It’s impossible to talk about gut health without coming across the word “Microbiome”. It’s a relatively new (about 25 years) area of study, but has changed everything we know about diets, aging, illness and health. In fact, focusing on your gut, specifically your gut microbiome may be the biggest change you can make to improve your overall health.


Despite it being new, there’s an overwhelming amount of information relating to the microbiome out there. Much of it, difficult to digest. To make it easier to understand, I’ve done the research and broken it down to help you understand what it is, how it develops, why it’s really important what it impacts and how you can improve it.


Defining the Microbiome

The American Microbiome Institute describes the human microbiome as the “assemblage of microbes that live in the human body”. They inhabit all parts of our body exposed to the environment, but most reside in our guts where they have a constant supply of nutrients.


According to Dr Aviva Romm, your gut microbiome is made up of a trillion diverse microorganisms (bacteria, fungi and viruses), which weighs in at about 1 kilogram, the same weight as your brain.


Over the past 25 years, studies into the human microbiome have increased and researchers have shown how those organisms making up your gut microbiome impact nutrient absorption, detoxification, the health of your gut lining, your moods, appetite, food cravings and mental function. When your microbiome is out of balance it can result in inflammation, obesity, diabetes, hormonal problems, anxiety, depression and brain fog.


In her book, The Adrenal Thyroid Revolution, Romm explains how your microbiome extracts calories and nutrition from your food, detoxifies chemicals and hormones, and synthesizes vitamins and iron for absorption. There are about 400-600 strains of bacteria in your gut, some healthy and some not. Healthy bacteria help keep your gut lining in tact and healthy. Unhealthy bacteria in your gut on the other hand, release toxins which can disrupt the integrity of your intestinal lining.


In addition, 70% of your immune system is in the lining of your gut. The bacteria on your gut border communicates with your immune system and nervous systems, including your brain. Inflammation in your gut can thus affect your entire immune system including your mood.


What Effects the makeup of your Microbiome?


It’s highly probable that the majority of us have a microbiome that is out of whack, thanks to years of being exposed to not so healthy food choices like GMOS, sugar, artificial sweeteners and even medication.  Our microbiome is also constantly evolving starting from when we are born. The following things can impact the makeup of your Microbiome and thus your overall health.


  1. Your birth – Scientists believe that the mode of delivery can impact the initial infant gut microbiome and normal immune development. Babies born via C-section have a gut microbiome that resembles their mother’s skin right after birth and are more likely to develop an autoimmune disease later in life. Babies born vaginally have a gut microbiome that resembles their mothers’ vaginas and are at lower risk for asthma and allergies.


  1. Anti-biotics – the number of times you have been on a course of anti-biotics impacts your microbiome, as it disrupts the microbiome killing the bad bacteria along with the good. The more you’ve been on anti-biotics, the likelier you are to suffer from gut issues. And it could take years for your microbiome to recover.


  1. Exercise – exercise can change the composition of your microbiome over time for the better. Researchers found that exercise increases certain microbes that can help to produce substances called short-chain fatty acids. These fatty acids are said to aid in reducing inflammation in the gut and the rest of the body. They also work to fight insulin resistance, a precursor to diabetes, and boost one’s metabolism.



How the Microbiome Influences your Physical and Mental Health

As research continues to show the microbiome has major impacts on your nutrition, likeliness of getting certain diseases, immune system and even your mental health.



Your gut bacteria are responsible for breaking down many of the complex molecules found in foods. These bacteria not only harvest energy for themselves from the plants we eat, but also break down the plants into smaller molecules which our body is able to digest. Scientists have discovered that different diets can impact the makeup of one’s microbiome.


Furthermore, Food cravings (whether you go for sweet or salty foods) may be a factor of what’s going on in your gut microbial community. According to Romm your gut can manipulate you into eating certain foods that specific organisms in it need to survive and thrive. It does this by creating a food craving for the foods it needs for its own growth by making your brain register those foods as tastier and more appealing. It also produces toxins that make us feel unwell and alter our mood, through affecting various neurotransmitter levels until we eat the foods that satisfy them.


Immune System

Your gut bacteria play a huge role in developing your immune system when you’re young. It starts as discussed above by birth as you’re exposed to your mother’s microbiome. As you grow, your body is exposed to germs and other foreign antigens and develops a tolerance to them.  Once a homeostasis is established, non-pathogenic microbes and other harmless antigens will not induce an inflammatory response. Unless there are allergies or autoimmune diseases in which case your body will develop an inflammatory response.


Disease and Hormones

The gut microbiome is being shown to impact many diseases. Especially symptom based gastrointestinal diseases, like Crohn’s disease, ulcerative colitis and IBS, which have strong links to shifts in bacterial gut populations.  While the microbiome is normally quite robust, the ingestion of antibiotics, as well as sustained diarrhoea can permanently alter our flora as new bacteria repopulate the gut.


