The Microbiome Effect

Book review of The Microbiome Effect, How Your Baby’s Birth Affects Their Future Health by Toni Harman and Alex Wakeford, Pinter and Martin, 2016

What is a microbiome?

A human microbiome refers to all the microorganisms (mostly different kinds of bacteria) that live on our skin and within our bodies. The Microbiome Effect is a basic introduction to how important the microbiome is to our health and well being and how it is being changed—a change which could be threatening long term human health. It is a fairly easy-to-read book with less than 200 pages made up of nine short chapters each with their own helpful summary of key points.

The microbiome is not new

The book discusses how the human body has always had a mutually beneficial (symbiotic) relationship with bacteria and in fact our bodies contain far more microorganisms than human cells. There are even microbes in our brains which may influence brain development and behaviour and microorganisms in our gut to help to digest food and protect us. This relationship with the microbiome primarily begins at birth when as babies we are “seeded” with very specific bacteria that proliferate in a mother’s birth canal and skin, and via the bacteria within breast milk. Harman and Wakeford explain that the same microbiome has been historically passed down from mother to daughter to granddaughter, generation after generation. Until now.

Is the microbiome changing?

That the microbiome could be changing is the focus of this book. Changes in birth practices, the use of formula instead of breast milk, and a rise in antibiotics are linked with altering and degrading the microbiome. Researchers are making links between changes in the human microbiome and rises in non-communicable diseases such as cardiovascular disease, chronic respiratory disease, diabetes and cancer. Increases in food allergies, reflux, coeliac disease, autism and obesity could, explain the authors, also have connections with a changing microbiome.

Book cover for The Microbiome Effect

Natural birth and the microbiome

According to The Microbiome Effect, birth is the main “seeding event” for a baby’s all important gut microbiome. In other words, it is during birth that your baby’s skin, mouth and gut receive the first important types (or species) of bacteria. Bacteria are said to arrive in a set order. The first to arrive are Lactobacilli. Prior to the birth, Lactobacilli proliferate in the mother’s vagina, and literally crowd out other less desirable species. Lactobacilli bacteria are thought critical to seed the baby’s microbiome along with Bifidobacteria which are found in the gut and are also picked up at birth. The significance of Lactobacilli being the first to arrive are threefold. Firstly they help the baby digest breast milk and extract energy from lactose (the main sugar in breast milk). Secondly they also have defences to inhibit competing or dangerous bacteria so protecting the baby and thirdly, they “train” or teach the baby’s developing immune system. Skin-to-skin contact and breast milk continue to complete the seeding process of the microbiome.

The microscopic exposures happening right at that moment, in the time during and immediately after birth, help lay the foundations for lifelong health and immunity

Surgical births

A typical modern labour in hospital is full of intervention. Synthetic oxytocin alone can have profound effects setting off a chain of events that may result in a surgical birth. The significance of this for the microbiome, say the authors, is that babies born by caesarean section are not exposed to the vaginal and fecal bacteria thought necessary to seed the microbiome in the correct order which could affect the final balance of organisms. Harman and Wakeford speculate that these babies are incomplete because their microbiome is incomplete. Caesarean birth is associated with fewer species of bacteria in the microbiome, and delayed colonisation of Bacteroides (another particular useful bacteria). If these babies then miss out on breast milk, they have lost another opportunity to seed and feed the microbiome for themselves and potentially for all future generations of babies in that family.

A C-section in one family member, therefore, may have serious consequences for the health of future generations of that family.

The Microbiome Effect discusses whether a caesarean section’s altered microbiome has links with higher rates of diabetes, obesity, allergy (including coeliac disease) and asthma. There is also speculation that a vaginal birth enables desirable epigenetic changes to direct future health in a way that a caesarean birth does not.

As well as being more likely to develop mild breathing difficulties and respiratory problems, babies born surgically, are—in the short term—more likely to have low blood sugar levels, be less alert, and be sleepier, and they may find it more difficult to feed properly.

Breast milk and the microbiome

The Microbiome Effect focuses on birth but points out that vaginal birth is not the only event impacting on a baby’s health. A major repeating event impacting the microbiome and intended to follow birth for at least a couple of years, is breastfeeding. Breast milk not only contains nutrients and microbes for baby it offers indigestible oligosaccharides to feed baby’s gut microbiome which in turn train a baby’s immune system. Formula in comparison has missing ingredients, and the first microbes developing in a formula fed baby’s gut could cause the microbiome to take a different form with potentially higher risks of various health issues.

Antibiotics and the microbiome

Antibiotics and antibacterials have been used in vast quantities over the last 70 yrs in farming and medicine. Antibiotics often go hand-in-hand with surgical births, wiping out important friendly bacteria in the microbiome and creating changes that may persist for twelve months according to The Microbiome Effect. Harman and Wakeford explain that removing just one species from a food web can change the dynamics of a whole ecosystem and losing important “keystone” (vital) species could have devastating effects on the microbiome.


If you’re looking for an introduction to the way birth can impact on the microbiome with a useful bibliography and an overview of the latest research, you will be interested in The Microbiome Effect. The way natural caesarean, skin-to-skin contact after birth and breastfeeding can support the microbiome when a caesarean is necessary are discussed. However, overall the role of breastfeeding is given very little place in the book. I would have liked much more information on breast milk’s role as a seeding event for the microbiome and felt the importance of this was neglected.


This article should not be construed as medical advice. Information found online should always be discussed with your own IBCLC lactation consultant and doctor to ensure it is appropriate for you and your baby’s situation. Contact your doctor, paediatrician or health care provider with any concerns about your baby’s health and welfare.