Microorganisms are long believed to only cause diseases in the body. However, this has been debunked following the discovery that many microorganisms benefit the body. Our own body houses trillions of bacteria, both good and bad. Specifically, more than 40 trillion bacteria or microorganisms currently reside in different parts of the body, including the skin and the gut.
What is a microbiome?
A microbiome is described as a community of microorganisms that exists in a specific environment [1]. These microorganisms range from bacteria to viruses and fungi. In humans, microbiomes are microorganisms that live in the gut, skin, mouth and urogenital area. These microorganisms are commensal and harmless and protect the body by killing pathogenic microorganisms or limiting their growth.
While several microorganisms are present in the microbiome, bacteria are the most extensively studied microorganisms in the body. The bacterial population outnumbers the population of cells, with 40 trillion microorganisms over 30 trillion of our cells.
In the gut alone, at least 1,000 bacterial species perform different functions and boost immunity. However, there are also harmful or pathogenic bacteria present in the gut. The population of these pathogenic bacteria is checked and controlled by commensals or harmless bacteria.
These bacteria weigh approximately 1-2 kg, roughly as heavy as your brain. Interestingly, the microbiota network is unique for each person and is influenced initially by one’s DNA.
How microbiomes develop in the gut
The gut is an important site in the body that houses important commensal bacteria. However, how does the gut microbiota or microbiome develop? It is now known that an infant is first exposed to microorganisms during childbirth and through breast milk. Depending on the type of birth, infants born through caesarean delivery have more microorganisms present in the skin compared with infants born through vaginal delivery. The latter group of infants are more exposed to microorganisms present in the birth canal. Notably, the diversity of microorganisms depends on the mother’s health.
Infants who receive breastmilk from mothers who are obese tend to have less diverse microbiota compared with infants who breastfeed from mothers with average body mass index (BMI) [2]. Although it is well established that exposure to microorganisms during childbirth and infant feeding help form the microbiota of the infants, current research [3] provides evidence that the gut microbiota is formed even when the foetus is still developing in the mother’s womb.
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Later, when an infant grows older, they are exposed to different microorganisms from the food they eat. One’s diet directly impacts the diversity of microorganisms in the gut and other body parts. A healthy and plant-based diet is associated with higher populations of good bacteria, while diets rich in food additives and red meat are associated with reduced levels of good bacteria [4]. The food that individuals eat dictates whether an individual is at higher risk of diseases such as type 2 diabetes or is at reduced risk of chronic conditions.
What is dysbiosis, and how can this impact overall health?
Dysbiosis refers to the imbalance of the good and bad bacteria in the gut and other body parts. When homeostasis or balance of the gut is disrupted, this often leads to several health problems. Some of the health issues arising from dysbiosis are discussed below:
Dysbiosis and type 2 diabetes
Accumulating evidence from animal model studies [4] revealed that gut dysbiosis is associated with obesity and type 2 diabetes. Type 2 diabetes and obesity are characterised by the following:
- Altered gut microbiota
- Inflammation
- Gut barrier disruption
Although obesity and type 2 diabetes are believed to be complex diseases caused by several factors, there is evidence that these conditions may also be related to disruptions in the balance of the gut microbiota.
The lack of diversity of the gut microbiota may also contribute to developing obesity and type 2 diabetes mellitus. For example, a study of obese and non-obese Danish individuals revealed that patients with low diversity of gut microbiome demonstrated insulin resistance, low-grade inflammation and fatty liver compared with those with a high diversity of the gut microbiome. This study suggests that the gut microbe’s composition can influence disease development.
It would appear that lack of diversity and dysbiosis of the gut microbiota influence development of chronic conditions such as obesity and type 2 diabetes mellitus.
Gut microbiota and obesity
Recent studies have shown that gut microbiota appears to have a critical role in the development of obesity and its progression. Many studies on obesity demonstrated dysbiosis or an imbalance between good and bad bacteria. Those who are obese were seen to have a lower diversity of microorganisms in their gut.
Studies on twins [5] showed that microorganisms belonging to the genus called Christensenella were not present in overweight and obese people. Organisms belonging to this genus are found to prevent weight gain. Low microbiota diversity and low fibre intake have all been associated with obesity.
What are the benefits of the microbiota in the body?
