What are the microbiota and microbiome?

The microbiome is a collection of microorganisms that live in different places in your body, for example on your skin, in your mouth, ears, intestines and even in our lungs. In general, they live on all surfaces that have direct contact with the outside world. The microbiota is the part of the microbiome that consists only of bacteria. This is by far the largest group within the microbiome, covering as much as 95%. The other microorganisms such as fungi, yeast, viruses and nematodes (worms) also live in our gut, but cover only 5% of your microbiome. There is also less research on their role and function. Therefore, we focus on the remaining 95%: bacteria. The role of bacteria is still being studied, (logical, as there are more than 2,000 different species found in every gut!), but we can already tell you a lot about yourself based on the bacteria in your gut! 

Microflora is also often used; but, since this is not about plants, the term microbiota is better. The term microbiome and microbiota are often used interchangeably, but remember: When we talk about microbiota, we mean your bacterial community and when we talk about the microbiome, we mean all microorganisms.

Who discovered microorganisms? 

We're going back in time for a moment to set the scene. More precisely, Antonie van Leeuwenhoek made a discovery in 1676 that forever altered the course of science. With a fascination for lenses, this Delft businessman invented the first microscope capable of magnifying objects up to 300 times, large enough to view microorganisms as small as 1 millimeter (1 millionth of a meter or 1 thousandth of a centimeter). Van Leeuwenhoek dubbed these microbes animalcules, or minute beings, and discovered them in almost everything he investigated with his microscope. You name it: saliva, feces specimens, and even water samples. Because of his numerous reports of what he witnessed in scholarly journals, history and the scientific community regard him as the creator of microbiology. 

Anthonie van Leeuwenhoek with a drawing of the animalcules he saw

The microbiota in numbers 

According to estimates, the gut microbiota contains 1014 (100,000,000,000,000) bacteria, or more than 1000 times the Earth's population. The DNA of all these cells collectively referred to as the microbiome, has 3 million unique genes. Compared to the approximately 23,000 genes included in the human genome, it is clear that bacteria can perform many more activities than our body's cells. 

Since their discovery, we've identified over 2000 unique bacteria, and we're constantly uncovering new ones. Each individual has between 400 and 600 unique species (estimates vary), which changes in response to the bacteria we consume and our genetic predisposition, among other variables. As a result, each person possesses around 30 different species of bacteria, which we refer to as the core microbiota. 

How does the microbiota form?

At birth, a person comes into contact with germs first (although some studies show that bacteria already exist in the womb). It occurs when an infant leaves the mother's body via the vagina, and various types of germs land on and in the newborn child. The newborn child then comes into contact with the mother's skin, which has a high concentration of germs. Finally, breastfeeding ends this initial wave of "contagion." 

We believed that breast milk was sterile, but we now know it includes a diverse array of bacteria, including streptococci, lactobacilli, and bifidobacteria. We can find many of them in the intestines of any infant because human breast milk contains unique sugar chains (polysaccharides). These polysaccharides are a superfood for bacteria called Bifidobacterium Infantis frequently found in the stomachs of nursing infants. 

Little toddlers use their tongues to explore their environment, tasting and licking their way through the world as they grow. This is a wonderfully effective method for introducing new bacteria into your body. Additionally, as toddlers move to solid food, they contract additional pathogens, impacting the initially present bacteria. Exposure to new foods enables certain bacteria to grow more rapidly while others grow more slowly. For example, Bifidobacterium Infantis degrades slowly in the stomach and is not detected in most people. 

Genetic predisposition is another critical factor in the formation of our microbiota. This affects the bacteria that remain in our intestines and those that do not. Except for around 30 to 50 species present in every person, this leads to a microbiota that is unique to each individual. 

During the second and third years of life, a more or less developed microbiota emerges, the composition of which remains consistent for an extended period. Only as we age does the variety of bacteria in our intestines diminish steadily. 

What does the microbiota do?

So, now we know how you get it. But what does having a microbiota mean to you? So, the first function we'll look at relates to developing our immune systems.  

Immune System 

Germs in our stomachs help our immune systems distinguish between benign and pathogenic bacteria. Notable species, such as Bifidobacterium Infantis, benefit our immune system by stimulating it. However, modern science is still unsure of how these systems work. Nonetheless, we know from mouse experiments that mice born completely infertile have underdeveloped immune systems. 

A healthy microbiota aids in the successful fight against infections (pathogens). This can take place in a variety of ways. Bacteria in our gut, for example, compete with pathogens in the intestines for food and attachment sites. Additionally, several bacteria can combat illness through the secretion of antibiotic chemicals (bacteriocins). 

