Eating probiotic foods contributes to a healthy microbiome and plays an important role in promoting health and the correct functioning of the human body.
Content – All About Probiotic Foods
- Prebiotics vs. Probiotics: What’s the Difference and Why It Matters
- The Importance of the Microbiome: What You Need to Know
- Why Fermented Probiotic Foods Are Good for Your Health
- What is food fermentation?
- The Hidden Benefits of Fermented Foods
- Why You Should Care About Repopulating Your Microbiota
Prebiotics vs. Probiotics: What’s the Difference and Why It Matters

Prebiotics (PRE-biotics) are foods that nourish the human microflora, such as fiber.
So, prebiotics are food for the healthy bacteria that populate our guts.
Eating fiber-rich foods is very important for our health and one of the key benefits comes from their prebiotic effect.

Probiotics (PRO-biotics) are foods or supplements that directly contain live microorganisms that can maintain or even improve the “good” bacteria in our body. These good bacteria are also known as our microbiome. Eating probiotic fermented foods is very important for our health because they repopulate our guts with healthy bacteria. A few examples of healthy probiotic foods are fermented foods such as: yogurt, milk kefir and water kefir, fermented vegetables like sauerkraut and pickles, tempeh, kimchi, miso and kombucha. When you eat these types of foods, you are eating trillions of healthy bacteria that are going to find place and live in your guts, joining your microbiome and helping you stay healthy.
The Importance of the Microbiome: What You Need to Know
The content of this article is based on the research presented by The Nutrition Source of Harvard T.H. Chan School of Public Health and the work of the Italian nutritionist Stefano Vendrame.
The human microbiome consists in trillions of microorganisms (also called microbiota or microbes) of thousands of different species that reside in our body. These microorganism include mainly bacteria, but also fungi, parasites, and viruses. The largest amounts of bacteria in the human body are found in the small and large intestines, but these also present throughout the body including the skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract.
The bacteria of the microbiome are both helpful and potentially harmful. Most of them are symbiotic (this means that both the human body and microbiota benefit from the symbiosis) and some, in smaller numbers, are pathogenic (promoting disease). In a healthy body, pathogenic and symbiotic microbiota coexist in harmony. But if there is a disturbance in that balance, for example because of infectious illnesses, certain diets, the prolonged use of antibiotics or other bacteria-destroying medications, these normal interactions can be negatively impacted and the body may become more susceptible to disease.
Each person has an entirely unique network of microbiota that is originally determined by one’s DNA. A person is first exposed to microorganisms as an infant, during delivery in the birth canal and through the mother’s breast milk. Exactly which microorganisms the infant is exposed to depends on the species found in the mother. Later on, environmental exposures and diet can change one’s microbiome to be either beneficial to health or place one at greater risk for disease.
Until a few years ago it was thought that the cells of the microorganisms that inhabit our bodies were about nine times more numerous than those of the human body and that the total weight of the microbiota of an average-sized man was about 1.5 kilograms. In an article published in the journal Plos Biology in 2016, these estimates have been revised downwards a bit: the ratio between microbiota cells and human cells seems to be almost equal, and the overall weight of the microorganisms lower than assumed previously. In any case, humans are colonized by many microorganisms; for every single cell of our body there is one microbiota cell inside us. So, the microbiome remains a substantial component of our body. It could be even considered a supporting organ because of its importance in promoting the correct functioning of our body.
Why Fermented Probiotic Foods Are Good for Your Health
Eating prebiotic and probiotic foods is fundamentally important to build and maintain an healthy intestinal microbiome, which in turn brings the following health benefits.
Digesting better the food we eat: for example by secreting digestive enzymes that help us with the digestion of certain nutrients which can then be absorbed by the colon walls. For example, intestinal bacteria ferment soluble dietary fiber, turning it into organic acids which serve to nourish the colon walls keeping them intact and in good health.
