Microbial Genomics (GEM)

Our goal is to advance in the development of more effective and personalized treatments for microbial-based human diseases, through a better understanding of the biological determinants of health and disease at the population level. To achieve this goal, we focus our research on three main areas of interest:

1. Understanding the role of the gut microbiome in human health and disease. We use next-generation sequencing to characterize the distribution and function of the human gut microbiota in different conditions of health and disease. We are currently working on:

• Analysing how the gut microbiome influences the ability of HIV-1 infected individuals to achieve adequate immune reconstitution, control HIV-1 replication and limit chronic inflammation.
• Characterizing the co-evolution of the gut microbiome and inflammatory response after acute HIV-1 infection.
• Understanding how the human microbiome can influence the AIDS vaccine response and vice versa, that is, how vaccines and other strategies for eliminating HIV-1 affect the human microbiome.

2. Improving genotypic viral diagnostic tools to maximize antiretroviral efficacy. We pioneered the introduction of next-generation sequencing of HIV-1 in Europe, leading a number of seminal studies to evaluate the clinical value of ultrasensitive tests of HIV-1 resistance and tropism in response to antiretroviral treatment. We work in close collaboration with diagnostic companies and academic centres in Europe, the USA and several African countries.

3. Defining the global clinical epidemiology of HIV-1. We work with leading European clinical cohorts (EuroCOORD, ESAR and EuroSIDA) and with African and American research groups in order to understand how the virus responds to treatment and affects clinical progression to AIDS and death.