The Microbiome and Human Health

The Microbiome and Human Health

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The microbiome has become somewhat of a ‘hot topic’ in recent years, and like any new  specialty area there is a lot of generalisation and misinformation out there.  This article will attempt to clarify what the microbiome is, how it functions, and the factors that can affect it.  Following this I will discuss ways in which we can promote gut health, including the use of probiotics and explore the role of breastfeeding in the development and function of the microbiome.

The Microbiome

Most people associate the microbiome with gut health, however the microbiome actually refers to a population of microorganisms that exist in and on the entire human body, and upon whom we humans are dependent on to keep us alive and healthy, including fungi, parasites and bacteria (1).  In fact, there are as many microbes in/on the body as human cells (2).  According to (3), the most critical period for the development of the microbiome occurs during infancy and early childhood (the first 3 years), and having medical interventions can have lifelong consequences for our gut and overall health. 

The Role of the Microbiome

Different microbes dwell in specific areas of our bodies, meaning that there are various specific microbiome’s present in the body including the gut, brain, lungs, and skin.  The theory is that these microbiome’s are connected and that microbial dysbiosis or disharmony is leading to the rise in many chronic conditions such as infant overweight and obesity (4), skin issues, auto-immune conditions such as inflammatory bowel disease, multiple sclerosis, diabetes, allergies, asthma, autism and cancer (4, 5, 6).  There is also emerging research in the area of mental health, whereby our gut and brain microbiomes are connected.  Many of our mood-enhancing hormones are made in the gut (such as serotonin-the ‘happy’ hormone), and if our gut is not in harmony, it cannot function optimally (7).

The gut microbiota have three main functions:

  1. Protection: they serve as a barrier against the proliferation of unwelcome pathogens.
  2. Metabolism: they play a vital role in the metabolism of colostrum, breastmilk, formula, solid foods, and medications.
  3. Maintenance: they enable the healthy growth of intestinal epithelial cells, which ensure the maintenance of the immune system (including intolerance to food antigens) (8). 70% of our immune system is located within the gut (2)

It is easier to think of the gut microbiome as a layer of protection or filter between our intestinal contents and the gut wall.

Factors that affect the microbiome:

Mode of Delivery

It has been espoused that the mode of delivery plays a significant role in the development of a healthy microbiome, and indeed there have been differences found in the early microbial balance of a newborn. According to the systematic review by Rutayisire (9), babies born via vaginal delivery had a more diverse pattern of gut microbiota during the first three months of life. However, after 6 months the observed differences disappeared.  

Aagaard (10) casts further uncertainty on the debate in suggesting that intrauterine life may have more of a role to play than previously thought, and that microbial presence in the maternal uterus, upper reproductive tract and preterm placenta may be just as important as the mode of delivery. More research is needed in this area.

Infant Diet

Breastfeeding provides the most consistent early source of probiotic bacteria, which includes staphylococcus (mums skin bacteria), infant saliva bacteria and bacteria produced in the milk glands (1). Breast milk delivers 800,000 bacteria daily directly to the baby’s mouth and GI tract. Babies who are formula fed will receive environmental pathogens and will have higher amounts of gut bacteria, but they are far less diverse and are missing the highly specialised human milk microbiome (1).

Breastfeeding stage

Breast milk is not a static substance. It changes depending on the time of day, frequency of breast emptying, infant illness or dehydration, maternal illness and so on. However, breast milk also alters in composition as mother and baby move through various ages and stages (11). When our babies start to leave our family circle, and attend crèche or childcare, they start to pick up more bugs and viruses. A mother’s more mature immune system makes antibodies for these germs and transmits them to her child through her breast milk.  Therefore we are giving our babies significantly more protection by breastfeeding them for longer.  The World Health Organisation (12) recommends that babies be exclusively breastfed for 6 months, with continued breastfeeding along with appropriate complementary foods for up to 2 years and beyond. 

Gestational age

Term babies are far more likely to remain with their mothers after birth, therefore building their microbiome and immune system within their family unit.  When a baby is born preterm, they are far more likely to need neonatal assistance which involves separation from their mothers, and the possible introduction of very necessary medical interventions.  This will give those babies a different microbial cocktail, but giving these baby’s breastmilk is hugely protective of their overall health and gut health (4).  Also, mothers of preterm babies produce breast milk that is higher in immune components and anti-infective properties than mothers of term babies (12). In fact, the American Academy of Paediatrics (13) recommends that preterm infants should receive human milk as an essential medical intervention, and in the absence of their mother’s milk should receive donor human milk. 


Antibiotics are a well-known cause of microbial imbalance within the body.  They work very well by killing bacteria that are harmful to us, but they also kill our resident good bacteria that are very important to maintaining our gut health and immunity.  If the balance of these microorganisms is compromised, we can have health repercussions both short term, and for life.  This is often seen when we have a yeast imbalance and candida as a result (otherwise known as thrush).  This imbalance most often occurs after antibiotic use.  Antibiotic use during pregnancy and while breastfeeding has also been linked to an increase in the rates of obesity, irritable bowel disease, and asthma in older children (4).


We, as humans, have evolved over thousands of years with our own specific range of microbes.  These microbes are likely to be found in our parents and our grandparents.  However our individual microbiome is completely unique to us (2).

