The microbiome is a collection of microorganisms that inhabit not only the intestines but also the skin, respiratory tract, mucous membranes, urogenital system, and even the surrounding environment. The human body contains more microbial cells than its own: for every human cell, there are approximately 1.3 microbial cells. The total mass of the microbiome is estimated to be 1.5–2 kg, and its genes outnumber human genes by 150 times.
The external microbiome is an invisible cloud of microorganisms surrounding each person at approximately one meter. It consists of bacteria, fungi, archaea, and viruses, and it can change depending on lifestyle, diet, and environmental interactions.
The internal microbiome refers to the microbes living inside the body. They play a key role in metabolism, pathogen protection, immune regulation, and even nervous system function. The balance of these microorganisms affects overall health, and any disruption in the microbiome composition may be linked to various diseases, from allergies and inflammatory bowel disorders to neurological and metabolic conditions.
The Role of the Microbiome in the Body
The microbiome plays a crucial role in human health by supporting metabolism, immunity, and even mental well-being. Normally, we exist in symbiosis with a vast array of microorganisms, and this cooperation is essential for life:
- Metabolism: Aids in digesting food, synthesizing vitamins (K, B12), and regulating blood sugar levels.
- Pathogen Protection: Suppresses the growth of harmful microorganisms and maintains the integrity of mucosal barriers.
- Immune Regulation: Helps distinguish between safe and harmful bacteria, reducing the risk of autoimmune diseases and chronic inflammation.
- Nervous System Interaction: Influences serotonin and dopamine levels, as well as inflammatory responses, affecting cognitive function and mood.
- Skin Health: Reduces the risk of inflammatory skin conditions (acne, dermatitis, eczema).
- Respiratory System: Regulates microbial balance in the nasopharynx and lungs, lowering the risk of infections and allergies.
- Urogenital System: Helps prevent infections and maintain a healthy pH balance.
However, not all microorganisms are beneficial. Even in a healthy microbiome, conditionally pathogenic bacteria exist. Under unfavorable conditions (such as stress, dysbiosis, or weakened immunity), these microbes can become dominant and cause diseases. Maintaining a balance between beneficial and potentially harmful microbes is key to a healthy microbiome.
Environmental Influence on the Microbiome
The human microbiome is shaped by numerous factors. While internal mechanisms determine its baseline composition, external conditions influence its dynamic changes.
A person releases approximately 37 million bacteria into the air per minute, and up to 80% of the microorganisms in an indoor environment originate from its occupants. These microbes settle on surfaces, transfer through touch, and circulate in inhaled air.
Spending extended periods in the same environment (6–12 hours or more per day) leads to active microbial exchange, forming a microbial ecosystem that can either support health or contribute to imbalance.
Factors Affecting the Microbiome and Its Changes
Internal Factors:
- Age – In infants, the microbiome is still developing, stabilizes in adults, and declines in diversity in the elderly.
- Hormonal Balance – Estrogen, testosterone, insulin, and other hormones can alter microbiome composition.
- Diet and Medications – Fiber supports beneficial bacteria, whereas antibiotics, NSAIDs, and excessive sugar can disrupt microbial balance.
- Emotional State – Stress and anxiety affect the gut-brain axis, altering bacterial equilibrium.
External Factors:
- Environmental Exposure – Interaction with natural microorganisms (soil, plants, animals) increases microbial diversity.
- Lifestyle – Physical activity, sleep patterns, and exposure to pollution can weaken beneficial bacteria.
- Hygiene and Household Chemicals – Overuse of antiseptics reduces microbiome diversity.
- Water Quality – Chlorination and contamination can suppress gut microbiota.
Maintaining microbiome balance is crucial for overall health, as its disruption can lead to chronic conditions, including inflammatory, neurological, autoimmune, and metabolic disorders. Since microbiome imbalances are linked to numerous diseases, it is essential to understand how the environment impacts its state and what steps can be taken for restoration.
How Microbiome Changes Affect Health
Sudden microbiome shifts can disrupt various bodily systems:
- Urogenital System – Changes in sexual partners lead to microbiome exchange, sometimes resulting in “honeymoon cystitis.”
- Skin – Adapting to a new environment can alter 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 disturbances like traveler’s diarrhea.
- Immune System – Seasonal or geographical microbiome changes can impact immune response, increasing susceptibility to infections and triggering allergies.