Studies have also found that our bacteria (or lack thereof) can be linked to or associated with obesity, malnutrition, heart disease, diabetes, coeliac disease, eczema, asthma, multiple sclerosis, colitis, some cancers, and even autism.


Your microbiome may also affect your hormones. Healthy gut flora has bacteria with genes capable of breaking down and helping your body eliminate oestrogen. They help prevent excess oestrogen from recirculating in the intestine. When a microbiome is damaged, oestrogen recirculates in a particularly toxic form, this increases a women’s risk of becoming oestrogen dominant and increasing the risk of breast, ovarian and endometrial cancers.


Behaviour and Mood

There’s a strong connection between mind, mood and microbiome. Above we discussed how your microbiome can influence what foods you crave. Some beneficial species of Gut Flora produce Butyrate which reduces anxiety and depression. When the micobiome is perturbed, Butyrate levels drop.


As Romm explains, the gut has two major ways of communicating: The enteric Nervous system and your microbiome. The enteric nervous system is called the “second brain” and is made up of a network of some hundred million neurons that are embedded in the lining of your gut. Majority of your serotonin (the feel-good hormone) is produced in the gut.  95% of the information passing through the vagus nerve (one of the largest in your body) goes from the gut to the brain. Disruptions in your gut can cause unhappy moods and thoughts to the extent that the emotions you experience may reflect what’s happening in your gut.


Your microbiome may also cause brain fog. This happens because of the chemicals and gasses produced by fermentation in your gut, which are determined by your particular microbial community and the foods you eat that cloud your thinking. Eating a high sugar and highly refined carbohydrate diet can lead to the production of by-products that make you feel groggy.


How do you know if Your Microbiome is out of whack?

It’s said that when your gut is off the rest of you is off, but how do you know? While there are tests that test one’s microbiome, the science is still in it’s infancy,  Doctors say it’s more of a science project than a diagnostic test.


There are however some indications that your gut isn’t that healthy


  1. Digestive issues – the number one indicator that your gut is out of whack is having any digestive issues. If you listen to your gut after eating, you’ll also be able to see what’s good for it and what’s not. For example, feeling jittery or anxious after a cup of coffee means you’re a slow metaboliser as it’s hanging in your body longer and it may be better to give it up. Dr Vincent Pedre also suggests noticing how you feel after a high fat meal, if you generally feel tired it’s not good for you.
  2.  Brain Fog, Depression and Anxiety – while not definitive, they can indicate a gut issue.
  3. Mineral Deficiencies – you are what you absorb, not what you eat. If you’re eating well but still lack certain vitamins and minerals it may indicate that your gut isn’t properly absorbing the nutrients.
  4. Inability to manage stress – if you find it difficult to handle stress you may want to take note of your gut and what you eat.
  5.  Skin conditions like eczema, psoriasis, rosea and acne can be linked to your gut.
  6.  Autoimmune diseases have been strongly linked to a compromised gut microbiome.


How to Make Your Microbiome Healthier

There are a number of things you can do to improve the health of your gut. Dr Pedre advises choosing one thing – one thing you can change to make your gut healthier. This way the chances of you sticking to it are higher than if you overhaul your entire diet and life.


  1. Eat Fiber – “Fiber is the currency by which we communicate with the microbiome”. According to Dr Pedre, when bacteria takes fiber and digests it – it produces something called short chain fatty acids, they get absorbed into the body and have effects everywhere, they regulate blood sugar, regulate brain behaviour, regulate which genes are expressed. Foods that contain fiber which friendly bacteria feed are called prebiotics and include onions, tomatoes, garlic, leeks and radishes.
  2.  Eat lots of plants – specifically dark leafy greens.
  3.  Know where your food comes from – stay away from corn fed, grain fed and pasteurised sources of meat and dairy.
  4.  Eat fermented foods – things like sauerkraut, kimchi and kefir have natural bacteria to protect your gut.
  5. Drink filtered water – chlorine in tap water kills microbes in soil, and thus the chlorine in unfiltered water will alter your bacterial balance.
  6.  Limit your sugar intake – this is not only refined sources but also hidden sources in carbohydrates and sweeteners added to food.
  7.  Variety – eat a variety of foods and colours have a broad representation in colours of your food and rotate so you can feed different aspects of your microbiome.
  8.  Exercise – it improves your gut bacteria and also helps manage stress.
  9.  Avoid preservatives, artificial ingredients and artificial sweeteners as they disrupt your microbiome


Please note this article is not meant to be used as medical advice. The information is based on the following sources

Dr. Aviva Romm, The Adrenal Thryoid Revolution

The Microbiome Institute

Mind Body Green Podcast with Dr Vincent Pedre

Nourish Noshes Podcast on Microbiome

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