Dr Alexandre Almeida

The study of the human gut microbiome has emerged as a new frontier of biomedical research. With the advent of high-throughput DNA sequencing, a strong link between the human gut microbiome composition and various aspects of human health is being increasingly recognized. However, thousands of bacterial species and viruses in the human gut microbiome are largely unknown, as they remain difficult to culture and experimentally characterize in vitro. This technical limitation represents a major hurdle to understanding the biological mechanisms and beneficial role of the gut microbiome in host health.

Our research group develops and applies large-scale, high-resolution metagenomic approaches to understand the biological role of hidden gut microbes across multiple kingdoms (including bacteria, viruses and archaea) and explore their impact on human health. Some of our key questions are:

• Which uncultured microbiome species are the most clinically relevant?
• What is the role of the gut microbiome in ageing and neurodegeneration?
• How does the gut microbiome influence pathogen colonization and evolution?
• Can viruses and bacteriophages be used as biomarkers of health and disease?
• How does the multi-kingdom microbiome differ across human body sites?

By providing an integrated view of the physiology and functions of the commensal microbiome, we seek to improve our understanding of their role in human health and open new avenues to develop innovative therapeutic applications.

If you are interested in pursuing a PhD or Postdoctoral position in my group feel free to get in touch with a CV and cover letter/statement explaining your interest in our research, so we can discuss future opportunities.

Throughout my research career I have specialized in the development and application of bioinformatics and genomic approaches to make biological discoveries with relevance to human health. I obtained my PhD in Microbiology at the Institut Pasteur in Paris, where I studied the opportunistic pathogen group B Streptococcus to identify genomic traits linked to host adaptation (Almeida et al. Environ. Microbiol. 2016), virulence and pathogenicity (Almeida et al. J. Bacteriol. 2015 and Almeida et al. mSystems 2017). Using comparative genomics methods, we were able to identify candidate genes and single nucleotide variants linked with disease onset and progression (Almeida et al. mSystems 2017).

After my PhD, I was awarded an EBI-Sanger Postdoctoral (ESPOD) Fellowship and relocated to Cambridge to expand my research to metagenomic studies of the human gut microbiome. Using large-scale computational methods, we discovered thousands of uncultivated bacterial species in the human gut microbiome, more than tripling the number of gut-associated species previously known (Almeida et al. Nature 2019 and Almeida et al. Nat. Biotechnol. 2021). I have also been involved in a number of national and international collaborative projects, one of which led to the discovery of over 140,000 distinct viruses in the human gut microbiome, of which 50% were unknown before (Camarillo-Guerrero et al. Cell 2021).

Now, I have established a new research team at the Department of Veterinary Medicine in Cambridge, funded by an MRC Career Development Award, to understand the role that the hidden, uncultured microbiome plays in human health and disease.