Microbiome – what is it and how does it affect our health?

Microorganisms are an essential part of the human body, playing key roles in its daily functions. Bacteria, archaea, fungi, viruses, and eukaryotes are the various microbes that make up the microbiome. Where is the microbiome located? What is the microbiome? What factors affect its composition? What is the gut microbiome? How to restore the gut microbiome?

Microbiome - what is it? Impact of the microbiome on human health

The term "microbiome" was first used in 2001 by American geneticist and microbiologist Joshua Lederberg to describe the collective set of microorganisms living in a particular environment. It refers to the microorganisms in the human body, including bacteria, fungi, viruses, archaea, and eukaryotes (also known as nucleated organisms). The term is used to describe the collective genome of all commensal microbes (those that benefit from another organism without affecting its function), as well as symbiotic and pathogenic microorganisms.

Microbiomes can be found not only in humans but also in plants, animals, and soil. Interestingly, the microbiomes of different environments are remarkably similar to one another.

The term "microbiome" is most commonly used to refer to the microorganisms living inside the human body, which can be found in various parts of the body. For example, we distinguish between the oral microbiome, respiratory microbiome, gut microbiome, and skin microbiome, as well as microbiomes of the vagina and urinary tract. Thus, the human microbiome is considered a complex and diverse group of microorganisms that play a vital role in the immune system, and significantly affect the digestive and metabolic systems.

Microbiome vs. microbiota

In discussions of microorganisms inhabiting a given environment, you'll encounter both the term "microbiome" and "microbiota". While these terms are often used interchangeably, there are some key differences between them.

Strictly speaking, "microbiota" refers to all the microorganisms living in the human body, while "microbiome" refers to the collective genomes of these microorganisms. Therefore, "microbiome" is more closely associated with the genetic structure of the microorganisms, while "microbiota" pertains to their presence in a given environment.

Another term sometimes used is "gut flora," which, while often used interchangeably with "microbiome" and "microbiota," is a less precise term and is increasingly being avoided in scientific circles.

Impact of the microbiome on human health

The human microbiome plays a critical role in the body, affecting its functions in numerous ways. It helps maintain homeostasis and contributes to:

• digesting food components
• synthesizing B vitamins and vitamin K
• producing nutrients
• regulating metabolism
• supporting the immune system
• protecting against pathogens and toxins
• enhancing the absorption of electrolytes and minerals
• influencing the development of the nervous system
• maintaining the integrity of the intestinal lining

The most diverse and abundant microbiome in the human body is found in the gastrointestinal system, particularly in the gut microbiome. The bacteria in the digestive tract are responsible for breaking down food remnants, metabolizing fats in the liver, improving nutrient absorption, stimulating the immune system, and protecting against harmful microorganisms.

Factors affecting the composition of the microbiome

Each person has a unique microbiome, which can change throughout life. Research suggests that the microbiome begins developing in the fetal stage and is influenced by the mother's natural bacterial flora. Studies indicate that microorganisms from the mother's mouth may have a significant impact on the baby's microbiome, with the colonization of microbes intensifying immediately after birth.

Several factors can influence the composition of the gut and other microbiomes in the human body, including:

• age
• birth method and feeding practices
• diet
• medications
• antibiotic use
• living environment
• animal contact
• stress levels
• sleep quality and duration
• physical activity
• use of recreational substances
• previous illnesses

Genetics also plays an important role in shaping an individual's microbiome, impacting enzyme production and food intolerances.

Microbiome and allergies, chronic diseases

The complex and multifaceted influence of the microbiome on human health means that imbalances, known as dysbiosis, can negatively affect the body, contributing to conditions like allergies and chronic diseases.

Microbiome and the development of food allergies

Studies suggest that early diet can influence the microbiome and, in turn, the risk of developing food allergies. Children who were formula-fed in infancy are more likely to develop food allergies compared to those who were breastfed. Additionally, the method of birth can impact the microbiome — babies born via C-section tend to have fewer bacteria than those born vaginally, making them more susceptible to allergies.

Research also indicates that exposing infants to a variety of foods in the first year of life may reduce the risk of developing food allergies.

Interestingly, the skin microbiome can also influence allergies by supporting the skin's protective barriers, preventing excessive immune reactions to allergens.

Microbiome and chronic diseases

The microbiome supports not only immune system function but also may reduce the risk of chronic diseases. Evidence suggests that a balanced microbiome may lower the likelihood of conditions like diabetes and obesity. The microbiome can also influence the risk of mental health disorders, such as depression, autism, Alzheimer's disease, and sensory abnormalities.

Imbalances in the microbiome can lead to dysbiosis, which increases the risk of autoimmune diseases like Hashimoto's thyroiditis and celiac disease. Dysbiosis can also disrupt the digestive system, increasing the likelihood of conditions like inflammatory bowel disease, irritable bowel syndrome (IBS), ulcerative colitis, Crohn's disease, and peptic ulcers.

SIBO - a dangerous consequence of microbiome overgrowth

A growing concern in modern health is Small Intestinal Bacterial Overgrowth (SIBO), a form of dysbiosis that involves an overgrowth of bacteria in the small intestine. SIBO can lead to digestive and nutrient absorption issues, affecting the body’s overall functioning.

