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Go With Your Gut

By Rhoda Frost

Photo credit: Pixabay


We tend to think of bacteria in terms of ‘germs’ or ‘bugs’ – annoyances that make us sick, things which have no benefit for us. In fact, bacteria are vital to the normal functioning of your body. There are more bacteria living inside your gut than all the cells in your body, around 10-100 trillion microorganisms of many different species, weighing around the same mass as your brain [1][2]. They can break down foods that we can’t digest, help our immune system, produce hundreds of chemicals, and may even have further-reaching, untapped health benefits. This is just a quick look at the research, which has exploded recently around the human body’s bacteria, particularly in the gut – the gut microbiome.

What affects the microbiome?

Photo credit: Pixabay

So, how do these trillions of bacteria get inside of us? In fact, it begins the second you are born. In a normal delivery, a baby picks up microbes from its mother, and from its immediate hospital environment [3]. Even babies born via caesarean section show a different composition to babies born naturally, as do babies who are bottle-fed compared to breast-fed [3]. The gut microbiome is also affected by the gestational age at birth, genetics, and whether the baby has been treated by antibiotics or hospitalised. The gut microbiome remains changeable and unstable until solid foods are commenced, and becomes stable when the baby is weaned [3]. In these early times, the composition of the gut microbiome can have an effect on the immune system and digestive system, which persists throughout life.

In adulthood, the microbiota is very stable, and is only disturbed transiently, e.g. by taking antibiotics [3]. This affects the gut because the antibiotic cannot discriminate between helpful and harmful bacteria, so many beneficial bacteria are killed, causing some disturbance to the gut ecosystem. This will generally resolve shortly after treatment is stopped, and rarely causes any serious damage. One factor that will affect the microbiota composition is diet [4]. Different bacteria are better at breaking down and using certain food substances than others are, so if diet is changed significantly, either short-term or long-term, then the gut bacteria will also change in response to this [5]. This may also explain the finding that people in different countries have very different microbes in their gut, as do people following vegetarian or vegan diets, compared to those who eat meat [3].

Photo credit: Pixabay

As old age approaches, the diversity of the microbiota decreases [3]. This may be both a cause and an effect of the ageing of the immune system. The reduced ability of the body to fight off disease causes wide-spread inflammation, which allows growth of inflammation-promoting bacteria [5]. The immune system is also less able to control normal bacterial growth in the gut, so bacteria multiply and grow more quickly, causing even further inflammation. It is this link between the gut and the immune system which may be responsible for some of the diseases which have been linked to an imbalance in gut bacteria.


In many diseases (with more being discovered all the time), the gut microbiota is in a state of ‘dysbiosis’, which means that there is an imbalance between bacteria which promote health, and those which either have no benefit, or cause disease in the host [6]. The most obvious diseases associated with dysbiosis are the gastro-intestinal diseases – those affecting the gut directly. Irritable bowel syndrome (IBS) is a common disease causing poor digestion of food and motor and sensory dysfunction of the intestines. It also has immune and psychological links and is characterised by a reduced diversity of the microbiota [3]. Inflammatory bowel disease (IBD) is another disease affecting the intestines, which may be caused by an immune reaction against something in the gut – whether against the gut wall itself, or the bacteria found there. In IBD the microbiome is very variable, and generally less diverse and stable than in healthy people [3]. Even in obesity, the function and composition of the microbiota is altered and there is mild inflammation, which leads to some of the health problems caused by the disease, including the onset of type 2 diabetes [3][6]. Interestingly, lower microbial diversity has also been seen in patients with colorectal cancer [7].

I have talked so far purely about the gut microbiome, but bacteria are everywhere, and the microbiome of the lung is also involved in certain lung diseases. It is possible that abnormalities in the lung and gut microbiota in early life may cause asthma in some people [8]. In cystic fibrosis, though it is a genetic disorder and thus present from birth, there are links between reduced lung microbiota diversity and a poorer lung function, as well as bacterial infection and resulting inflammation being responsible for sickness and death in the majority of cystic fibrosis patients [8].