Maternal diet and lifestyle

‘You are what you eat’ is a famous phrase that is as true today as it was when it was first coined in 1826 by the French Lawyer Anthelme Brillat-Savarin.  A diet that is high in sugar, processed foods and low in fibre has a negative impact on gut health (14).  Stress can also play a role in affecting gut health and is a leading cause of irritable bowel syndrome (7). Chronic stress and anxiety can cause abdominal pain, diarrhoea, and lack of appetite. In fact (15) found that resilience to stress- and immune-related disorders may be dependent on the diversity and complexity of our gastrointestinal microbiota.  

Geographic location

Studies have found that microbial composition varies from country to country, and even within rural or urban communities. However it is still unclear whether this is due to dietary influences or genetics or the geography of the land (6). 

Promoting a Healthy Infant Microbiome

Taking into account all of the factors that affect the microbiome, it is not difficult to surmise ways in which we can promote a healthy infant microbiome.  In the antenatal stage it is important to maintain a healthy diet, reduce stress, and keep active.  

The preferred mode of delivery is a vaginal delivery (if possible).  Postnatally, there should be minimal mother-baby separation, uninterrupted skin-to-skin for the first 3 hours, unrestricted infant access to the breasts with breastfeeding on demand (11).  

If there is mother-baby separation for any reason, the mother should be assisted to hand express/pump off her colostrum/mature milk every 2-2.5 hours so that it can be fed to her baby via syringe, cup or tube feeding.  This will also protect the mothers supply until she and her baby are reunited and direct feeding can resume. 

When a newborn drinks colostrum, it coats the gut wall in a thick honey like substance that is packed with probiotics, good bacteria, and proteins that optimize immunity. These proteins are full of immunoglobulins, antibodies  and live cells that give baby an amazing boost to their immune system. The more breastmilk a baby drinks, and the longer they breastfeed for, the greater the immunity (11).

Parents should be made aware of the effects of antibiotic use, so that they are not used without due consideration for the dangers of using them as well as the benefits.  Where antibiotics are used, probiotics should also be encouraged (under their doctor’s supervision), in order to promote the rebalancing of the infant gut microbiome. 

Parents should be encouraged to breastfeed their babies well into toddlerhood, and as long as both mum and baby are happy to do so.  Breastfeeding isn’t just for small babies.  Breastmilk continues to provide immunities and vitamins and is an excellent parenting tool in providing nutrition, comfort, security and reassurance (16).  

Prebiotics and Probiotics


Simply put; prebiotics provide the food for bacteria to grow and flourish, while probiotics provide the bacteria.  They are promoted as helping with digestive issues such as diarrhoea, constipation, infant reflux, and yeast infections (17).

Prebiotics are food components (complex sugars) that may provide a health benefit by helping bacteria to grow in your gut.  Foods such as onion, garlic, asparagus, oats and avocado are considered prebiotic foods.  Commercial prebiotics are available in Ireland but they are only recognised by the Food Safety Authority of Ireland (18) as a ‘health claim’ not a ‘health benefit’, and neither prebiotics or probiotics have yet been approved by the EU as authorised for use as a ‘health benefit’.

However, breast milk contains its own natural prebiotic: HMOs (Human Milk Oligosaccharides).  HMOs are complex sugars that are the 3rd most abundant component of breastmilk after lactose (milk sugar) and lipids (fats), but they are indigestible to babies.  In fact, for years scientists didn’t know why they were in breast milk if they could not be digested by the baby.  HMOs provide sugars to feed the beneficial gut microbes in the infant gut, so that they can multiply and colonise the infant gut microbiome, which is the basis for babies’ immune systems.  When babies breastfeed, they get all the nutritional goodness of that milk, which includes: milk sugars that are digestible, and complex milk sugars that are NOT digestible, but are digestible to your baby’s gut microbes (19).


Like prebiotics, probiotics are also considered a ‘health claim’ product, and not a ‘health benefit’ product.  Probiotic foods include fermented foods such as kefir and yoghurts [which can only be called ‘live’ if they contain at least 10 of the main colony forming starter microorganisms such as Lactobacillus acidophilus and Bifidobacterium infantis (18)].

Probiotic supplements come in pill, powder or liquid form and seem to be everywhere, but are they safe or effective?  Firstly, not all probiotics are created equal. Manufacturers use different strains of bacteria or yeast, in different quantities.  Therefore there is no one size fits all (17,20).  Probiotics are not recommended for immunocompromised persons or persons with open wounds following major surgery (2)

In general, probiotics are considered safe for use, but should only be used after consulting with a doctor.  It is also preferable to choose a reputable, well-known brand that has probiotic strains formulated specifically for various complaints such as digestive issues or candida.  Pharmacists should also be able to assist with choosing a reliable well-known product.

In general, it is considered that if a healthy varied diet is consumed, there should be no need for prebiotics or probiotic supplements.  However in times of illness or antibiotic therapy, probiotics may play a role in recovery.  Interestingly, Nami et al (21) envision probiotic therapy as a possible future preventative treatment so that antibiotic use is decreased, but more research is required in this area. 


The microbiome plays a significant role in the health of us humans.  It is considered by many as another organ, such is its extensive impact.  However, because it is not visible to the naked eye like the heart or lungs, it is difficult for us to be mindful of.  Processed and heavily engineered foods are all around us, and it can be difficult and expensive to make consistent healthy food choices. 

However, when it comes to the health of our babies, there are very clear steps we can take to ensure we give them the very best start in life.  Mode of delivery, infant diet (breastfeeding), and maternal/infant antibiotic treatment, seem to be the most important factors in optimal microbiome development (22).  

Information is key, and knowledge is power.  Parents need to be informed about the importance of the microbiome, and the ways in which they can promote gut health within themselves and their family. 


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