We may not be aware that we live with 2 kg of microscopically small bacteria in our gastro-intestinal tracts (gut), which play a vital role in the functioning of our bodies. Bacteria are found on the skin, in the mouth, the nose, the urogenital system, but the vast majority are found in the gut, particularly in the large intestine (colon). These bacteria can be beneficial, harmless or harmful to the human body.

This collection of bacteria, along with their genetic material, make up the microbiome. The word “microbiome” combines two concepts, where “micro” refers to microorganisms and “biome” refers to a specific habitat that is home to a living community. The terms “microbiome” and “microbiota” are sometimes used interchangeably, but microbiota usually refers to specific microorganisms that are found in a specific environment, for example in the gut.

The gut microbiome is established at birth and later on there are estimated to be more than 1 000 different species of bacteria, which live in a delicately balanced symbiotic relationship with the human host. Although many species are commonly found, every person has a unique microbiome, which contributes to how the individual digests food, fights disease, and it even affects the brain and mood. Scientists view the microbiome as an “essential organ” of the human body.

The role of the gut microbiome:

The microorganisms in the gut microbiome are not invaders, but beneficial colonizers that play an important role in four broad areas of health, namely nutrition, immunity, behaviour and disease.

• Nutrition: The food that we eat plays an essential role in the proper functioning of the microbiome. Gut bacteria assist in breaking down complex molecules in food such as meat and vegetables, and help with the fermentation of non-digestible substrates such as dietary fibers. Plant cellulose would be indigestible without the aid of gut bacteria. The diversity of one’s diet affects the diversity of the gut microbiome. A higher microbiome diversity, which refers to how many different species can be identified, can reflect how healthy the gut microbiome is considered to be. Specific foods and dietary patterns can all affect the diversity of bacteria in the gut, which in turn can affect health.

• Immunity: The gut microbiome plays a vital role in immune surveillance of the body and how the body responds to infection, through communication between the gut microbiome and immune cells, of which 70-80% are found in the gut wall. Interactions between the gut microbiome and the immune system are complex and bi-directional. Healthy interaction between the gut microbiome and the immune system supports protective responses against pathogens and promotes tolerance to harmless microbes, as well as helping to maintain the ability of the immune system not to react harmfully to our own body proteins. The gut microbiome maintains the homeostasis of our immune system and can influence the immune response by having an effect on the intestinal barrier strength, and permeability of the gut wall. The immune system controls inflammation in the body, but, in turn, the microbiome manages the immune system.

Behaviour: The gut microbiome is deemed to affect the central nervous system, which controls brain function. Molecules that are released by the activities of gut bacteria can trigger the responses of nerves in the gut and can affect neurobehavioural traits. The gut microbiome has been linked to psychological disorders, such as depression and autistic spectrum disorder (ASD).

Disease: The microbiome has been identified as a key modulator of human health. An imbalance between healthy and unhealthy microbes is referred to as gut dysbiosis and has been linked to a variety of diseases. (Details in next section.)

The gut microbiome and your health:

The state of the gut microbiome has a significant impact on our health. The composition of these bacterial colonies can alter the absorption as well as the metabolism (degrade or activate) of nutrients or toxins in the gut before they are absorbed into the bloodstream.

Studies have linked a number of diseases and heath conditions to dysbiosis of the gut microbiome, and a lower diversity in species is associated with a number of diseases.

• Obesity: Studies suggest that the gut microbiome plays a key role in the development of obesity, as our dietary habits affects the composition of the gut microbiome. The gut microbiome of obese people is characterized by a low bacterial diversity. Dietary patterns and specific foods can all influence the abundance of different types of bacteria in the gut microbiome. The gut microbiome can affect the amount of energy that is extracted from food during digestion, which in turn can predispose individuals to obesity and the development of obesity-related illnesses such as insulin resistance and cardiovascular disease.

Cardiovascular disease: Recent investigations have shown that the gut microbiome composition is associated with hypertension, atherosclerosis and arterial stiffness markers. Studies have also indicated that the diversity of beneficial bacteria in the gut microbiome plays an important role in regulating levels of triglycerides and LDL cholesterol in the bloodstream. Reduced diversity of beneficial bacteria can lead to an increase in blood triglycerides and LDL cholesterol, as well as increases in inflammation and insulin resistance.

Diabetes: Diabetes has become the third major disease worldwide after cancer and cardiovascular disease. The composition of the gut microbiome is dependent on the available nutrients, so it follows that the generation of metabolites (end products of cellular metabolism) are reliant on food intake. The development of Type 1 diabetes is likely to be influenced by specific individual bacteria rather than the overall balance of organisms in the gut microbiome. Scientists have suggested that future studies on anti-diabetic treatments should target specific bacterial strains.

Autoimmune diseases: Dysfunction in the gut microbiome has not only been linked to diabetes, but also to other autoimmune diseases such as multiple sclerosis, muscular dystrophy, fibromyalgia, and rheumatoid arthritis.

