Health implications of the baby biome?

New research by Sanger Institute scientists and their colleagues, published today (18 September), investigates the differences between the microbiomes of babies born by C-section and those born vaginally^[1]. The important findings shed light on the types of microbes that are the very first to colonise a baby’s gut – and found very different types in the two groups. But, as the babies grew those differences evened out.

The effects of our first gut microbes on our health remains unknown. So why is the microbiome such an important topic?

What is a microbiome?

A microbiome is the genetic material of all the microbes – viruses, plus single-celled bacteria and fungi – living in particular place. In this case, that place is us.

We all have a thin layer of microbes on our skin. Our mouths, nasal passages, ears and eyes each have their own, distinct, populations. Our guts contain the largest numbers and variety of species. In total, it’s thought that our bodies are home to somewhere in the region of 40 trillion microbes, mostly bacteria, from 10,000 different species^[2]. Microbes outnumber our human cells by about three to one.

While some bacteria are harmful and can cause disease, most do not. Over the last 20 years, scientists have come to appreciate bacteria’s roles in our health, even behaviour. We have evolved together, and our bodies simply wouldn’t function without them. Some researchers have gone as far as describing people as ‘holobionts’ — not autonomous beings but biological ‘networks’ with human and microbial parts^[3].

Gut microbes help us digest our food by breaking down fibre, fats or proteins, and making them into nutrients we can absorb. Some microbes produce anti-inflammatories which can regulate the immune response. They may also regulate the immune system in other ways.

Why  is the microbiome important?

It is the links between gut microbes and the immune system that could be important for disease^[4],^[5]. It’s thought that a disruption between microbes and immune cells could be linked to autoimmune conditions like irritable bowel syndrome (IBS), Crohn’s disease and asthma^[6].

Gut microbes could also affect how we respond to particular medicines, like chemotherapy^[7], and so may be important to consider in the development of cancer treatments.

Other studies have linked the gut microbiome to conditions including obesity^[8], cardiovascular disease^[9] and arthritis^[10].

But it’s important to note that most of these links are, at the moment, associations. They could be the effects of a certain condition, rather than the cause.

So we know the microbiome is important, but at the moment its exact role in long term conditions isn’t clear. The questions of precisely how the microbiome, and which specific species, might be contributing to a disease, are yet to be resolved.

Our gut microbiota can be thought of as an ecosystem - thousands of species and millions of individuals living together, interacting with each other and with their environment. Uncovering which are important for disease, and how they might be harnessed to improve health, is no easy task. Understanding where it comes from is an important piece of the picture.

Where does the microbiome come from?

In the womb, we are sterile; microbes aren’t usually present. It is during birth that babies encounter their first microbes. This new study shows that when a baby is born vaginally, it is bacteria from the mother’s gut that transfer to the baby’s gut^[11]. These are encountered as the baby passes the perineum (the area between the vagina and anus). While a baby does come into contact with bacteria in the vagina, contrary to previous assumptions, very few of these vaginal bacteria colonise a newborn’s gut. If a baby is born by caesarean, the bacteria which colonise its gut are not transferred from the mother, they are mainly bacteria from the hospital environment, the new research finds.

After babies are born, they continue to acquire bacteria from the people and environment around them. Drinking milk, and chewing on toys or peoples’ fingers takes up a lot of time in the first few months of life. As they grow, they begin to eat solid foods and yet more things go into their mouths – beakers, toys, clothes, more fingers. And as they start to crawl or shuffle around, they find a whole new range of things to munch on. (My children had a fondness for eating sand from our local park – you’d think that once you’d tried it once that would be enough, but apparently not.) Everything is a potential source of microbes.

By the age of about three, our gut microbiome has stabilised. It’s not a constant though, and changes throughout our lives. Illness, stress, long-term diet and drugs – especially antibiotics – all have an effect on our gut microbes.

Long-term effects - the baby biome study

The long-term effects of how the gut microbiome forms in the first phase of life remain unknown. This is one of the reasons that the controversial practice of ‘vaginal seeding’ (swabbing a baby born by C-section with fluids from the mother’s vagina) is not recommended [12]. It could also unintentionally transfer harmful microbes.

The research published today is part of the ‘baby biome’ study^[13]. The researchers want to follow up the children who took part and assess their health and their microbiome as they grow. Once they have that data they will be able to investigate the links between the two.

It may be that in the future, if certain bacterial species are found to be important, then therapeutics (referred to as ‘crapsules’ by some), could be developed to replace them if they are missing.

We’re beginning to understand that ‘our health’ is a broader term than we thought. Knowing how and when our microbiome forms will offer up insights into health and disease that we would never have considered even a few years ago. There is much more to uncover about the millions of microbes that call us home.

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