What comes to your mind when you hear the word bacteria, virus, or fungi? If you’re like most people, you probably think of some pathogens that can infect your throat, skin, gut, or urinary tract and make you sick. Or perhaps microorganisms that can spoil your food.
But did you know that your body is home to hundreds of trillions of microbes even if you’re healthy? In fact, the more diverse the bacterial population living inside your gut is, the healthier you are. That society of microbes living on your skin and inside your body is called microbiome or microbiota.
Your microbiome literally is a society of different microorganisms. To understand it better, you can think of it as a society of humans on earth, but in a microscopical size. Our body is a planet for those microbes. Just as each of us in the human population has a different personality, expression, and function (doctors, lawyers, builders, bakers, taxi drivers, etc.), microbiota living in our body works the same way. These microorganisms influence not only their immediate environment, thus creating a more suitable environment for similar (good or not so good) bacteria. But the particular microbes in your body also have either positive or negative impacts on your health via the metabolites they produce.
What microorganisms are in the human microbiome?
Hundreds of trillions of microorganisms live inside and on the skin of our bodies. Our microbiota consists of multiple different microorganisms:
Bacteria
Bacteria is the most known microorganism in our body, with the most significant impact on our metabolism and health.
Most bacteria are harmless or helpful (probiotics), but some can cause disease. These potentially harmful bacteria are called pathogens.
Bacteria are prokaryotic because they have cell walls that contain peptidoglycan. Their genetic material (DNA) is not housed within a true nucleus.
Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio).
Bacteria have a wide range of metabolic capabilities. They can grow in various environments, using different combinations of nutrients, making different niches of the human body suitable for different types of bacteria.
For example, our skin is colonized mainly by aerobic bacteria (needing oxygen), while our gut is an ideal environment for anaerobic bacteria (oxygen-free environment). The human gut is the most extensive reservoir of bacteria.
Archaea
Similar to bacteria, archaea are also unicellular prokaryotic organisms. Archaea have a slightly different evolutionary background than bacteria, and there is also some difference in their DNA, metabolic pathways, and the composition of their cell walls and membranes.
Archaeal cell walls are usually composed of a substance called pseudopeptidoglycan and not peptidoglycan as bacterial cell walls. Archaea also live in the human body but are much less populated than bacteria and are usually not human pathogens.
Viruses
Significant participants in the human microbiome are viruses. Viruses are acellular microorganisms – their “body” is not composed of cells. A virus consists of proteins and genetic material—either DNA or RNA (never both). They are inactive outside of a cell; however, by inserting their DNA into a host cell, viruses can co-opt the host’s cellular mechanisms to multiply and spread, causing the infection.
Viruses can infect all types of cells, from human cells to the cells of other microorganisms, including bacteria.
There are hundreds of different viruses, and not all of them are created equal.
While some human viruses are responsible for numerous diseases, such as the common cold, Ebola, or HIV, some viruses are actually beneficial for humans.
These viruses don’t infect human cells but instead bacterial cells. They are called bacteriophages or phages. Phages can target specific pathogenic bacteria such as S. Aureus and kill them by inserting their DNA into the bacteria. The new viruses then grow from the infected bacteria, which kills the bacteria in the process. That’s how viruses are helping to keep the microbiome balanced and healthy.
Fungi
Fungi (singular: fungus) are also eukaryotes. There are more than 1000 known species of fungi. Some multicellular fungi, such as mushrooms, resemble plants but are quite different. Fungi are not photosynthetic; their cell walls are usually made of chitin rather than cellulose.
Fungi haven’t been as extensively studied as bacteria in the microbiome. Yet emerging scientific studies are beginning to reveal that fungi in the gut can have a significant impact on host metabolism.
Some yeasts that are used in foods have beneficial use not only in the food industry but also in our gut after consuming the food containing them. Again not all fungi are created equal, and while some are beneficial, others can cause annoying diseases, such as vaginal yeast infections and oral thrush.