Synthesizing vitamins: Some vitamins, like vitamin K and some B vitamins, can be synthesized by intestinal bacteria and then absorbed, so our intestinal microbiota can help us meeting the daily recommended intakes of certain vitamins.
Producing protective substances: Gut bacteria metabolize some nutrients into other substances that may be more beneficial. Most importantly, a good intestinal microbiota produces healthy substances while fermenting soluble fiber, such as short-chain fatty acids, which are associated with a series important health benefits. For example, they prevent colon cancer locally in the intestine, and beyond the guts they have a cholesterol-lowering effect by inhibiting the synthesis of cholesterol in our liver.
Neutralization of toxic substances: The intestinal microbiota synthesizes detoxifying enzymes, which help us to neutralize or reduce the toxicity of toxic substances or pollutants that we introduce with food.
Protection from toxin infections: A good intestinal microbiota keeps other harmful microbial species away, and protects us from the risk of food poisoning caused by pathogenic bacteria thanks to competitive mechanisms. This means that when a pathogenic bacterium arrives in the intestine, before being able to develop and cause infection or intoxication, it must first “fight” with the bacteria that are already present there, which have no interest in ‘giving way’. It’s normal that some pathogenic bacteria are present in what we eat, like some Listeria or Salmonella. But luckily these bacteria normally don’t harm us thanks to the acidity of our stomach, and thanks to this mechanism of microbial competition in the intestine. The good bacteria in our guts are not welcoming the new guests and they react by fighting and killing them. This is why when we take antibiotics, which can wipe out our intestinal microbiota, we must make an effort to repopulate it quickly with our army of good bacteria by eating prebiotics and probiotics foods (potentially including probiotics supplements).
Intestinal epithelium integrity and protection from inflammation, allergies, and autoimmune diseases: Healthy microorganisms adhere to the walls of the colon, nourishing it and maintaining the integrity of the intestinal epithelium. This helps prevent harmful substances from entering the bloodstream. These substances, such as viruses, bacteria and toxins, trigger inflammatory responses within our body, and activate the immune system, increasing the risk of allergies and autoimmune responses. Many important diseases, such as cardiovascular, diabetes, and cancer, have an important inflammatory component. Clinical evidence shows that probiotics can reduce systemic levels of subclinical inflammation.
Strengthening the immune system: A good intestinal microflora helps us stimulate our immune defenses by acquiring information from the surrounding environment and passing it on to the immune system. Bacteria, in fact, exchange information with each other through exchanges of genes and plasmids. In this way, the bacteria that live in our intestines acquire information from those passing by through the exchange of a few pieces of DNA, and then in return they instruct our immune system.
Promotion of intestinal transit: An healthy intestinal microflora produces microbial biomasses that favor intestinal transit. By increasing the volume of feces they accelerate its passage, thereby reducing the contact time with the intestinal walls, which is a risk factor for colon cancer.
Protection from the risk of intestinal tumors: In addition to optimizing intestinal transit, a good microbiota protects against the risk of colon cancer through the production of protective substances such as butyric acid, nourishing and keeping the intestinal epithelium healthy and intact, and neutralizing potentially toxic substances.
Body weight control: A healthy intestinal microflora produces substances that help regulate the feelings of hunger and satiety, and molecules that regulate the way fat is deposited in our reserves. As a consequence, a healthy microbiota contributes to prevent overeating and fat accumulation.
Stress reduction: A recent research study indicated that eating more fermented foods and more fiber daily can have an impact on your stress levels by reducing perceived stress after just four weeks. The study researched a so called psychobiotic diet and its impact on stress levels. Quoting from the article presenting the study findings: “The foods in focus of the psychobiotic diet included those known to influence the microbiota, namely, whole grains, prebiotic fruits and vegetables, fermented foods, and legumes while discouraging consumption of “unhealthy” foods such as sweets, fast food or sugary drinks.”
What is food fermentation?
