The microbiome – a significant element at the intersection of human genome and the environment

The work carried out in the Human Microbiome Research programme (HUMI) ranges from Parkinson's disease to inflammatory bowel disease and antibiotic resistance. Faecal microbiota transplantations are only the beginning – a great deal is expected of microbiome research in the coming years.

In the past, medicine considered the only good bacteria to be dead bacteria. Today it is understood that the lack of appropriate bacteria can also cause diseases.

Knowledge is steadily increasing. Through the efforts of seven research groups and approximately 60 researchers, the Human Microbiome Research programme of the Faculty of Medicine is expanding knowledge pertaining to bacteria and other microbes that affect health.

Not only does knowledge increase but it also changes the treatment and diagnostics of diseases. Among other things, the programme is investigating the effect of the environment and lifestyle choices on microbiomes and the spread of antibiotic resistance, as well as explaining the mechanisms with which microbiomes and individual microbes influence diseases.

What is the exact basis of the therapeutic effect of faecal transplantations? Can multiresistant bacteria be eliminated with bacterial viruses, also known as phages? Which biomarkers of bacterial origin could predict secondary allergies in babies or identify latent metabolic or neurological diseases in adults?

The researchers are interested in both the normal human microbiome as well as pathogens, which are investigated in relation to, among other things, infections, skin diseases, inflammatory bowel disease, irritable bowel syndrome, cervical cancer and obesity.

In addition to identifying the relevant associations, the aim of the programme is to scrutinize the causal relations and mechanisms of host-microbe interactions in medical microbiome research. This will increase understanding of the causes of the etiology diseases. Above all, new avenues to promoting health through microbes will be opened.

“A lot of anticipation related to microbes is also directed at early diagnostics, treatment responses and progression prognoses,” says Docent Anne Salonen, deputy director of the research programme.

Attempts are being made to improve all of the above in the case of Parkinson’s disease, among others. It may even result in the ability to stop the progress of the disease.

Like a new planet

Anne Salonen says that the knowledge gained on the existence of the human microbiome and its characteristics through the latest research techniques has been compared with the discovery of a new planet.

In search for explanations for diseases, it is now understood that the microbiome is a significant element at the intersection of host genome and environmental factors. Taking this into account is now an established element of biomedical research aiming for personalised medicine.

“Previously, it was thought that the lower part of the gut was only a waste-disposal unit. Now its microbiome is equalled with an organ that has a central effect on our physiology,” Salonen says.

“It’s becoming difficult to identify a disease without a connection to the gut microbiota. The effects are not limited to the gut, but extend all the way to neurological diseases. The bacteria on the skin, in the airways and the birth canal are also an important factor in, for instance, the regulation of mucosal immune responses. And microbes produce metabolites which travel from the gut to both the central nervous system and the liver. These are the things we are trying to understand,” she adds.

Bacterial therapy on the horizon

Not much can be done for gene defects in humans. In contrast, what makes individual microbiomes exceptional is that they can be modified even in adulthood and therapeutically transplanted easily from one person to another.

For the time being, the only microbiota-based therapy approved for clinical use is faecal transplantation in the case of antibiotic-associated diarrhoea. The efficacy of this therapy is almost 100%. A number of therapeutic trials are ongoing on treating other diseases with faecal transplantations, as well as on phage therapy.

Salonen believes a lot will happen in microbiome research in the coming years. The research will generate novel tools for managing both infectious and chronic diseases. Bacterial therapy is one such concrete research result.

“We will certainly see new kinds of bacterial therapy products that are fervently being developed to fill the gap between faecal transplants and traditional probiotics. Researchers and rapidly expanding business in the field are developing live biotherapeutics — single or multi-strain bacterial cultures, also known as next generation probiotics. In the pipeline are products that affect mental health or diseases associated with obesity.”

Salonen believes that microbiome research can make an important addition to the currently used data sources for predicting complex traits in biomedicine. In the future, the analysis of the microbiome will most likely become part of a range of diagnostic tests.

When data on the microbiome, genes, laboratory measurements and the patient’s history are combined with the help of AI solutions, latent links will be identified which can be used to classify people for risk assessment and therapeutic choices.

To the mainstream

DNA sequencing was broadly adopted in microbiome research roughly 10 years ago, something which Salonen compares to opening the curtains. Computing has advanced to analysing large datasets.

For example, microbiome specimens collected from birth cohorts and electronic data collection make it possible to carry out extensive longitudinal studies on the causes and consequences of microbial variation.

Last year, big news was heard in the field of microbiome research. According to several articles published in the Science journal, the gut microbiome has an effect in the treatment efficacy of cancer.

“Even the last holdout was finally convinced of the importance of the microbiome. I don’t think anyone still thinks that microbiome research is a marginal field,” Salonen says.

What Salonen, a microbiologist by training, finds most interesting in microbiome research is its multidisciplinary nature. There are specialists of various medical fields, nutritional scientists, microbiologists, biochemists and computer scientists involved.

Despite different background, everyone in the research groups and the programme must find a common language and learn from each other.

“We really are on the cusp of something big. Breakthroughs will be made in my research or that of my colleagues. We will find new bacteria, good or bad, and describe the mechanisms through which they impact human physiology. It’s fascinating how we get gradually closer to the truth by piecing together complex matters,” says Salonen.

The Research Pro­grams Unit of the Fac­ulty of Medicine

The Research Programs Unit (RPU) of the Faculty of Medicine is a high-level research community.  An international scientific advisory board evaluates and selects the research programmes and groups through a competitive application procedure every four to six years. RPU director is Associate Professor Henna Tyynismaa.

The current Research Programs are the following (until the end of 2025):