Digestion 

Our bodies break down food using enzymes generated by specific cells in our mouth, stomach, intestines, and pancreas, a vital source of enzymes. Our bodies break it down into minute components and molecules easily absorbed and transported by intestinal wall cells. 

However, some components, like plant fibers, are inaccessible to human bodies. But have no fear; our intestines are teeming with bacteria that know just what to do with them. They convert these fibers to compounds that humans can absorb, other bacteria can use them as food, or our intestinal wall cells can use them directly. These by-products consist primarily of short-chain fatty acids like butyric acid (butyrate) , propionic acid (propionate), and acetic acid (acetate). Butyrate, in particular, is crucial for the health of our gut bacteria. It helps maintain a healthy intestinal wall by feeding our epithelial cells (the cells that line the surface of our intestines). 

Different bacteria in our intestines can produce substances that our bodies cannot produce. For example, several bacteria produce vitamins (K, B12, and folic acid) and amino acids. In addition, certain bacteria produce signaling chemicals recognized by the nervous system and serve as indicators of feeling satisfied after eating (satiation) or cause bowel movements (peristalsis). Other signaling molecules can excite the brain, therefore affecting our mood. 

Want to learn more about the role your microbiota plays in your immune system, nutrient production and digestion? Click here!

Research into the microbiota

Not so long ago, research into the microbiota relied on culture methods, in which we grew and examined bacteria individually. Unfortunately, that was not easy because most bacteria in our gut are anaerobic, meaning they die when they get in contact with oxygen. In addition, some bacteria need nutrients made by other bacteria, so as long as you don't know which these are, you can't grow them separately. This kind of research was accessible to only a few specialists who had special equipment to grow bacteria without coming into contact with the external air.  

Want to learn more and use the right terms like a pro? Dive into the differences between microbiome and microbiota in this blog!

Nowadays 

These days bacteria are researched without having to culture them separately. To do so, we use a technique called 16s rRNA analysis. It works like this: Every bacteria has a core that contains their DNA. This DNA consists of two strands and contains 'recipes' for all things of a bacteria. To create all these things, a recipe (piece of DNA) is first copied into a single strand of DNA that can move to outside the core. This piece is called a RNA strand. The recipe on the RNA is then processed in a ribosome. Ribosomes are little factories that create proteins. The ribosome itself is made of proteins and RNA molecules. One of these RNA molecules is called the 16S rRNA. Pieces of this RNA are different for each bacterial species. Therefore, by analyzing this piece of DNA, we can find out which species it belonged to. 

Discover how the 16S rRNA gene sequencing revolutionizes our understanding of gut bacteria. Learn about the crucial roles of genes and proteins in bacterial survival and how this gene acts as a biomarker to identify different bacterial species. Click here to read our informative blog and enhance your knowledge about the microscopic world within us.

What role does the microbiota play in disease?

We previously concentrated on the microbiota’s function, and there is much we can learn about how it influences human health. For example, a weak gut wall might result in issues with nutrition absorption, intestinal inflammation, and colon cancer. Allergies might be a result of an immature immune system. Excessive or insufficient signaling molecules for our nervous system may result in nervous system diseases. The diseases and disorders associated with abnormal microbiota are already long and growing. 

Bacterial diversity, which refers to certain types of bacteria prevailing over others, is a critical feature shared by all of these microbiota illnesses. Consequently, we may deduce from microbiota studies that variety is now the most critical component of health. Regrettably, it is impossible to account for all symptoms, diseases, and microbiota research. So that monstrous volume would no longer fit through your letterbox! 

However, the following is a list of conditions linked to the composition of your microbiota: 

• Metabolic diseases: obesity, type 2 diabetes, non-alcoholic fatty liver, liver cirrhosis, cardiovascular disease, chronic intestinal inflammation (ulcerative colitis, Crohn's disease) 
• Allergies: eczema, asthma, hay fever, house dust mite allergy 
• Colon cancer 
• Neurological Disorders: MS, Autism, Depression 
• Antibiotic-associated intestinal infection (Clostridium Difficile infection) 

The researchers' primary concern is with cause and effect. For example, are microbiota abnormalities a result of the disease? Is it the reverse? 

Antibiotics and the microbiota

Antibiotic usage has taught us essential lessons in more ways than one, and it has given rise to a whole new field of research to answer this question. Antibiotics are drugs used to treat bacterial infections. Antibiotics, however, do not discriminate between wanted  and less wanted bacteria and can severely upset your microbiota. In addition, according to research, antibiotic usage in early childhood has been linked to the development of allergies such as asthma and hay fever and obesity later in life. 