Mold is also a type of fungus, and it is made up of long filaments that form visible colonies. Molds are found in many different environments, from soil to rotting food to dank bathroom corners. While molds are critical for the decomposition of dead plants and animals and in nature, when they get to the human body, they can cause allergies and other adverse reactions due to metabolites called mycotoxins. For example, brain fog is a common symptom of mold toxicity.
Parasites
The human microbiome also often contains parasites. These are multicellular organisms that can only survive by extracting nutrients from a host organism, for example, worms. Technically, they are not microbes, but they are included in microbiology because their eggs and larvae are often microscopic.
All these microorganisms (except some larger parasites) are so tiny that the human body is literally a planet for them.
But wait. Aren’t we born without bacteria? Yes, we are. So then…
How did trillions of bacteria, viruses, and other microorganisms get in on our bodies?
To understand how these microorganisms got into our bodies, we have to look all the way back to our birth and our first weeks, months, and years of life. That’s when the first microbes colonize our bodies.
If we are born via vaginal delivery, we begin by getting a dose of microbes from the birth canal, but if born by cesarean section, our first dose is from the skin of our carers.
The healthy vaginal microbiome composition consists mainly of Lactobacillus bacterial species (ca 70%). However, it is often the case that the vaginal microbiome is disrupted (the state called dysbiosis). In that case, other bacterial species that are not supposed to be there (pathogens) are present, and the child is also exposed to those at birth.
Once the child emerges fully into the world, it is quickly exposed to myriad other bacteria from doctors’ and nurses’ hands, air and environment, surfaces it touches, etc.
Then there is the mother’s breast, skin, and saliva, and a little later in life, the child is exposed to the bacteria from food, other people it comes to contact with, and the environment it lives in.
As the child ages, it comes to contact with all kinds of environments, people, and foods, and the microbiome diversity increases accordingly. Sometime between six months and three years of age, a stable microbiome composition is attained and changes only mildly unless there is some significant disruption, for example, by antibiotic treatment.
The first bacteria that colonize our body right after birth and subsequent months are called pioneer species. These bacteria can set a course for further bacterial selection and, therefore, influence the composition of our core microbiota.
In the ideal case, a “good” healthy microbiota colonized your gut and skin shortly after birth, programmed your immunity, and prevented other bacterial species (pathogens) from residing in your body. As you can imagine, it is essential.
Probiotics versus pathogens
There are thousands of different bacteria, fungi, and viruses, and most that can survive in our body long-term are neutral or helpful (probiotics). But there are also harmful bacteria, called pathogens, which can cause severe illness or even death when they get the upper hand in our microbiome.
What are probiotic bacteria?
Probiotics are the type of bacteria that help their host to be healthy. Probiotic bacteria help digest the food you eat by producing enzymes. Those enzymes break down fiber and other food components that are otherwise undigestable, turning them into fatty acids, vitamins, and other metabolites that the body needs for optimal functioning. Probiotic bacteria also produce enzymes that repel pathogenic bacteria, keeping the gut or skin healthy and with optimal PH.
Some of the most common probiotic bacteria are Lactobacillus and Bifidobacterium species, but also other bacteria such as:
Bacillus subtilis
Enterococcus faecalis
Enterococcus faecium
Lactococcus lactis
Leucnostoc mesenteroides
Pediococcus acidilactici
Saccharomyces boulardi
Sporolactobacillus inulinus
Streptococcus thermophiles and others…
Pathogens
While most bacteria living in our body are neutral or beneficial, there are also pathogens. Pathogens are bacteria that can cause inflammation, infection, and even severe health problems or even death, sometimes very rapidly when the immunity is weak.
The microbiome of most people has some pathogens, but only in minimal quantities and therefore not causing any problems. When our microbiome is diverse and balanced, our immunity system is robust and keeps pathogens at bay. However, when the pathogens have the opportunity to grow, for example, during stressful periods when our immunity is weakened or our microbiome balance is disrupted, these pathogens can take over and cause health problems.
