Microbiota: part 2

So what is the Microbiota or Microbiome?

Everybody seems to be talking about it. The short answer is the microbiota is a group of bacteria and fungi along with other organisms that live in and on us. Many of them inhabit the gut.

Although there is a lot of talk about bacteria we know that fungal species and viruses also can play a role in modulating and enhancing our immunes systems response.

Like it or not and as yucky as it might sound to some we are a super-organism (meta-organism). Our body is composed of human cells and many types of microbes who we co-evolved with over many millions of years. This is not entirely surprising given that bacteria were some of the first living creatures on the planet. All other organisms came later and so it makes absolute sense that we evolved with these bacteria. There is solid evidence that the mitochondria in our cells, our cellular power stations are actually derived from bacteria that took up residence inside larger cells millions of years ago, swapping power production for the host cells who in return provide shelter.

It has been argued that larger animals including ourselves evolved to provide warm mobile homes for complex colonies of bacteria. We are essentially their planet earth. Our habitats are as complex and diverse to them as our earth is for us.


Let's deal with the names first, the correct name for the organisms that live in and on us is the microbiota. The microbiome is the genetic material contained within that community. But honestly it's semantics, pretty much everyone refers to the microbiota as the microbiome.

Every part of our body, and I mean every part, has its own colony of microorganisms. Our skin is like the desert, dry and harsh but within this desert are oases, places like our armpits and groins are moist and have unique ecosystems. Our back is different from our front, our palms different from the soles of our feet. Our nose has a different colony from our mouth. Our intestines provide the richest environment of all. The species of organisms present are different horizontally. Spaces along the gut, the mouth, oesophagus, stomach, small intestine and large intestine are vastly different environments with their own characteristic species. Exactly like different ecosystems on our planet. Totally different animals live in the desert as compared to a forest or a river. There is also vertical habitats just like in a rainforest. Animals and birds living in the tops of trees, the so called canopy are completely different form those living on the forest floor.

We have known about this system for 300 years with the discovery of animalcules in the mouth by a Dutch scientist Antoine van Leeuwenhoek in 1676. In the late 1800 a scientist called Metchnikov who discovered macrophages wrote about the probiotic benefits of yogurt in 1902 incorrectly thinking that our native microbiota was poisonous. He later won the Nobel prize in 1908 for his discovery of macrophages and how they interacted with our microbiota. Another Albert Döderlein in 1910 wrote about the way lactobacillus in the vagina protected women from colonization by disease causing bacteria. As is often the case with important scientific discoveries all this information was ignored for many decades.

Specific colonies of organisms are influenced by their environments. If you change the environment you change the colony. This has significant effects on your health.

Every aspect of how you choose to live your life influences your microbial colonies’ health.

The type of shampoo, soap or perfume you use. Whether your house “sterile" or just clean. But nothing influences the colonies more than the food available to them locally.

The master colony lives in your intestine, your gut and is by far the largest with probably 30-100 trillion bacteria weighing about 1.5 kilo (3 lbs) which is the same weight as a human brain. This colony has the greatest number of species and the greatest diversity. It is one of the densest bacterial ecosystems on the planet. In a healthy gut it forms an incredibly complicated and sophisticated ecological group consisting of about 2-3000 species. In some traditional hunter gatherer groups it is significantly higher up to 6-7000 species. These bacteria contain over 46 million unique genes in the mouth and gut and possibly over 232 million genes in the total human microbiome compared to 30,000 in the human genome. The colonies produces many chemicals that influence how our entire body operates.

We are just beginning to recognise the immense significance and important role that they play in human health. They have an enormous influence not only over our digestive processes and general metabolism but also our mental health.

The microbiota influences our neuro-immune system.

The microbiota not only educates in early life but continues to influence our neuro-immune system throughout our entire lives. They control inflammation and thus ultimately our health and aging. The colony which is inherited from our mother and then other family members is required for the normal development of our immune system as an infant and toddler. We now know that it influences every phase of immune response throughout the entire body. Thus your microbiota influences your response to infection and vaccines. Your response to injury. Your response to many medications including modern cancer therapies. They influence your body’s response to cancer. They also control immune responses in autoimmune disease. This includes eczema and asthma. In short the bacterial colony in your gut influences every aspect of your life.

The nervous section of the neuro-immune system, including our brain also requires a healthy balanced microbiome to develop normally. What happens in the first three years of life as the colony develops has a profound effect on our lifelong health journey. Life stress along with an inappropriate diet amongst other things all shape the colony and our neuro-immune system. It is of course influenced by the amount of exercise you take and the quality of your sleep.

