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Utilizing community ecology to examine the role of environmental niches of Histoplasma capsulatum to better understand host-environment dynamics

Project Description

In this project we seek to:

Identify environmental niches of Histoplasma in households and within communal gathering points in endemic regions, namely Ethiopia and The Gambia.

Describe and compare the role Histoplasma plays within the environmental microbial community in households with, and without active clinical cases of equine Histoplasma.

Explore the community ecology in environments supportive of the maintenance of Histoplasma and identify potential routes of transmission (and opportunities for intervention). This will include an exploration of the role of vectors and geological variables.

This will be achieved through the combined use of community ecology and disease modelling methods to identify key niches, interactions between microbiome and Histoplasma in sites with and without infections. You will be a highly motivated ecologist or microbiologist with an interest in disease modelling. This study aligns with an existing project aimed at understanding the epidemiology and ecology of Histoplasma through 3 large scale population based field studies. This PhD would provide training in key molecular and ecological skills, provide grounding in research in International global health, and benefits from support through an international collaboration of scientists and veterinarians with expertise in clinical disease, epidemiology, and fungal environmental microbiomes.

Funding Notes

Competitive funding of tuition fee, research costs and stipend (£14,777 tax-free, 2018-19) from the NERC Doctoral Training Partnership ACCE, View Website. ACCE – a collaboration between the Universities of Sheffield, Liverpool, and York – is the only dedicated ecology/evolution/conservation Doctoral Training Partnership in the UK.

Applications (CV, letter of application, 2 referees) by email to , deadline: January 9 2019. Interviews in or after the week commencing: 11th February 2019. Shortlisted applicants will be interviewed for only one project from the ACCE partnership.

This project is also available to self-funded students. A fees bursary may be available.


Scantlebury, C.E., Pinchbeck, G.L., Loughnane, P., Aklilu, N., Ashine, T., Stringer, A.P., Gordon, L., Marshall, M., Christley, R.M., McCarthy, A. (2016) Development and evaluation of a molecular diagnostic method to rapidly detect Histoplasma capsulatum var. farciminosum, the causative agent of Epizootic Lymphangitis, in equine clinical samples. Journal of Clinical Microbiology 54 (12): 2990-2999.

Scantlebury CE, Zerfu A, Pinchbeck GP, Reed K, Gebreab F, Aklilu N, Mideksa K, Christley R (2015) Participatory appraisal of the impact of epizootic lymphangitis in Ethiopia. Preventive Veterinary Medicine 120 (3-4): 265-276.

Ransom-Jones, E., McCarthy, A. J., Haldenby, S., Doonan, J., & McDonald, J. E. (2017). Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity. MSPHERE, 2(4). doi:10.1128/mSphere.00300-17

de Menezes, A. B., McDonald, J. E., Allison, H. E., & McCarthy, A. J. (2012). Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78(9), 3495-3499. doi:10.1128/AEM.07314-11.

Rooks, D. J., McDonald, J. E., & McCarthy, A. J. (2012). Metagenomic Approaches to the Discovery of Cellulases. Methods in Enzymology, 510, 375-394.

Hibbett, D., Abarenkov, K., Kõljalg, U., Öpik, M., Chai, B., Cole, J., et al. (2017). Sequence-based classification and identification of Fungi. Mycologia.

Cotton TEA, Fitter AH, Dumbrell AJ, Miller, MR, Helgason T, (2015) Fungi in the future: inter-annual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities. New Phytologist. 205:1598-1607 doi: 10.1111/nph.13224.

Morrissey BJ, Helgason T, Poppinga L, Fünfhaus A, Genersch E, Budge G (2015) Biogeography of Paenibacillus larvae, the causative agent of American foulbrood, using a new MLST scheme Environmental Microbiology 17:1414-1424 doi: 10.1111/1462-2920.12625

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