Microbiome: The Invisible Ecosystem Within and Around Us

Microbiome refers to the collection of microorganisms that inhabit not only the gut, but also the skin, respiratory tract, mucous membranes, urogenital system, and even the surrounding environment. The human body contains more microbial cells than human cells: for every human cell, there are about 1.3 microbial cells. The total mass of the microbiome is 1.5–2 kg, and its genes outnumber human genes by a factor of 150.

External microbiome is the invisible cloud of microorganisms surrounding each person within approximately one meter. It consists of bacteria, fungi, archaea, and viruses, and can vary depending on lifestyle, diet, and environmental contact.

Internal microbiome includes the microbes that live inside the body. They play a key role in metabolism, protection from pathogens, regulation of the immune system, and even the functioning of the nervous system. Their balance affects overall health, and disruption of the microbiome composition may be associated with a wide range of diseases — from allergies and inflammatory bowel diseases to neurological and metabolic disorders.

The Role of the Microbiome in the Body

The microbiome plays a vital role in human health by supporting metabolism, immunity, and even emotional well-being. Under normal conditions, we live in symbiosis with many microorganisms, and this cooperation is essential:

• Metabolism: helps digest food, synthesize vitamins (K, B12), and regulate blood sugar levels.
• Protection from pathogens: suppresses the growth of harmful microorganisms and maintains the integrity of mucous membranes.
• Immune regulation: helps distinguish between safe and harmful bacteria, reducing the risk of autoimmune diseases and chronic inflammation.
• Connection with the nervous system: influences levels of serotonin, dopamine, and inflammation, affecting cognitive functions and mood.
• Skin health: reduces the risk of inflammatory conditions (acne, dermatitis, eczema).
• Respiratory system: regulates microbial balance in the nasopharynx and lungs, reducing the risk of infections and allergies.
• Urogenital system: helps protect against infections and maintain normal pH levels.

However, not all microorganisms are beneficial. A healthy microbiome naturally includes conditionally pathogenic bacteria that can dominate and cause disease under unfavorable conditions (stress, dysbiosis, weakened immunity). The balance between beneficial and potentially harmful microbes is key to a healthy microbiome.

Environmental Impact on the Microbiome

The human microbiome is shaped by many factors. Internal mechanisms determine its basic composition, while external conditions influence its dynamic changes.

A person emits about 37 million bacteria into the air every minute, and up to 80% of indoor microorganisms come from the people who inhabit the space. These microbes settle on surfaces, are transmitted through touch, and are inhaled.

Spending extended periods in one room (6–12 hours a day or more) leads to active microbial exchange, creating a microbial ecosystem that can either support health or contribute to its imbalance.

Factors Affecting the Microbiome Composition and Its Changes

Internal Factors:

• Age – in infants, the microbiome is just forming; in adults, it stabilizes; and in the elderly, its diversity decreases.
• Hormonal balance – estrogens, testosterone, insulin, and other hormones can alter the composition of the microbiota.
• Diet and medications – fiber supports beneficial bacteria, while antibiotics, NSAIDs, and excess sugar disrupt microbiome balance.
• Emotional state – stress and anxiety affect the “gut-brain” axis, altering bacterial balance.

External Factors:

• Contact with the environment – interaction with natural microorganisms (soil, plants, animals) increases microbial diversity.
• Lifestyle – physical activity, sleep patterns, and environmental pollution can weaken beneficial bacteria.
• Hygiene and household chemicals – excessive use of antiseptics reduces microbiome diversity.
• Water quality – chlorination and contamination can suppress the gut microbiota.

Microbiome balance is essential for maintaining health, and its disruption can lead to chronic diseases, including inflammatory, neurological, autoimmune, and metabolic disorders. Since microbiome imbalance is linked to many diseases, it is important to understand how the environment affects its state and what steps can be taken for recovery.

How Microbiome Changes Affect Health

Sudden changes in the microbiome can disrupt the function of various body systems:

• Urogenital system – changing sexual partners involves the exchange of microbiomes, which may lead to honeymoon cystitis.
• Skin – adaptation to a new environment may alter the bacterial composition, causing irritation or inflammatory reactions such as eczema.
• Gastrointestinal tract – changes in water and diet, especially while traveling, can lead to temporary digestive disorders like traveler’s diarrhea.
• Immunity – seasonal or geographic changes in the microbiome may affect immune response, increasing susceptibility to infections and triggering allergies.

