Gut Health - A basic guide

[Updated 3 April 2017 - Check out the video at the end of the post! ]

Believe it or not, not all bacteria are bad. In fact, some are really good for us. Our bodies are home to 100 trillion bacteria, most of which live in our gut [1]. Of course, there are the ‘bad guys’ that cause illness and infection, which we aim to kill off using antibiotics, but there are also many ‘good guys’, which form part of the microbiome in our gut that plays a major role in keeping us healthy [1]. The trillions of microorganisms that call our bodies home play a significant role in the proper functioning of our digestive tract, immune system, skin, and a number of other body systems [2].


Current Research

The relationship between good bacteria and health was first noted and researched by Dr. Matchnikoff in 1906 but remained unappreciated for many decades up until about 20 years ago [1]. In recent years the human microbiome has attracted more and more attention from scientists worldwide. The Human Microbiome Project is currently underway, with the aim of mapping out all of the microbes found in the human gut to discover their role in promoting health and preventing disease [1]. The Center for Microbiome Informatics and Therapeutics was launched a few years ago as a dedicated center for advancing research in this field that should help us better understand the role that the microbiome plays in the human body, as well as the development of treatments for a number of related illnesses [2].

Treatment for conditions such as inflammatory bowel disease (IBD), Crohn’s disease, ulcerative colitis, and chronic digestive tract inflammation all stand to benefit from new research being done to advance microbiome-based medicine [2]. Based on the results of some studies done on patients with IBD, treatment options are moving towards dietary adjustments and targeted therapies that are designed to remove, replace, or even modify specific gut bacteria [2]. Another condition that stands to benefit from new research into the role that gut bacteria play in health and illness is Chronic Fatigue Syndrome (CFS) [3]. CFS is a debilitating condition that is characterised by long-term fatigue and a host of other unpleasant symptoms that prove to be incredibly debilitating, often limiting a person’s ability to live their life normally [3]. A group of researchers based at Melbourne University have been studying the metabolites produced by gut bacteria in CFS patients to figure out how understanding gut bacteria can improve their understanding of what causes and maintains this condition [3]. They discovered that there is a distinct microbial difference in patients with CFS, compared to a normal healthy individual [3]. To read a bit more about this study and to gain a better understanding of what this means for future research and treatment, check out this link.

Where does it all begin?

Before we’re born we have absolutely no microbes growing inside of us. A foetus grows inside its mothers' womb, which is a completely sterile environment, for 9 months before being born [1]. When a baby is delivered through vaginal delivery, he or she passes through the uterine canal with an open mouth to pick up a whole lot of mom’s microbes before entering the world [1]. Babies born by caesarean section pick up some microbes from the air and their mother’s skin, but do not get the same microbial intake through the mouth during birth [1]. Throughout the years that follow birth, an infant will obtain microbes from their mother’s milk, the food that they eat, the dirt that they tough, and the air that they breathe, and will usually establish it's own unique microbiota by three years of age [1].

The role of microorganisms in the body

So how exactly do the ‘good guys’ keep us healthy? They: 

1. Directly attack infective agents and prevent the ‘bad guys’ from wanting to colonise our body 

Viruses, pathogenic bacteria, and unwanted fungi can be fought off to some extent by the healthy microbes found inside of us [1]. Bacteria are able to produce their own antibiotics, which can kill off pathogenic bacteria, and can also neutralise toxins produced by viruses [1]. Furthermore, healthy microbes have a greater ability to adhere to the lining of our lower digestive tract than the ‘bad guys’ [1]. As long as we give them the nutrients that they need, and don’t consume things that prevent them from protecting the lining of the gut, these ‘good guys’ will prevent the adherence of pathogenic microbes that might want to colonise the gut wall [1].


2. Help us digest our food

Our gut microflora has the ability to synthesise enzymes that can breakdown food components such as lactose and starch [1]. When we have a well-functioning colony of good bacteria working inside of our digestive tract, we have a greater capacity to break down these carbohydrates into simple sugar molecules that can be absorbed into the body.


3. Synthesise some vitamins

Many bacteria are able to synthesise small amounts of some of the vitamins that are essential to keeping our bodies in a healthy, working order. A healthy microbiome is likely to produce vitamins such as niacin, biotin, folic acid, pantothenic acid, vitamin K, C, and B12, which our bodies can absorb and utilise [1].


4. Strengthen our immune system


What happens when our gut flora is out of whack?

Our microbiota can change due to things like medication, such as the pill and antibiotics, changes in our diet, our lifestyle, stress, and infections [1]. A change in our microbial balance is also known as dysbiosis. It can make us more susceptible to illness and disease, including things like:

  • Colds & flu

  • Irritable bowel syndrome (IBS)

  • Constipation

  • Thrush / Candida

  • Urinary tract infections

  • Eczema

  • Autoimmune conditions

  • Colon cancer

  • Inflammatory bowel disease, Crohn’s disease, and ulcerative colitis

  • Gastrointestinal infections that cause diarrhea

This is all a bit scary, but is there anything that we can do when our gut microbiota is out of balance? Repopulating your gut with the ‘good guys’ is key to regaining a good balance of gut microbes. Lactobacillus plantarum 229v, for example, is a strain of bacteria that has has been shown to possibly help restore the gut microbiota of IBS sufferers whilst reducing unpleasant symptoms such as bloating and wind [1].

