The Human Microbiome and Your health

The Human Microbiome and Your health | The White Pigeon Said

What is a microbiome?

When we refer to a microbiome we’re talking about the collection of microorganisms that live in a particular environment or organism; including bacteria, fungi, viruses, and other microbes.

We use the term to describe the highly complex community of microbes that live in and on the human body, better known as the human microbiome; no doubt you’ve heard this term before.

The human microbiome is made up of trillions of microorganisms; an estimated 38 trillion microbes live in and on us (Sender, et al. 2016). Just to put that in perspective, recent estimates suggest we have about 30 trillion of our own cells that make up the human body. So yes, more microbial cells live with us than our own cells.

This blog explores the intriguing connection between the microbiome and crucial facets of human health, backed by some notable research findings.

We have several microbiomes.

Microbial populations or microbiomes (I’ll use the terms interchangeably) don’t just live in your gut (and throughout your entire digestive system), which you have probably heard a lot about, but also in and on other parts of the body; on your skin, in your nose and mouth, and in the reproductive organs; each of these hosting unique, diverse and highly complex microbial communities. Anywhere our insides meet the environment, we have a microbiome there to play a role.

These microorganisms play crucial roles in most physiological processes and can have a significant impact on our health; impacts we are only just scratching the surface on research wise.

Where does our microbiome come from?

It is largely thought that the womb is a sterile environment so before we are born, we are in effect, a blank canvas. So how is it that we acquire this abundance of microbial species?

There are several factors that influence what strains we are ‘seeded’ with when born. The method of birth, i.e., vaginal or caesarean, method of feeding, skin of other caregivers (and strangers too), surfaces you’re exposed to and whether you have a pet in the home will all influence which microbial strains initially land and populate your system.

Then after the first year of life, when solids are introduced, we see a shift in the microbial populations present. It is thought that these personal and what we call native microbial populations remain relatively stable into adulthood but can differ between people based on a variety of factors like Body Mass index (BMI), cultural and dietary factors, lifestyle and frequency of exercise (Rinninella et al., 2019).

So, what happens where our gut microbiome and our cells meet?

Just for a moment I’d like you to think of your gut (or large intestine if I’ve got my scientific hat on) as a large bustling city.

It has a protective wall, the gut lining, protecting the city (you) from unwanted intruders (pathogenic microbes). Protecting this wall (or barrier) is a vibrant neighbourhood, a community of trillions of bacteria, viruses and other inhabitants, our microbiome. And, to keep the peace in this bustling city, we have the immune system, our body's very own security force on the other side of the wall; just in case anyone or anything untoward gets through!

Now, let's delve into the science of this crucial but complex relationship:

The Gut Lining; Our Great Wall of Defense:

Your gut lining is like the city's protective wall, serving as the first line of defense against harmful invaders. It's a single layer of cells that separates the bustling city from the outside world, ensuring that only the good stuff gets in – like nutrients from your food. So, this interface is composed of a single layer of intestinal mucosal cells (or colonocytes), a mucous layer and our immune cells just sitting and waiting for instructions.

The Microbiome, our lively neighbours: Along this protective wall lies the microbiome – a diverse and teeming community of microorganisms. These friendly residents include a multitude of bacterial species, viruses, fungi, and more. Think of them as the quirky neighbors who play a big role in keeping the city running smoothly. They help with digestion, produce essential nutrients, and even influence your mood and health, more on this in a moment.

The Immune System - The Security Squad: Now, let's introduce the immune system – your body's vigilant security force. They are like the police and firefighters of the city. Their job is to maintain order and respond to any threats. The immune system is constantly patrolling the gut lining to ensure everything is A-OK.

What is Leaky gut syndrome?

We have mentioned that the gut lining (protective wall) keeps the contents of our gut where it needs to be but is really just a single layer of cells and some mucous. Sometimes things go awry.

