• Sarah Hickson

A Journey into the Human Microbiome

Updated: Aug 12, 2020

Poor germs. For years their infectious counterparts had us trying to avoid them at all costs for the sake of our health, leading us to be meticulous with scrubbing them away and “disinfecting” them with the most hygienic of products to ensure that the family house was safe and bug free!

Of course, certain microbes do have the potential to induce harmful infections, but until fairly recently we knew very little about how other microbes could help us. With the advances of science and the explosion of research into this area we are discovering that there are microbes that are actually protective against disease. Instead of making us feel ill, there are microbes that contribute towards our overall wellbeing as part of a thriving community that exists both within and outside the human body. According to animal studies, disruptions to the balance of this ecosystem or the absentee of certain strains of beneficial microbes can in fact, can spell disaster for our health too, not just physically but also mentally and emotionally.

Understanding the Human Microbiome

The microbial community that I’m referring to is collectively known as the human microbiome and includes an assortment of microscopic creatures such as bacteria, fungi, viruses and protozoa. Containing almost equal amounts of these non-human cells to human cells (we originally believed them to outnumber our cells by a ratio of 10 to 1 but that figure has since been updated), microbes are found on surfaces throughout the body including our skin, mouth, nose, ear, throat, lungs, gut and urogenital tract, and a whopping 70% of these microbes are found in our large bowel. The makeup of each human microbiome has strong diversity form person to person and is influenced greatly by our external and internal environment, genetics, diet, medications, stress and disease states. Quite curiously, using our body as a host there are commensal microbes that co-exist with our human cells without causing us any harm. Then there are microbes that play quite an active role in supporting our wellbeing, forming a synergistic relationship with our human cells. For example, prebiotics found in wholegrains, fruits and vegetables, human breast milk and some formulas provide food to nourish Bifidobacterium. This bacteria in turn performs tasks that benefit the human body, e.g. protecting against the overgrowth of bad bugs and maintaining the strength and integrity of our intestinal wall. Then there are strains of bacteria that are not directly harmful, yet if the conditions are favourable they can produce toxins that correlate with inflammatory and autoimmune conditions.

How a Community is Built

Prior to birth babies were believed to be essentially germ free, with ‘seeding’ first taking place through exposure to their mother’s microflora, that is if they had undergone a vaginal birth. However, exposure may occur even earlier than that with more recent studies finding a presence of microorganisms inside the human placenta. Indeed, if born via a vaginal delivery the newborn’s skin is coated with their mother's microflora with microbes entering their eyes, ears, nose and digestive system and contributing towards the microbial community. The environment (especially if born via a caesarian) and the child’s nutrition plays a big role too. By the time a child reaches the age of 3, their microbiome is similar to that of an adult’s.

How our microflora supports infant development

Studies done on the infant microbiome so far have found beneficial strains in infant microflora (e.g. Bifidobacterium) to play a valuable role in:

  • Helping babies to break down and absorb their food

  • Training their immune system on how to recognize friend from foe (having a protective effect against asthma and allergies later in life)

  • Supporting cognition and brain development

  • Regulating gene expression, potentially having a protective effect against many diseases including cancer and autoimmunity

  • Regulating metabolism. Remarkably, animal studies have shown that microflora can also have a protective effect against the development of obesity

How our microflora influences our wellbeing from infancy and beyond

Scientists have found that beneficial microorganisms play a wide variety of essential roles important for our long-term health and vitality. Some of the benefits are discussed below.

Maintaining the integrity of our gut lining.

Beneficial strains of our microflora are important for maintaining the function of our intestinal wall. A healthy gut lining absorbs nutrients while preventing the absorption of harmful toxins and microbes. If not functioning properly these toxins can enter our bloodstream, activate the immune system and trigger an inflammatory response.

Producing short chain fatty acids through fermentation of food fibres.

These fatty acids are not only important for regulating intestinal cell growth while protecting against cancer (butyric acid is the sole fuel source for cells lining the large bowel), they also play a role in brain metabolism, with beneficial effects being found in brain and psychological disorders including Alzheimer’s disease, autism and anxiety.

Producing vitamins and other nutrients

Beneficial intestinal bacteria produce a large number of nutrients that are essential for healthy cell development, metabolism and supporting our mental wellbeing. These nutrients include B group vitamins, vitamin K and amino acids.

Assists in the production of mood regulating chemicals

Fun fact: Over 90% of our serotonin, a chemical that is exerts feelings of calm and happiness and is a common target for antidepressant medication, is produced inside our gut!

Protecting against infection by preventing the overgrowth of harmful bacteria

Microorganisms such as Bifidobacteria help to protect us against the overgrowth of bad bugs, building our resilience against infection.

Communicating with and regulating our immune system

This role not only helps to support our immune cells in fighting off viral, bacterial, fungal and parasitic infections but also helps in preventing or down-regulating immune hypersensitive reactions such as autoimmunity and allergy.

Nourishing Our Microbes Supports Our Health Overall

The above information only touches on the amazing role our microflora plays in supporting our wellbeing (and we are only at the beginning of understanding its full complexity), yet this is when the community is rich in diversity with synergistic microbes high in number. Obvious symptoms of a disrupted internal ecosystem (termed dysbiosis) can manifest as frequent constipation or diarrhoea, bloating, wind and abdominal discomfort. Studies done on animals have found long term dysbiosis to be been linked to a multitude of chronic diseases that include inflammatory bowel disease, obesity, cancer and autism, and even mental health conditions such as anxiety and depression. When it comes to treating chronic illnesses, supporting our gut health will always be a worthy complement to any holistic or medical treatment.

As I mentioned at the beginning of this post, there are many factors that can compromise the balance of our microbiome, a diet lacking in fibre and phytonutrients being a major influence. In my next blog post from this series I will discuss the term prebiotics and how we can nourish and nurture the growth of our microbiome so that in turn we are supporting the health of the whole body. Meal ideas and recipes will be included!


Mueller, N.T., Bakacs, E., Combellick, J., Grigoryan, Z., Dominguez-Bello, M.G., 2015, The infant microbiome development: Mom matters, Trends Mol Med, Vol 21 (2), p.109-117

Morelli, L., 2008, Postnatal Development of Intestinal Microflora as Influenced by Infant Nutrition, Journal of Nutrition, Vol 138, no 9, p.1791S-1795S

Vyas, U., Ranganathan, N., 2012, Probiotics, Prebiotics, and Synbiotics: Gut and Beyond, Journal of Gastroenterology and Research and Practice, Vol 2012, p.1-16

Castro-Nallar E, Bendall ML, Pérez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA. (2015) Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.

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