Healthier habits, healthier microbiome: RSU explores the connection

11 November 2026

RSU in the news

Research

What can we do today to improve our health by taking care of our microbiome? Could the oral and gut microbiomes help detect diseases before they show symptoms? Researchers at Rīga Stradiņš University (RSU) have already found answers to some questions, and they continue to study others: what are the differences in the oral microbiome of ancient and modern humans; what do the studies conducted so far tell us about the microbiome and depression and cancer; what daily habits can help improve your microbiome.

It is the totality of all the microbes that live in the human body. It can vary from organ to organ, so we can study the microbiome of the mouth, the microbiome of the gut, for example. There are differences even within a single body part: the microbiome on the tongue differs from the microbiome on the gums or the inside of the cheeks. The microbiome contains not just bacteria, but also viruses and fungi. Researchers worldwide have been studying the microbiome for more than 20 years.

Microorganisms can cause disease, but they can also help the body perform important functions: they participate in the processing of nutrients, the functioning of the immune system, and various metabolic processes.

Therefore, it is important for scientists to understand not only what microbes are living in the human body, but also how their overall composition and function change.

Ancient humans had a more diverse microbiome

When Alisa Kazarina, a lead researcher at the RSU Faculty of Dentistry, began studying microorganisms of ancient people during her doctoral studies, her main research material was dental calculus.

Kazarina says: ‘I studied the microbiome of people who lived in the 16th and 17th centuries by analysing archaeological human remains. I realised pretty quickly in my research that if I wanted to have any hope of finding the remains of ancient microbes, the only material that I could realistically look for them in was dental calculus. So, my archaeologist colleagues brought me ancient human calculus, and I studied what ancient human microbes were left in there and compared them to what we find in calculus today.’

The researcher used sequencing, a method that can read the genetic material of microorganisms preserved in dental calculus.

Like other studies, the work of the RSU researcher also confirmed that the microbiome of the modern human is “dying out” – its biological diversity is decreasing.

The researcher raises the question of whether these changes could be linked to so-called diseases of civilisation. The decline in microbiome diversity may be influenced by changes in human lifestyles, such as diet, environment, and exposure to microorganisms in the world around us. For example, people today are more likely to live in cities, have less exposure to natural environments, and use a variety of antibacterial products.

How the microbiome develops in childhood

Although the microbiome changes throughout life, its development during the first three years is particularly important. These questions have been analysed in scientific research by Ilze Maldupa, lead researcher and lecturer at the RSU Faculty of Dentistry.

The development of the microbiome is influenced by the very earliest life conditions: the type of birth, breastfeeding, the first foods, and the first dietary habits.

For example, babies born vaginally have a healthier microbiome compared to babies born by C-section. But regardless of how the baby is born, if the baby is exclusively breastfed afterwards (meaning fed only breast milk for the first six months), the baby's microbiome becomes more diverse and healthier compared to the microbiome of formula-fed babies.

Breast milk contains both microorganisms and substances that promote the growth of certain gut bacteria.

Thus, breastfeeding helps to shape the infant gut microbiome, supports immune system development, and facilitates endocrine, nervous system, and cognitive development.

When introducing complementary foods, a varied diet is important, in which vegetables, fruits, cereals, and other age-appropriate products are gradually introduced. These products create a more favourable environment for intestinal microorganisms than sugar-containing industrially prepared food. Ilze Maldupa emphasises that the composition should be carefully studied even in ready-made baby food: it often contains sugar even if it is indicated that it is not added.

Childhood is an important time for microbiome development, but its composition is not pre-determined for life. The microbiome continues to change throughout adulthood, influenced by diet, medications, lifestyle, and the environment.

Could microbiome research help detect diseases earlier and improve treatment?

The study of the microbiome opens up new possibilities for the diagnosis and treatment of diseases. Scientists are investigating whether changes in the microbiome could signal the onset of disease before symptoms appear, allowing for early detection and, potentially, prevention. At the same time, there are efforts to find ways to treat specific diseases by targeting the microbiome.

