Metabolomics and lipidomics have transformed how we understand health, disease, and physiological response to environmental stress. Recently, pioneering work at Leicester has begun applying these approaches to human remains, reconstructing past diet and disease across centuries of human history. Here, we explore how much further these boundaries can be pushed: what can we learn about biology, ecology, and health if we extend metabolomic analysis across tens of thousands of years and to the remains of other species?
Surprisingly Rock Hyrax middens offer an extraordinary opportunity to test these limits. The communal latrines of Rock Hyraxes (Procavia capensis), which inhabit semi-arid landscapes across southern Africa, accumulate into stratified organic archives which can be preserved for more than 50,000 years. These deposits preserve organic molecules under exceptional conditions: we have identified intact animal and plant metabolites such as cholesterol, hippuric acid and plant derived terpenoids and leaf waxes (Chase et al. 2012). The plant lipids in these archives carry ecosystem-scale isotopic climate records, but the animal metabolome remains entirely unexplored. No study has reconstructed the metabolome of an ancient, long-lived animal community at this temporal depth. This is a methodological and a conceptual frontier. We do not yet know how far metabolic information survives, what a 50,000-year record of community biochemistry contains, or what information it has about how organisms and their health responded to shifting climate and environment over deep time.
Working with Leicester’s van Geest Laboratory (Prof Jones) and the School of Heritage and Culture (Dr Inskip), this project in the School of Chemistry, Earth and Environmental Sciences (Boom and Carr) will develop and extend established archaeological metabolomic methods to this new and promising deep-time archive. The doctoral researcher will develop analytical workflows combining mass spectrometric, spectroscopic, and stable-isotope approaches, characterising the organic composition of midden material and its ancient metabolome. They will link these signatures to the rich climatic and environmental records these deposits provide. The result will be a new platform for deep-time metabolomics: a new way to read millennial-scale biochemical responses to environmental change, with direct relevance to understanding human health in a changing climate.
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The doctoral researcher will develop and validate an integrated analytical workflow for characterising the organic composition and ancient metabolome of Hyrax middens. Bulk organic structure and composition will be assessed using pyrolysis-GC/MS and FTIR spectroscopy. Metabolomic and lipidomic profiles will be obtained through solvent extraction and gas chromatography–mass spectrometry (GC/MS), with solid-phase microextraction (SPME) capturing volatile and semi-volatile fractions. Metabolomic analyses will employ high-resolution LC/MS in Leicester’s van Geest Laboratory. Environmental DNA and metabarcoding sequencing will be conducted in collaboration with the National History Museum (Jungblut). Stable carbon and nitrogen isotope analysis, including compound-specific isotope measurements, will provide metabolic, dietary, and environmental context, enabling ancient metabolic signatures to be linked to the climatic and environmental records these same deposits preserve.
DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
In addition to the training provided by CENTA, the supervisory team will provide appropriate training for a wide range of mass spectrometric applications (Boom and Jones). Inskip leads a bioarcheology discussion group which will open for participation. Boom, Carr and Chase will provide further training on Hyrax midden research, stable isotope analysis, age-depth modelling of radiocarbon chronologies and the environmental and climatological setting.
Sarah Inskip is a UKRI Future Leaders fellow and Philip Leverhulme Prize winner. Her work concerns the emerging discipline of archaeometabolomics and she is the bioarcheology group leader at Leicester.
Donald Jones is an expert on metabolomics and cancer biomarker research. He is the Co-Director of the van Geest Multi-OMICs Facility.
Brian Chase is a research director at CNRS France and is the leading authority on Hyrax middens and palaeoclimates of southern Africa.
Anne Jungblut is an environmental microbiologist at the Natural History Museum. Her expertise lies in molecular biology, environmental DNA sequencing, genomics and museomics.
Year 1: Learning the principles of the analytical methods and developing new methodologies. Extraction of metabolites requires new protocols due to the different nature of the sample matrix compared to traditional samples. Mastering the practical application of mass spectormetry and FTIR spectroscopy will be a key goal, along with developing new analysis methods and workflows on these platforms.
Year 2: Sampling of B Chase’s midden achives in Montpellier, collecting data to reconstruct the Hyrax metabolome over time and space, using specialised software.
Year 3: Continuation of data collection and more in depth ananyses and interpretation of data. Working with the palaeoenvironmental supervisory team to interpret past repsonses to climatic changePreparing manuscripts for pubication. Presenting at inernational major conference.
Journal:
Carr, A.S., Boom, A., Chase, B.M. (2010). ‘The potential of plant biomarker evidence derived from rock hyrax middens as an indicator of palaeoenvironmental change’. Palaeogeography, Palaeoclimatology, Palaeoecology, 285, pp. 175-183
Chase, B.M. et al., 2023. ‘Linking upwelling intensity and orbital-scale climate variability in South Africa’s winter rainfall zone: insights from a ~70,000-year hyrax midden record’. Quaternary Science Advances 10, 100081
Chase, B.M., Scott, L., Meadows, M.E., Gil-Romera, G., Boom, A., Carr, A.S., Reimer, P.J., Truc, L., Valsecchi, V. & Quick, L.J. (2012). ‘Rock hyrax middens: A palaeoenvironmental archive for southern African drylands.’ Quaternary Science Reviews 56, 107–125. DOI: 10.1016/j.quascirev.2012.08.018.
Website:
Kaufmann, R. (2010) Fuzzy Critters’ Crystallized Pee Changes Climate Record? Available at: https://www.nationalgeographic.com/animals/article/101015-urine-pee-rock-hyrax-climate-science-ancient-prehistoric
For further information please contact Arnoud Boom [email protected].
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 6th January 2027.