What we know about our inner microbiome

Our gut houses 300-1000 different species of bacteria.  The majority of these are harmless and, indeed, friendly.  Some on the other hand are harmful, and others still can be harmless or harmful, depending on one’s gut health.  These bacteria form a mutual relationship with us, feeding off the fibre and other substances that go through our gut.  In return they secrete useful nutrients for us, including B vitamins, vitamin K and short-chain fatty acids.  All of these contribute towards our health and immune function.  Our inner microbiome also protects us from disease by forming the first line of defence against invading harmful bacteria.  The majority of these bacteria come from 30-40 species; however no one microbiome is the same as another.

It appears that we have a core set of functions that the gut needs to meet.  However there are multiple species of microbes that could enact each function in the gut.  Think of an ecosystem: there can be a variety of plants that can exist in one space.  A variety of predators exist for one animal, and a plant has a variety of pollinators.  So the species present in an individual’s gut vary depending on age, location, health, exposure to bacteria or antibiotics and diet, but each individual’s inner microbiome carries out similar functions.

Different types of microbes

Most studies have focused on the bacteria in the gut, but interestingly, there are a variety of other microbes in a gut that can contribute to health and illness.  They include fungi, archaea and viruses (yes, viruses!).  Unfortunately, we know much less about these microbes and their functions.  We do know that Candida, a fungus which can be problematic if its population explodes, is present in healthy guts.  Some of the microbes can prevent disease breakouts, including cholera.

gut bacteria acupunctureAs a result of this complexity and the sheer variety of species that have overlapping functions it becomes very hard to fully understand what is responsible for what.  The current approach is to look at the gut as an ecosystem with multiple feedback loops.  Greater resilience, and thus health of the individual, is found in guts with a greater diversity of microbes.

Gut resilience and diversity

Our gut microbiomes tend to be quite resilient.  They are able to fend off harmful as well as friendly bacteria, essentially, they are a relatively self-sustaining community.  They are able to do this as they are so rich in species varieties and these species have a good deal of independence: they are specialised to survive off specific nutrients.  The species are also interdependent, i.e. they all look after each other.  In such conditions, it can be very hard for other microbes to get in and build a community.  This works well when gut conditions are healthy.  However if gut conditions change, and there is an influx of one type of nutrient, then the species that survives best on that nutrient will suddenly flourish, potentially causing negative health impacts.  If this condition continues then the resilience of the colonies and the long-term gut health can be affected.

The degree of resilience to incoming microbes, diet changes, drugs – including antibiotics, and other internal states such as chronic inflammation needs to be further researched, especially for its important implications upon health.

One interesting quirk of this resilience is that it appears that microbiomes are susceptible to insertions of other microbiomes, which can be used to shift a harmful microbiota to a healthy one.  This could be very important for healthcare.

What can change this balance

As alluded to above, changes can occur in the microbes in the gut.  It seems the most common reasons for these changes are due to diet, chronic stress and inflammation and compounds that are damaging to the microbes, especially antibiotics.

Antibiotics are the most powerful disruptors of the microbiome.  More resilient guts can regain a healthy equilibrium after a few months, following a course of antibiotics.  But others can take years to repair the microbiome, which leaves individuals open to a wide variety of disease states.

Physiological and psychological stress can reduce the diversity in your gut, reducing resilience and allowing harmful microbes to increase.  This state can also affect our mental health, as we produce less of the compounds our brain needs, and as more inflammation ensues.  A lack of diversity in the gut can also weaken our intestinal lining and allow harmful microbes and compounds into our body, causing strong immune responses.

Diet and our inner microbiome

Dietary changes can affect our inner microbiome.  Generally, shifts to high fibre, low fat, low sugar diets improve gut health and changes to high fat, high sugar and low fibre lead to negative changes in the gut health.  Whilst such changes can change the gut colonies in as little as three days, it can take months if not years for such states to reach a stable equilibrium.


Studies revealed that mice on high fat, high sugar and low fibre diets expressed diseases that we see mainly in developed countries.  These findings have led to the ‘disappearing microbiome hypothesis’.  This is that people in developing countries have a much more diverse and resilient gut microbiome than those in developed countries, and display the diseases of affluence that we mainly see in developed countries far less often.  Mice recover their gut health if fed a low fat, low sugar and high fibre diet, but after 4 generations this option was lost as the microbes were not passed down from previous generations and so could not recolonise.  This is a hugely important point as we are now reaching the 4th generation of our overly insulated and sterilised life style.

How it can affect our health

When our gut health becomes disrupted we develop a condition known as dysbiosis.  This state has been associated with obesity, malnutrition, inflammatory bowel diseases, multiple sclerosis, diabetes (type 1 and 2), allergies, asthma, autism, celiac disease, cardiovascular disease, diverticulosis, HIV enteropathy, acute diarrhoea, neurological disorders, autoimmune diseases and even cancer.

On top of dysbiosis, obese people also have fewer microbes in their guts than leaner people.  This compromises the functions their gut carries out, including nutrient production.  Nutrient production is especially important, as some of the compounds made by the gut bacteria are essential for our immune system.  They reduce inflammation, prevent cancer and even look after our brain health.  Hence all the diseases above.

Also, if our intestinal wall is breached due to harmful microbes and rampant inflammation then all kinds of harmful compounds can get in and cause a wide variety of negative health conditions.  In other words, without a healthy microbiome, a diverse and resilience ecosystem, we cannot have full health and wellbeing.

What we can do to improve gut health

As mentioned earlier it can take time and persistence to improve the condition of your microbiome.  Whatever is there currently will try to prevent any other microbes from colonising.  Therefore, it is essential to work for long-term health and not expect changes overnight.

There are a variety of things we can do to protect our inner microbiome.  Top of my list would be;

  • Avoiding antibiotics as far as possible, including food sources of antibiotics.  This includes animals that have ingested antibiotics (essentially any animal product that is not organic or wild). Of course, if you have a life-threatening infection that requires antibiotics, you should use antibiotics.
  • Changing eating patterns – move towards a diet low in sugar, low in fat and high in fibre.  Also try to eat as much live or homemade fermented foods as possible.  These will bring in healthy microbes to recolonise your gut.  They include sauerkraut, kombucha, kefir, yoghurt, fermented pickles, miso, tempeh, wild homebrew and many, many more.  I would strongly recommend reading Wild fermentation by Sandor Katz for more information on this.
  • Reducing stress with meditation and exercise – both of these are essential to keeping the system calm and happy and have dramatic beneficial impacts on health and wellbeing, especially gut health.
  • Seek other methods that reduce inflammation.  When symptoms or diseases states are particularly extreme you will probably need some outside specialist help as well.  Acupuncture and herbal medicine can both be particularly effective for this.
  • Supplementation may also be useful.  Certain supplements can be calming and healing for the gut and may be necessary in extreme cases.  I would suggest seeking professional advice in this area, something I would be more than happy to help with.


Another interesting option that is being developed is the introduction of whole microbiotas.  These seem to be able to colonise our inner microbiome more effectively than individual microbes.  Live fermented foods will do this too as they contain a variety of microbes).  This is known as bacteriotherapy or, more enjoyably, as crapsules.  Yes, it is getting the microbiome from healthy individuals and inserting it rectally or orally (in capsule form) and has been shown to be useful in some conditions.  Again, I would suggest consulting a professional for more advice on this.

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