Caesareans linked to microbiome disruption

Babies born by caesarean section are missing normal bacteria and their guts are colonised instead by bugs found in operating rooms and intensive care units, according to a new British study in the journal Nature.

Worryingly, those hospital bacteria include strains that are antibiotic-resistant.

The finding is the latest in a wave of research on the “gut microbiome”, the trillions of bacteria that call your intestine home and collectively weigh up to two kilograms in adults.

Far from being passive free riders, these gut bugs are increasingly known to have a hand in illnesses from depression to cancer and even autism. Hence the deep interest in cultivating the right class of passenger.

The kinds of bacteria that lurk in your darker recesses depend in part on what the researchers, led by microbiologist Trevor Lawley at the Wellcome Sanger Institute in the UK, call “pioneering microorganisms”.

These first settlers stake an early claim in the race to colonise your gut.

Their ranks are swelled by bacteria bub picks up on its way through the vagina, mingled with more bugs from mum’s poo, which tends to put in a showing at delivery due to pressure from the baby’s head.

But as medicine intrudes on the birth process – global caesarean rates have almost doubled since 2000 – the bugs in the guts of tiny tots are changing, something linked to asthma and allergy in childhood.  

Until now, however, understanding how early life shapes our bacterial inheritance has been limited by small studies with limited poo samples. 

The current study aimed to address that by examining nearly 600 babies from the UK Baby Biome Study, 282 of whom were caesarean and 314 vaginal births.

All tackers had poo samples taken in the first month and 300 or so were re-sampled at around nine months. In addition, 175 mums submitted their poop for scrutiny.

The findings suggest that which bugs take up residence in the alimentary canal comes down in no small part to how you were born.

Nearly 70% of the bacteria in the poo of babies born vaginally were so-called “commensals” – healthy bacteria that cohabit in relative peace – including some called Bacteroides. But when the researchers examined the poo of caesarean babies, the bacteria profile had undergone a frame shift.

“The gut microbiota of babies delivered by caesarean section were depleted of these commensal genera,” the authors write.

To put a precise number on it, Bacteroides species were low or absent in 99.6% of samples taken from the caesarean babies.

Instead, their poop played host to a rather different class of organism. Species of Enterobacter and Klebsiella, which cause pneumonia and blood poisoning and are often found in hospitals, had largely replaced the commensals, making up nearly 70% of the samples.

These bugs are known as “opportunistic pathogens” because they tend to cause illness when a person’s defences are down; for example, because they are already sick.

Which is why another of the study’s findings is especially concerning. These bacteria had, the authors report, “clinically relevant antimicrobial resistance”.

The researchers believe antibiotics given during caesarean section play a role in the altered neonatal microbiome. Consistent with that, mothers who delivered vaginally but received antibiotics also had fewer healthy commensal bugs.

All of which means another birthing mode could be called up in the quest to learn how hospitals shape the nascent microbiome.

“This highlights the need for large-scale, long-term cohort studies that also sample home births to better understand the consequence of hospital birth and establish whether perturbation of the neonatal microbiota negatively affects health outcomes in childhood and later life,” the authors conclude.