Research is unveiling the surprising, lifelong impact of what enters a baby's gut in the days after birth.

It's 2017 and two technicians at Queen's Hospital pathology laboratory in London wait anxiously for the day's mail.

On a good day, this lab might receive 50 individual tightly-wrapped packages, each containing a treasure within – a tiny sample of baby poo, carefully scraped from the nappies of newborn infants by their loving parents.

These technicians are the front line soldiers of the Baby Biome study, which aims to understand how a baby's gut microbiome – the trillions of microbes living in their digestive tract – affect their future health. Between 2016 and 2017, the lab analysed the poo of 3,500 newborns.

It was a lot of poo. But the results were very revealing.

"It's not until about three or four days after birth that you start to get a really good signature of microbes in the gut, so it takes a couple of days to start colonising," says Nigel Field, professor of infectious disease epidemiology at University College London (UCL), who leads the Baby Biome project.

"You're essentially sterile when you're born. So it's a pretty extraordinary moment for the immune system, because until that moment, all the body surfaces don't come into contact with microbes."

Every single one of us, once we've passed those initial few days of life, develops a gut microbiome. Scientists now believe this community of bacteria, fungi and viruses play a vital role in our health. As adults they help break down hard to digest fibre and provide the enzymes necessary to synthesise certain vitamins. Simply by being there, they protect us from harmful pathogens, while some even release natural antibiotics to kill off invaders.

And the benefits of having a healthy gut microbiome stretch beyond even this. Emerging research suggests that a well-functioning gut microbiome could protect against conditions like anxiety, depression and even neurodegenerative diseases such as Alzheimer's.

The flip side of this coin, though, is that having an "unhealthy" gut microbiome as an adult is linked to a long list of conditions including cardiovascular disease, colorectal cancer, chronic kidney disease, diabetes, inflammatory bowel disease and obesity.

Yet while scientists have conducted lots of studies into the role that gut bacteria have on adult health, until recently they knew little about their impact during childhood. That has started to change, however.

"The first microbes that colonise a baby's gut are like the architects of the immune system," says Archita Mishra, senior lecturer at the University of Sydney in Australia, who studies the role of the microbiome in early-life immune development. "They help 'train' the body to distinguish friend from foe, teaching immune cells how to tolerate food antigens [and] harmless microbes, and mount defences against pathogens."

According to Mishra, the bacterial communities that establish in the first six to 12 months are responsible for allergy risk, how well the child responds to vaccines, and how well the gut barrier – the layer that separates the gut's contents from the rest of the body – functions.

"The first thousand days of life appear to be a window when the gut microbiome leaves an imprint that lasts decades," says Mishra.

The placenta is widely believed to be a bug-free zone, meaning babies don't have a gut microbiome when they are inside the womb. Instead, babies seem to inherit most of their bacteria from their mother's digestive tract – not their vagina, as previously thought.

"Nature has a very refined method of establishing the gut microbiome in a newborn infant," says Steven Leach, a........

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