The colony influences our mood and plays a role in motivation and psychological health and disease. We have demonstrated that we can transfer anxiety between mice with faecal transplants. There is evidence that probiotics and diet can influence both mood and emotional reactions in humans. Finally in this realm of gut brain connectivity we are beginning to understand the mechanisms that the microbiota plays a role in a diverse group of psychologically challenging syndromes including autism spectrum disorders and functional pain syndromes.

The colony controls the metabolism in the body.

It influences many processes indirectly by the production of many chemicals including hormones and neurotransmitters that influence the neuro-immune system in the gut wall. This interaction in turn influences the entire body. We now know that you can transplant obesity and slimness between individuals by faecal transplants. Long done in mice we have now demonstrated this in some human subjects. The process is not without risk as doctors inadvertently transplanted the metabolic syndrome into a patient. Another good example of how medical intervention however well intended always carries risk. But the concept is remarkable. We know that following bariatric surgery for obesity there is an immediate change in the structure of the colony and many patients who were previously diabetic are cured.

To be healthy we probably benefit from a diverse colony and in the western world we have lost a great deal of this diversity compared to less evolved societies like the Hadza hunter gatherers who still live in our ancestral homeland in East Africa.

It has been suggested that loss of bacterial diversity has significant consequences and plays a part in the ongoing deterioration of the health of modern societies. But it’s not that simple. We all develop a colony relevant to our environment and regional diet. The Hadza have a microbiota that is shaped by their specific local nutritional environment and needs. With so many genes being present in all our colonies there is a great deal of genetic redundancy and it might be that it is the chemical functions of a colony that matters more than its composition. The evolution of our western colony reflects our environment which has been very different from that of the Hadza for many thousands of years.

There is a lot of research into the structure and function of our microbiota. Currently we are stuck looking at this ecosystem at a pretty high level. Researchers talk about phyla for example, Bacteroidetes and Firmicutes, genus and species. There is a little bit of information about strains, but not enough. I mentioned this so you can appreciate that it's much more complicated than a few probiotics.

Similar but different

Our genotype is the DNA we possess, and our phenotype is how that DNA is expressed. In other words genotype is the possibility of we could look like or our potential life history. Phenotype is what we actually look like or what actually happens to us. We all share similar but subtlety different DNA, our genotype. But some of us are athletic and some of us are not. We have different eye colour, intelligence level and so forth. Similar genome, different phenotype. Similarly we might inherit a high risk of developing a certain cancer but how we live decides if we actually get that cancer.

The microbiota is no different. All of us share microbiota that have similar genetic compositions, genomes. That is because we carry many of the same species. But we have different and distinct strains. This means that everybody's microbiome (remember microbiome is the DNA contained in the microbiota) is unique. In other words each microbiota has a unique phenotype which in part contributes to our own phenotype making us the individual that we are.

Our microbiota is so unique that forensic specialists can tell whether you have been in a room or used a computer by analysing the bacteria you leave behind when you leave the room or use the computer.

You inherit your microbiota colony from your mother, the rest of the family and pets, especially dogs living in the house. The colonisation of the gut occurs during the first three years of life and this is one of the reasons why antibiotics given to young children are so damaging to longterm health.

Once you have inherited the basic colony, the structure is predicated by your lifestyle. Primarily your diet, but also the amount of exercise, sleep and levels of stress. Your environment city or country and the number of pets and animals you come in contact with also have a profound influence. Whether you go for walks in the country or woodland. On the whole the closer you get to nature the better off you are.

The presence of dogs in the household confers a more diverse and beneficial colony. An interesting observation that perhaps speaks to the co-evolution of dogs and humans over the last 15,000 years.

There are two basic extremes. One is a colony that causes inflammation not only locally in the gut wall but also systemically, throughout the whole body. The other end of the spectrum is a microbiota that is quite the opposite being anti-inflammatory in nature. This of course is the one you want.

High fibre diet

We have discovered over the last few years that the best way to encourage an anti-inflammatory colony in your gut is to have a high fibre diet. In contrast the standard North American and British diets, high in sugars and refined carbohydrates, animal fats and vegetable oils, promotes an inflammatory microbiota. This is exactly the opposite situation and promotes both physical and mental ill-health. This is why when you clean up your diet by removing manufactured and highly processed food, everyone feels better.

People who have a high proportion of plan based foods in their diets, which translates into high fibre content, have lower inflammatory markers in their blood and are generally much healthier and most important feel mentally and physically better.
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