Prebiotics vs. Probiotics

What exactly are probiotics? And what is the difference between probiotics and prebiotics? Probiotics are the live strains of different microorganisms that are ingested in the form of a powder, capsule, or in food. Specific strains of bacteria and yeast are used in probiotic supplements because they have been shown to benefit humans in one way or another [1]. Prebiotics, on the other hand, are the foods that help microbes grow and thrive inside of our GIT [4]. This video by Joyous Health does a great job of explaining the difference between the two, and the important role that they play in promoting good gut health.


What can I do to help my gut microbiome stay in tip-top shape?

Here are some top tips for looking after your microbiome [1]:

  1. Eat fibre-rich, prebiotic foods – Some of the best prebiotic foods include onions, leeks, garlic, bananas, apples, pears, dandelion, oats, barley, asparagus, and celeriac [4].

  2. Eat fermented, probiotic foods that contain lots of healthy microorganisms – Some of the top fermented foods eat regularly include yoghurt, kefir, kimchi (you can find a fantastic recipe for this here), sauerkraut, kombucha, and fermented soy products such as miso and tempeh [5].

  3. Maintain healthy levels of stomach acid – Our stomach acid acts as a line of defense against unwanted bacteria that try enter our systems through the food that we eat. To support good stomach acid levels, try to not drink anything 30 minutes before and after, or with meals [1].

  4. Stop using so much hand sanitizer and antimicrobial products – We’ve been scared into using antibacterial soaps and wipes at every turn. TV adverts and magazine articles make us think that every surface we encounter is full of harmful bacteria that are going to make us sick [1]. The truth of the matter is that the more we use antimicrobial cleaning agents, the more good guys we are killing in our immediate environment along with the bad guys [1]. Good bacteria play a role in suppressing or competing with the growth of bad microbes, such as the super-bugs that are starting to become more prevalent throughout the world. So, practice good hygiene, and wash your hands after using the toilet and before preparing food, but stop using antibacterial soaps and wipes all the time.

  5. Use antibiotics only when absolutely necessary – Antibiotics kill most kinds of bacteria. If you're taking a long-term dose of antibiotics you're most likely killing off both the bad guys and the good guys. Antibiotics are not only found in our prescription medication, but even in our meat, dairy, and egg supply. It's important to be mindful of what we eat and feed our body with foods that promote healthy gut microflora [5].

  6. Use a daily probiotic – When choosing a probiotic, make sure that the different strains and the dosage are both optimal. A good probiotic supplement should include a variety of different bacteria that have been scientifically proven to be beneficial to improving the health of humans. Ensure that the probiotic that you are taking contains no less than 15 billion active live bacteria per dose. The probiotic bacteria need to make it through the winding maze of your GIT from your mouth and through your acidic stomach before they will reach the small intestine and colon. Finally, choose to buy a probiotic from a reputable brand that has been produced and stored in a way that maintains the life and effectiveness of the bacteria that it contains [1].

A good-quality probiotic yoghurt, whether it's dairy based or coconut yoghurt, is one of my favorite probiotic-rich foods. Yoghurt bowls for breakfast are the best, especially when your toppings include fibre-rich fruits, nuts, seeds, or coconut. Another probiotic-rich breakfast option is making a good nutrient-packed smoothie with kefir. Oats with an apple make a great prebiotic-rich breakfast. If you need a delicious recipe for overnight oats take a look at this link.

Some more gut-health resources

I really hope that this post and all of the additional resources help you understand a bit more about your gut, why having a healthy gut microbiome is so important, and the role that probiotics and fermented foods play in keeping our gut healthy. This is such an interesting, current topic that is gaining more and more interest worldwide, so stay posted for new discoveries in the years to come, I'm sure there are going to be many!


[1] Hebblethwaite, C. Getting to know your gut. [Internet]. 2014 - [cited 2017 Feb 14]. Available from:

[2] MIT News. New interdisciplinary center at MIT to focus on the microbiome and human health. MIT News. [Internet]. 2014 - [cited 2017 Feb 15]. Available from:

[3] Brancatisano, E. The Huffington Post. How Gut Bacteria Is Helping To Unpack Chronic Fatigue Syndrome. [Internet]. 2017 - [cited 2017 Feb 14]. Available from:

[4] McCarthy, J. Prebiotics vs. Probiotics. [Internet]. 2017 - [cited 2017 Feb 25]. Available from:

[5] Hill, M. Nutrition Stripped. Guide to Probiotics. [Internet]. 2014 - [cited 2017 Feb 25].  Available from:

Featured image credit - I haven't been able to find the original source of this adorable picture. If anyone knows where to find it and who to credit, please let me know