Some of the most common pathogenic bacteria are Staphylococcus aureus (MRSA), Clostridium difficile, Campylobacter, Clostridium botulinum, Listeria monocytogenes, Norovirus, Salmonella, Shigella, Vibrio vulnificus, and Toxoplasma gondii.
Different microbiome compositions at various body sites
There are bacteria, viruses, and fungi all over our body, but different sites have different microbial compositions depending on nutrient profile, moisture, temperature, PH, and other environmental factors. Whether on our skin, mouth, nose, ears, gut, or urogenital tract, they thrive where they have optimal conditions for life.
Mouth (Oral) microbiome
Most people consider the gut microbiome an essential indicator of human health, and yes, it is critical. But oral microbiome seems to be equally important.
Our mouth is a gateway into our body. It is the first place where the food we eat enters our system. More than 250 different bacterial species live in our mouth, including several pathogens, such as Streptococcus mutans, Porphyromonas gingivalis, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans, involved in the etiology of dental caries and periodontal disease.
Enormous fluctuations in temperature, PH, different foods, and other substances constantly impact the oral microbiome. Such circumstances are defining factors for the selection of colonizing microbes and their ability to survive in this environment.
Pioneer microbial colonizers of the mouth, such as Streptococcus mitis, Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, are some of the common bacteria found in the oral microbiome. They can bind to the tongue and cheek cells before the teeth emerge, outcompete other microbial species and pathogens, and prevent them from colonization.
Throughout the history of humankind and especially in the last hundred years, there has been a tremendous shift in the composition of our diet. The western diet contains a lot of farmed animal meats, dairy products, refined vegetable oils, and processed cereal grains and substantially diverges from pre-agricultural diets. Such changes in our diet are parallel by changes to the oral microbiota and a greater representation of acid-producing and acid-tolerant organisms and periodontal pathogens.
Recent data indicate that the oral microbiota or at least some bacterial species can have a say regarding our dietary preferences. Hence the cravings for certain junk foods. It is not always you who craves that chocolate, pizza, or a can of soda, but the bacteria living in your mouth and gut, for example, some Clostridia and Prevotella species.
Oral hygiene habits are another consistent source of influence on your oral microflora. Toothbrushing and flossing can be a powerful way to disrupt bacterial plaque (biofilm), the microbial inhabitants of which can cause tooth demineralization and gingival inflammation long-term.
Scientific studies revealed that mouth bacteria have also been detected in other body parts, including the small intestines, lungs, heart, and even placenta and brain. Establishing associations between oral microbes, specifically those implicated in periodontal disease, and other common chronic conditions, such as IBS/IBD, cardiovascular disease, and high blood pressure.
Researchers demonstrated that oral microbiota can also influence immune responses and disease pathogenesis outside the mouth and that their ability to colonize ectopic sites depends on that site’s current state of health.
The oral microbiome may therefore serve as a reservoir for pathobionts that can either contribute to or exacerbate diseases of remote body niches or organ systems.
Gut microbiome
The largest reservoir of microbiota is in our intestinal tract, especially the large colon. The colon provides ideal conditions for the growth of anaerobic bacteria. There they are turning previously undigested food, like plant fiber, into metabolites that can be absorbed into our bloodstream and utilized by the body.
Hundreds of trillions of microorganisms (mostly bacteria, viruses, fungi, and protozoa) live in the human gastrointestinal tract. We have approximately 1-2 kg of bacteria in our gut, which is mind-blowing when considering the size of a single bacteria.
It will probably not surprise you that bacteria are among the fastest reproducing organisms in the world. Some bacteria can reproduce in ideal conditions extremely fast, like doubling every 4 to 20 minutes! Because of such rapid growth, bacteria make up about 30-50% of the weight of contents of our intestines. Yes, each poop is not just the processed food you ate hours or days ago but consists of 30-50% of bacteria!
More than 1300 bacterial species live in the human gut, and these species fall into five main phyla: Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia. Of these, Bacteroidetes and Firmicutes are usually the most common.
