top of page
  • Writer's pictureCheryl Penna

The Human Microbiome

Updated: May 31, 2022

Your microbiome is the unique collection of trillions of microorganisms in and on your body. They play a big part in your wellness. There are as many microorganisms as there are cells in your body and most of them live in your gut.

Your microbes help to keep you healthy. Some enable your gut to digest fibre and manufacture vitamins. Others are less helpful, and some are actually harmful.

When your gut is healthier, you're healthier.

Balance in your gut microbiome is key to wellbeing.

The human microbiome, includes the microbes that find their home not only in the gastrointestinal tract (GI), but also on the skin, respiratory tract, urogenital tract and even the brain. These microbes predominantly consist of bacteria, although nonbacterial organisms such as viruses and fungi are also represented.  The term “microbiome” refers not only to the microbiota and their habitat but also the collective genomes of the microbes, known as the “metagenome”.  

Whilst the exact number is not known, it is estimated that the ratio of bacteria to human cells lies somewhere around 1-3:1, indicating that the body relies on a substantial microbial population whose function impacts not only the interfacing epithelial tissues but also the function of our body within.

Development of the Gut Microbiota

By far the largest population of microbes is found in the GI tract, which is home to a diverse mix of microorganisms that is unique to each of us.  As we consider how this population becomes so complex, we must roll back to clock to infancy and beyond to understand the development of this unique ecosystem the serves up from birth till death. Factors such as the health and wellbeing of the mother both before and during pregnancy predetermine seeding of our microbiome.  

Birthing practices such as vaginal vs C-section determine the bacterial diversity or “richness” in the gut.  C-section and bottle-fed children have been shown to have a less diverse richness of microbes that may influence obesity, food allergy, atopic dermatitis and asthma risk in early development as well as later in life. 

The neonatal gut continues to populate and diversify though childhood until it reaches a high level of diversity at around the age of 2 years.  During this period the gut microbiome is heavily influence by antibiotic use as well as medications such as steroids and PPI’s that may reduce or wipe out complete species of bacteria that will impact the health of the gut for many years to come.  

Diet and environmental factors also impact the richness of the developing gut and a broad range of whole foods as well exposure to playing in the dirt and having a family pet add to the microbial diversity. 

Feeding the Gut Diversity

Human breast milk contains a rich source of Oligosaccharides (HMOs) prebiotics, that not only serve as a food for bacteria to feed on but have also been found to have antimicrobial effects that modulate the developing immune system, whilst protecting the infant.  There are many substances that are found in the diet and are available as supplements that contain prebiotics; foods that feed our microbes.  

In 2011 the World Gastroenterology Organisation defined prebiotics as “dietary substances (mostly consisting of non-starch polysaccharides and oligosaccharides poorly digested by human enzymes) that nurture a select group of microorganisms living in the gut.

Prebiotic fibres include; Inulin, lactulose, fructooligosaccharides (FOS), xylooligosaccharides (XOS) and galactooligosaccharides (GOS).  High levels of prebiotic fibres are found in foods such as onions, garlic, Jerusalem artichoke, leeks, green bananas and chicory root.  

Mechanisms of Action Prebiotics serve as substrates for fermentation by the bacteria in the colon, and may support health by a variety of mechanisms;

  • Increasing levels of Lactobacillus and Bifidobacterium species in the colon

  • Decreasing GI transit time

  • Improving mineral absorption

  • Promoting satiety and reducing food consumption

  • Protecting against infection by inhibiting pathogen attachment and or supporting immune function

  • Increasing levels of short-chain fatty acids (SCFAs) in the colon, including butyrate\

  • Reducing cholesterol levels

Health Benefits

Prebiotics have been shown to potentially be beneficial in settings of inflammatory bowel disease (IBD), bone health, infant and childhood allergies and atopic dermatitis as well as cardiovascular disease.

Adverse Effects

Although prebiotics are generally safe for consumption and are predominantly found in our diets, higher doses of prebiotics fibres can lead to undesirable effects such as increased flatulence, bloating and diarrhoea.  These fibres are not suitable for people who have been told to follow a low FODMAP diet or have been diagnosed with SIBO (Small Intestinal Bacterial Overgrowth).

These adverse effects can be averted by increasing the dosage gradually or spreading intake throughout the day.  The best advice to follow when introducing these foods and fibres into your diet is to GO SLOW and LOW. Introduce one type of fibre supplement at a time and if you have a reaction then stop, reduce the dose or try a different prebiotic fibre. 


Probiotics are defined as living organisms that when administered promote a transient increase in flora that may benefit the host. Specific strains have been shown to be beneficial for many health conditions such as genitourinary tract infection, atopic dermatitis, mood disorders, autoimmune disease, metabolic syndrome and autism spectrum disorder.

Mechanism of Action

Probiotics are intended to affect the health of the host and the microbiota balance via local and systemic immune mechanisms as well as non-immune mechanisms.  These include;

  • Enhancing intestinal barrier function

  • Stimulating production of protective epithelial mucin

  • Increasing production of health promoting SCFAs in the colon

  • Enhancing the local mucosal immune activity by increasing secretory IgA, which helps protect against pathogens and toxins

  • Lessening systemic antigen exposure (e.g., food allergens)

  • Systemically modulating immune system function

  • Protecting from microbial invaders by; Competition for nutrients at adhesion sites, Production of bacteriocins proteins, that can inhibit the growth of other bacteria, including pathogens, Alteration of the local pH to create an environment unfavourable for pathogen growth.

Selected Clinical Applications

The primary families of probiotics that have been studied are Lactobacillus and Bifidobacterium species.  Other commonly used probiotics include; Steptococcus thermophilus, Saccaromyces boulardii (yeast), Lactococcus lactis, Enterococcus faecalis and spore-forming anaerobe Bacilllus coagulans.

The past few years has seen an explosion of research in this area that have highlighted several species that have shown beneficial effectiveness in clinical therapy. 


Les commentaires ont été désactivés.
bottom of page