Microbiome is a fascinating topic and once you learn abou it, then maybe some of the dots which do not seem to be connecting in your health journey, will finally make sense. Understanding the microbiome may help explain your struggles with weight loss, problems with inflammation in your body, gut related symptoms and various other health symptoms. You may have even given up on certain aspects of your health, not realising that there is something that YOU can do to help improve your symptoms or in some cases treat your symptoms. 

Microbiome is being discussed and discovered more and more by Scientists and Physicians. Traditionally none of us doctors had any training on this in medical school so I was also very surprised when I started researching on this. The mysterious habitat of the microbiome in our body is vital for our survival from the moment we are born. The picture below is an illustration of the gut and how we find so many bacteria in there.

So let us try to understand this Microbiome in more depth. Microbiome refers to the collective genomes of the micro-organisms in a particular environment.  In simple terms this means that the bacteria exist in harmony within that environment. This is applicable inside our body too where microbiome consist of these complex communities of microbes. These microbes colonise many sites of our body such as the skin and the gut. Our gut microbiome has over 30 trillion microbes which includes bacteria, viruses, fungi and even parasites. 

99% of the gut microbes exist in the large intestine. Even our mouth has a microbiome. The microbes interact with the gut lining and create a protective layer or a barrier, consisting of mucous and the good bacteria. This creates a defence against pathogens, toxins, chemicals and food particles, therefore this plays a vital role in our immune system. The microbiome also has bad bacteria however it is a particular balance of good and bad microbes which is what keeps the microbiome happy. This is known as symbiosis.

The microbes in our gut digest or break down our food so that it can be readily available for absorption. For example they break down proteins in to amino acids. They make Short Chain Fatty Acids such as butyrate which contributes to the healthy barrier on the gut lining. They also utilise many phytonutrients from the plants in our food such as prebiotics and probiotics and produce important postbiotics or metabolites. This includes neurotransmitters, enzymes, vitamins and other vital chemicals that are needed for various biochemical and physiological processes in our body. If for any reason the microbiome becomes disrupted such as overgrowth of bad bacteria, then this is known as dysbiosis. Dysbiosis is associated with a leaky gut where un wanted pathogens, toxins and other chemicals leak through the gut epthelim, in to the blood stream, initiating an inflammtory process in the gut and then the whole body.

Where did this microbes come from? Before birth, a baby has no microbiome at all. When a baby is born via a normal delivery, his or her mother colonises the baby with her microbiome. As the baby grows s/he gets the poole of microbiome from the people s/he lives with, the surrounding environment and the foods s/he is fed. More so, even breast feeding introduces a lot of microbes in to the body. The microbiome is important for the normal neurodevleopment, the immune system, metabolic processes and various biochemical and physiological processes. It is even important after death because the microbiome allows a natural decomposition of the body after burial.  Without the microbiome we would not be able to survive. A symbiosis helps us stay in good health. However a dysbiosis can cause many inflammatory diseases. The picture below shows what happens in a leaky gut syndrom. In a symbiosis state, the gut barrier is intact and protects us against un wanted pathogens and chemicals. Either the microbiota can augment pathways to benefit the gut in the human body, while sometimes they encode for pathways that will benefit the microbiome. However in dysbiosis, the protective lining breaks allowing the pathogen to enter through the falty tight junctions of the gut cells.

Scientists have been carrying out studies on the microbiome in order to establish the links with nutrition and disease.  There was a study done on rats which were born sterile with no microbiome. Those rats failed to develop neurologically and they hardly moved, neither behaved like rats. Scientists then injected microbiome in to them and they started to develop and behave like rats! There are a lot of studies that have shown the connection between microbiome and health or disease.

About 13 years ago, I did my very first project on Microbiome, there was not so much data available for me to analyse. Over a decade plus later there is a surge of published data and we are learning so much about the microbes. Studies have given us information on how fibre and polyphenols are important for the gut microbes. 

We always recommended patients to eat fibre because it seemed to help with constipation. Even as physicians, we did not really understand that the fibre was not for us. The fibre is infact a food for our gut microbes. They are able to fully or partially digest this fibre which helps in our gut transit. Furthermore, the concept of eating polyphenols is more emphasised now by encouraging people to get their 30 plants were week. The polyphenols are a food for the gut bacteria because they use these phytonutrients to make metabolites that are useful to the humans. For example they have antioxidant effects, anti inflammatory effects and contribute to various cellular processes. The polyphenols also increase the diversity of good bacteria. 