The gut microbiome influences the host’s fitness, phenotype, and health. Approximately 70% of the immune system is located in the gut. The microbes in the human gut produce thousands of metabolites and have several essential functions, such as breaking down foods, manufacturing vitamins, and training our immune system. Because of this, scientists consider the gut microbiome a virtual body organ.
Therefore, probiotic supplementation is an excellent way to promote a healthy immune and digestion system.
Genital microbiome
The Human Microbiome Project, which started more than ten years ago, has provided significant findings. The genital microbiome is not only associated with the development of numerous diseases of the human genital tract but is also involved in fertility.
Especially for women, genital health is of the utmost importance because urinary and reproductive tract diseases can lead to painful and protracted inflammation and reduce the protective effect against infections.
The increase in bacterial diversity and thus of pathogens associated with bacterial vaginosis (BV) are also associated with infertility.
Bacterial vaginosis is problematic not only because of the unpleasant smell but also due to the risk of infertility, failure of artificial insemination, and/or complicated pregnancy.
Dysbiosis also makes it easier for other viral and bacterial sexually transmitted pathogens to colonize the urogenital tract, further increasing the risk of serious disease.
The male genital tract is not much different regarding microbiome composition and consequences of dysbiosis. Seminal microbiome dysbiosis can negatively influence sperm quality and thus cause male infertility.
Changes in the microbiome composition leading to dysbiosis can be associated with restrictions in sperm function, such as reduced sperm motility, fragmentation of sperm DNA or even the absence of sperm in the ejaculate (azoospermia).
And it’s not just because of certain germs (e.g., chlamydia, ureaplasma, or mycoplasma) that are typically associated with infertility in both men and women but also due to the overall shift in the genital microbiome and its biochemical environment.
Research also revealed the link between the genital microbiome and the occurrence of varicocele which requires surgical removal of the veins from the testicle(s). It is worth keeping your genital microbiome healthy.
A properly balanced microbiome essentially maintains urogenital health.
Skin microbiome
Your skin is the biggest organ of your body. It is a vital organ, not only because when it’s healthy, it makes you look and feel good, but because it is a part of the immunity system.
Just like the healthy intestinal barrier in the gut prevents pathogens, food particles, and toxins from leaking into the bloodstream and causing autoimmune reactions and inflammation, the skin has the same purpose – to protect your body from pathogens and toxins from the environment.
Your skin is also home to hundreds of bacteria species and other microorganisms. If the bacterial composition is healthy, it has a protective function and will not allow pathogens and toxins to penetrate the skin and enter the bloodstream. With a healthy skin microbiome, wounds heal faster because microbiota directly cooperates with your skin’s immune cells.
Factors that influence our microbiota during our life
One study, looking at the first six months of life, revealed a great diversity in microbial populations between babies, with a surprisingly wide variation in what constitutes a ‘healthy’ microbiota.
As we grow and begin to put all kinds of things into our mouths (not just a variety of foods, but all those other goodies kids like to taste test), we introduce new microbes into our gut.
Sometime between the age of six months and three years, we attain a relatively stable microbiome composition. That happens with the adoption of an adult-like diet and the completion of immune development.
The research found that our microbiome is not significantly associated with genetic ancestry. Genetics plays only a minor role in determining our microbiome composition.
Even identical twins have the same microbiome at only 34 percent if they don’t live together. For the rest of the population, the match is around 30 percent, so there is no significant difference.
Another study showed significant similarities in the compositions of the microbiomes of individuals who were not genetically related but shared a household.
Despite the microbiome being relatively stable in adults, other factors than genetics can alter its composition, including environmental influences, disease states, changes in diet, intake of food supplements and prescription drugs, especially antibiotics, probiotics, and indeed exercise/fitness, and age.
