The evolution of host-associated microbiomes through time and space Funding Status: Funding is in competition with other projects and students through Doctoral Training Programs (NERC E5 and Darwin Trust) Project Description Host-associated microbiomes are essential for the survival of macroscopic hosts, including mammals. Yet, our understanding of where they come from, how they adapt to living in and on the host, how they move through the host organs, and how they contribute to host’s physiological and ecological adaptations is limited. We also have only rudimentary idea about how changes in the environment affect these microbial communities and what consequences changing microbiomes have for the hosts. What we know is primarily uncovered in the gut, a very distinct microbial community that is kept safe from environmental influence through the inhospitable conditions in the stomach. There is very little data on other host-associated microbial communities. This project will use dental calculus, the preserved oral microbiome that forms on the teeth of many mammalian species. It calcifies on the living host, remaining unchanged over hundreds of thousands of years, and can be easily collected from museum and archaeological specimens. It hence allows the study of temporal, ecological and host-specific processes that govern a microbial community. The mouth is exposed to the outside through breathing and food intake, and is also connected to internal respiratory and digestive tracts, providing a testing ground for environmental microorganisms on route to colonising the host. Key research questions We have collated a shotgun metagenomic dataset of oral (dental calculus) microbiomes for 34 mammalian species, from okapis to sea lions, from hippos to muskox, and there is a possibility to collect additional samples for targeted research questions. Due to the degraded nature of DNA in historical collections, the datasets are effectively ancient DNA. Because the entire field of (temporal) comparative metagenomics is young, there are many questions that can be explored and adapted to the specific interest of the candidate. They span from areas in microbial genome evolution, to host ecological adaptations, to function. Some initial ideas include: - Does the mouth serve as a testing ground for environmental bacteria on route to colonise internal host organs, such as the gut, respiratory tract, etc.? How often do we find transitions from the environment into the host? And what is the order of these transitions – environment-mouth-gut or a different route? What are the genomic changes that enable these transitions and what functions do the newly acquired environmental taxa fulfil in the host? - Does the oral microbiome differ across populations of the same host species and what ecological conditions experienced by the host best explain these differences? Are these differences in microbial communities adaptive for the host? Understanding this would further our knowledge on the contribution of microbiomes to rapid host adaptations, a question that is particularly important in the face of ongoing climate and environmental change. - How does the oral microbiome change with captivity and domestication? So far, this question has only been explored in the gut. However, gut microbiomes rarely preserve through time, whereas dental calculus does. Uncovering the microbial hallmarks of domestication would allow exploring the rich archaeological record that is often struggling with identifying early domesticates. - Our previous work indicated that diet has a strong effect on the composition and function of oral microbial communities. So, do dietary specialists contain a less diverse, more streamlined oral microbiome and is it uniquely adapted to the nutrients that are available to the host? Dietary specialist are often consuming foods rich in secondary compounds that are toxic, so could microbial commensals help the host in utilising novel dietary sources? We have vast experience dealing with the challenges of historical metagenomic datasets short reads, post-mortem damage, contamination. It will also be possible to collect and generate additional data for targeted samples through our extensive collaboration with natural history museums across Europe, the UK, and Australia and to obtain training in ancient DNA molecular lab techniques. However, the bulk of the project is computational, relying on metagenomics analyses, using group-internal and publicly available data. It will be conducted in collaboration with researchers in the UK, Germany and the USA. Candidate requirements To be eligible for a PhD-student position, the applicant should have at least an upper 2.1 degree in evolutionary biology, bioinformatics or a related field. In the British system, candidates who have successfully finished their undergraduate degree (Honours) are eligible to apply. The technical skills of the candidates will be evaluated based on the experience with large-scale genomics/metagenomics analyses and bioinformatics proficiency. The ideal candidate will have a strong interest and documented knowledge in evolutionary biology, with a drive to understand processes involved in the evolution of host-associated microbiomes. Perseverance and high intrinsic motivation are necessary to successfully complete a PhD project and overcome the unavoidable obstacles with data and analyses. You will be highly reliable, driven and well-organised, curious and willing to think outside the box, with the ability to quickly acquire new skills, and enjoy working both independently and as part of a team. The position will begin Fall 2027. The deadlines depend on the DTP (2nd December 2026 at noon [UK time] for E5 and some time in January or February for Darwin Trust), but supervisors have to propose candidates to be considered, particularly for candidates applying from outside of the UK. Interested students should send a CV, a copy of transcripts, and a brief letter of interest to Dr. Katerina Guschanski (Katerina.Guschanski@ed.ac.uk) by November 16, 2026. Please also reach out with informal questions. E5 DTP (NERC), deadline 2nd December 2026 (noon) https://e5-dtp.ed.ac.uk/project?item=1865 Darwin Trust (for international students only), deadline January or February 2027 https://biology.ed.ac.uk/darwintrust/phdstudenships More information about the research group https://www.research.ed.ac.uk/en/persons/katerina-guschanski (to manage your EvolDir subscription: https://evoldir.net/django/subscriptions/manage/)