There are now enough studies to support that inflammatory processes in the body start with gut dysbiosis where the bad bacteria outgrow the good bacteria or there are not enough diverse species. In many people, some of the good bacterial species have been totally wiped out from the Western diet. The advances in science means that we have identified so many species of gut microbes with their own names and are able to see which are good and which ones are bad. Furthermore we are able to see which ones of those or lack of microbes predispose to more inflammation, more weight gain, poor glucose response, poor fat response. As a physician who had no training about this in medical school, these findings are simply revolutionary and it definitely changes my personal perspective of health and disease.

We know that the microbiome consists of good and bad bacteria. Do you know that there are more microbes in our microbiome than there are cells in our body? It makes me think who is in control here? Our interaction with the microbes produces thousands of postbiotics or metabolites that regulate many of the functions in our body. Studies have shown that external environmental factors (such as diet and drugs, antibiotics, pesticides) and genetic factors both have an impact on the microbiome and therefore the metabolite production. It has been shown that gut microbes even in twins are also different therefore can manifest in different health conditions. As a family we share a common poole of microbiome too but our gut microbiome is unique to each one of us. Genetically we are able to recognise that we must not attack these microbes. We can not change our genes but we can certainly alter our own microbiome through many external factors including good nutrition.

What kind of things can alter the gut microbiome. Lets us consider an example like antibiotics. When you take antibiotics for infections, unfortunately they are wide specturm, meaning they will target other bacteria in your body too. Antibiotics can kill a lot of the protective colonies of microbes. The development of thrush ( a fungal infection ) following antibiotics is well known, for example the female readers may relate to developing vaginal thrush following a course of antibiotics. This happens because the antibiotics cause the protective colonies to die out which are responsible for keeping the fungi in control. As soon as those colonies die, the fungi overgrow in the wrong places. So it is your own micorbiome dysfunction as a result of the antibiotics which results in thrush. This is why doctors are trying to avoid giving antibiotics. Not only does it cause antibiotic resistance but the antibiotics can have side effects. You may be familiar with being screened for MRSA before having any surgcial procedure. This resistnat strain is a consequence of using too many antibiotics over the years. Another example is antibiotic related colitis which can end up in hospital admissions. Ofcourse I am not implying never to use antibiotics because many clinical infections have to be treated with antibiotics. It is important to understand what the antibiotics do to our microbiome. It can take up to 6 months following antibiotics for our gut bacteria to recover. 

Diet can have positive or negative impacts on our gut microbiome. It is recommended that we try and eat 30 plus plant varieties per week. A plant rich diet helps keep the microbiome in balance. Plants have many phytonutrients such as polyphenols and fibre mentioned above, which are important for the good bacteria in our gut. Our diet must be rich in prebiotics and probiotics to feed our good bacteria. Fermented foods provide a good variety of probioitics. In contrast a diet rich in sugar can have a detrimental effect because the bad bacteria overgrow. The biggest culprit in table sugar is the Fructose which joins on the glucose. Fructose is associated with Non Alcoholic Fatty Liver disease. It is metabolised just like alcohol and yet the food industry puts this in all the soft drinks and so many Ultra processed foods. Ultra processed foods negatively impacts our microbiome too because they contain harmful chemicals such as emulsifiers, additives, stabilisers. Even wholefood is not the same anymore as it also has pesticides which are disruptive for the microbes. Lack of fibre in our diet, too much sugar, eating refined oild, certain medications, chronic stress and even lack of sleep all have a negative impact on our gut microbiome.

