Alexandre Almeida (Group Leader)

Alex is an MRC Career Development Fellow leading the Microbiome Function and Diversity group at the University of Cambridge. His team focuses on understanding the role that the uncultured microbiome plays in human health and disease. He obtained his PhD in Microbiology at the Institut Pasteur in Paris, studying the opportunistic pathogen group B Streptococcus. After his PhD, he relocated to Cambridge with an EBI-Sanger Postdoctoral Fellowship to expand his research to metagenomic studies of the human gut microbiome. Using computational genomic methods, his work contributed to the discovery of thousands of uncultivated bacterial species in the human gut microbiome, more than tripling the number of gut-associated species previously known.

Efrat Muller (Postdoc)

Efrat is a postdoc in the Microbiome Function and Diversity group interested in the understudied components of the gut microbiome, particularly bacteriophages. She completed her PhD at the Borenstein lab (Tel Aviv University, School of Computer Science), studying computational approaches for integrating multi-omic data in the context of the human microbiome. Prior to her PhD, Efrat worked at Medial EarlySign and at Intel, using data-science to tackle healthcare challenges.

Jacob Lapkin (MPhil student)

Jacob is an MPhil student in Biotechnology at the University of Cambridge, working with the Microbiome Function and Diversity group. Inspired by breakthroughs like AlphaFold’s impact on protein structure prediction, he transitioned slowly to biotechnology to explore new frontiers where computational approaches can advance more ubiquitous problems. Prior to joining Cambridge, he worked as a Research Software Engineer at Ingram Micro, where he architected backend systems and APIs for insights and recommendations, developing expertise in cloud infrastructure, API design, and software architecture. With an MSc in Computer Science from University College London and a BSc in Economics from the University of Utah, he brings a unique interdisciplinary background combining software engineering, data science, and biotechnology.

Luis Gonzalez (PhD student)

Luis is a PhD student at the Wellcome Sanger Institute, currently performing his PhD project at the Microbiome Function and Diversity group at the University of Cambridge. Luis was trained as a biologist at Universidad Peruana Cayetano Heredia before receiving graduate training in genomics at Sanger. During his MPhil at the Lawley group, he constructed the most extensive Bifidobacterium breve collection to date to understand its phylogenetic diversity and relationship with its host. In his PhD, he is researching the composition, diversity, and functionality of the respiratory microbiome and how they play a role in the host’s health status. Luis is interested in building resources for developing better treatments to tackle public health problems.

Qi Yin (Postdoc)

Qi is a visiting postdoc in the Microbiome Function and Diversity group interested in the discovery of novel probiotics and antimicrobials in the human gut microbiome. She finished her PhD in 2016 at the University of Chinese Academy Sciences and was a postdoc until 2020 when she began her appointment as an Associate Professor at the Chongqing Medical University. Her current research interests centre around the study of host-microbe interactions in the lung/gut microbiome, the molecular mechanisms of bacterial infection and development of novel antimicrobial agents.

Rahul Arora (PhD student)

Rahul is a member of the Royal Society of Biology and a visiting PhD student in the Microbiome Function and Diversity group. He works with the brain transcriptomics to identify the shared biological pathways in neurodegeneration at the centre for misfolding diseases in his PhD at Cambridge. He is interested to understand the role of gut microbiome evolution in neurodegeneration and its impact on disease onset and progression. His project is focused on using metagenomic data from a diverse group of neurodegenerative diseases to understand the links between strain level microbial abundance in human gut and how their functional pathways interact with the brain altering the transcriptomic landscape.

Samriddhi Gupta (BSc student/Amgen Scholar)

Samriddhi is an undergraduate student at Trinity College Dublin who was accepted into the Amgen Scholarship programme at the University of Cambridge to develop a project in the Microbiome Function and Diversity lab. Her research aimed to build a phylogenetic history of the human gut microbiome and perform comparative genomic analyses of bacterial genomes colonizing the intestinal tract of various mammalian hosts to identify host-specific and host-generalist genetic features. She also developed a research project in the MFD lab as part of her undergraduate to investigate the emergence of opportunistic pathogens in the human gut microbiome.

Ana C. da Silva (Postdoc)

Ana is a microbiologist who has transitioned from wet to dry-lab science. In her work, she uses the lens of bioinformatics to look at biological questions from the perspective and context of the data. She has worked at the interface of basic and translational research, having explored different branches of the Tree of Life: Drosophila (undergrad and MSc in Cell and Molecular Biology – Portugal, exploring molecular basis of cold resistance), Microbes (post-doc & PhD at Nottingham, using phenotypic and genomic approaches to investigate ecology and evolution of polymicrobial chronic wounds) and Plants (MSc in Bioinformatics & post-doc at Nottingham, finding genomic factors underlying salinity tolerance). During her time in the Microbiome Function and Diversity team, Ana used bioinformatics approaches to investigate the role of uncultured bacteria in the human gut, with the goal of understanding how the composition of the gut microbiome may influence the incidence of gut-related human diseases.