‘All disease may begin in the gut, but the key to a healthy gut is the microbiome’.

Microbiome is the name given some 10 trillion bacterial cells that make their home inside your gut (1). There are more than 1000 different species in each gut and the species vary from person to person. Research shows the micobiome effects many aspects of human health. These include weight gain (2), autoimmune conditions (3), digestive problems, mood (4), hormonal issues and susceptibility to colds and flues.

Bacteria that live in your gut come in the good, bad or neutral varieties.  These little critters keep each other in check by competing for space and resources. One type will tend to dominate the other which can mean a state of good health for us or a state of dysbiosis.  Dysbiosis is when the ratio moves in favour of the bad bugs. This is when your health can take a dive. Ideally we should have around 85% good and neutral to 15% bad (5).

Your Microbiome and Your Digestive System

Most microbes live in the large intestine, but some live small intestine. The further down the intestine you go, the more microbes you tend to find. Friendly bacterial species will produce nutrients that heal and protect the gut. The body in return produces mucous that provides nutrients for the friendly bacteria while prohibiting the growth of the unfriendly ones.

We have all heard names like lactobacillus and bifidobacteria . These friendly microbes cling to the gut wall and discourage the growth of harmful bacteria like staphylococcus or clostridium difficile . C diff is a well know cause of fever and diahorrea (6)Problems in the microbiome can arise due to bad diet, antibiotics, toxins or infections. The good bacteria take a can take a hit leaving the bad microbes space to reproduce unchecked. When this happens the gut becomes inflamed due to toxins produced by the unhealthy microbes.

Unfavourable yeasts, bacteria and parasites can feed off sugars and starches promoting inflammation in the gut. Animal fats also promote inflammation but only in the absence of good species of bacteria such as Bifidobacterium (7). Inflammation makes the gut leaky which allows undigested food particles to enter the body and trigger the immune system. The immune system responds to this in turn by increasing inflammation and so the cycle continues. Bloating, gas, pain, constipation and diahorrea can all result from this. Generally this is referred to as IBS.

It’s also worth noting that states of inflammation promote the growth of unhealthy microbes like Candida Albicans (8). That’s a downward cycle you don’t want to be on. Elimating all sources of inflammation is a must in gut recovery.Alcohol, caffeine, transfats, processed foods, sugar, gluten and dairy all have to go if you want to heal your digestive tract. At least until you’ve healed your digestion and improve the colonisation status of your microbiome.

Your Microbiome and Immune System.

Do you get frequent colds and flus? Do you suffer with hayfever and sinusitis? Your microbiome plays a huge part in regulating your immunity. Most of our immune system is located in our gut. A good 70% or so. Our guts are the doorways between what’s outside and what’s inside our bodies. Something really isn’t inside us until it’s been absorbed through the gut wall, so our immune system is there in force to make sure no unwanted intruders get inside.

Having the right microbes can make all the difference to your health. In one Swedish study, it was found that those you supplemented Lactobacillus reuteri (9) took only half the sick days than those who did not. In another study, it was found that collage students supplementing Bifidobacterium bifidum  lost less days in school and recovered faster from colds then there class mates (10). Not all studies show a strong correlation between probiotic supplementation and colds and flu though. It seems the types of bacteria used make all the difference (11).

Your Microbiome and Auto-Immune Disease

The bacteria in your gut are in constant communication with your body. Through interacting with healthy and unhealthy species of bacteria your immune system learns what to attack and what not to attack. Friends and foes become identified. Without interaction from the microbiome, the immune system cannot calibrate itself correctly. Too much stimulation from toxins and food intolerances can lead it to attack the body’s own cells, as in the case of an auto-immune disease (12).

An essential part of dealing with any auto-immune condition is having a healthy microbiome. Good bacteria produce anti-inflammatory agents that soothe the gastro-intestinal tract and calm the immune system. This has systemic effects, reducing inflammation throughout the body (13). This helps to calm and prevent auto-immune flare ups while reducing pain and inflammation through out the body. They also produce short chain fatty acids which heal and seal the gut preventing unwanted toxins, microbes and food particles from entering the body.

At the moment specific species are being studied for their role in preventing different types of disease. For example, various strains of Lactobacillus have been shown to powerfully reduce inflammation and symptoms in suffers of Irritable Bowel Disease (14). The science is still in its infancy. We still know relatively little about the microbiome but one thing is for sure; a new medicine is emerging.

Your Microbiome, Mood, and Cognition

Perhaps hard to believe but your microbiome actually has an effect on your mood and cognition! This is done through what’s known as the microbiome-gut-brain axis.  Certain metabolites produced by bacteria can have a powerful effect on your neurotransmitters. Your microbiome is literally talking to your brain. As per usual the friendly ones attempt to improve your life while the unfriendly ones will try to disrupt it.

Our friend Lactobacillus rhamnosus has been shown to reduce anxiety in mice by increasing the number of GABA receptors in the brain (15). GABA is responsible for calm and tranquil sensations. On the other hand the not so friendly c. diff can create a toxin know as HPHPA which can block the breakdown of dopamine in the brain (16). This can contribute to cases of autism and schizophrenia.

Keeping micobiome healthy is essential for a healthy mind. Serotonin is the feel-good neurotransmitter and 90% of it is made by your friendly bacteria. Feeding your friendly bacteria (with fiber) could be the most important thing you do for a happy and stress-free life!

Your Microbiome and Weight Gain

For some people losing weight seems incredibly difficult. Recent research shows that the type of bugs you have in your gut may be the driving factor on whether your fat or skinny. Simply put, try hard dieters may not have the right bugs to actually lose weight! Like everything with the microbiome this area is really new but has potential. Studies are finding a direct correlation between your weight and the types of bugs in your gut (16)

Some bugs seem to produce a lot of energy that the body can use. Even on a restricted diet, a person may be getting a lot of calories from their microbiome. Scientists have actually transferred the microbiome from fat rats to skinny ones and the skinny ones have become fat! (17). Visa Versa is also held true. This tells us that it may be possible to therapeutically alter a person’s microbiome to promote weight loss.

It’s well known that giving animals antibiotics fattens them up. The antibiotic