One such study forms part of the doctoral research conducted by Ilona Vilkoite, a gastroenterologist and doctoral student at RSU, on the relationship between the gut microbiome and colorectal adenomas, or precancerous growths of the colon.

Adenomas are growths, some of which can become cancerous over time. Therefore, their early detection and removal are an important part of the prevention of colorectal cancer.

Ilona Vilkoite compared the gut microbiome of people with colorectal adenomas and people without such formations in her doctoral research. Her findings showed that patients with colorectal adenomas had reduced relative abundance of several microbial metabolic pathways, including those involved in the biosynthesis of vitamin K₂ (menaquinone), fermentation of certain amino acids, and the production of the short-chain fatty acid propionate.

‘Our study showed that differences in both the composition and functional potential of the gut microbiome can be observed as early as the precancerous stage in the colon.

This suggests that metabolic changes in the microbiome may be associated with early processes of colorectal neoplasia.

However, further research is still needed to find out whether these changes are among the factors that contribute to the development of the disease or the consequences of existing changes,’ Vilkoite explains.

The researcher found that the composition of microorganisms differed between the two groups of study participants, as did their possible activity.

‘In patients with colorectal adenomas, we found a reduced relative abundance of six microbial metabolic pathways. So, this means that the microbiome is not only different in its composition of microorganisms, but also in its potential metabolic functions. Changes in the processes related to the formation of vitamin K₂ and propionate are particularly interesting, as these substances may play a role in the regulation of intestinal mucosal homeostasis and inflammation. However, in our study, the concentrations of these substances were not directly measured.

These findings are consistent with other international studies that suggest that dysfunction of the gut microbiome may be one of the early mechanisms in the development of colorectal cancer,’ says Ilona Vilkoite.

It should be noted that the analysis of the microbiome does not yet replace the currently used methods of screening for colorectal cancer. But these studies open the door to understanding disease development at a much more detailed level.

Alisa Kazarina, meanwhile, continued her research on the microbiome in her postdoctoral studies, focusing on periodontitis, a disease that affects the gums and the tissues that support the teeth. The development of the disease is influenced by changes in the oral microbiome and the body's inflammatory response.

Currently, the researcher is conducting a clinical study to investigate whether harmful pathogens associated with periodontitis can be controlled using a gentler approach, while maintaining the balance of the oral microbiome important for health. In the third stage of the disease, patients are usually prescribed strong antibacterial agents such as chlorhexidine mouthwash. It can cause noticeable side effects, including changes in taste and dark staining of the teeth. And, in the long run, along with the bad bacteria, it kills off the good ones that are necessary for health. It can have negative consequences for health in general. For example, bacteria in the mouth reduce dietary nitrates to form nitric oxide, a very important signalling molecule that helps maintain cardiovascular health. If these bacteria are destroyed, the amount of nitric oxide in the body drops, and this can cause blood pressure to rise.

Kazarina is investigating whether the treatment could be changed to a mouthwash with essential oils from medicinal plants grown in Latvia.

‘We tested coriander, caraway, and chamomile, but it was the coriander oil that made it to the clinical trial with patients. The coriander grown in Latvia, which is cultivated by the Institute for Environmental Solutions, has a unique chemical composition that allows it to effectively limit harmful pathogens while maintaining the balance of the oral microbiome important for health,’ emphasises the researcher.

She also addresses another question: could changes in the oral microbiome help detect periodontitis earlier? Periodontitis can progress for a long time without any obvious symptoms, so patients often only go to the doctor when more serious tissue damage has already occurred. A second area of her research therefore focuses on how to study the oral microbiome so that we can use it as a tool for early diagnosis. Certain changes in the microbiome might be detectable early enough to prompt people to seek medical advice and potentially reduce their risk of developing certain diseases. In addition, analyses of the oral microbiome could also serve as a tool for monitoring the effectiveness of treatment, allowing for the follow-up of microbiome changes during and after therapy.

Does the gut microbiome affect depression and anxiety?

There is also increasing research into the link between mental health and the gut microbiome. You may have heard of the gut-brain axis, which is the way that scientists refer to the communication between the gut and the brain. The brain influences gut function, while processes in the gut may affect brain function and our wellbeing. This communication involves the nervous and immune systems, as well as hormones and substances produced by gut microbes.