Bacteria are responsible for example for the brownish and soft patch that form on an apple when left too long in the basket, or for the white and green bloom on a lemon that was forgotten for too long in the fridge. Despite this is a somewhat macabre process of rotting decomposition, this same process is the basis of the production of a large variety of foods. In such cases, instead of talking about decomposition, we use the term fermentation. But in essence the process is the same, with the exception that in fermentation the decomposition is controlled and stopped at the right time.
About two third of the foods we eat are the result of fermentation. It is thanks to this controlled decomposition of plants or animal foods that we can radically transform foods, here are some examples of transformations done by fermentations:
- Grapes are turned into wine
- Barley into beer
- Wheat into bread
- Milk into yogurt or in kefir or cheeses
- Pork into ham or salami
- Wine into vinegar
- Tea into kombucha
- Soy into tempeh, natto, miso, or in soy sauce
- Tomato into ketchup
- Taro into Poi
- Teff into Injera
- Fish into a number of fermented fish sauces such as Bagoóng, Budu sauce, Cincalok, Garum, Worcestershire sauce
To learn more, see this comprehensive list of fermented foods on Wikipedia.
In probiotic foods, for example in fermented vegetables like sauerkrauts or pickles, the beneficial microorganism that produce the fermentation are normally present in the final product, bringing the probiotics health benefits that we described above. This is normally the case when these fermentations are hand made at home. For industrially produced foods, however, the process of pasteurization unfortunately kills all the microorganism, including the good ones. Therefore when you buy sauerkrauts or pickles in the supermarket you can assume that normally they don’t have a probiotic effect.
In some organic supermarket, however, you can buy fermented vegetables that are also probiotics, in this case you should look specifically for the indication “unpasteurized” in the food label. The same problem may occur with other fermented foods that one may think to be always probiotic, such as kombucha, the nice sparkling fermented drink whose popularity is currently on the rise. If you want to buy a kombucha that still has the health probiotics bacteria in it, you have to search for it in the fridge and best if it has “unpasteurized” written in its label.
In the pictures below you can find some examples of fermented probiotic foods, beyond the well known yogurt (click the images to enlarge):





The Hidden Benefits of Fermented Foods
Not all fermented foods are probiotics.
In many cases fermentation is only a stage of the food production process in which at the end the microorganisms that drove the fermentation are no longer there. An example is bread that is produced with yeasts that ultimately die in the oven during the cooking, another example is the production of alcohol in wine, beer, or cider, in which at the end the yeasts that produced it die intoxicated by their own alcohol.
Even when fermented foods don’t have a probiotic effect, fermentation offers a range of advantages. In the first place it helps preserving longer otherwise perishable foods, which was very useful in the past when there were no refrigerators or pasteurization. In fact, virtually all cultures in the world have traditional fermented products made with local ingredients.
Fermentation also allow to create a more intense aromatic and gustatory profile than the starting product, for example by freeing ketones from lipids, small peptides from proteins, or forming acids or alcohol. Halfway between fresh and putrefied there is a whole range in which we can create the most delicious flavors.
Fermentation also have strictly nutritional advantages, for example it often makes the starting food more digestible by pre-digesting proteins, carbohydrates, and lipids in smaller molecules that are then easier to digest and absorb. It often eliminates anti-nutrients such as phytic acid from cereals and legumes, or oxalic acid from vegetables. In some cases it even eliminates toxic substances, for example ammonia.
Fermentation can also eliminate substances that can cause intolerances, for example consuming lactose in yogurt or cheese. In addition, fermentation can add proteins that come from the biomass of the microorganisms that multiply during the process.
Fermentation also produces vitamins, especially those of group B. For example beer has more vitamin B and more proteins than the starting barley, or vitamin C is formed when cabbage if fermented to make sauerkraut. Fermentation can also produce potentially useful enzymes such as nattokinase in natto, which is a fibrinolytic enzyme that helps to keep the blood fluid, or anti-cancer isothiocyanates such as sulforaphane in kimchi, starting from glucosinolates that are present in cabbage.