Microbiome imbalance is associated with a wide range of diseases: obesity, diabetes, autoimmune disorders, depression, Parkinson’s disease, autism, ADHD, and dementia. Modern research confirms these links, highlighting the importance of the environment in maintaining a healthy microbiome.

How Quickly Does the Environment Affect a Person and How Can the Microbiome Be Restored?

As mentioned earlier, 6–12 hours a day spent in an indoor environment can already significantly influence the microbiome composition. Therefore, regular and periodic exposure to a polluted environment leads to the accumulation of harmful effects and, over time, may result in chronic health problems.

How Quickly Does an Indoor Environment Affect a Person?

• Hours – Days: Initial symptoms (nasal congestion, coughing, eye irritation, headache) can appear immediately after entering a contaminated environment.
• Weeks – Months: Prolonged exposure may weaken the immune system, trigger allergies, gastrointestinal issues, and chronic fatigue.
• Years: Long-term presence in an unhealthy environment is associated with inflammatory, autoimmune, and respiratory diseases. In addition, continuous exposure to carcinogens (mold mycotoxins, heavy metals, volatile organic compounds, radon) increases the risk of cancer, especially of the lungs, liver, and urinary system. This risk depends on the duration of exposure, individual sensitivity, genetics, and overall health.

Why Is Cleanliness of the Indoor Environment Critically Important?

• In cases of serious chronic diseases, without cleaning the environment or moving to a clean space, therapies can only slow disease progression but not achieve full recovery.
• Even during treatment, there may be periodic symptom relapses, not only due to detox reactions but also because of repeated contact with a polluted environment.
• It is minimally essential to ensure cleanliness in the home, especially in the bedroom, since the body recovers during sleep and the microbiome restructures.
• If changing the work environment is not possible, it’s important to minimize contact with contaminated spaces and create a safe resting zone. This could be one room where the person spends most of their time and sleeps.

How Quickly Can the Microbiome Be Cleansed?

• 2–4 weeks: After leaving a polluted environment, a detox reaction begins — a temporary worsening of well-being due to the release of accumulated toxins. Possible symptoms include headaches, skin rashes, fatigue, and symptom flare-ups.
• 1–3 months: Even after prolonged time in a clean environment, without a comprehensive approach (clean space, diet, probiotics, detox), full recovery does not occur. With supportive therapy, gradual improvement begins, but residual symptoms may persist for a long time.
• Long-term: Full recovery can take several months to a year or longer, depending on the degree of toxic exposure, individual body characteristics, age, diet, stress levels, physical activity, and immune system condition.

How Can Old Belongings Contaminate a New Space?

One factor affecting the microbiome is the environment in which we live. Cleaning the space is important, but it is equally crucial to avoid contamination from old items.

• Furniture, carpets, books, clothing accumulate mold spores, bacteria, toxins, and chemical pollutants.
• Moving belongings from a contaminated space can lead to contamination of the new environment and prolong toxic exposure.
• It’s important to thoroughly clean or dispose of items that were in a moldy or toxic space. In some cases, cleaning is ineffective, and porous items (upholstered furniture, mattresses, books, carpets) are better discarded, as deeply embedded mold spores and toxins can persist even after treatment.

Microbial Diversity and Its Impact on Health

Microbial diversity refers to the quantitative and species-level diversity of microorganisms inhabiting the human microbiome. High microbiome diversity is associated with resilience to external stressors, more efficient immune system function, and a reduced risk of chronic disease.

When microbial diversity is sufficient, even potentially pathogenic organisms such as Clostridia or Helicobacter pylori do not cause problems, because balance is maintained through interspecies competition. However, when diversity decreases, control over the growth of certain bacterial groups is lost, which can lead to inflammation, infections, autoimmune reactions, and metabolic disorders.

Therefore, maintaining health requires not only controlling harmful microorganisms but also preserving microbiome diversity. Modern scientific research shows that insufficient microbial diversity may be linked to a number of serious diseases.

