their mothers than babies who were born by cesarean," says the study. It adds, "In place of some of the mother's bacteria, the babies born via cesarean had more bacteria that are typically acquired in hospitals, and were more likely to have antimicrobial resistance."

The guts of cesarean section babies had "high-level colonization by opportunistic pathogens" associated with the hospital environment, including Enterococcus, Enterobacter and Klebsiella. (Getty Images)

The researchers isolated, grew and sequenced the genomes of more than 800 of these "potentially pathogenic bacteria," confirming that they were the same as strains causing bloodstream infections in UK hospitals. Although these bacteria do not usually cause disease while in the gut, they can cause infections if they get into the wrong place or if the immune system fails, say experts. The researchers recommend extensive follow-up studies to determine if the early differences influence health outcomes. 

According to Dr. Alison Wright, consultant obstetrician and vice president of The Royal College of Obstetricians and Gynaecologists, the study findings should not discourage women from having a cesarean birth as it is a life-saving procedure for many. "In many cases, a Caesarean is a life-saving procedure and can be the right choice for a woman and her baby. The exact role of the microbiome in the newborn and what factors can change it are still uncertain, so we don't think this study should deter women from having a cesarean. This study shows that more research is required to improve our understanding of this important area," says Dr. Wilson.

Experts say that women who have a cesarean are now offered antibiotics before the delivery to help prevent the mother from developing postoperative infections, meaning that the baby also receives a dose of antibiotics via the placenta. This, say scientists, could also cause some of the microbiome differences seen between the two birth methods.

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