Alise Stugle, a graduate of the RSU Medicine study programme, who is currently a resident doctor in psychotherapy, analysed scientific literature on the possible role of the gut microbiome in the development of depression and anxiety in her final research paper. Here are some of the findings from the research.

Stress hormones can alter gut motility and permeability, and changes in the gut microbiome may be linked to the body’s stress response.

Studies have shown a possible link between the gut microbiome, inflammatory processes, and symptoms of depression or anxiety. An imbalanced microbiome can decrease neurotransmitter production, increase inflammation and oxidative stress.

It has also been shown that beneficial dietary habits may be associated with a lower risk of anxiety and depression, by influencing the composition and functional activity of the gut microbiome, as well as reducing inflammation.

Scientists have found that patients with depression often have lower levels of certain groups of bacteria, including Firmicutes involved in short-chain fatty acid (SCFA) production. SCFA deficiency can weaken the gut barrier, increasing permeability and inflammation. SCFA have anti-inflammatory effects that help maintain the integrity of the intestinal barrier and reduce symptoms of depression.

Scientists are also studying the interaction of microbes with substances that transmit nerve signals and hormones that affect appetite, mood and stress regulation.

Stugle admits: ‘Currently, the therapeutic options that target the gut microbiome are relatively few.

There is a growing body of research in the literature on psychobiotics. Psychobiotics are agents that aim to influence mental health by modulating the gut microbiome.

These include prebiotics, probiotics, nutrition, and exercise. In the future, for patients with irritable bowel syndrome and anxiety or depression, a possible therapy could be targeted probiotic therapy, used together or separately with medication.’

Scientists still need to establish which microorganisms are most important, who might benefit from interventions targeting the microbiome, and whether the observed effects are sufficiently long-lasting to be used in treatment.

What can we do for our microbiome today?

We have already discovered enough about the relationship between the microbiome and daily habits to be able to give practical advice on how to improve the microbiome.

Ilona Vilkoite emphasises that studies show that a varied diet rich in fibre and polyphenols, which also includes fermented products (kefir, yoghurt, and fermented vegetables) and olive oil, can have a beneficial effect on the composition of the gut microbiome and metabolism.

For example, it is recommended to regularly include vegetables, whole grains, legumes, fruits, berries, nuts, and seeds in the menu.

Such dietary patterns are also associated with more favourable inflammatory and metabolic health markers. However, the mechanisms of these benefits are complex, and not all can be directly attributed to changes in the microbiome.

Ilze Maldupa reminds us not to forget legumes, which have a beneficial effect on the microbiome. ‘I recommend avoiding products that require reading the ingredients list: if the product is packaged and one cannot name what it consists of without reading the label, it cannot be healthy for us or our bacteria. The term “ultra-processed food” is widely used to describe such industrially produced products, which can almost always be regarded as part of an “unhealthy diet”’, emphasises Ilze Maldupa.

Special attention should be paid to the consumption of added sugars, especially in childhood

The literature review developed by the RSU Institute of Public Health identified studies that used historical data on sugar access restrictions during and after World War II. These circumstances created a unique natural experiment that allowed researchers to assess the relationship between early life sugar intake and health later in life.

Studies have found that people whose exposure to sugar was restricted from pregnancy through their first years of life had a lower risk of certain metabolic and cardiovascular diseases later in life.

Sugar also affects the oral microbial environment. Frequent consumption of sugary foods and drinks promotes the formation of acids in dental plaque, which in turn damages tooth enamel and promotes the development of caries.

Antibacterial products should also be used judiciously. Alisa Kazarina reminds us that not all microorganisms are harmful. Therefore, strong antibacterial mouthwashes should not be used for prolonged periods unless there is a clear need and a healthcare professional has recommended them.

Science has already helped us understand the importance of the microbiome in human health. Researchers worldwide, including those at RSU, continue to find out how changes in the microbiome are related to the development of diseases and whether this knowledge will allow diseases to be detected, prevented, or treated earlier in the future. Meanwhile, we can take care of our microbiome today by adopting science-based healthy habits.

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