There are various environmental factors that can shift the balance of microbial populations out of balance. Things like chronic stress (sadly, so common in this day and age), exposure to environmental toxins (yes, in the air and environment but also those we put on our skin and in our bodies, like pesticides), a poor diet, antibiotic use can all cause dysbiosis in our microbiome.

Leaky Gut Syndrome | Leaky gut symptoms | Human Microbiome | The White Pigeon Said

When out of balance, some bacteria can damage the mucous and colonocyte layer causing ‘holes’, or a leaky gut. Our once balanced fortress, the gut now allows molecules to pass through that shouldn’t; microbes themselves, toxins and some particles from our diet, leaking from the gut into the bloodstream.

Now, this is when our army of immune cells on the other side launch an attack, which often causes inflammation.

Leaky Gut symptoms

A damaged intestinal lining can lead to an array of leaky gut symptoms from minor ones (though they don’t feel minor) to more serious diseases like (Camilleri, 2019):

Gastrointestinal: Bloating, cramps, pain, allergies, heartburn, gas or sensitivities

Skin: Acne, rashes, Eczema, Rosacea, Itchy and irritated skin, Psoriasis

Neurological: Fatigue, headaches, General brain fog, Anxiety, Depression, Insomnia, ADD/ADHD

Autoimmune and Metabolic: Celiac disease, Crohn’s disease, Inflammatory Bowel Disease (IBD), Diabetes and Multiple Sclerosis.

So, what's the difference between prebiotics, probiotics and postbiotics?

Now is as good a time as any to introduce and clarify a few terms:


These are foods or supplements that feed our microbiome. They allow our beneficial microbes to grow and flourish and to make metabolites that benefit us. Prebiotic foods are generally those that are high in fiber like whole grains, legumes, fruit and vegetables.

Prebiotic can also be purified forms of fibre, like Fructo-oligosaccharides (FOS) (fancy name for a carbohydrate chain) and Galacto-oligosaccharides (GOS) (Davani-Davari et al., 2019). These are generally found in low levels in food and so are now purified for an extra prebiotic boost.


These are the microbes themselves. The good guys. There are many gut health probiotics now available, different strains, different doses… a lot.

Whether these bacteria can actually pass through the entire digestive tract and are then able to populate the colon is up for debate. However, recent studies have shown the benefits of ingesting fermented foods, teeming with live good bacteria, on microbial diversity and improved immune responses (Wastyk et al., 2021) as well as antiviral support (Varsha et al, 2022).

I recommend consulting with your functional medicine doctor before taking any probiotics.


So, these are the byproducts of our gut microbiota. They eat what we feed them, and then they produce a host of beneficial metabolites, like short chain fatty acids, more on this in a moment.

Why does having a healthy microbiome matter?

So far, scientists have identified key biological functions of the human microbiome which include but are not limited to:

  1. Digestion:

Microbes in the gut help break down and digest food, helping us absorb vital nutrients. Not only do they break down some nutrients that we can’t (think indigestible carbohydrates like dietary fibre and resistant starch), but the kicker with this is that through this process microbes generate metabolites (or postbiotics) that significantly impact human health. Not only are they beneficial, many of which are actually essential for optimal health and wellbeing.

Probably the most well studied microbial metabolites are short chain fatty acids, SCFA, mainly butyrate, propionate and acetate which are produced by some colonic bacterial strains in the Firmicute species (like Lactobacillaceae strains).

SCFA have been shown to influence microbiota-gut-brain communication affecting brain physiology and behaviour (O’Riordan et al, 2022) as well as other organs and most biological systems to some degree.

Some microbially produced metabolites are beneficial but others are not. The table below shows how varied the biological effects of some of these microbial products are.

Short Chain Fatty Acid

Documented effect


Increased satiety, weight loss, suppress appetite, improves insulin sensitivity, reduce proinflammatory cytokines, may serve to promote cancer cell survival


Anti-obesity effect; reduces weight gain, intra-abdominal adipose tissue distribution. Decreases proinflammatory cytokines


Supports mucosal integrity, modulates both local and systemic immunity, protects against colonic neoplasia (uncontrolled cell growth), anti-obesity effects; stimulates the release of anorexigenic hormones and leptin synthesis.

