The microbiome: as unique to you as your fingerprint

There are trillions of microbes living on and inside us, mostly in our gut: the gut microbiota. Although they may seem scary, we now know that most of those microbes are essential for our health – provided a balance is maintained.

Microbes are tiny organisms, such as bacteria, fungi and viruses, found everywhere: in the water, in the soil, in our food and even in our bodies. Trillions of symbiotic microbes live in and on each person, but 90%-95% of them live in the gut, especially in the colon.

While scientists have not yet been able to pinpoint what amounts to an ideal gut microbiota, they have demonstrated that microbes keep up healthy by reinforcing the gut barrier, improving gut motility and function, protecting us against pathogens and synthesizing metabolites, vitamins and hormones, just to mention their main benefits.

Scientists analyse microbiota activity by studying the microbiome, i.e., the genetic material within the microbiota. The genes in our microbiome outnumber the genes in our genome by 150 to 1, which gives an idea of the vast amount of information contained within the microbiome of any given human. This is also what makes the microbiome as unique to each person as their fingerprint. Collecting, storing and processing such vast volumes of data requires big data analytic tools.

 

It’s all about balance

The microbiota is composed of some 10,000 different microbial species cohabiting peacefully in our bodies. When their environment is disturbed for whatever reason – e.g., by an immune alteration caused by HIV infection – the resulting imbalance can lead to a wide range of disorders.

We can imagine the gut microbiota as a kind of internal ecosystem, with many different virus, bacteria and fungi living together symbiotically – as in a highly diverse garden of lush plants. Those microorganisms have a beneficial impact on body functioning when microbiota composition is balanced. However, as happens with any ecosystem, even small changes can disturb that balance, allowing opportunistic pathogens and prejudicial microbial activities to proliferate. Imagine an abnormal temperature change affecting our garden: some plants would continue to thrive, but others would die, transforming our garden.

Many factors can influence gut microbiota composition, including genetics, drugs and diet.  MISTRAL’s focus is to understand how infections, and especially HIV infection, alter microbiota composition and balance and how changes in microbial composition can be a marker of disease and disease progression.

 

HIV infection alters the microbiome

Immune disorders like HIV infection can modify the balance of microbes in the gut microbiome. Scientists hope to be able to decipher the “ideal microbiome” so as to apply that knowledge in treatments.

HIV is a virus that infects T-cells, crucial for the immune system. HIV kills the T-cells in order to be able to reproduce and multiply. In time, HIV weakens immunity, leading to the emergence of immune disorders.

Scientists have demonstrated that there is a direct relationship between the immune system and the gut microbiome. Therefore, any damage to the immune system will change the gut environment and its composition in microbes.  There is emerging evidence that the vaccine response varies, depending on a person’s microbiome. For instance, it is known that people living with HIV have a different microbiome from people without infection, a fact that poses several questions. Is there a link between a person’s microbiome and their clinical HIV complications? Who will be responsive to a vaccine? Can we enhance a person’s response to a vaccine?

In order to find answers to such questions, scientists need first to understand what amounts to an “ideal microbiome” and then need to find a way to modify microbiomes “on demand”. Such information would be the basis for the development of clinical tools aimed at improving the vaccine response and enhancing immune systems.