Microbiome, macro possibilities

You may or may not have heard about the concept of the micro biome – that is, the multitude of bacteria housed in your gut, on your skin, in your genital area, up your nose, and in your mouth. There are 10-fold more bacteria living in and on you than there are cells in your body! So is it a surprise then that these microscopic organisms may hold crucial information as to the origin of many diseases we see today as well as potential to not only use them in therapeutic pursuits but also to optimise their diversity through our own lifestyle choices? Let’s delve deeper…


Under normal physiological circumstances, the gut microbiota are commensal and are involved in both digestive function, producing metabolites which further impact human health, as well as immune function, through the maintenance of self-tolerance and through protection of the human host from invading pathogens. Dysbiosis, or an imbalance in the gut micro biome, has thus been implicated in various disease states through failure of these two primary functions of the microbiome.


The two biggest sources contributing to our gut microbiota are our mode of delivery (vaginal versus Caesarean section) and long-term diet. It has been found that the predominant bacterial group as well as the diversity of gut flora differs whether one is exposed to vaginal flora or maternal skin flora (as in C-section), whether one is born at home or in a hospital setting, whether one is breastfed or not, the levels of protein and animal fats versus carbohydrates in the diet, and whether one follows a vegan versus omnivorous diet. If we have to accept our mode of delivery now that we are adults, then changing our microbiome and warding off certain disease states may lie in what we choose to put into our mouths and the lifestyle we choose to live. Known as the father of modern probiotics, Russian scientist Ilya Metchnikov, postulated that the gut microbes had a huge influence on health and disease and he saw that supplementation with lactic acid bacteria from fermented milk products (kefir, yes please!) in Bulgarian peasant populations was associated with health and longevity. Problems with culturing bacteria and detecting DNA have limited the potential of this field of medicine, but as technology advances, we are beginning to discover increasing links between the microbes and disease. Next generation sequencing is currently facilitating metagenomic studies, and the Human Microbiome Project has sequenced 1300 reference strains from the human body thus far – the research is on the rise and worth watching out for!


So what role do microbiota play in health and disease? Well, quite a few associations have been found between predominant gut bacteria and autoimmune disease, and it may be that the gut dysbiosis that occurs results in a altered intestinal permeability, or “leaky gut”, allowing things from the environment into our blood stream that would  otherwise have been blocked had the function of our commensal bacteria been intact. It is about immune system homeostasis: in order for the human host to exist concurrently with these bacteria, a symbiosis has developed whereby our immune systems have developed a self-tolerance to our commensal gut bacteria while the gut bacteria protect us from foreign pathogenic bacteria through the maintenance of physical barrier to entry as well as through the production of antimicrobial enzymes. It is postulated that a breakdown of this symbiosis and changes in specific bacterial species may be the cornerstone of autoimmune disease. Let’s take a quick look at some of the diseases that have been associated thus far…

  1. Inflammatory bowel disease: it has been shown that impaired recognition of commensal bacteria leads to IBD – specific gene mutations in host cells of the gut lining are associated with differences in the gut micro biome, both in terms of diversity and predominance of species. This unbalanced micro biome leads to dysregulation of the immune response and results in chronic inflammation in the gut.
  2. Rheumatoid arthritis: it has been shown that implantation of specific bacteria called segmented filamentous bacteria into the gut of mice causes differentiation of certain white blood cells (CD4 cells, if you’re interested) into another type of white blood cell (T helper 17) which then migrate to peripheral lymphoid tissue (places of immune activation) and produce a chemical (IL-17) that causes autoantibody production in the spleen. These autoantibodies are directed against target joints
  3. Type 1 Diabetes: at the heart of this disease is destruction of pancreatic cells that release insulin – an association has been found between the predominant gut bacteria present and the development of type 1 diabetes through the interaction of these bacteria and the immune system causing autoantibody production
  4. Multiple sclerosis: studies in mice have shown that colonisation with certain gut bacteria lead to increased T-helper-17 differentiation and Il-17 production in both the gut and spinal cord, and it has been suggested that altering the gut microbiota can change the immune response towards an anti-inflammatory T-helper-2 response
  5. Obesity: a different micro biome composition and diversity has been shown in obese versus lean individuals, and the transfer of faeces from obese mice into lean mice has been shown to induce weight gain in these mice in the absence of increased food intake!


Cause or consequence? An association between the micro biome and disease states does not necessarily imply causation – it may be that the alteration in the gut micro biome is a consequence of disease instead. However, the use of antibiotics to alleviate disease severity in conditions like rheumatoid arthritis as well as the clinical manifestations resulting from faecal transplantation, point towards a likelihood that this may be “cause” rather than “consequence”.


So then what can we do to optimise health? How can we heal a “leaky gut”? Here are a couple of suggestions that I have picked up:

  1. Eliminate foods that damage the gut: this includes grains, legumes, and dairy. Some grains and legumes contain high amounts of saponins which, due to their chemical structure (basically like soap detergent which allows for oil and water to mix), interact with cholesterol and cause pores to form in cell membranes. Other grains and dairy contain protease inhibitors which result in impaired breakdown of all proteins in the gut at that time – this causes an imbalance of digestive enzymes with one pancreatic enzyme, trypsin, ending up in large concentrations. This enzyme has been shown to weaken the connections between the cells of the gut lining resulting in “leaky gut”.
  2. Eat foods that reduce inflammation: foods high in omega-3s like grass fed meat, wild caught seafood, fish oil, a wide variety of vegetables, and berries
  3. Fix your microbiota: eat fermented foods like sauerkraut, kimchi, kefir, and kombucha or supplement with probiotics
  4. Eat healing foods: coconut oil has been shown to be antimicrobial and it also contains medium chain triglycerides that can be passively absorbed and used for energy requiring no processing. Bone broth is another great addition to the diet as it has a variety of nutrients that support different functions: gelatine supports digestion, proline and glycine are amino acids that are anti-inflammatory and help repair cells, calcium and magnesium support bone health, and chondroitin sulphate and glucosamine promote joint health. It is so cheap and easy to make too!
  5. Get sufficient sleep and reduce stress: easier said than done! I’m terrible at this myself but as I learn more ways to improve sleep quality and how to make meditation a part of my routine, I’ll have to update you 😉 but the research is out there on how sleep may be more intricately related to disease than food…


That’s a wrap for now folks! I hope you have gained a bit more insight into the micro biome and how we can improve our own gut population while we watch and wait for more research to be done on this fascinating topic. Follow the hyperlinks to the articles used for this post. And as always, drop a comment, question, or suggestion – I’d love to hear your feedback!


Have an epic week!




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