Table 1: Summary of effects of gut microbial SCFA (Adapted from Rahman et al., 2023)

Interestingly, low levels of SCFA have been associated with Alzheimers (Zhang, 2017), Autism spectrum disorder (ASD) (Liu, et al., 2017) and chronic stress so, these SCFA-producing bacteria are the good guys that we want to feed well to help them propagate and flourish.

  1. Immune System Support and Inflammation:

The microbes that share your body help to train and regulate your immune system which aims to protects you against harmful pathogens. Growing research highlights the impact of a diverse and healthy microbiome to a well-balanced immune system.

The previously mention postbiotics, produced by our microbiome can mediate crosstalk between the colonocytes that line the gut and our immune cells on the other side.

In a healthy system, specialised cells in the gut called goblet cells produce mucous to help keep our microbiome where they need to be so that the integrity of intestinal barrier is maintained. A healthy microbiome supports little permeability to unwanted molecules (i.e. no leaky gut). If no nasty foreign materials cross this barrier then we have happy and calm immune cells on the other side.

Extensive research suggests that certain microbial species promote immune tolerance, which stop the immune system from overreacting to harmless substances while other microbes trigger immune responses (including inflammation) to ward off any potential pathogens.

It’s all fine balance as those of us with autoimmune issues know all too well.

Commensal bacteria, like those belonging to the Bacteroides and Clostridium genera, produce SCFAs (as discussed above), which play a key role in modulating immune cell function and promoting anti-inflammatory responses (Honda and Littman, 2016).

It should be no stretch, based on what we’ve covered thus far that these interactions have a significant impact on the body's ability to fend off infections and maintain a balanced immune response.

Microbial dysbiosis, where there is disruption between the microbiome and the host has been implicated in several types of cancers, metabolic deficiencies and autoimmune diseases among others.   

  1. Metabolism:

Microbes can influence metabolism and may play a role in conditions like obesity and diabetes.

Interestingly, the microbiome can modulate energy intake by directly affecting the digestion of complex marconutrients (i.e. complex carbohydrates) or indirectly by influencing the production and/or secretion of molecules that control hunger and satiety through the neuro-endocrine axis (Fettisov, 2016).

Obesity is linked to several diseases of metabolic dysregulation like fatty liver disease, Type 2 diabetes and cardiovascular disease and recent studies have shown links between the microbiome and these diseases (Bäckhed et al. 2004; Kahn et al., 2014).

  1. Protection:

Beneficial gut microbes play a key role in our immune function, as noted above. They work to protect us against pathogenic (disease causing) strains by:

  • eating up all the nutrients which inhibits their ability to survive and grow and also by
  • producing bacteriocins, molecules that change the environment, making it unsuitable for these harmful strains to thrive,

These tools ultimately ensure that these harmful bacteria cannot colonize and cause infection (Rinninella, et al., 2019).  

  1. Synthesis of Vitamins and Nutrients:

While we get many of our essential vitamins from our diet, many are synthesized by our gut microbes; how clever is this symbiotic relationship!

Several microbes are involved in the production of vitamins and other essential nutrients. Studies have shown gut microbes are able to synthesize vitamin K2 and most water-soluble B vitamins (Pham et al., 2021).

The pathways for their synthesis vary but have been shown to be produced by various bacteria like Bacteroidetes, Firmicutes and Fusobacteria (Yang and Cong, 2021). Again, good guys we want to continue to feed and nurture.

  1. Mood, Brain Function and mental health:

Emerging research supports the connection between the gut microbiome and mental health, with potential implications for mood and cognitive function; there is so much great info out there on this and it’s termed the Gut-Brain Axis.

