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Microorganisms live all around us. Louis Pasteur ‘had’ to invent the process of pasteurisation so that we could store food for longer without the risk of it spoiling. Bacteria, fungi, viruses, and other microorganisms can be found on every surface of our planet. They can be found in every drop of ocean, in the air, in the glaciers of Antarctica, or in the most extreme conditions of the Dead Sea and hot deep-sea chimneys. Some are able to survive the presence of radioactive waste, or even live off the molten core of the Chernobyl reactor. We cannot be surprised, therefore, to find micro-organisms on the surface of the human body as well as inside it. We refer to these micro-organisms and their environment as the microbiome.
Micro-organisms have always influenced the evolution of life on Earth, and they have an equally important impact on human health.
What is the microbiome?
The microbiome is the sum total of all microorganisms living on the surface (skin) and inside the human body. These microorganisms include bacteria, viruses, fungi (yeasts) and protozoa. Ideally, these microorganisms are your good friends and live in symbiosis with you and I. They help to protect you from the “bad” microorganisms.
The most well-known bacterium found in the microbiome of humans and other warm-blooded animals is Escherichia coli. It is relatively easy to culture in laboratory conditions and its entire DNA sequence is known. It has therefore become the workhorse of molecular biology and makes a significant contribution to biology and medical research.
Depending on the site of occurrence, microbiomes such as gut, skin, oral microbiome, as well as brain and lung microbiomes are distinguished. The latter two are often states of infection. The gut microbiome (formerly known as the intestinal microbiota) has been the focus of attention in recent years because it significantly influences the functioning of the whole body.
The gut microbiome represents the most numerous and diverse part of the human microbiome. It contains approximately 1013 (10 and 13 zeros or 100 trillion) bacterial cells, which is about the same as the number of cells in the human body, and can total up to 0.2 kg. [1]
What influences the composition of the microbiome?
The composition, i.e. the amount of different types of microorganisms in the microbiome, is influenced by several factors:
- the food you consume
- genetics
- the environment in which you live
- use of antibiotics
- overall lifestyle (alcohol and smoking have a negative effect on the composition of the microbiome)
The composition of the human microbiome is also influenced by the mode of delivery. In the case of caesarean delivery, the baby does not pass through the natural birth canal and is not exposed to the mother’s vaginal microbiome. The gut microbiome of babies born by caesarean section thus has a different composition, which increases the risk of certain diseases during life. [2]
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What does the gut microbiome do?
Bacteria living in the human body are living organisms that carry their own DNA. Their genes can be thought of as an extension of themselves, as they carry out a variety of important functions. The products of microbial metabolism in the gut are beneficial to your health.
1. Promotes digestion and nutrient absorption
Microorganisms in the gut come into direct contact with what you eat. In order to survive, these microorganisms need something to consume, and this they find in your already digested food. They thus help you with digestion of substances that you cannot digest on your own.
Among the substances that can not be digested are fibres (called prebiotics). This is not one single substance, but a group of indigestible substances derived from plants that serve as food for the bacteria in your digestive tract. They can be classified according to their solubility (soluble and insoluble fibre), viscosity (density) and fermentability. Fermentability tells us to what extent it can be digested by the microorganisms of the gut microbiome.
2. Produces beneficial substances
The microbial digestion of fibre results in substances (called postbiotics) that enter the blood and can be used by the body. At the same time, substances are produced that are involved in the signalling of the immune system. The gut microbiome also produces up to 30% of the daily dose of vitamin K and B vitamins. [3]
3. Affects the immune system
The good micro-organisms that you can sustain through your diet help to keep the bad (pathogenic) ones at bay by blocking their access to food. Their influence on the immune system also enables them to fight infections better [4]
Up to 80% of all immune system cells are located in the digestive tract. It is one of the possible access points for entering pathogens, which must be guarded and, if necessary, destroyed. The presence of immune system cells in the colon suggests that beneficial bacteria are interacting extensively with the immune system. [5]
The gut microbiome is a source of so-called SCFAs, which are short-chain fatty acids. These fatty acids have their own receptors on the cells of the immune system, which allows the gut microbiome to regulate its functions immediately. [6]
4. Affects mental health
The gut microbiome is part of the brain-gut axis, which is the communication axis between the digestive tract and the brain. Substances produced by the gut microbiome influence brain development in early childhood. Changes in the composition of the microbiome, and thus the substances it produces, can contribute to the development of psychiatric illnesses such as depression and anxiety disorders. [7]
There are also claims on the internet that up to 90% of all serotonin is produced in the gut. This is true, but this serotonin is involved in digestion and does not pass to the brain where it could influence mood. [8]
Consumption of fermented foods, which are considered probiotics in the true sense of the word, has a positive effect on symptoms of social anxiety in people who are prone to social anxiety.[9]
What if the microbiome is in an imbalance?
Dysbiosis, or an imbalance of microorganisms in the gut, is caused by a low diversity of species, but also by pathogenic bacteria that cause disease. Commonly, its consequences are indigestion, which comes after eating spoiled food in which pathogenic bacteria have overgrown. If these predominate over the beneficial ones, treatment with antibiotics is necessary.