Microbiome imbalance is associated with a vast range of conditions, including obesity, diabetes, autoimmune diseases, depression, Parkinson’s disease, autism, hyperactivity, and dementia. Modern research continues to confirm these connections, emphasizing the critical role of the environment in maintaining a healthy microbiome.
How Quickly Does the Environment Affect the Human Microbiome and How Can It Be Restored?
As previously mentioned, spending 6–12 hours per day in an indoor environment can already have a significant impact on the microbiome. Regular exposure to a polluted environment leads to the accumulation of harmful effects and, over time, can contribute to chronic health issues.
How Quickly Does an Indoor Environment Affect the Body?
- Hours – Days: Initial symptoms (nasal congestion, coughing, eye irritation, headaches) may appear immediately after exposure to a polluted environment.
- Weeks – Months: Prolonged exposure can weaken the immune system, trigger allergies, cause gastrointestinal issues, and lead to chronic fatigue.
- Years: Long-term residence in an unhealthy environment is associated with inflammatory, autoimmune, and respiratory diseases. Additionally, continuous exposure to carcinogens (mold mycotoxins, heavy metals, volatile organic compounds, radon) increases the risk of cancer, particularly lung, liver, and urinary tract cancers. The risk depends on exposure duration, individual sensitivity, genetics, and overall health status.
Why Is Indoor Cleanliness Critically Important?
- For individuals with chronic conditions, recovery is difficult without cleaning the indoor environment or moving to a healthier space. Treatments alone may slow disease progression but not fully restore health.
- Even with treatment, symptoms may recur periodically due to detox reactions or re-exposure to contaminants in the living space.
- Maintaining cleanliness in the home, especially in the bedroom, is crucial, as the body undergoes restoration during sleep, and the microbiome rebalances.
- If changing the workplace or living environment is not possible, minimizing exposure to polluted areas and creating a safe space for rest (such as a clean bedroom) can be beneficial.
How Quickly Can the Microbiome Be Restored?
- 2–4 weeks: After leaving a polluted environment, a detox reaction may occur, leading to temporary symptoms such as headaches, skin rashes, fatigue, and an increase in existing symptoms due to the release of accumulated toxins.
- 1–3 months: Even with prolonged exposure to a clean environment, full restoration does not occur without a comprehensive approach (clean air, proper diet, probiotics, and detoxification). Gradual improvements begin, but residual symptoms may persist.
- Long-term recovery: Full microbiome restoration may take several months to a year or more, depending on the severity of toxic accumulation, individual health factors, diet, stress levels, physical activity, and immune system function.
How Can Old Belongings Contaminate a New Space?
The environment in which we live is a major factor influencing the microbiome. While cleaning the living space is essential, preventing contamination from old belongings is equally important.
- Furniture, carpets, books, and clothing accumulate mold spores, bacteria, toxins, and chemical pollutants.
- Moving items from a contaminated space into a new environment can introduce toxins and microbial contaminants, prolonging exposure.
- Proper cleaning or disposal of affected items is crucial. In many cases, porous materials (such as soft furniture, mattresses, books, and carpets) cannot be fully cleaned, making disposal the best option since deeply embedded mold spores and toxins may persist even after treatment.
Microbial Diversity and Its Impact on Health
Microbial diversity refers to the quantitative and qualitative variety of microorganisms that inhabit the human microbiome. A highly diverse microbiome is associated with greater resilience to external influences, more efficient immune system function, and a lower risk of chronic diseases.
When microbial diversity is sufficient, even potentially pathogenic microorganisms such as Clostridia or Helicobacter pylori do not necessarily cause harm, as their growth is controlled by competition among species. However, a decline in diversity disrupts this balance, allowing specific bacterial groups to overgrow, which can lead to inflammation, infections, autoimmune reactions, and metabolic disorders.
Thus, maintaining health requires not only controlling harmful microorganisms but also preserving microbiome diversity. Modern research indicates that insufficient microbial diversity is linked to numerous serious health conditions.
Key Bacterial Groups in the Gut Microbiome
The gut microbiome consists of a vast array of microorganisms, but several key bacterial groups play essential roles in health and metabolism:
- Actinobacteria – Aid in breaking down complex carbohydrates, synthesizing B vitamins, and regulating immune function.
- Bacteroidetes – Responsible for fiber digestion, regulating fat and carbohydrate metabolism, and influencing immune system responses.
- Firmicutes – Play a role in fermenting dietary fibers and synthesizing short-chain fatty acids (SCFAs), which are crucial for gut barrier integrity and metabolism.