Studies have shown how several bacterial strains can alter levels of neurotransmitter (NT) precursors in the gut and even synthesize (or control production of) several neurotransmitters themselves, including:

  • Gamma Aminobutyric acid (GABA): an inhibitory NT with low levels linked to anxiety, depression, insomnia and epilepsy.
  • Serotonin: involved in controlling mood, reward, learning, memory and so much more with deficiencies linked to anxiety and depression.
  • Dopamine: associated with feelings of pleasure and motivation. Dopamine dysregulation has been strongly associated to psychiatric and neurological disorders like anxiety, depression, autism, and Parkinson’s.
  • Noradrenaline: essential in regulating arousal, attention, memory, learning as well as our stress reactions with deficiencies having been linked to various neurological issues. (Miri et al., 2023)

So, what is a ‘healthy’ gut microbiome?

Our microbiomes are unique and composed of an array of bacterial species, yeast and viruses. Bacteria are classified by phyla, classes, orders, families, genera and species – a complex system with only a few phyla represented in our microbiome.

For those of you who love science, the dominant gut microbial phyla are Firmicutes and Bacteroidetes, which represent approximately 90% of our gut microbes with others like Actinobacteria, proteobacteria, Fusobacteria and Verrucomicrobia also represented (Arumugam et al., 2011).

The Phyla Firmicutes represent more than 200 species; including Lactobacillus, Bacillus and Clostridium, some of which you may have heard of.

The composition of the human microbiome can vary widely between people depending on a bunch of varying factors like diet, genetics, age, antibiotic use, BMI, ethnicity and environment as well as the prenatal and postnatal periods of development, as mentioned previously (Rininella et al., 2019).

A balanced and diverse microbiome is generally associated with better health, while disruptions or imbalances in the microbiome can contribute to various health issues.

Gut dysbiosis has been linked to the development of many metabolic, behavioural and neurologic outcomes like diabetes, IBD, Crohn’s Disease, Depression, Parkinson’s disease, Alzheimer’s Disease and Autism Spectrum Disorder (ASD) and many more (Silva, Bernardi and Frozza, 2020; Rininella et al., 2019).   

So, we need a healthy, balanced and diverse gut microbiome to;

  • Aid in digestion
  • Maintain barrier function (that protective wall)
  • Talk to our immune system and keep inflammation in check
  • Produce crucial metabolites and
  • Protect us against pathogens
  • Regulate our metabolism

Do you have a healthy microbiome?

Firstly, it’s important to be able to identify whether you have poor gut health. Some signs might include;

  • Chronic upset tummy (bloating, cramping etc)
  • New food allergies or sensitivities
  • Bouts of skin irritations (like eczema or rosacea)
  • Poor sleep quality
  • Changes in appetite/ eating habits or unexplained weight gain/loss

There are tests available that analyse a sample of your poo and identify what microbial populations live in your gut and in what proportions. BUT, and it’s a bit but, there is not yet a universal method for determining whether what is found in your gut is necessarily healthy or not and how to completely interpret this data.

While it’s known that certain bacterial strains are beneficial, developing a symbiotic relationship with us, there is no unique and optimal gut microbiome. We are all different. What is healthy for you or one population is not necessarily so for another.

What we do know is that there needs to be a healthy balance of commensal (beneficial) bacterial strains that outnumber the pathogenic (ones that cause disease) ones. This gut microbiota balance is crucial for maintaining a healthy metabolism and immune system while preventing disease.

Scientists are pumping out fascinating research into the human microbiome so we can better understand its role in health and disease. This knowledge has led to the development of therapies like prebiotics and probiotics, which aim to promote a healthy microbiome and improve overall well-being.

Sometime in the not-so-distant future, there is likely be individualised treatments based on analysis of your microbiome to improve health outcomes.

Can I change my microbiome?

The short answer is yes, you absolutely can. While this topic is a blog on its own, there are ways to alter your microbiome to help the good guys flourish and sometimes, if needed, start over.