Imbalance and low diversity of the gut microbiome is associated with changes in the immune system. Although substances produced by the microbiome influence the functioning of the immune system, it is not always clear whether a malfunctioning immune system is the cause of dysbiosis or whether dysbiosis has affected the immune system. [10]
Similarly, dysbiosis of the microbiome is associated with obesity, diabetes, allergies and even depression. It is unclear in these cases what was the cause to begin with and the relationship between dysbiosis and disease is likely to be reciprocal – one causing the other and vice versa.
Bacteria from the large intestine can also overgrow into the small intestine, causing SIBO (small intestinal bacterial overgrowth). A person suffering from SIBO has frequent indigestion, flatulence (bloated abdomen), diarrhoea and abdominal pain. They also suffer from reduced absorption of certain vitamins and fatigue.
SIBO is associated with several diseases:[11]
- diabetes mellitus
- hypothyroidism
- Coeliac disease
- cirrhosis
- pancreatitis
How to foster a healthy microbiome
There are a number of options to support the gut microbiome, which include lifestyle changes.
1. Follow a balanced diet rich in fibre
The gut microbiome requires a constant supply of fibre (prebiotics) to not only produce substances beneficial to the human body, but also to survive. Fibre helps maintain the diversity of beneficial bacteria. It is therefore advisable to have plenty of fruit and vegetables, legumes and some cereals such as oatmeal in the diet
2. Limit excessive use of antibiotics
Too frequent use of antibiotics not only kills the bad, pathogenic bacteria, but also some beneficial ones, leading to a sharp change in the balance of the gut microbiome. Whenever taking antibiotics, it is advisable to take probiotics – beneficial bacteria that can again colonise the colon.
3. Take probiotics
The use of probiotics is important when taking antibiotics. An alternative that could be added to the diet are fermented products such as kefir or kimchi. These have the same health benefits. [12]
In addition to taking probiotics, it is advisable to take substances that the microbiome itself needs, i.e. prebiotics, which is most often fibre. The combination of prebiotics and probiotics is called synbiotic.
4. Healthy lifestyle
Getting enough sleep, getting enough exercise and better stress management lead to better eating habits and lower rates of overeating unhealthy foods. Processed and nutritionally poor foods lead to an imbalance of the gut microbiome.
Conclusion? In a healthy gut, is a healthy spirit!
The gut microbiome has coexisted with each of us for millions of years, during which time its relationship with the human body has become a symbiosis. Its health affects your health, both physical and mental. A healthy lifestyle, including a varied diet rich in fibre, taking probiotics and reducing the consumption of industrially processed foods, will help to maintain beneficial gut bacteria in sufficient quantities.
[1] Flint HJ. The impact of nutrition on the human microbiome – https://pubmed.ncbi.nlm.nih.gov/22861801/
[2] Inchingolo F, Inchingolo AD, Palumbo I, Trilli I, Guglielmo M, Mancini A, Palermo A, Inchingolo AM, Dipalma G. The Impact of Cesarean Section Delivery on Intestinal Microbiota: Mechanisms, Consequences, and Perspectives – https://www.mdpi.com/1422-0067/25/2/1055
[3] Nysten J, Van Dijck P. Can we microbe-manage our vitamin acquisition for better health? – https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011361
[4] Frances Spragge et al. ,Microbiome diversity protects against pathogens by nutrient blocking – https://www.science.org/doi/10.1126/science.adj3502
[5] Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ. The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies. – https://www.mdpi.com/2072-6643/13/3/886
[6] Yao, Yao et al. “The role of short-chain fatty acids in immunity, inflammation and metabolism.” – https://pubmed.ncbi.nlm.nih.gov/33261516/
[7] Xiong RG, Li J, Cheng J, Zhou DD, Wu SX, Huang SY, Saimaiti A, Yang ZJ, Gan RY, Li HB. The Role of Gut Microbiota in Anxiety, Depression, and Other Mental Disorders as Well as the Protective Effects of Dietary Components – https://www.mdpi.com/2072-6643/15/14/3258
[8] El-Merahbi, Rabih; Löffler, Mona; Mayer, Alexander; Sumara, Grzegorz . (2015). The roles of peripheral serotonin in metabolic homeostasis – https://pubmed.ncbi.nlm.nih.gov/26070423/
[9] Hilimire, Matthew R et al. “Fermented foods, neuroticism, and social anxiety: An interaction model.” – https://pubmed.ncbi.nlm.nih.gov/25998000/
[10] Levy, M., Kolodziejczyk, A., Thaiss, C. et al. Dysbiosis and the immune system – https://www.nature.com/articles/nri.2017.7
[11] Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review – https://pmc.ncbi.nlm.nih.gov/articles/PMC3099351/
[12] Soemarie YB, Milanda T, Barliana MI. Fermented Foods as Probiotics: A Review – https://pubmed.ncbi.nlm.nih.gov/34820306/
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