FERMENTING SHORT CHAIN CARBOHYDRATES or better known as dietry fibre or FODMAPs are consumed by us in our diet. After certain meals, that odd bloating, belching or flatulence may be annoying but it just shows that our microbiome is working and the microbes are pretty happy right now. Now rather than getting annoyed, celebrate your freinds inside the gut! Our gut microbes ferment the non-digestible dietry fibre, which promotes the growth of much needed specialist microbes which produce Short Chain Fatty Acids (SCFA) and gases (the oops moment). The major SCFAs are acetate, propionate and butyrate. This is getting complex for sure but keep reading to be even more fascinated by this world inside your body. Butyrate is used by our colon cells (enterocytes) as the preferred energy source and has anti-inflammatory effects and even antitumor activity. It helps the intestines make more glucose (gluconeogenesis) which is vital for our energy levels. Furthermore, it is useful for maintaining the balance in gut oxygen levels, vital to keep a healthy microbiome. Another SCFA, Propionate helps in production of glucose and once absorbed it goes to the liver and helps regulate satiety signaling. Therefore this tells us when we are full and avoids those hunger pangs which many people have trouble with while trying to lose weight. Acetate is the most abundant SCFA produced by the fermentation process and it is needed for the growth of other bacteria as well as cholesterol metabolism. Studies have shown that higher production of SCFA's is associated with lower diet-induced obesity and lower insulin resistance. The consumption of dietary fibre and probiotics increases the SCFA production which itself can also help balance out the microbiome. This highlights the importance of addressing our microbiome when we tackle obesity. Microbiome dysfunction can be a cause of obesity and can hinder weight loss. In fact, a lot people with obesity have a tendency to develop Small Intestine Bacterial Overgrowth (SIBO), which is another type of gut dysbiosis. In clinical practice this may be treated with antibiotics but actually SIBO can be treated with a short term Low FODMAP diet, followed by re introduction of the FODMAPs and building a healthy microbiome. Furthermore there is evidence that Intermittent Fasting can treat SIBO. Furthermore, it is very worrying how many patients have the clinical signs and symptoms of metabolic syndrome (diabetes, obesity, high cholestrol, insulin resistance). Insulin resistance itself has a major role in difficulty losing weight, obesity and diabetes. This is all interconnected to our nutrition and microbiome and gut health!

For the purpose of my discussion, it is important to discuss some other metabolites made by the gut microbes because from this we are able to demonstarte how our diet can initiate inflammtory processes. When we consume meat and dairy products in our diet, the gut microbes use the digested metabolites to produce another metabolite called trimethylamine. Once absorbed through the gut lining, trimethylamine reaches the liver and gets oxidised to trimethylamine N-oxide (TMAO). TMAO produced by the gut microbes may have a role in the increased risk of atherosclerosis and major cardiovascular events. 

Another culprit in chronic inflammation is Lipopolysaccharide (LPS). LPS is part of the bacterial wall of gram negative bacteria which can leak through the gut. It can cause acute infections or chronic inflammation. Low level of inflammation is associated with diabetes, cardiovascular disease, chronic kidney disease, obesity and non alcoholic fatty liver disease, In the pathogenesis of cardiovascular disease the LPS can attach on to the LDL cholestrol. It changes the LDL cholestrol to small density LDL and this causes a cascade of inflammatory responses. Small density LDL has been found to be in high concentrations in atheroscelrotic plaques.

Other ways in which our gut microbiome can impact the human body is by altering the availability of certain drugs to the body. The opposite can happen where drugs like the NSAID's can cause a leaky gut to develop. Microbiome can have an impact on cholestrol levels because the gut microbe enzymes have a role in bile acid metabolism. Any dysbiosis can negatively effect the bile acid metabolism thus the cholestrol and lipid metabolism. Microbiome dysbiosis can impact the immune system by altering how the cells lining the gut respond to a pathogen. The normal microbe colonies are a protective wall in the gut as they prevent external pathogens to invade. Any disruption to the colonies could potentially lead to pathogens invading by causing local infections or systemic infections or the development of inflammatory disease like diabetes and cardiovascular disease.

I recall 15 years ago following the Atkins diet which was predominantly a protein onl diet. I realised that on a long term it was not going to be healthy for my heart. In retrospect that diet was no good for my microbioe either! None of the restrictive diets are going to be useful for our health in the long term, unless they are prescribed to us by Health Professionals. A diet should be all about balance and not a permanent exclusion of foods. That is why I also hold some skeptical opinions about high carbohydrate only diets, low calorie diet, low protein diet, low FODMAP diets on a long term and even many of these weight losing programs available easily for the public. More on this in weight loss section.

This concludes my somewhat simplified explanation of the Microbiome. I think it is vital that we understand our microbiome which is a balance between good and bad bacteria. We should eat for our microbiome. There are factors which disrupt the good balance and there are steps to take which improve our microbiome. A happy microbiome means a happy gut. Good gut health itself is important in preventing many diseases and overall good health. Looking after the microbiome is the key to good health.