Geographical location or country of residence also makes a difference in gut microbiome composition. For example, researchers found that populations of western countries have different microbiota composition from people living in developed countries. Specifically, people in western countries have, on average, 300 bacterial species less and with a different composition than people in developing countries. That decreased bacterial diversity and shift in the microbiome structure negatively correlates with the increase of autoimmune diseases and mental health disorders that are on the rise in developed western countries.
So it’s not surprising that there are still differences in the microbial make-up of individual adults. Our microbiota is unique to each of us, just like our fingerprints.
Why you should care about your microbiome
The human genome consists of about 23 000 genes, whereas the microbiome encodes over three million genes(!). In other words, microbes are a large part of us, and from the genetic standpoint, we are more microbes than humans, however crazy that sounds.
The bacteria in our bodies produce thousands of different enzymes that directly impact our body’s functions.
The microbiome has a significant effect on most aspects of our health. As well to absorbing energy from food, gut microbes are essential to helping us take in nutrients. Gut bacteria help us break down complex molecules in meats and vegetables, for example. Without the aid of gut bacteria, plant cellulose is indigestible.
In addition to a role for specific microbes or groups of microbes, the importance of microbial diversity has been recognized in many studies, with a decreased diversity associated with multiple gastrointestinal conditions such as IBD, certain cancers, and Type 1 diabetes. An altered microbiome can also affect energy metabolism and immune function and increase obesity and oxidative stress, which are vital for physical performance and overall health.
Speaking of health, your microbiome does not only affect your physical health but also your mental health. Many scientific studies are now linking gut microbiome dysbiosis and depression, autism, anxiety, and other mental health and mood disorders.
Equally important is the fact that people with disrupted microbiome composition (dysbiosis) are more vulnerable to acquiring other pathogens, for example, Covid 19, which causes a downward spiral effect with sometimes rapidly worsening health.
How to keep your microbiome healthy, diverse, and balanced?
It is not that hard to keep your microbiome healthy and happy. It is even easier when your microbiome returns that favor and does the same for you.
All it takes is a healthy and balanced diet with enough plants (fruits, vegetables, herbs) and therefore fiber, minerals, and vitamins. On top of that, irrigate your gut with enough water (1-2 liters a day) and give your body some physical stimulus in the form of exercise. Science found that exercise improves the gut microbiome and promotes healthy bacteria, so physical training is helpful on multiple levels.
Okay, Michal, but what if I cannot tolerate most foods? What if everything I eat triggers pain, cramps, diarrhea, or other reactions… What if I am too tired to go to the gym or even take a walk? Is it even possible to modify or change my microbiome once it is in a state of dysbiosis?
In my opinion, it is possible to reverse dysbiosis and improve your microbiome at any age and stage of dysbiosis, whether it is mild IBS or severe IBD.
Some people have tolerated their gut issues for decades. Then they are in their 40s, 50s, 60s, or 70s and their problems are so severe that they finally start thinking about some serious solution before it’s too late.
Obviously, the longer you have the dysbiosis and the worse your condition is, the longer it will take to reverse it. Not only because the chronic condition and inflammation change your physiology but also because the older you are, the harder it is to change your habits that have been forming for decades and led to that condition.
That being said, you can hugely improve your microbiome and health at any age. All you need is to stick to the new routines and dietary changes and maintain that momentum long enough. Then it will be self-sustaining.
How long does it take? For some people, it can be two years. For others, it might be more or less. It took me about three years of consistent effort to turn around the ship. The momentum of habits is strong. The power of your current microbiome is strong. But with consistent effort, you can reverse any condition and change any habit.
If you decide and commit to it, you can vastly transform your microbiome just like a gardener can transform the garden. You can update your microbiome with new bacterial species or even completely transform it by wiping out your existing microbiome and introducing a new microbiome. That’s what I did in 2020, and it changed my life.
In any case, you should become a gardener of your gut microbiome and take care of it the best you can because your health and well-being depend on it.
Maybe you will even start loving your new bacterial friends living inside your gut and think of them every time you eat a meal. That alone should change your food preferences and improve your health 🙂