Should Caesarean-section babies be smeared with a sample of their mother's vaginal fluids as soon as they are born?

"Vaginal seeding" is not mainstream medicine, but it is growing in popularity.

The idea is to give these newborns something they missed when they emerged into the world - the good bacteria that live in their mother's vagina.

A swab is taken of mum's vaginal fluid, which is then rubbed on to her child's skin and mouth.

The hope is this microbial gift will boost their child's long-term health - particularly by reducing their risk of immune disorders.

It is a crucial time.

We might have been sterile in the womb, but in our first few moments of life an invisible bond is being established between baby and bacteria.

It's a relationship that will last a lifetime, and the first contact is as important as a first date.

"The first time a baby's own immune system has to respond are to those first few bacteria," says Prof Peter Brocklehurst, from the University of Birmingham.

"That we believe is important for, in some way, setting the baby's immune system."

There is a noticeable difference between the microbiomes - the collection of bacteria, viruses, fungi and archaea - of babies born vaginally and by Caesarean section.

It lasts for about the first year of life.

A baby born vaginally is first exposed and colonised by microbes from their mother's vagina and gut.

But for Caesarean-section babies, the first exposure "if they're lucky", says Prof Brocklehurst, comes from the very different organisms on their mother's skin.

He is running the Baby Biome Study to see if these different microbial colonists on Caesarean-section babies explain why they have higher rates of diseases such as asthma and allergies later in life.

The microbiome

You're more microbe than human - if you count all the cells in your body, only 43% are human

The rest is our microbiome and includes bacteria, viruses, fungi and single-celled archaea

The human genome - the full set of genetic instructions for a human being - is made up of 20,000 instructions called genes

But add all the genes in our microbiome together and the figure comes out at between two million and 20 million microbial genes

It's known as the second genome and is linked to diseases including allergy, obesity, inflammatory bowel disease, Parkinson's, whether cancer drugs work and even depression and autism

More than half your body is not human

Gut Instinct: Why I put my poo in the post

The early interaction between the immune system and microbes appears crucial.

Obviously our bodies do attack the dangerous ones - but the overall relationship between microbial and immune cells is about more than conflict, it's a far deeper dynamic.

Graham Rook, a professor of medical microbiology at University College London, says the microbiome is the immune system's teacher.

"This is a learning system, it is like the brain. Now, the thing about the adaptive immune system is it needs data, just like the brain needs data."

Listen to The Second Genome on BBC Radio 4.

The next episode airs 11:00 BST Tuesday April 17, repeated 21:00 BST Monday April 23 and on the BBC iPlayer

And that "data" is coming from microbes and the chemicals they produce. They provoke a reaction in the immune system that can last a lifetime.

Prof Rook says: "The initial setting up of the immune system occurs during the first weeks and months of life.

"We know that because there's a window of opportunity during those first months of life when if you give antibiotics you can disrupt the microbiota and then in adulthood those individuals are more likely to have immunological problems and are more likely to put on weight."

This is the idea that some parents are buying into when they perform vaginal seeding.

Do dogs boost a baby's microbiome?

Even the type of home you bring your baby back to may affect their long-term health.

Research has shown households with dogs have lower rates of asthma.

The idea is they help us swim against the hygiene tide by traipsing their muddy paws round the house and sticking their noses into everything.

"The speculation has always been that the dog brings, from the outside, microbes that are helpful in stimulating the infant's immune system," says Prof Anita Kozyrskyj, from the University of Alberta.

She is analysing data on about 3,500 families in the Canadian Healthy Infant Longitudinal Development Study.

One of its findings is that the microbiomes of three-month-olds is far richer and more diverse (a good sign) if there is a pet in the house.

Two types of beneficial bacteria seemed to be more common.

"The Oscillospira have been associated with leanness and the Ruminococcus have been associated with reduced risk of allergic disease."

Breastfeeding or formula, antibiotics and method of delivery all affect the microbiome.

But studies into the microbiome and long-term health have often been too small to be definitive.

The Baby Biome study is aiming to collect faecal samples from 80,000 babies.

That will be a lot of soiled nappies to analyse, but it will be an unparalleled resource for interrogating the impact of decisions made around birth.

Many of those will be out of parents' hands.

No doctor or parent would hold back on life-saving antibiotics because of an uncertain long-term impact.

Breast milk feeds gut bacteria

This study will let scientists see which microbes the body first hooks up, what that means years later and, tantalisingly, whether damaging relationships with the wrong bacteria can be repaired.

The faecal samples will end up at the Wellcome Sanger Institute in Cambridge and in the hands of microbial enthusiasts such as Dr Trevor Lawley.

"My latest favourite microorganism is Bifidobacterium," he says.

"It is one of the first bugs to colonise humans early in life, and we believe they feed off sugars in the breast milk.

"So, there's a very sophisticated evolutionary set-up where the bugs are passed from the mother to child and the mother nurtures that bug to establish the early microbiome."

Dr Lawley's lab will be trying to uncover every microbe that colonises a newborn and what that means later in life.

He thinks the end result of the project will be to change policy around avoidable antibiotic use and Caesarean sections.

Or, alternatively, "maybe we could culture the bugs from the mums to purposefully colonise the babies to allow their microbiome to mature and develop properly" - in other words, a scientifically controlled version of vaginal seeding.

So are some parents just ahead of the game?

Prof Brocklehurst says: "At the moment some parents believe this hypothesis enough that they are doing their own vaginal seeding.

"Now, there could be real downsides to that."

One concern is dangerous bugs could be transferred.

Up to a quarter of women are thought to carry group-B strep in their vagina, and exposing babies to this bacterium could be fatal.

Prof Brocklehurst says: "It too early to start introducing bacteria artificially into the baby until we've got a good handle on how likely this is to be the mechanism or not."

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Illustrations: Katie Horwich