• Cancer: The gut microbiome and its possible complex relationship in the development of cancer has become an increasingly researched topic. A higher abundance of particular strains of gut microorganisms have been identified for each of a number of different types of cancer, such as prostate, colorectal, and gastric cancer. A higher abundance of certain strains of gut microorganisms have also been linked to a better response to immunotherapy.

Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS): Dysbiosis of the gut microbiome is often associated with intestinal diseases. Certain strains of bacteria may have evolved to thrive in an IBD gut environment, while certain other species of gut bacteria can help seal gaps between intestinal walls and prevent leaky gut syndrome.

• Gout: A metabolic disease with symptoms of severe pain in the joints, the gut microbiome of these patients has been shown to be dysregulated when compared with healthy individuals, also showing a higher abundance of opportunistic pathogens and certain other microorganisms, as well as a lower abundance of certain beneficial species.

• Depression: Studies have shown that the gut microbiome may be involved in some neuropsychiatric disorders such as depression. Some probiotic species were able to reduce depression scores in patients with major depressive disorder. Certain species of bacteria in the gut can help to produce chemicals used in the brain, called neurotransmitters. Serotonin is such a chemical that is mostly made in the gut and acts as an antidepressant neurotransmitter. The gut is directly connected – via the enteric nervous system, also known as the second brain – to the central nervous system. There is direct communication between first and second brain. There are, however, still a lack of well-designed human studies and understanding of the influence that gut microorganisms have on the brain.

• Infant health: Colonisation of the intestine starts at birth and babies born by Caesarean section have different gut bacteria to babies born vaginally. Breastfeeding for at least six months is important for the development of beneficial bacteria in the infant’s gut microbiome. By the time babies are weaned (usually 6-9 months), the differences in gut microbiome composition between C-section and vaginal births have mostly disappeared.

• Longevity: The core gut microbiome of Italian and Chinese centenarians, who live in secluded areas characterized by a healthy lifestyle (diet, exercise and strong family ties), have shown typical decreases in the abundance of certain microorganisms and typical increases in the abundance of other microorganisms. The species of bacteria found in the Italians were somewhat different from those found in the Chinese, which can be ascribed to differences in diet and geographical location.

• Clostridium difficile infection: This is a disease of the large intestine that results from toxins produced by spore forming bacteria called clostridium difficile, which can cause severe diarrhea. This condition follows on critical changes to the gut microbiome, often occurring after the use of antibiotics.

Looking after the gut microbiome:

“We are what we eat” is very appropriate for the gut microbiome, as a varied and balanced diet plays an essential role in maintaining the diversity and proper functioning of the trillions of microorganisms in the gut.

• Eating a diverse range of foods can lead to abundance of diversity in the gut microbiome, which represents good gut health.

• Fermented foods such as yogurt, kefir, sauerkraut, kombucha, tempeh, miso, kimchi and sourdough bread have become popular, due to their suggested health benefits for the gut. However, an overview by the Department of Nutritional Studies at the King’s College, London, have found very limited clinical evidence for the effectiveness of most fermented foods in gastrointestinal health and disease. One study found some evidence to suggest that kefir may have beneficial effects in lactose malabsorption.

• Prebiotics (also referred to as fermentable fiber) are types of plant fiber that pass through the small intestines undigested and stimulate the growth and activity of certain beneficial bacteria in the large intestine. Prebiotics are naturally present in fruit (such bananas, apples, plums, nectarines, persimmon, grape fruit); in vegetables (such as beetroot, garlic, onions, asparagus, leeks, artichokes); in grains (such as bran, oats, couscous, whole grains); and in nuts and seeds. Balance and variety are essential when including prebiotics in your diet.

• Foods that are rich in polyphenols (plant compounds found in red wine, dark chocolate, olive oil, green tea, whole grains) help to stimulate healthy bacterial growth in the gut microbiome when broken down during digestion.

• Diets rich in plant material can help to reduce levels of inflammation, cholesterol and certain disease-causing bacteria.

• Probiotics are food supplements that contain live bacteria which can help restore dysbiosis in the gut and maintain digestive health. Other benefits of probiotics include assistance with the maintenance of digestive comfort, regulation of the immune system, and balancing the gut microbiome when it has been affected by antibiotics, infections, poor diet or external factors such as chronic stress.

Genetic material in the microbiome:

Just like the genetic material (“genome”) contained in virtually every cell of the human body, these trillions of microorganisms carry their own genetic material. There is currently relatively little known about the genome of the microbiome and it has been described as the next new frontier in science.

The term “genome” refers to the genetic material of a living organism – the entire set of hereditary instructions for building, running and maintaining an organism. The genome is found in the nucleus of cells, which are the microscopic structures that make up an organism. The bacteria of the microbiome each carries its own genome, in a similar way that virtually each of the cells in your body contains a copy of your unique genome. The human genome is made up of chromosomes, which in turn contains thousands of genes, and each gene is built up of DNA.


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