Scientific Foresight (STOA) By / February 10, 2022

What if we killed all microorganisms in our bodies? [Science and Technology podcast]

It is possible to raise animals completely free of microorganisms (i.e. bacteria, viruses, fungi and parasites).

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Written by Gianluca Quaglio with Virginia Mahieu.

While killing all microorganisms in our bodies may seem tempting to some germaphobes, scientific evidence indicates that beneficial microorganisms (that live in nearly ubiquitous communities called microbiota) are an essential component of human health, and could form a new frontier for personalised medicine to fight non-communicable diseases and improve human health.

It is possible to raise animals completely free of microorganisms (i.e. bacteria, viruses, fungi and parasites). These ‘germ-free’ animals can survive (with supplementation of vitamins), but show marked differences in health and development, such as abnormal digestion, metabolism, respiration and circulation, as well as behavioural and neurological dysfunction.

These models make it possible to study the interplay between human microbiome (all microbiota in the body) and host, revealing some interesting and perhaps unexpected links.

The microbiome is essential to human life in many ways, including not only digestion, but also hormone regulation and the immune system, and even mental health. Humans and our microbiomes are an example of a symbiotic relationship: we provide them with shelter and food, and they provide us with many ‘services’ in return.

The microbiota in our gut feed on prebiotics (a group of nutrients that are degraded by gut microbiota) such as dietary fibre – a substance commonly found in cereals, vegetables and nuts – that we cannot digest. In return, they break down essential nutrients and they help keep infections at bay. In addition, the microbiota have been shown to be a key regulator of the gut-brain axis, and thus the microbiota-gut-brain axis has been proposed.

Probiotics (foods and supplements containing specific microorganisms that can contribute to health such as yogurt, miso and kefir) are gaining increasing popularity, not only for increasing general wellbeing, but also for treating a number of medical conditions.

Potential impacts and developments

Diet, physical activity, medical treatments and environmental factors can all affect our microbiome. There is indication that the human microbiome could be detrimentally impacted by societal changes of the past few decades, especially in terms of nutrition, lifestyle and the use of antibiotics. It is increasingly plausible that a substantial rise in a large host of non-communicable diseases (NCDs) could be at least partially attributed to changes in our gut microbiome. As NCDs currently represent over 70 % of global deaths, these place an enormous burden on healthcare systems and economies.

At least partly responsible for this rise in NCDs may be a shift in the consumption of fresh versus processed food, and an increased use of food additives such as emulsifiers and artificial sweeteners. In the USA, a country with one of the highest rates of obesity in the world, healthier food is markedly more expensive and often less readily available.

Some doctors are now prescribing probiotics as medical treatment for gastrointestinal conditions and allergies, but their full health potential is not yet widely demonstrated or recognised by the medical community. In fact, pending a deeper biological understanding and wide-scale clinical trials, probiotics could have the potential to treat other conditions such as obesity, hypertension, diabetes mellitus, rheumatoid arthritis, respiratory tract infections, and several other pathologic conditions. Perhaps most intriguingly, gut microbiota can influence brain physiology and pathology via the ‘gut-brain axis‘ and treating dysbiosis could in some cases influence anxiety and depression, as well as multiple sclerosis, Alzheimer’s and Parkinson’s diseases. Probiotics are even being suggested as an alternative to chemical disinfectants in hospitals.

Antibiotics, though effective at killing pathogens, can also kill some of the ‘good bacteria’ in our gut. The balance of the microbiome is delicate, and shifts in that balance can leave space for flare-ups of certain types of bacteria that, while helpful in small quantities, may not be good in larger quantities. Misuse and abuse of antibiotics can therefore have several potential side-effects.

Furthermore, persistent and excessive prescription of antibiotics can lead to antimicrobial resistance (AMR), meaning that we increasingly have to resort to more potent broad-spectrum antibiotics. Deaths from multi-drug resistant (MDR) bacteria accounted for more than 33 000 deaths in Europe in 2015. Recent research suggests that the future combat against AMR may involve probiotic-based approaches.

In short, killing infectious bacteria is important, but it can damage the balance of the human microbiome. If this is not prevented or managed it can ultimately lead to health problems in itself. There is evidence that taking probiotics can mitigate some of the side effects of antibiotics. Furthermore, probiotics could become part of a more personalised form of medicine in which treatments for a range of conditions are adapted based on the composition of the patient’s microbiome. They could open a path for preventing certain NCDs, and they could reduce the need for antibiotics in healthcare (both as medical treatment and as disinfectant).

Anticipatory policy-making

To safeguard the future of public health, we need to respect the ‘invisible’ microorganisms that live with us and are currently largely ignored or even unknowingly harmed. Though their role is becoming increasingly evident, there is currently no EU guidance, legislation or regulation on microbiomes in the context of human health.

Furthermore, EU food law does not yet contain any provisions for evaluating the safety or composition of probiotics in food, or how our food processing or intake can affect the human microbiome. The European Food Safety Authority (EFSA) is currently investigating the scientific evidence on microbiomes and working to integrate it into regulatory assessments.

There are major limiting factors for research into the potential applications of probiotics in healthcare and general wellbeing, so many health claims are currently associated with a lack of a clear causal pathway. Probiotic products can be subject to fad marketing and hype, so without proper governance they can lack credibility and quality control.

In addition, there is a need for new microbiome-oriented diagnostic tools in medical care. For the potential benefits of targeting the microbiome to reach society, the EU should consider standardisation, protocols, and a regulatory framework to support research and innovation. This research is essential to further understanding the processes that underlie the human microbiome and how to treat it.

The health of the microorganisms in our bodies and our food goes hand in hand with the health of the planet. A better understanding of the role of microorganisms in soil and in the ocean could also contribute to sustainable agriculture and plant protection by improving crop yields and reducing the need for pesticides. They could also contribute to a circular economy through improved waste degradation, helping to mitigate pollution and closing gaps in the production chain. As such, they could contribute to the successful achievement of several of the United Nations Sustainable Development Goals (SDGs) as well as the EU circular economy action plan, and the European Green Deal.


Read this ‘at a glance’ on ‘What if we killed all microorganisms in our bodies?‘ in the Think Tank pages of the European Parliament.

Listen to policy podcast ‘What if we killed all microorganisms in our bodies?’ on YouTube.


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