Research Overview

We are interested in the co-evolution of humans with their microbiomes. Our basic science investigates the evolutionary history of gut microbes, how they have adapted to life inside humans and how they affect human biology and health.

Microbiome Science



Ruth Ley

How human is the human gut microbiome? The thousands of species that make up the human gut microbiome are environmentally acquired, yet their interactions with the host belie a close relationship built of reciprocal adaptations. From molecular mimicry of host cell surface structures, to host immune evasion and manipulation, the commensal microbiota of the gut have assimilated into the human gut environment. Combined with our recent evidence that humans and certain gut species share an evolutionary history, these adaptations indicate a profoundly specific relationship to the human host. The research questions we address in the Department of Microbiome Science…

Microbiome Genetics & Engineering


Departmental Group Leader:

James Marsh

The community of microorganisms within the human gastrointestinal tract is one of the most diverse ecosystems known, yet we currently have limited tools to unravel its intrinsic complexity. Next-generation sequencing approaches have been invaluable for the characterisation of gut microbial distribution, abundance, and evolution, but elucidating the mechanistic basis for these dynamics requires an ability to perturb the system through manipulation and testing. By developing novel microbiome engineering techniques, we are genetically reprogramming diverse, non-model organisms associated with the human gut to understand both their ecological niche and the intertwined interactions that drive the emergent properties of the community….

Microbiome Bioinformatics: Ecology and Co-Evolution


Departmental Group Leader:

Alexander Tyakht

Host-associated microbial communities demonstrate remarkable diversity and dynamics while maintaining stability, reflecting their co-evolution with humans. The gut microbiome, particularly for humans, is integral to various bodily functions. We aim to understand the principles underlying its temporal stability and rapid response to external influences, as well as how the vast functional potential encoded in gut microbial genomes is realized. To address these questions, we employ algorithms, software pipelines, and statistical methods to analyze microbiome sequencing data in the context of health, disease, diet, and geography. Our approach encompasses conventional metagenomics and modified techniques such as high-throughput conformation capture (Hi-C…