Mental health

I mentioned that IBS was an intestinal disease with psychological aspects, and the mechanism by which this link occurs is the gut-brain axis, which is dysregulated in this disorder. However recently, the existence of a microbiome-gut-brain axis has been postulated, via which bacteria themselves can affect brain activity [9].

This is a fascinating possibility, that mental health, and even mental health disorders, could be caused or influenced by the bacteria in the gut. Recent studies have found a specific strain of gut bacteria that only grow when fed with specific neurotransmitters – chemicals released by cells of the brain and nervous system [10]. There is another bacterial species, Lactobacillus rhamnosus, which can change brain activity in mice, and affect their response to stress [10]. This bacterium can also reduce behaviour associated with anxiety, depression and OCD, and improve memory abilities in mice [9].

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This could change the face of treatment of mental health disorders. Record levels of antidepressants are being taken and prescribed currently, and the thought that problems such as anxiety or depression could be treated or alleviated by the administration of one or more specific bacterial species is incredible [1]. While obviously still in its infancy, and still being heavily researched, these discoveries could provide a distant light at the end of the tunnel for sufferers of these neuro-behavioural disorders.


Having mentioned all of this, you may be thinking “Wait a minute, what about those probiotic yoghurt drinks?” I was thinking the same thing. Probiotics are bacteria which beneficially affect your health, particularly the health of your gut [1]. They can compete with harmful gut bacteria for resources, inhibit the chemicals they produce, and stimulate the immune system in a positive way [2]. The term ‘psychobiotic’ has also been proposed for those bacteria with a mental health benefit, as I just described [1]. So, should we all be dosing up with probiotics then to protect ourselves from all these diseases? Well, maybe it’s not as simple as that.

Photo credit: Pixabay

The point of probiotics is to maintain health and reduce risk of illness, and this can definitely occur in some cases with some bacteria – termed ‘pharmabiotics’ [3]. However, in some groups of people (including premature babies and those with immune systems functioning abnormally), these bacteria could cause more harm than good [3].Even if don’t fall into either of these categories, have you ever considered how the bacteria reach your gut? Grown in a factory far away, stored for an unknown length of time, transported to a store, bought and put in your fridge… Can the bacteria survive all this storage and transport? Even if they do, will they survive the travel through your highly acidic and inhospitable stomach to reach the intestine where they can have their positive health effects?

I speak hypothetically, and I dare say the efficiency and numbers with which the bacteria reach the gut varies between brand of yoghurt and species of bacteria used. Although regulations on the claims companies can make have become much stricter recently, I’d say don’t believe everything you read. This is not to say that probiotics are a bad idea – with the right conditions in the right person, it’s clear they can be beneficial.


So to summarise, bacteria are NOT always the enemy. Your constant companion from birth, they complement and assist your digestive system, your immune system, and even your nervous system. When they are removed or disrupted, something is going badly wrong, and it could even cause further health problems. As probiotics are known to be beneficial in the gut, interaction between microbes and the brain gives hope for future ‘psychobiotic’ treatment of mental health disorders. The potential for these tiny microorganisms to influence our wellbeing currently seems endless, and I am fascinated to see the discoveries that will be made next.


  1. [1]New Scientist, available from [accessed 22/7/16]
  2. [2] D Compare et al., Nutrition, Metabolism and Cardiovascular Diseases, 2012, 22(6), 471-476
  3. [3] SE Power et al., British Journal of Nutrition, 2014, 11, 387-402
  4. [4] KP Scott et al., Pharmacological Research 2013, 69(1), 52-60
  5. [5] E Biagi et al., Pharmacological Research, 2013, 69(1), 11-20
  6. [6] J Shen, MS Obin, L Zhao, Obesity, 2013, 34(1), 39-58
  7. [7] J Ahn et al., JNCI J Natl Cancer Inst.,, 2013, 105(24), 1907-1911
  8. [8] MK Han et al., Thorax, 2012, 67, 456-463
  9. [9] JA Bravo et al., PNAS, 2011, 108(38), 16050-16055
  10. [10] New Scientist, available from [accessed 22/7/16]

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