More friend than foe? Linking food microbiome and human health

Humans are constantly exposed to different food-associated bacteria depending on the types of products they consume. Even though some bacteria may be pathogenic, recent research has taught us that a healthy balance of diverse bacteria is beneficial to us.1 While unpleasant odor and taste may speak for rotten food and the potential of toxic compounds, the good bacteria are not so easy to observe. However, there is an increasing amount of knowledge about the micro-organisms that are needed to sustain good health.

Hands, plants

Picture 1. Plants we consume include billions of microbes.

When it comes to the microbiome of food, most of our knowledge concerns probiotic sources such as yoghurt and other fermented food. However, a considerable share of the plants on our plates is consumed fresh and each meal can include billions of microbes. Despite the washing or rinsing of the food surfaces, we are expected to enjoy many bacteria with our food. Given that traditional food has not been much processed and sterilized before eating, the intake of various bacteria can be seen as a natural part of our diet throughout human history.1

How does our food influence our health? The microbiota describes the range and composition of microorganisms in our body. When a healthy balance of microorganisms in their hosts exists, the microbiota is stable. The microbiota in the human gut serves many beneficial functions like metabolites production, detoxification, defense against pathogens, and help in the development of the immune system. Conversely, dysbiosis, an altered symbiosis of the host and the microbiota, is associated with various diseases such as inflammatory bowel disease, obesity, allergy, and autoimmune diseases.2

The plant microbiome and microbial diversity are important for humans as it contributes to the diversity of the gut microbiome and acts as a stimulus and aid for our immune system’s responses, most microorganism are primarily received through edible plants, especially unprocessed ones. Bacterial diversity and immune-mediated diseases are likely to have a correlating association. The diversity also affects the anti-inflammatory markers that play a key role in maintaining immunologic tolerance to harmless substances – some of the bacteria are known to have a protective effect against allergies as well as potential for immunomodulatory actions.1

Washing plants

Picture 2. Despite cleaning or rinsing the food surfaces, the intake of microbes is still expected.

Early life matters…

The bacterial colonization takes place already during in-utero period, but the gut microbiota is established after birth. The two big steps are during the breastfeeding phase, followed by the weaning period when the introduction of solid foods begins alongside breast feeding. Breast milk is known to contain as many as 600 different bacterial species making it technically unsterile. This said, the newborns are exposed to multiple bacteria, and it is only good news, since this ‘critical window’ period is needed in the creation of gut microbiota and is associated with immune system development. Disturbances in this process have been shown to cause food allergies, atopic dermatitis, and asthma.2

Even though sometimes necessary, antibiotics may also have a negative impact on the gut since they may cause perturbations in the microbiome. Some epidemiological data are indicating that early life antibiotic use can increase the risk of immune-mediated diseases like asthma, atopy, and even type 1 diabetes. This is likely to happen as the antibiotics are known to cause temporary alterations in the microbiota, which can negatively impact the immune system and onset of allergies. Many researchers have presented the association of lifestyle and gut microbiology in the frame of the hygiene hypothesis, which we introduced in a previous blog post. The importance of the relationship between the dietary microbiota and health is also supported by the hypothesis.2

…but changes can be done later, too

There is a wide documentation of differences in gut microbiota composition in individuals with vegan and vegetarian diets compared to those with omnivorous diet. While only a marginal difference in gut microbiota between vegans and vegetarians exists, omnivores are known to have significant differences in their microbiota composition.3

What are the components causing the difference? Studies suggest that there are three basic bacterial enterotypes; genus Prevotella, genus Bacteroides and genus Ruminococcus. Prevotella is associated with anti-inflammatory functions and protection, and it appears to be significantly more frequent in those following a plant-based diet. Prevotella has also been exclusively present in African children who consume a diet low in fat and animal protein as well as rich in starch, fiber, and plant protein. Interestingly, those children living on a Western diet with high consumption of animal protein, sugar, starch, and fat, but low consumption of fiber, have less abundance of these bacteria.3

Long-term dietary patterns do have a considerable influence on gut microbiota composition. Research findings suggest that a vegan diet together with lower body weight potentially increase microbial diversity and consequently protect against inflammation.3

Picture 3. Food microbiome is a remarkable part of the exposome, particularly because it affects the composition of gut microbiota. (Picture source: Microbiome & Health (

A deeper look at the gut’s inside gives us a hint of the diets’ impact on our health. Consumption of fruits, vegetables, and legumes seems to help the creation of microbial metabolites, such as short-fatty acids, propionate, and butyrate. One does not need to be on a fully plant-based diet to increase their short-fatty acid levels, which are associated with an improved immune system. A Mediterranean diet might be enough for this, since it is rich in fruit, legumes, and vegetables. Intake of these, however, is important for the gut to produce vitamins such as K, B9, and B2. Due to a greater intake of plants, vegans show a greater enrichment of B9-vitamin (folate) biosynthesis in comparison with non-vegans. Also, a microbial metabolite called Trimethylamine N-Oxide is believed to be linked with cardiovascular and neurological diseases and is mostly found in animal-origin products (pork, beef, eggs). Research shows that increased vegetable consumption lowers the levels of this metabolite.3

In conclusion, vegetarian or vegan diet is considered beneficial in creating a diversified ecology of helpful bacteria to support both the human gut microbiome and general health.3 However, the way of cultivation also matters. Crops grown intensively in mass agriculture are frequently characterized by a decreased microbial diversity compared to crops grown organically or in natural ecosystems. Since microbial diversity is crucial for human food and health, we should take care of both soil- and plant-associated ecosystems and biodiversity and use sustainable ways of food production to protect our and future generations’ health.1

HEDIMED contributes to food microbiome research

Among other issues, our work considers the food microbiome as part of the exposome.  During early life, introduction to external exposures such as the consumption of solid foods can contribute to the development of the gut microbiota. Fruits and vegetables are among the solid meals that are often taken during early life, making them essential parts of a healthy human diet. So far, our research has shown that the processing of certain food products can affect microbiota, thus affect the intake of different bacteria. Apple fruits with a high bacterial diversity and abundance have been shown to reform depending on the way of processing. While drying and boiling do not eliminate all the indigenous bacteria from the fruit, the microbiota might be affected by heat and mechanical processing.4 If we become more aware of the microbiota that we expose our children to, this kind of knowledge is worth considering!

Want to learn more about microbiome and health?

Get familiar with a MOOC course ‘Microbiome & Health’ by our partner Graz University of Technology : Microbiome & Health (


The background information for this blog blogpost was provided by Wisnu Wicaksono. It was drafted and written by Henna Numminen with edits by Daniel Schmidtmann and Wisnu Wicaksono.

Pictures from Pexels and Pixabay.


  1. Berg, G., Erlacher, A., & Grube, M. (2015). The edible plant microbiome: importance and health issues. In Principles of plant-microbe interactions(pp. 419-426). Springer, Cham.
  2. Tanaka, M., & Nakayama, J. (2017). Development of the gut microbiota in infancy and its impact on health in later life. Allergology International66(4), 515-522.
  3. Tomova, A., Bukovsky, I., Rembert, E., Yonas, W., Alwarith, J., Barnard, N. D., & Kahleova, H. (2019). The effects of vegetarian and vegan diets on gut microbiota. Frontiers in nutrition6, 47.
  4. Wicaksono, W. A., Buko, A., Kusstatscher, P., Sinkkonen, A., Laitinen, O. H., Virtanen, S. M., Hyöty, H., Cernava, T. & Berg, G. (2022). Modulation of the food microbiome by apple fruit processing. Food Microbiology108, 104103.

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