Published on 17th December 2017


Can how we are born really impact the diversity of our gut bacteria? Catherine Morgan writes

Research into the microbiome (our inner ecosystem of trillions of microscopic microorganisms and their collective genetic makeup) has revealed that the diversity and balance of microbes lurking within our guts could have long-term implications for our health — starting in infancy.

In 2016, a study published in Nature Medicine showed that new-born babies who had a particular pattern of gut microbes were three-times more likely to develop allergic reactions by the age of two, and asthma by the age of four.1,2 Babies in the highest risk group had lower levels of certain normal gut bacteria (e.g. Bifidobacterium, Akkermansia and Faecalibacterium) and abnormally high levels of certain fungal species (Candida and Rhodotorula).

The study is part of a growing body of evidence suggesting that developing a ‘healthy’ gut microbiome from birth is essential.

This complex microbial system plays a key role in just about every aspect of our health, from digestion and vitamin production, to the regulation of our immune systems. A shift in microbial balance (i.e. dysbiosis) has also been associated with an increasing number of health problems, from allergies and gastrointestinal disorders3 to autoimmune diseases like multiple sclerosis4 and rheumatoid arthritis,5 and even obesity.6

“Two studies... also found an association between antibiotic use during childbirth and dysbiosis of the infant gut microbiota

Where does it all begin?
It has been commonly accepted that whilst in the womb, babies live in a sterile environment — receiving their first dose of bacteria from their mother whilst in the birth canal, and then through skin-to-skin contact, and breastfeeding. But there is now a view that we may receive bacteria from our mothers even before birth.7,8,9

Compared with an adult’s microbiota (the community of microbes), the infant gut typically has fewer species of bacteria, so less diversity, and is less stable. But it develops rapidly from birth until two to three years of age, when a more complex, stable, adult-like composition is established.

A number of factors reportedly contribute to this development.

Some studies have shown that babies born by C-section have a different microbial pattern to those born vaginally.9 Whilst it has been suggested that infants born vaginally have intestinal microbial content similar to the mother’s vaginal and intestinal flora (i.e. Bacteroides, Bifidobacterium and Escherichia coli), C-section babies are instead colonised with microbes associated with skin surfaces and the hospital environment.10,11

A 2013 study, for example, reported lower abundances of Escherichia–Shigella bacteria and an absence of Bacteroides in babies born by C-section — although, interestingly, the findings also indicated that colonisation of the infant gut may be affected differently by elective or emergency caesarean.12 A 2014 study also reported an association between caesarean delivery and delayed colonisation of Bifidobacterium and Bacteroides.13 Despite these findings, however, more recent research, found no discernible differences in the microbiomes of babies born via vaginal or caesarean delivery at four and six weeks of age.14

Feeding patterns
Breast milk contains, amongst many other essential components, special sugars called human milk oligosaccharides (HMOs) which help feed the beneficial bacteria in the infant’s gut, as well the mother’s milk microbiome. A study published in JAMA Pediatrics reported that breastfed infants received almost 30 per cent of their gut bacteria from breast milk during the first 30 days of life, with a further 10 per cent coming from the skin on the mother’s breast.15 Microbial differences have been reported in breast-fed versus formula-fed infants.10,12

Antibiotic use
A 2015 review reported that: “Even short-term antibiotic treatment can significantly affect the evolution of the infant gut microbiota; in fact, the colonisation pattern of Bifidobacterium seems to be particularly disturbed up to eight weeks after treatment while Proteobacteria are increased”.16 Two studies published in 2016 also found an association between antibiotic use during childbirth and dysbiosis of the infant gut microbiota; in both cases, breastfeeding modified some of these effects.17,18

“...eating fruit and veg, playing outside and getting dirty make sense when it comes to supporting a child’s gut microbiome

Supporting a healthy microbiome
So does this then mean that our microbial fate is sealed in the first years of life? No-one can predict what is going to happen at birth, or in the following months. And what if the mother’s microbiome is less than desirable to begin with? Will future generations be paying the microbial price for years to come? And what constitutes a ‘healthy’ microbiome anyway?

Dr Maya Shetreat-Klein, a paediatric neurologist and author of The Dirt Cure: Growing Healthy Kids with Food Straight from Soil, told Optimum Nutrition: “Certainly, there are window periods of development, such as birth, that confer specific risk or benefit for things like allergy and autoimmunity. For instance, babies who are born by C-section have a higher risk of developing asthma or coeliac disease later in childhood.” But this may not be entirely due to birth. “On some level,” she says, “these risks may be a result of epigenetic changes as well.”

Diversity of microbiome may also be inherited. “It is very possible that less diverse flora, and the associated epigenetic risks associated with that, can absolutely be passed down through generations,” she says. “Babies born by C-section, or to mothers who have been on numerous antibiotics, or who weren’t breastfed, can have altered flora — and unless steps are taken to reverse this, they can eventually pass these less diverse flora to their children, and on, and on.”

But the good news, she says, is that — as far as we know at this time — none of this is set in stone. “This goes along with the idea that, like the brain, the body has the plasticity to adapt and change, depending on its  environment. While a child may or may not start life from a position of microbial advantage, the possibility to become more microbially diverse is available.”

Shetreat-Klein says that several studies show ways that children can restore their guts with diverse flora, including: “Eating fermented foods like sauerkraut, kefir, unsweetened yoghurt, kimchi and the like; eating plenty of prebiotic foods like onions, garlic, leeks, burdock, chicory, and banana, which nourish the gut flora; having a pet; washing dishes with a sponge rather than by dishwasher (at least occasionally!); playing outdoors, gardening, hiking in the forest and generally getting dirty; and being social with other children.”

So whilst there is still much to learn about the microbiome, some experts agree that we can, to some extent, help nurture and balance the microbes within. Professor Tim Spector, doctor, scientist, and author of The Diet Myth told Optimum Nutrition: “The best way to improve a new-born’s microbiome is to breast feed, avoid antibiotics and introduce diverse plants early”. (Note, antibiotics are sometimes necessary, but appropriate use is key.)

There is also some evidence to suggest that probiotics (live microbes that act as temporary visitors to the gut) can help remodel our microbiome if we’re recovering from antibiotic treatment, although further research is needed to better understand the mechanisms.19
Kate Delmar-Morgan, a nutritional therapist who specialises in children’s health, points to research showing that probiotic yoghurt can be effective in reducing the incidence of antibiotic-related diarrhoea in children.20

However, when it comes to giving children probiotics to promote digestive health and immunity, and to prevent allergies, she says that the evidence is mixed — although there has been some suggestion to support the practice. She says that more research with standardised study designs is needed, and advises caution in giving probiotics to infants and children who are seriously ill or who have a compromised immune system.

A spokesperson from the American Gut Project, the world’s largest crowd-funded microbiome project, also said that the age-old recommendations of eating fruit and veg, playing outside and getting dirty make sense when it comes to supporting a child’s gut microbiome. And, well, it really does make sense: plant foods are an important source of fermentable dietary fibres that feed the beneficial bacteria in our guts, and contact with nature exposes us more to the microbial world around us. Writing in Rewild, a book that focuses on the microbiome, Jeff Leach, anthropologist and co-founder of the American Gut Project, states his belief that eating a greater diversity and quantity of whole plants is “the single most important dietary strategy for improving the diversity and health of your gut microbes”.21

There are other research directions too: the benefits of early-life exercise,22 or the impact of having a pet.23 But we are really only beginning to scratch the surface. There is perhaps one reoccurring idea, though, and that is: disease really can begin in the gut — and at birth.



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