Prof. Vassillios Fanos on Metabolomics and Microbiomics

Prof. Fanos, addresses how COVID-19, AI, Big Data and the future of medicine may impact our relation with the microbiome.

An Interview with Prof. Vassilios Fanos

Article translated from the original Italian version

At the recently concluded Congress of the German Society of Internal Medicine you addressed the topic “Microbiome in COVID-19: An unrecognised player?”. What were the main take-home messages of your speech?

The microbiome plays a key role in determining our health status. Therefore, it comes as no surprise that several studies report on the role of the microbiome in COVID-19. The disease's outbreak, its course, degree of severity, response to treatment and vaccines, and its outcome can be greatly influenced by the microbiome, not only the gut microbiome, but also that of other areas.

Patients with an altered microbiome have a very different susceptibility to disease and a distinct clinical picture than patients without such dysbiosis. Even before the pandemic, there was an abundance of literature suggesting that administering probiotics to modulate the microbiota is useful to achieve or maintain a eubiotic state; not only to prevent disease, but also to treat it.

Moreover, the microbiome plays a role in the spread of the Sars-CoV-2 virus in the body, influencing the immune system. The phenomenon of “more gut in the lung” can lead to bacterial translocation, with gut bacteria colonising the lung. This disrupts the delicate balance within the lung microbiota, triggering an immune response, which in some individuals can lead to a cytokine storm, with IL-6 and IL-8 predominating. Studying the gut-lung axis can help us greatly in our clinical practice.

Could the microbiome also play a role in long COVID?

The microbiome of patients with COVID-19 differs not only from that of healthy patients, but also from patients with other forms of pneumonia. In some patients, this dysbiosis persists over a long period of time and is responsible for what is commonly referred to as long COVID. Some studies seem to link certain strains of bacteria more than others to increased vulnerability of certain organs.

By analysing the microbiome, we might be able to predict which patients are likely to suffer from the syndrome and which are not. Targeted steps could be taken to regulate the dysbiosis using probiotics to avoid the long-term effects of COVID-19. 

You frequently recommend a "microbiomic" approach to treat diseases, looking at the person as a holistic being rather than an isolated one. How can we put this approach into practice?

Metabolites in our body fluids influence our entire existence. Modern medicine is becoming increasingly aware of this fact. Studies now clearly show that we are not individual beings but true ecosystems. And the influence of the microbiome on the individual is as significant as that of the genome when it comes to our personality and susceptibility to certain diseases. The microbiome affects every human being from the very first moments of life, from the moment of conception onwards. 

However, it is essential to have data on this specific aspect for an initial evaluation of a patient. Hopefully, in the near future, we will be able to quickly examine a patient's metabolites to gain a comprehensive understanding of their microbiome. Easy-to-use and quick-to-read test kits could enable us to understand which groups of bacteria are deficient or abundant, and then intervene to restore the missing balance.

We still need time and money for research in metabolomics before we can perform a metabolic test in the emergency room or in a GP's office with a handy test kit (like the one for urine). 

Could artificial intelligence and Big Data play a role in creating a completely personalised human medicine?

Artificial intelligence is fundamental to modern medicine. It helps physicians make sense of the wealth of data and variables in order to draw conclusions.

Without the use of current and future technologies, we would not be able to gather all the available information about each individual patient and correlate it with that of thousands of other patients. Personalised medicine cannot work without the massive help of artificial intelligence in data collection and analytics.

Of course, all this has to be done in a practical way, otherwise there will be no benefit for the individual patient who presents to the GP with some symptom.

A customised treatment for each patient, like a custom-made suit from a tailor. Is this what the realistic future of medicine looks like?

In most of the diseases we encounter today, analysing environmental factors is fundamental, sometimes almost more important than genetic factors. Metabolomics plays an important role in this. In the immediate future, we aim to positively modify the microbiome to create a customised artificial microbiome, if needed, to address a specific condition and maintain health. The real revolution will come when we no longer have to wait for a cancer diagnosis before intervening, but when we can assess the health of each individual patient in advance and take all measures to prevent them from becoming ill in the first place.

References and further resources
  1. Fanos V. Metabolomics and Microbiomics. Personalized Medicine from the Fetus to the Adult. Academic Press 2016
  2. Fanos V, Pintus MC, Pintus R, Marcialis MA. Lung microbiota in the acute respiratory disease: from coronavirus to metabolomics. J Pediatr Neonat Individual Med. 2020;9(1):e090139. doi: 10.7363/090139.
  3. Fanos V, Pintus R, Pintus MC, Mussap M, Marcialis MA. Seven secrets of COVID-19: fever, ACE2 receptors, gut-lung axis, metabolomics, microbiomics, probiotics, diet. J Pediatr Neonat Individual Med. 2021;10(1):e100145. doi: 10.7363/100145.
  4. Mussap M, Fanos V. Could metabolomics drive the fate of COVID-19 pandemic? A narrative review on lights and shadows. Clin Chem Lab Med. 2021 Jul 30;59(12):1891-1905. doi: 10.1515/cclm-2021-0414. Print 2021 Nov 25.
  5. Bardanzellu F, Fanos V. Metabolomics, Microbiomics, Machine learning during the COVID-19 pandemic. Pediatr Allergy Immunol. 2022 Jan;33 Suppl 27:86-88.
  6. Liu Q, Mak JWY, Su Q, Yeoh YK, Lui GC, Ng SSS, Zhang F, Li AYL, Lu W, Hui DS, Chan PK, Chan FKL, Ng SC. Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome. Gut. 2022 Mar;71(3):544-552. doi: 10.1136/gutjnl-2021-325989. Epub 2022 Jan 26. PMID: 35082169; PMCID: PMC8814432.
  7. Fanos V, Puddu M, Mussap M. OMICS technologies and personalized vaccination in the COVID-19 era. J Pediatr Neonat Individual Med. 2022;11(1):e110114. doi: 10.7363/110114.
  8. Cortes GM, Marcialis MA, Bardanzellu F, Corrias A, Fanos V, Mussap M. Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin. Front Microbiol. 2022 Mar 21;13:856165. doi: 10.3389/fmicb.2022.856165. PMID: 35391730; PMCID: PMC8981987.
  9. Fanos V. COVID-19 and microbiota. Gut-Lung axis, metabolomics, nutrition and probiotics (in Italian: COVID-19 e microbiota. Asse intestino-polmone, metabolomica, alimentazione e probiotici). Hygeia Press, 2021