More benefits of breastfeeding? Oksana Kuzmina/Alamy

A healthy set of gut bacteria seems to play a vital role in protecting us from a host of disorders – but what about the billions of viruses that interact with these bacteria? Although babies seem to be born without any such viruses, their guts become home to billions within the first month of life – and the community of viruses is shaped by whether the baby was breastfed or not.

Plenty of studies over the past decade have shown that the collection of bacteria in our guts – known as the microbiome – is involved in a range of disorders. Disruption in gut bacteria have been linked to obesity, diabetes, depression and Parkinson’s disease, among others. But little is known about the viruses.

Most of the viruses in our guts seem to infect the bacteria that line them. But we don’t really know what they are doing – the vast majority don’t show up in existing virus databases. That’s partly because there are so many viruses that have yet to be studied.


“In a healthy adult, if we take some poop and purify the virus-like particle, we find something like a billion particles per gram,” says Frederic Bushman at the University of Pennsylvania.

Following babies

To find out more about the viruses, Bushman and his colleagues studied 20 babies. They collected faecal samples within a few days of birth, and again when the infants were 1 month old and 4 months old.

The team searched for virus-like particles in each sample. These particles are thought to be viruses and look like viruses, but haven’t been through various tests to confirm that they really are.

At birth, only three of the babies seemed to have any virus in their meconium – their earliest stool. This suggests that babies are born virus-free, and collect their first bugs either during birth or shortly after, says Bushman. But within a month, the babies had adult-levels of virus.

As with adults, most of these viruses seem to be of the type that infect bacteria. But some are known to infect human cells. Viruses of this type were less common in babies that had been breastfed, the team found.

Bushman thinks that proteins and sugars in breast milk might be working to discourage the growth of these viruses. Having fewer of the viruses might protect a baby from infections, says Bushman. He points out that breastfeeding has been linked to other positive health outcomes – we don’t yet know how much of this effect might be linked to the presence of viruses in the gut.

The team found the same pattern among a group of 125 babies in the US aged between 3 and 4 months, and 100 babies in Botswana who were 4 months old.

Journal reference: Nature, DOI: 10.1038/s41586-020-2192-1