Antibiotic treatment in the elderly can frequently result in unpleasant bowel infections accompanied by severe diarrhea. We now know that disruption to the microbiota causes these consequences, altering immune system development and permitting bacteria that are typically innocuous to thrive and unexpectedly cause disease. 

Researchers discovered that replacing patients' microbiota with healthy people's microbiota can have significant benefits and is a powerful approach to examining cause and effect. Fecal Microbiota Transplantation is the name given to this procedure (FMT). For numerous years, this approach successfully addressed, for example, persistent Clostridium Difficile infections. 

What does a healthy microbiota look like?

It is still difficult to define a healthy microbiota because every person is unique and has a unique microbiome. Each person has 30-50 species which we find in many people, but the other species found (between 400 to 600 per person) can vary wildly. 

There is also still a lot of research to be done to determine precisely which factors of the microbiome are most important for health or influence illness. However, we do know that a high diversity, high butyrate-production and low score of unwanted bacteria are all indicators of a healthy gut. 

To better understand the elements that impact a healthy microbiota and the relationship between lifestyle and nutrition and our microbiota, we must compare the microbiotas of thousands of people and (preferably) track them over time. We aim to contribute to this through MyMicroZoo's citizen science project. 

Explore the secrets of a thriving microbiota! Visit our blog to learn more about what a healthy microbiota truly is about.

Contact us!

What results can I expect?

After giving us your sample to analyze, you will receive your results in a very elaborate report.  You can also access your results in the online dashboard, where you are able to look up specific bacteria and can compare your microbiome to those of other users. 

In the report you will be given an overview of your:

• Composition: An overview of the different species we found and in which abundance.
• Diversity: A higher diversity is an indicator for a healthy gut
• Enterotype: your microbiome type that is based on which bacteria you encountered as a child and your diet choices 
• Keystone species: These species fulfill a key role in the microbiota. 
• Butyrate producing bacteria: Butyrate is thé most important energy source for your gut. A score within or above the reference range is an indicator for a healthy gut. 
• Propionate producing bacteria: Propionate plays a major role in the feeling of satiety and in the sugar metabolism
• Lactate producing bacteria: Lactate producing bacteria (also called lactic acid bacteria) are known for their production of lactate. Lactate is an important food source for other bacteria who cannot live off sugars from food sources.
• Gas producing bacteria: Gas production in the gut is a natural process which provides the gut and body with energy. However, too much gas production can cause abdominal complaints such as bloating.
• Unwanted bacteria: Some bacteria are less wanted in your gut since they are known to cause irritation in your intestines. 
• Tips to improve your scores: The second part of the report contains tips on how you can improve each of your scores. 

To become acquainted with the data that you will see later, you can check out this overview of the common groups you can encounter: 

Faecalibacterium Prausnitzii 

Without a doubt, the most well-known is Faecalibacterium Prausnitzii. We know this bacterium very well for its anti-inflammatory capabilities and can account for up to 20% of all intestinal bacteria in your colon. Additionally, like many others in this phylum, this bacterium generates butyrate. Butyrate is a butyric acid derivative that provides critical sustenance to our intestinal cells and promotes gut health. Another lesser-known species is Christensenella Minuta. A study of 977 participants revealed that those with a higher proportion of Christensenella bacteria in their stomachs had a lower BMI (less fat) than those with a lower proportion of Christensenella bacteria. 

This group includes several (possible) infections, including Listeria, Staphylococcus, and the species Clostridium Difficile (which has recently been renamed Clostridioides Difficile). 

Firmicutes 

This is the phylum that is most prevalent in the western population. The most abundant species (or, more precisely, genera) discovered in the human gut are Anaerostipes, Blautia, Dorea, Flavonifractor, Lactobacillus, Pseudobutyrivibrio, Roseburia, Ruminococcus, and Sarcina. Additionally, this phylum contains numerous microorganisms that are strongly associated with health.  

Bacteroidetes 

Bacteroidetes are the second most prevalent group in Western populations and are frequently the most common group in non-Western people. They are all Gram-negative bacteria that are generally rod-shaped. Prevotella, Alistipes, and Bacteroides are the most prevalent genera. Many other species (not all!) are pathogens and so are not or only rarely seen in healthy people's microbiota. 

Actinobacteria 

This phylum often makes up only a few percent of the entire population in the gut and consists of primarily beneficial bacteria. Species commonly encountered are Collinsella and Bifidobacteria. We know the latter from the healthy yogurts from the supermarket, like Bifidobacterium Animalis, which is also referred to by cryptic names such as Bifidobacterium Regularis, Bifidobacterium Actiregularis or Bifidobacterium Digestivum. Other Actinobacteria genera that occur are Actinomyces, Adlercreutzia, and Cryptobacterium. 