- Proteobacteria – Include potentially pathogenic species, and their excessive growth is associated with inflammation and dysbiosis.
- Mycoplasmatota – May impact immune regulation, though their role in the gut is not yet well understood.
- Verrucomicrobiota – Mainly represented by Akkermansia muciniphila, which reinforces the gut mucus barrier and regulates metabolism.
Maintaining a balanced ratio among these bacterial groups is essential for a healthy microbiome. Disruptions in their equilibrium are linked to various metabolic disorders, autoimmune conditions, and inflammatory bowel diseases.
Bifidobacteria and Their Impact on Health
Bifidobacteria are key representatives of Actinobacteria, playing a crucial role in digestion, immune regulation, and mucosal protection. A decline in their levels is associated with metabolic, immune, and neurological disorders.
- In infants (especially those who are breastfed), Bifidobacteria can make up to 80% of thegut microbiota, aiding in carbohydrate digestion, vitamin synthesis, and immune system development.
- With age, their levels decrease: in adults, they comprise 5–10%, while in the elderly, they drop even further, which may impair digestion, weaken immune defenses, and increase the risk of inflammatory diseases.
A reduction in Bifidobacteria has been linked to a wide range of diseases, including autoimmune and allergic conditions, inflammatory bowel diseases (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. A more detailed read can be found in the article: Bifidobacteria: The Key to a Healthy Microbiome and Strong Immunity.
Fecal Microbiota Transplantation: Restoring the Microbiome
Fecal microbiota transplantation (FMT) is a method for restoring intestinal microbial diversity by transferring the gut microbiome from a healthy donor to a patient (available in some hospitals in BC, Canada). Unlike probiotics, which contain a limited selection of bacterial species, FMT provides a complete microbial ecosystem, making it highly effective in cases of severe dysbiosis. Currently, FMT is widely used to treat Clostridioides difficile infections and is being studied for its potential benefits in inflammatory bowel disease (IBD), metabolic disorders, immune dysregulation, and various neurological conditions.
A carefully screened donor with a high-diversity microbiome is selected for the procedure. Before transplantation, the patient typically undergoes antibiotic and laxative treatment to reduce competition between their existing microbiota and the transplanted bacteria. After a 24-hour break, the transplantation is performed using one of the following methods.
The most effective method is administering the transplant via colonoscopy, with the cost of this procedure in the United States ranging from $5,000 to $8,000. A less invasive option is the oral intake of capsules containing lyophilized bacteria; however, their production is more complex, making the treatment more expensive—approximately $17,000. Alternative methods, such as enemas or a nasogastric tube, are used less frequently and provide less stable results.
The effects of FMT develop gradually, as the transplanted microbiome takes time to adapt within the new host. This process may take weeks or even months. The patient’s post-procedure lifestyle, including diet, stress levels, and overall health, plays a critical role in the success of the transplantation.
Bacterial Spore Transplantation
In addition to traditional fecal microbiota transplantation (FMT), alternative approaches such as bacterial spore transplantation are actively being researched. This method offers several advantages:
- Resistance to stomach acid and antibiotics – Bacterial spores can survive the harsh environment of the gastrointestinal tract and become active in the intestines.
- Safety – Reduces the risk of transferring pathogenic microorganisms, as spores are more controlled during production.
- Long-term effectiveness – Spores can colonize the gut and help restore microbial balance, providing prolonged benefits.
- Ease of administration – Spores can be taken orally in capsule form, eliminating the need for invasive transplantation methods.
This method represents a promising alternative to traditional FMT, particularly for patients who require a safer and more convenient way to restore their microbiome.
Conclusion
The human microbiome plays a fundamental role in maintaining health, influencing metabolism, immunity, nervous system function, and various other physiological processes. Its balance is shaped by multiple factors, including lifestyle, diet, medications, and environmental conditions. Microbiome dysbiosis has been associated with a wide range of diseases, from metabolic disorders to neurological and autoimmune conditions.
Current research confirms that maintaining microbial diversity and eliminating factors that suppress beneficial microorganisms can significantly improve overall health. A clean environment, balanced diet, cautious use of antibiotics, and microbiome support through probiotics and prebiotics are key strategies for preserving its stability.
Understanding the complex interactions between humans and their microbiome opens new perspectives for disease prevention and treatment. Microbiome-based therapies are evolving rapidly, and in the future, new and more effective methods for microbiome correction may emerge.