Immune system
The immune system plays a critical role in protecting the body against external harmful agents and pathogenic microorganisms that enter the body. The microbiota is believed to influence the immune system of the body.
It is recognised that humans and commensal or beneficial microorganisms evolved together, resulting in homeostasis and mutualism [6]. Evidence from published studies has increased knowledge of how the gut microbiome influences the immune system. It is now known that the commensal microorganisms present in the gut train and develop significant components of the host’s adaptive and innate immune system [6].
Notably, the gut is home to two-thirds or 70% of the immune system cells, particularly lymphoid immune cells along the intestinal lining. These immune system cells are collectively called the Gut Associated Lymphoid Tissues (GALT).
Production of vitamins and amino acids
The microbiota in the gut synthesises specific vitamins such as vitamins K and B and amino acids [6]. Bacteria only develop an enzyme needed to form vitamin B12 in the gut. In addition, the microbiota also breaks down toxic food compounds in the body.
Fermentation of non-digestible substances
Certain carbohydrates, such as cellulose, in the cell walls of plants are not digested in the small intestine. Instead, cellulose, which makes up the bulk of dietary fibres, is fermented and digested by the gut microbiota in the large intestine. Apart from dietary fibres, the gut microbiota also digests endogenous intestinal mucus.
Fermentation of dietary fibres supports the growth of specific microbes that are specialised in producing short-chain fatty acids such as acetate, butyrate and propionate.
Butyrate
Butyrate is crucial since it is the primary energy source of cells in the colon called colonocytes. Further, butyrate has been shown to induce apoptosis or cell death of colon cancer cells [7]. Butyrate benefits energy and glucose homeostasis by activating intestinal gluconeogenesis [7]. It also prevents dysbiosis of the gut microbiota by maintaining oxygen balance in the gut.
Propionate
Propionate is another short-chain fatty acid essential in regulating gluconeogenesis or glucose production and signalling appetite in the brain [8].
Acetate
Acetate is the most abundant short-chain fatty acid produced in the gut. It is an essential metabolite that other bacteria in the gut need for growth and metabolism. Like propionate, acetate is also vital for satiety, feeling hungry, or signalling the brain to eat. It is also essential in building and breaking down lipids in the body.
Many factors can disrupt the body’s balance of good and bad bacteria. Some specific foods and drugs can influence the abundance of microorganisms in the gut. Some food products and substances can increase the population of good bacteria, while others do the opposite.
Here are some examples of food products that can lower or increase good bacteria in the gut microbiota
Food products that can lower or increase good bacteria in the gut microbiota
Artificial sweeteners
Artificial sweeteners are present in our food, such as cola drinks and other commercial beverages. Artificial sweeteners are also found in junk foods or commercially prepared food.
When too many artificial sweeteners are taken, this can result in the overgrowth of Escherichia coli and Proteobacteria. Mice fed diets of artificial sweeteners developed glucose intolerance, leading to high glucose levels in the blood. Although there are still no long-term studies examining the effects of artificial sweeteners in the long term, small clinical trials consistently point out that artificial sweeteners can increase the risk of type 2 diabetes.
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Low FODMAP diet
A FODMAP diet is a diet low in certain sugars that can cause distress in the intestine. Individuals with small intestinal bacterial overgrowth (SIBO) and irritable bowel syndrome (IBS) should follow the FODMAP diet. The FODMAP diet is a temporary dietary plan that is very restrictive. It eliminates many foods, especially those that increase symptoms of IBS or SIBO.
FODMAP is an acronym for fermentable oligosaccharides, disaccharides, monosaccharides and polyols. These are sugars or short-chain carbohydrates that cannot be absorbed well in the small intestine. Eating FODMAP can result in the following symptoms:
- Gas and flatulence
- Stomach bloating
- Constipation
- Diarrhoea
- Cramping
The low FODMAP diet eliminates specific foods from your diet and slowly reintroduces each to see which ones can cause constipation, diarrhoea and other symptoms. Foods that have been identified to cause symptoms are then limited or avoided.
When a low FODMAP diet is introduced, this decreases the abundance of bacteria that are involved in consuming gas [9]. This diet also increased Actinobacteria, which are essential in maintaining a healthy gut and reducing symptoms of IBS.
Cheese
Cheese is a healthy dairy product that is enjoyed by many across the world. It adds flavour to dishes and is rich in proteins and minerals.