Proteobacteria 

These bacteria, like Actinobacteria, are uncommon in the human stomach. The most well-known examples are Escherichia coli and Helicobacter pylori. Even though there are many innocuous strains of Escherichia coli, this bacterium is best known as the "poop bacteria" and is frequently associated with food poisoning. Helicobacter Pylori is well known as a cause of stomach ulcers. The majority of Proteobacteria are (potential) pathogens. Salmonella and Campylobacter, both of which cause food poisoning, are well-known members of this group, as are Vibrio (Vibrio Cholerae, which causes cholera), Yersinia (Yersinia Pestis, which causes plague), and Haemophilus Influenzae (Haemophilus Influenzae, cause of respiratory diseases). However, these microorganisms are not necessarily doom and gloom. Sutterella Wadsworthensis is an unusual representative of the Proteobacteria usually found in the microbiota of healthy persons, where they undoubtedly contribute to a healthy microbiota. 

Verrucomicrobia 

The Verrucomicrobia form a phylum that we have to pay attention to briefly. As far as is known, only one representative of this occurs in our intestines, namely Akkermansia Muciniphila. This bacterium occurs in approximately 90% of the population and plays a vital role in our intestinal wall's health. According to several studies, it breaks down excess mucus secreted by the intestinal wall, has anti-inflammatory activity, and may protect against obesity, colon cancer, and autism. The following applies here: other bacteria will take over its various functions if you do not have the bacterium. There are several mucus-degrading bacteria, and the genus Christensenella is also associated with protection against obesity.

What influences the microbiota, and what can you do yourself?

Diet and lifestyle are factors you control yourself to have a positive influence on the gut microbiota. On the other hand, taking antibiotics can have a negative effect on the microbiota.

The adage "you are what you eat" is especially true for the composition of your microbiota. A one-sided diet leads to a one-sided microbiota. And a diverse diet leads to a diverse microbiota. As a result, diets that focus exclusively on one food group or completely exclude another are not always helpful for the microbiota and must be carefully regulated.  

A well-known example is a low-carbohydrate diet ("low carb diet"). In their research, scientists discovered that a low-carbohydrate diet reduces the production of butyrate. This phenomenon is due to a decrease in the abundance of many important butyrate-producing bacterial species belonging to the genera Roseburia and Eubacterium (Duncan et al., AEM 2007, 73: 1073-8). These bacteria feed on fibers to produce butyrate and are often left to starve in a low-carbohydrate diet if one does not pay attention to ensure other sources of fiber such as vegetables.  Not only are vegetables beneficial to the intestines, but they also decrease the risk of colon cancer! 

Exercising is a known way to influence your gut bacteria. For example, butyrate-producing bacteria are stimulated by partaking in cardio sports. Our research shows that more than two hours of cardio a week has a (positive) effect on your microbiota.

We already mentioned antibiotics earlier. Regrettably, they can have a detrimental effect on the microbiota. The finding that the microbiota plays a critical role in the immune system development of young children makes doctors increasingly hesitant to prescribe antibiotics. 

Probiotics 

With a story on microbiota, you can't escape briefly discussing probiotics. Ilya Metchnikoff, a Russian microbiologist, established around the turn of the century that the exceptional health of rural Bulgarians was primarily attributable to the usage of lactic acid bacteria in fermented dairy products such as yogurt (yep, Bulgarian yogurt!). Lactobacillus Bulgaricus is the name given to one of the bacteria resulting from this. In addition, it is still the case that items without these bacteria should not be labeled yogurt. 

This story demonstrates that microorganisms may positively impact our health. Most of the time, this entails stimulating the immune system. They also improve gut health by creating short-chain fatty acids like acetate and propionate that can be converted back to butyrate by other bacteria. In addition, many of these bacteria are responsible for the fermentation of fermented foods such as sauerkraut, kimchi, kefir, dry sausage, and, of course, yogurt. As a result, we regard these products as healthy foods (not only because of the bacteria but also the products that make them). 

Join us and learn more about your microbiota!

You now have a wealth of information at your disposal, and you may already have a better grasp of your initial investigation results. We will make every effort to keep you informed about new scientific discoveries concerning microbiota. Additionally, you may participate in the research yourself!  

To do so:  

Conduct a reasonable experiment to determine the effect on your microbiota. Learn how to diversify your microbiota and how to share your findings. By comparing data, we may learn more about the role of all microbes in your gut.  

In a nutshell, take on the role of a researcher and discover your tiny zoo. Discover how these organisms work and how they affect your health. Conduct a fundamental study to determine how to alter the blend. Participate in this citizen science project to help us better understand how bacteria work in our bodies!