Without going into detail here, there is research to support the numerous ways to modify your microbiome including:

  • Changing your diet to include fibre rich foods, fermented foods and polyphenol-rich foods.
  • Changing your diet to limit simple sugars, artificial sweeteners, processed foods (these really mess with your gut), alcohol, food additives, excessive alcohol, excessive saturated and trans fats and red meat.
  • Changing your diet to introduce Omega-3 fats.
  • Supplementing with prebiotics
  • Faecal microbial transplant

If you are suffering with or suspect poor gut health, please consult your functional medicine GP, Nutritionist and/or Naturopath.

A note on the Skin Microbiome

While we have focused on the gut here, the skin microbiome is also incredibly important. While the bacterial populations found on the skin differ from those in the gut, we also find some other critters on our skin, like fungi, many viruses and mites, yes, you read that right.  All of this found on the surface of healthy skin.

Our skin microbiome is involved in:

  1. Overall skin Health

A well-balanced skin microbiome plays a significant role in maintaining the health and appearance of your skin. It helps to regulate skin pH, moisture levels, and sebum production. An imbalance in the microbiome can lead to issues like dryness, oiliness, or sensitivity.

  1. Immune Support

The skin's microbiome interacts with the immune system (noticing a theme here?), helping it distinguish between harmful invaders and beneficial microbes. A healthy microbiome can bolster the immune response, reducing the risk of inflammatory skin conditions and allergies (Ferček et al., 2021).

  1. Wound Healing and Anti-aging

Beneficial bacteria on the skin can aid in the wound healing process by preventing infection and promoting tissue repair (Tomic-Canic et al., 2020). Interestingly, they also contribute to the formation of a protective biofilm which shield the wound and promote barrier restoration.

A balanced skin microbiome can help slow down the aging process by reducing inflammation and oxidative stress on the skin. It can also support the production of collagen and other skin-rejuvenating compounds (Ratanapokasatit et al., 2022).

  1. Skin condition management

Maintaining both a healthy skin AND gut microbiome is essential for individuals with chronic skin conditions such as eczema, psoriasis, or rosacea (Ellis et al., 2019). Imbalanced microbiomes (both gut and skin) can exacerbate these conditions, while well-regulated ones can help manage symptoms (De Pessemier et al., 2021).

  1. Holistic Health

Given the complexity of our symbiotic relationship between our microbes and us, it should be no surprise that dysbiosis in the skin’s microbiome has been linked to systemic health issues beyond the skin.

How to keep your skin microbiome in check

Just like we need to nurture our gut microbiome, the microbes on our skin also need some love. Here are a few tips to keep your skin microbes happy:

  • Limit the use of antibacterial products that can disrupt your beneficial microbes. This includes cosmetic products with preservatives.
  • Keep good hygiene: clean your mobile phone, keyboard, bed sheets regularly and keep your hands off your face unless they’ve been cleaned.
  • Eat a balanced diet; your gut microbiome impacts your skin!
  • Stop smoking and start to exercise (preferably out in nature)
  • Treat your skin to some prebiotics and probiotics (get in touch if you want to know how)

To sum up

The human microbiome’s impact on our overall health can’t be overstated. It influences our immune function, metabolism, brain function and mental health and most of our physiological processes.

Scientists are working to further understand and harness the potential of the microbiome and it is opening up a new world for personalised therapies and interventions to improve human health and quality of life. We have only just scratched the surface into microbiome research It’s remarkable really.

Here, we’ve highlighted the intricate interplay between the microbial world within (and on) us and our physiological and psychological wellbeing.

I trust that you now have a newfound respect for the trillions of microbes that share your body and will be a bit more conscious about nurturing them.

Here’s to living in harmony with our microbiomes,


P.S. If you are having gut issues and not sure where to turn for help, we've got your back, here is a list of local practitioners who have experience with gut health:

Andrea Murphy - Acupuncturist at Mornington Chinese Medicine 

Tessa Rickard - Nutritionist 



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