A review of the literature [9] reported that cheese intake increases Bifidobacteria. These bacteria are known to protect the gut against pathogens. They also produce metabolites that are needed to create short-chain fatty acids. These fatty acids are necessary for the gut to prevent intestinal infections and regulate glucose and lipid production. Hence, eating cheese would be beneficial to your gut and overall health.
Fibre and prebiotics
Fibre-rich foods include vegetables and fruits. Fibre from these foods helps improve your intestinal health since it protects your gut from colon cancer and other infections.
Prebiotics are specialised fibres that, once taken in by the body, could increase the diversity of the microbiota and increase the production of short-chain fatty acids. Evidence from published literature [9] has shown that both could reduce cardiovascular diseases and type 2 diabetes. Hence, if you want to protect your body against long-term conditions, increasing prebiotics in your diet and eating fibre-rich foods would be an excellent start.
Polyphenols
Polyphenols are groups of naturally occurring compounds found in many plants. Some polyphenol-rich food sources include the following:
- Coffee
- Tea
- Berries
- Vegetables such as artichokes, asparagus and olives
Polyphenols are known to increase the population of bacteria that protect the intestine. These include Lactobacillus and Bifidobacteria. These two groups of bacteria are regarded as good bacteria. High numbers of these bacteria in the gut promote gut health.
Polyphenols are also known to increase the population of bacteria that produce butyrate, a small-chain fatty acid that helps regulate glucose levels. Some of these butyrate-producing bacteria include Roseburia and Faecalibacterium prausnitzii. These gut microbiomes are essential in increasing the bioavailability of polyphenols.
Increased bioavailability of polyphenols would mean that these could be easily absorbed in the intestine and delivered by the blood to different cells and tissues. Polyphenols are essential antioxidants and have anti-inflammatory properties. Many studies support the role of polyphenols in reducing the risk of cardiovascular disease and type 2 diabetes mellitus.
Maintaining an appropriate balance of good and bad bacteria is necessary for optimising your gut health. However, some factors can cause dysbiosis. Here are some factors that could disrupt the balance of your gut microbiome.
Factors that can disrupt the balance of your microbiome
Age
Your age is essential in determining the diversity of your microbiome and the balance of good and bad bacteria. The gut’s microbiota is established following birth, although there is evidence that the microbiota might be developed while the fetus is still growing in the mother’s womb [10]. The mode of delivery determines the population of the infant’s gut microbiota.
Infants who are delivered through vaginal birth demonstrate populations of Lactobacillus and Prevotella bacteria that are present in the mother’s birth canal. In contrast, infants born through caesarean section have microbiota rich in Corynebacterium, Streptococcus and Propionibacterium. All these microorganisms are present in the mother’s skin. However, the populations are not limited to these bacteria alone as an infant’s gut microbiota becomes more diverse until three years old.
By the time a child is three years old, the gut microbiota resembles almost that of adults. However, a poor diet and a diet low in fibre lead to a low diversity of the gut microbiota. There is a link between the low diversity of gut microbiota and illnesses such as type 2 diabetes later in life [10].
Infant feeding
The microbiome of the infant’s gut is influenced by infant feeding. The mother’s milk is a source of commensal bacteria and probiotics since this is not sterile. A mother’s milk has at least 700 species of bacteria, most of which are suitable for infant development.
However, the mother’s body weight can influence the population of bacteria present in milk. Mothers who are obese tend to have low diversity of the bacterial population in the milk compared with mothers with regular weights [11].
An imbalance in the gut microbiota will occur if infants are fed with infant formulas rather than breastmilk. However, fortifying infant formulas with probiotics could prevent dysbiosis in the infant’s gut microbiota [11].
Antibiotics
Antibiotics play crucial roles in the treatment of numerous infections and diseases. Many lives have been saved since the discovery of antibiotics. However, prolonged intake of antibiotics can disrupt the gut microbiome.
Broad-spectrum antibiotics are associated with reduced diversity in the gut microbiome. When there is reduced diversity of gut microbiota, this could easily lead to imbalance as more bad bacteria flourishes with reduced diversity. Broad-spectrum antibiotics can kill pathogens but also destroy beneficial bacteria in the gut.
