Monday, 11 July 2022 13:46

How and why SPRINT are studying microbiomes Featured

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In the past year, we have gathered hundreds of samples across the SPRINT case study sites (Click here for more information). Many of these samples will be used in microbiome analyses, including: soil samples, gut samples from fish, fecal samples from humans and livestock, and nasal swabs from humans. We will analyse the composition of microbes in these samples. All of these samples contain millions of bacteria, fungi and other micro-organisms, which in combination, are called the microbiome.

Healthy microbiomes are important!
Whilst we all know pathogenic micro-organisms can be very harmful for plants, animals and humans, most microorganisms are not harmful or are even beneficial for our health. A diverse, balanced soil microbiome is important for plant growth, plant health and also resistance to stressors, such as drought, heavy metal pollution and parasitism. The soil directly surrounding the roots of plants is called the ‘rhizosphere’. Beneficial microbes in the rhizosphere form symbiotic relationships with the plant. The plant produces food for the microbes, while the microbes convert and hold on to nutrients in the soil, in their turn feeding the plant. Some microbes even act as antibiotics and secrete chemicals that kill pathogenic bacteria in the soil, thus, protecting the plant against diseases (1, 2).

A healthy gut microbiome is also important for humans and animals for some of the following reasons:

  • A disrupted gut microbiome can contribute to the pathophysiology of many diseases, including: cancer, obesity, coronary heart disease, diabetes, dementia, allergies, inflammatory bowel disease, autoimmune disorders such as multiple sclerosis (3), and mental health (4).
  • Helping us digest fibers and producing essential vitamins B and K (5).
  • Playing a role in resistance to pathogens. If you have a healthy microbiome, all bad bacteria entering your gut, for example via your food, have to compete for food and space with the good bacteria. Now imagine if there are no good bacteria in your gut. Suddenly the bad ones have a far easier job colonizing your gut and making you ill!  (6)

While the gut microbiome is heavily studied, other organs such as your skin (7) and your respiratory system (8) are also colonized by microbes. Again, most of these microbes are not harmful for you, and might even have beneficial effects, for example by preventing colonization by pathogens (9).


Maaike_Blog_P2.png.jpgAPC Microbiome Ireland

Why is SPRINT studying microbiomes?
The importance of microorganisms for our health has been gaining attention over the past couple of decades. Before this, we used to think ‘the cleaner, the better’. Now, we are starting to understand that damaging the microbiome can have detrimental effects on animal and human health. The effects on plant health are still largely unknown.

Several pesticides have been shown to have a disruptive effect on the microbiome, including glyphosate, chlorpyrifos, permethrin, pentachlorophenol, epoxiconazole, carbendazim and imazilil (3, 10). While most of these products (besides Glyphosate, 11) are no longer approved for commercial use in Europe, the effect of many other pesticides on (beneficial) microorganisms is less well studied. Therefore, it is important that SPRINT further explores the effects of current pesticide use on soil microbiome, animal microbiome and human microbiome, so we can advise farmers and policy makers to adapt pesticide use in a way that is safe for beneficial bacteria both in the soil and in our guts.


CSIRO, Australia Microbiome – To showcase capability in the Microbiome science capability. (

How are we studying the effects of pesticides on the microbiome?
Soil samples were taken at each of our case study farms. In the lab, the DNA of the microbes in the sample can be extracted. From this DNA, we can reconstruct which microbes were present in the sample; we can create a microbial composition profile for each sample. By comparing the samples from all the farms, and combining this with the collected data of pesticide use at each farm and pesticide residues found in the soil, we can identify soil bacteria that might be sensitive to specific pesticides. Similarly, faeces samples from animals at the farms have been collected and analyzed.

At each farm, one man and one woman from the household were asked to provide information on their health and to donate a fecal sample and a nose swab. Neighbours (living close to one of the farms) and consumers (subjects living further away from the farm, whom did or did not express a preference for organic food) were also asked to provide these samples. Again, the DNA from the fecal samples and the nose swabs was isolated, leading to a compositional microbiome profile for each sample. Also, urine, blood and stool samples were tested for pesticide residues.

This has provided us with a large and very complex dataset. By combining the data on pesticide use on the farms, pesticide residues found in human stool, urine and blood samples, and the microbiome profiles, we aim to identify gut or nose bacteria that might be sensitive to specific pesticides. Combining this information with the provided health data and with existing literature, we hope to unravel how potential shifts in the human microbiome, caused by pesticides, can affect human health. 

After identifying bacteria that appear to be sensitive to pesticides, we will, where possible, validate these findings in the laboratory by culturing these bacteria and monitoring their response when we expose them to the pesticide.

Take away message
Not all microbes are bad! Humans, animals, plants and soil all need a healthy microbiome in order to stay healthy. We do not yet know enough about the potentially detrimental effects of some pesticides on the microbiome. In SPRINT, we are gathering a lot of data to investigate this further. The results of these studies will be integrated in a toolbox which will help farmers and policy makers make decisions on pesticide use that reduce the impacts of their use on plant, animal, environmental and human health.

Further reading

1. Pathogen suppression by microbial volatile organic compounds in soils
2. Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens
3 The gut microbiota: a major player in the toxicity of environmental pollutants? - PubMed (
4 The role of inflammation and the gut microbiome in depression and anxiety - Peirce - 2019 - Journal of Neuroscience Research - Wiley Online Library
5. Gut microbiota functions: metabolism of nutrients and other food components - PMC (
6. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them - PubMed (
7. The human skin microbiome | Nature Reviews Microbiology
8. The microbiome of the upper respiratory tract in health and disease | BMC Biology | Full Text (
9. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them - PubMed (
10. Effects of environmental pollutants on gut microbiota - ScienceDirect
11. Glyphosate (

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