Why You Should Care About Repopulating Your Microbiota
The terror of microbes that the industry has inculcated in our minds is oversized and has led us to confuse the concept of microorganisms with that of pathogens. The bacteria that hurt are only an infinitesimal fraction of the bacteria that live around and inside us, and by trying to get rid at all costs of those few bacteria who hurt us we ended up eliminating also all the others that instead are needed for our health, without realizing that eating “sterile food” can create more risks than benefits for our health.
After the invention of pasteurization just over a century and a half ago, and other techniques of sterilization and food preservation, the food industry declared an absurd war on microorganisms, embracing the idea of eliminating as much as possible any form of micro organism from their products to preserve foods longer and eliminate any presumed risks of food poisoning. In doing so, food companies can also use scarcer starting products and worry much less about hygiene throughout the production process, because in the end everything is pasteurized or sterilized so all bacteria will die anyway. This paradigm has inculcated in us, the consumers, a perverse idea of hygiene for which any microorganism is seen with suspicion fear and must be kept away. Some people boil everything or disinfects vegetables with disinfectant because of fear of bacteria.
In the last two centuries, the science of nutrition has focused almost solely on how to feed the small intestine and therefore prioritized the concept of calories and macro nutrients such as carbohydrates, proteins, fats and micro nutrients such as vitamins and minerals, but it has forgotten that we must also nourish our colon. And for this you need fiber and healthy live bacteria in the food you eat.
Most people base their diets on super refined industrial products that are then pasteurized or sterilized. This diet only feed the small intestine with nothing left to nourish the the colon. Exposure to microorganism serves to develop the immune defenses by training them to distinguish the good from the bad ones. This sterilized nutrition is correlated to an unprecedented amount of allergies, intolerances, asthma, dermatitis, and autoimmune diseases. Although human beings have been eating cereals for 10,000 years without problems, celiac disease cases are skyrocketing in recent times, despite we are actually eating less cereals compared to the past because of the more varied diets we have today. Researches hypothesize that this may be linked to the war on microbes declared in the last century that changed our intestinal microbiota.
In general, developed countries have matured the idea that bacteria are associated with disease and therefore are something that must be fought and kept away at all costs. In reality, less than one percent of the germs that surround us are pathogens that cause diseases. In fact, the leading causes of death in our industrialized countries such as cardiovascular disease, cancers and diabetes have nothing to do with bacteria.
Actually, healthy bacteria can protect us even when they are still in food. In fact, if by mistake a pathogenic bacterium arrives in a sterile product, then it finds a free field in which it can proliferates easily. On the other hand, if the same bacterium arrives in a food that is full of other healthy bacteria, then it must compete with an army if it wants to proliferate. For the healthy bacteria this is an easy war to win.
The same happens in our body. As mentioned before, the food we eat every most likely contains some listeria or some salmonella, but we do not even notice it because our resident microflora fight it out immediately, preventing them from multiplying and progressing with an infection.
The reckless use of broad-spectrum antibiotics used for every little problem has led to the weakening of our defenses, killing our microbiome, and to a serious antibiotic resistance. This does not end up in the news every day but is already a catastrophe. In Europe there are 35.000 annual deaths from antimicrobial resistance, in other words people die simply because they arrive at the hospital and there is not a single antibiotic that works for them. This is something completely unthinkable only 20 years ago.
Our intestinal microbiome has changed more in the last 150 years than in the last 10 thousand years. Now, many health conscious people are realizing how urgent it is to repopulate our intestines with good bacteria by including fermented probiotic foods in their daily eating routines.
Our intestine is a garden that needs to be taken care of. The best way to approach our intestinal gardening is to make sure to include in your daily eating routines both prebiotic foods, typically high fiber foods, and probiotic foods such as yogurt, kefir, tempeh, kimchi, miso, fermented vegetables (like sauerkraut and pickles), and kombucha.