Antibiotics can also change the functional attributes of the gut microbiota. It can influence the formation of bacteria that are antibiotic-resistant and allow them to increase over those that are beneficial to the body. When this occurs, this will make the individual more prone to infections with pathogens.
Apart from disrupting the balance of the gut microbiome, antibiotics can also alter the production of metabolites such as short-chain fatty acids and amino acids [12]. When antibiotics kill microorganisms that produce short-chain fatty acids, it also changes the function of the microbiota and the metabolites produced.
A study on piglets fed a corn-soy basal diet showed that those who received antibiotics and the corn-soy demonstrated decreased production of amino acids and short-chain fatty acids in their gut [12]. Although antibiotics are crucial in treating illnesses, their prolonged use can impact the gut microbiota. However, there is still good news: the gut can be repopulated with good bacteria after antibiotic treatment.
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How to repopulate the gut microbiome
Here are some suggestions on how to repopulate your gut microbiome:
- Take a probiotic supplement. Probiotics are live bacteria that can help improve the diversity of your gut microbiome population. These probiotics are good bacteria that help other commensals in your gut to produce short-chain fatty acids, amino acids and other metabolites needed in your gut. An example of a probiotic supplement is yoghurt.
- Eat plenty of fruits and vegetables. A plant-based diet is essential in repopulating your gut microbiome. Fruits and vegetables are rich in fibre, which the gut needs to increase diversity and produce short-chain fatty acids and amino acids. Eating fruits and vegetables can also reduce the risk of colon cancer. Further, fruits and vegetables are rich in polyphenols and other antioxidants. Antioxidants are necessary for preventing early cell death and promoting cellular health.
- Take antibiotics as prescribed. Antibiotic regimens are often completed in 3-5 days, while some would take longer than five days. However, taking antibiotics according to the correct dose and frequency would be essential in preventing antimicrobial resistance. Further, a shorter duration of antibiotics would lessen the disruption of the gut’s microbiome.
- Eat prebiotic foods. Examples of prebiotic foods include asparagus, apples, bananas, artichoke and oats. These foods can stimulate the growth of good bacteria in the gut.
Repopulating the gut microbiota after the intake of antibiotics may take months. In one study [13], it took at least two months before the gut microbiota was restored to the same level before antibiotic therapy. However, you do not have to worry if you only take antibiotics for a short period. You can begin repopulating your gut microbiota as soon as possible with fruits and vegetables and a healthy diet. You can also choose to take probiotic supplements to optimise your health!
The gut microbiome plays a vital role in keeping your body healthy. Choosing the best probiotic supplement is one way of ensuring that you keep your gut healthy. In recent years, the gut-brain connection has sparked interest among researchers. This gut-brain connection is the interaction or communication between the brain’s nervous and digestive systems. These two systems communicate through the nervous system, hormones, metabolites produced by the gut’s microbiota and immune system.
Gut-brain connection and probiotics
A study [14] showed that taking a mixture of Bifidobacteria and Lactobacillus strains for eight weeks resulted in significant reductions in symptoms of depression. The same study also showed that patients taking the probiotics had reduced levels of inflammation. Additional analyses revealed that probiotics could relieve symptoms of the following:
- Psychological distress
- Anxiety symptoms
- Depressive symptoms
- Academic stress
You can reap the benefits of probiotics by taking these as supplements in addition to eating a plant-based diet and avoiding food rich in artificial sweeteners.
Finally, improving the diversity of the gut microbiome is essential in promoting overall health, including mental health. Talking to your doctor about probiotic supplements would be necessary for wellness and longevity.
[1] https://www.genome.gov/genetics-glossary/Microbiome
[2]https://www.hsph.harvard.edu/nutritionsource/microbiome/#microbiota-benefit
[3] https://pubmed.ncbi.nlm.nih.gov/25974306/
[4] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483960/
[5] https://www.bmj.com/content/361/bmj.k2179
[6] https://www.nature.com/articles/s41422-020-0332-7
[7] https://pubmed.ncbi.nlm.nih.gov/24251697
[8] https://pubmed.ncbi.nlm.nih.gov/24412651/
[9] https://www.bmj.com/content/361/bmj.k2179##
[10] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699480
[11] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483960/
[12] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756738/
[13] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831151/
[14] https://pubmed.ncbi.nlm.nih.gov/26706022/