SIBO manifests through symptoms such as bloating, gas, and abdominal pain, and can be triggered by a variety of factors. It often coexists with other conditions, like IBS, celiac disease, or gastroesophageal reflux disease (GERD), and can increase the risk of nutrient deficiencies, contributing to a larger waist circumference.

The impact of diet on the gut microbiome

To maintain a balanced microbiome and promote healthy growth of beneficial microorganisms, it's important to follow a nutritious diet. A well-balanced diet should include fresh fruits and vegetables, whole grains (sources of complex carbohydrates), healthy plant-based fats, and prebiotics, which nourish beneficial microbes. Foods rich in polyphenols and probiotics are also beneficial.

An unhealthy diet can disrupt the gut microbiome, leading to dysbiosis. Factors like fiber deficiency, excessive alcohol consumption, processed foods, fast food, excessive sugar, and high levels of trans and saturated fats can all negatively affect the gut.

10 foods that support gut health

To support gut health and balance the gut microbiome, consider adding these foods to your daily diet:

• green tea
• sauerkraut
• brown rice
• plain yogurt
• buttermilk
• pickled cucumbers
• garlic
• bananas
• oatmeal
• jerusalem artichoke

Delicious dishes for gut health

To support your gut health and microbiome balance, try incorporating foods that contain natural probiotics and prebiotics into your meals. Here are some ideas for dishes:

• oatmeal with soy milk, banana, and nuts
• plain yogurt with dark chocolate, banana, and walnuts
• fruit smoothie with kefir
• jerusalem artichoke hummus served with whole grain bread
• garlic cream soup
• citrus fruit salad
• brown rice with lentil patties and sauerkraut
• whole-wheat penne pasta with artichokes in an onion sauce

How to build meals that support the microbiome

When planning meals to support your microbiome, include sources of healthy fats and complex carbohydrates. Oats, peanut butter, and superfoods like inulin, spirulina, and vital fiber are great additions.

Microbiome testing - when should you consider it?

In cases of microbiome imbalances, your doctor may recommend microbiome testing to assess the state of your microbiome and identify any disparities among the microorganisms in your body. Depending on the test, it can also measure markers of inflammation, stool pH, and detect early changes in the gut.

Microbiome testing typically involves stool analysis to detect beneficial probiotics as well as harmful pathogens. It is recommended for patients who:

• are undergoing antibiotic treatment or have used antibiotics for extended periods
• experience digestive issues like bloating, nausea, gas, constipation, or diarrhea
• suffer from frequent bacterial or viral infections
• have irritable bowel syndrome (IBS) or inflammatory bowel diseases
• have food intolerances or allergies
• are dealing with stress, anxiety, or mood disorders

How to nourish and restore the microbiome

To support microbiome balance, focus on a diet rich in antioxidants, complex carbohydrates, dietary fiber, and probiotics. Regular exercise, good sleep hygiene, and stress management (through relaxation techniques) also play a key role.

In some cases, probiotic supplements containing live cultures can help restore and support the gut microbiota, improving the symptoms of dysbiosis. Probiotics can enhance gut barrier function, nutrient absorption, and modulate both the immune and nervous systems.

Prebiotics can also support gut microbiome dysbiosis. These are substances that gut microorganisms use for growth and reproduction. Among them are certain compounds classified as dietary fiber, such as inulin, fructooligosaccharides, and galactooligosaccharides, as well as CLA (conjugated linoleic acid) isomers and phenolic compounds.

Herbs and supplements that support the microbiome

When considering which supplements are most effective in maintaining the microbiome and which herbs and extracts may be helpful in balancing the microorganisms in the body, it's worth focusing on ingredients such as:

• Spirulina, which can positively affect gut health by reducing inflammation while providing many valuable nutrients.
• Inulin, a natural prebiotic that can stimulate the growth of beneficial gut bacteria.
• Garlic, a prebiotic that helps increase the number of health-promoting microorganisms in the body.
• Plantain (Plantago), which may protect the mucous membrane of the intestines.
• CLA (conjugated linoleic acid), which may promote the growth and multiplication of beneficial gut bacteria.
• Gotu Kola (Centella Asiatica), which contains asiaticoside, a compound known for its antioxidant properties that can positively impact gut health.
• Sodium butyrate, which may support the regeneration of the intestinal epithelium while nourishing enterocytes and reducing the secretion of pro-inflammatory cytokines.
• B vitamins, such as B6 and B12, which may have a beneficial effect on the balance of the gut microbiome.

Human microbiome - summary

The human microbiome contributes to the body's homeostasis, influencing processes such as immune system function, metabolic regulation, and digestion. Its composition, unique to each person, depends on various factors and can change throughout life.

Microbiome disturbances, known as dysbiosis, can negatively affect the body's functions, promoting the development of lifestyle diseases. Therefore, it is important to maintain the balance of microorganisms in the body.

To support the microbiome, it is recommended to follow a healthy and balanced diet rich in natural probiotics and prebiotics, engage in regular physical activity, and maintain proper sleep hygiene. Some herbs and dietary supplements may also support the balance of the microbiome, benefiting gut health.

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