Major Bacterial Groups in the Gut Microbiome

The gut microbiome consists of many microorganisms, but its main representatives belong to several key phyla, each performing important functions:

• Actinobacteria – involved in breaking down complex carbohydrates, synthesizing B vitamins, and regulating immunity.
• Bacteroidetes – responsible for fiber breakdown, regulation of fat and carbohydrate metabolism, and immune modulation.
• Firmicutes – participate in the fermentation of dietary fibers and synthesis of short-chain fatty acids (SCFAs), important for the intestinal barrier and metabolism.
• Proteobacteria – include potentially pathogenic species; their overgrowth is associated with inflammation and dysbiosis.
• Mycoplasmatota – may influence immune regulation, but their role in the gut is not yet well understood.
• Verrucomicrobiota – primarily represented by Akkermansia muciniphila, which strengthens the gut mucosal barrier and regulates metabolism.

The balance between these groups is essential for a healthy microbiome. Changes in their ratio may be associated with various conditions, including metabolic disorders, autoimmune processes, and inflammatory bowel diseases.

Bifidobacteria and Their Impact on Health

Bifidobacteria are key members of the Actinobacteria phylum, playing an important role in digestion, immune regulation, and protection of mucosal surfaces. A reduction in their levels is linked to metabolic, immune, and neurological disorders.

• In infants (especially those who are breastfed), they make up up to 80% of the intestinal microbiota, helping digest carbohydrates, synthesize vitamins, and form immunity.
• With age, their numbers decrease: in adults — to 5–10%, and even lower in the elderly, which may impair digestion, weaken immune defense, and increase the risk of inflammatory diseases.

A decline in bifidobacteria levels is associated with a wide range of conditions, including autoimmune and allergic diseases, inflammatory bowel conditions (IBD, SIBO, IBS), metabolic disorders (obesity, diabetes, insulin resistance), neurological disorders (depression, anxiety, Parkinson’s disease, autism), and a weakened immune response to COVID-19 and other viral infections. For more details, see the article: Bifidobacteria: the key to a healthy microbiome and strong immunity

Fecal Transplantation: Restoring the Microbiome Through Transfer

Fecal microbiota transplantation (FMT) is a method of restoring microbial diversity in the gut by transferring intestinal microbiota from a healthy donor to a patient (available in some hospitals in BC, Canada). Unlike probiotics, which contain a limited number of bacterial species, FMT delivers an entire ecosystem of microorganisms, making it effective in cases of severe dysbiosis. The method is currently used to treat Clostridioides difficile infection and is being researched for therapy of IBD, metabolic disorders, immune dysregulation, and various neurological conditions.

A carefully screened donor with high microbial diversity is selected for the procedure. Before transplantation, patients are given antibiotics and laxatives to reduce competition between their own microbiota and the transplant. Then, after a 24-hour break, the transplant is administered using one of several methods.

The most effective method is colonoscopy-based delivery, which costs between US$5,000 and US$8,000 in the U.S. A less invasive option is taking capsules with lyophilized bacteria, although this method is more complex and expensive — about US$17,000. Alternative methods like enemas or nasogastric tubes are used less frequently and typically yield less stable results.

The effect of FMT develops gradually, as the transplanted microbiome takes time to adapt to the new host — this process may take weeks or even months. The patient’s lifestyle — diet, stress levels, and overall health — plays an important role in the outcome.

Spore-Based Bacterial Transplantation

In addition to traditional fecal transplantation, alternative methods such as spore-based bacterial transplantation are actively being studied. This approach has several advantages:

• Resistance to stomach acid and antibiotics – bacterial spores can survive the harsh environment of the gastrointestinal tract and activate in the intestine.
• Safety – lowers the risk of transferring pathogenic microorganisms, as spores are easier to control during production.
• Long-term effect – spores can colonize the intestine and help restore microbial balance over time.
• Ease of use – spores can be taken orally in capsule form, eliminating the need for invasive transplantation methods.

This method represents a promising alternative to classical fecal transplantation, especially for patients who require a safer and more convenient way to restore their microbiome.

Conclusion

The microbiome plays a fundamental role in maintaining health, influencing metabolism, immunity, nervous system function, and many other processes. Its balance depends on numerous factors, including lifestyle, diet, medications, and the environment. Microbiome imbalance is associated with a wide range of diseases — from metabolic disorders to neurological and autoimmune conditions.

Modern research confirms that maintaining microbial diversity and eliminating factors that suppress beneficial microorganisms can improve overall health. A clean environment, balanced nutrition, sensible use of antibiotics, and microbiome support through probiotics or prebiotics are key strategies for preserving microbiome resilience.

Understanding the interaction between humans and their microbiome opens new perspectives in disease prevention and treatment. Microbiome therapy is rapidly evolving, and more effective methods of microbiome correction may emerge in the near future.