As the world continues to be affected by COVID-19, let’s take a moment to reflect on viruses within the microbiome.

By Bettina Schelkle, EUFIC.

Viruses are one of the many micro-organisms that are naturally present in microbial communities (a.k.a. microbiota). SARS-COV-2, the virus which causes COVID-19 in humans, is part of the microbiome of an animal: most likely bats, although this has yet to be confirmed. The virus has successfully managed to jump from its natural animal host, in which it does not cause disease, to humans in which it can cause quite severe health problems leading to death. Scientists call infectious diseases caused by pathogens that jump from animal hosts to humankind zoonotic diseases.

SARS-COV-2 is not the only virus known to humanity that is zoonotic in origin. HIV, which causes AIDS in humans, originated from apes. Malaria is caused by a parasite which gets transmitted to humans via mosquitos. Toxoplasma gondii is a microbe that is common in cats and when transferred to humans causes toxoplasmosis which can cause flu-like symptoms and is dangerous for pregnant individuals.

Common to these pathogens in humans is that none of them cause disease in their original animal hosts: there, these human pathogens are just part of the natural microbiota of the animals very much like our skin or gut microbiota is part of us. Indeed, the human microbiota itself contains numerous viruses most of which are actually deadly to bacteria, not us. Viruses that kill bacteria are called bacteriophages and are important in keeping the number and types of bacteria in beneficial microbial communities in check. Indeed, there is research ongoing to see whether bacteriophages can help combat anti-bacterial resistances.

With beneficial microbial communities everywhere in our food system, it is important to acknowledge that scientists may find that some microbes in the numerous microbiota in our foods and anything to do with our food production may cause disease in humans. Indeed, we know some of these microbes already: Salmonella bacteria and E. coli may cause food poisoning when food is not correctly stored or prepared. Moulds cause foods to go rotten. Given the right environmental conditions and time, harmful microbes will multiply in numbers and dominate other organisms within microbial communities. At high numbers, these natural members of the microbiota cause illnesses in human.

Key to clearly understanding not just potential opportunities of the use of microbes in the food system is to also find out potential pitfalls. CIRCLES will not just assess microbiomes for beneficial applications, but also gauge risks by looking at transmission pathways for microbes to jump from animal hosts to human handlers. By doing so, our researchers will ensure that disease outbreaks like the one we currently experience through the COVID-19 pandemic continue to be kept low and potential risks from microbiota uses in real life can be avoided whilst implementing microbial innovations in real life!