Dr Melanie Commins

BA BSc MSc PhD
Postdoctoral Scientist in Microbiomes and Metagenomics

Department: Pathobiology & Population Sciences

Campus: Hawkshead

Research Groups: Antimicrobial Resistance, IRLFS (Research Programme)

Melanie Hay is a postdoctoral scientist specialising in microbiomes and metagenomics. Her research explores the chicken gut microbiome and its links to antimicrobial resistance, welfare, and food safety. She contributes to international One Health projects investigating resistance and zoonotic pathogen transmission in poultry production systems.

Melanie Hay is a postdoctoral scientist at the Royal Veterinary College, specialising in microbiomes and metagenomics. She joined the RVC in 2020 as part of Professor Damer Blake’s group, where her research focuses on antimicrobial resistance, plasmid dynamics, and pathogen transmission in poultry production networks across India, Bangladesh and Vietnam (One Health Poultry Hub). She also contributes to the FADH Vet-AMR project, investigating how ionophore anticoccidials influence resistance in the chicken gut microbiome.

Melanie completed her undergraduate studies at Rhodes University, South Africa, graduating with a BA in English Literature and Psychology (2006). She later transitioned into the biological sciences, earning a BSc in Human Physiology and Genetics (2009), and a BSc (Med) (Hons) in Medical Microbiology (2010) at the University of Cape Town, where she also completed an MSc (Med) in Exercise Science (2013).

Following a period in science communication with Siyavula Education, developing open-access biology and natural science textbooks, she pursued a PhD at Aberystwyth University through the EU Marie Sklodowska-Curie MicroArctic ITN, using metagenomics to explore the biotechnological potential of cryospheric bacteria.

Her work at the RVC combines metagenomics, ecology, and One Health approaches to understand microbial communities in food production systems.

Melanie’s research integrates microbiome ecology, metagenomics, and antimicrobial resistance to understand how farming practices shape microbial communities in livestock.

Within the UKRI/ GCRF One Health Poultry Hub, she uses large-scale genomic datasets to trace the spread of zoonotic pathogens and resistance genes through poultry production networks in South Asia. Her recent work applies microbiome–resistome profiling to identify “enterotype–resistome” relationships that reveal selection pressures and help predict the emergence of unexpected resistance signatures.

Through the FADH: Vet-AMR project, she investigates how ionophore anticoccidial drugs influence the development and dissemination of antimicrobial resistance within the chicken gut microbiome.

In the Houghton Trust Dysbiosis Project, she studies the microbial and genetic factors underpinning dysbiosis in elite broiler breeding lines, linking gut ecology to host genotype, welfare, and productivity.

She also contributes to projects analysing antimicrobial resistance in cattle and welcomes collaborations on microbiome analysis across animal and environmental systems.

Together, these projects aim to build predictive frameworks for resistance evolution and inform sustainable antimicrobial stewardship in livestock production.

Gadhia, N., Smyrnakis, M., Liu, P.Y., Blake, D., Hay, M., Nguyen, A., Richards, D., Xia, D. and Krishna, R., 2025. A novel approach to differential expression analysis of co-occurrence networks for small-sampled microbiome data. IEEE Transactions on Computational Biology and Bioinformatics.

Hinsu, A., Dai, X., Dadousis, C., Hay, M., Fosso, B., Crotta, M., Pandit, R., Guitian, J., Tomley, F., Koringa, P. and Joshi, C., 2025. Unveiling host-genetic drivers of caecal microbial communities in chickens through genome-wide association studies. Frontiers in microbiomes, 4, p.1539923.

Raju, R., O’neil, L., Kerr, C., Lehri, B., Sarkar, S., Soni, T., Nguipdop-Djomo, P., Conan, A., Tu, N.D., Hung, T.T.M., Hay, M., ... and Stabler, R. 2024. Non-typhoidal Salmonella in humans in India, Vietnam, Bangladesh and Sri Lanka: a systematic review. JAC-antimicrobial resistance, 6(6), p.dlae190.

Mogrovejo-Arias, D.C., Hay, M.C., Edwards, A., Mitchell, A.C., Steinmann, J., Brill, F.H. and Neumann, B., 2024. Investigating the resistome of haemolytic bacteria in Arctic soils. Environmental Microbiology Reports, 16(5), p.e70028.

Hay, M.C., Hinsu, A.T., Koringa, P.G., Pandit, R.J., Liu, P.Y., Parekh, M.J., Jakhesara, S.J., Dai, X., Crotta, M., Fosso, B. and Limon, G., 2023. Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices. Frontiers in Microbiomes, 2, p.1301609.

Hay, M.C., Mitchell, A.C., Soares, A.R., Debbonaire, A.R., Mogrovejo, D.C., Els, N. and Edwards, A., 2023. Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss. Microbial Genomics, 9(11), p.001131.

Clason, C.C., Baccolo, G., Lokas, E., Owens, P.N., Wachniew, P., Millward, G.E., Taylor, A., Blake, W.H., Beard, D.B., Poniecka, E. and Selmes, N., ... Hay, M.C,... 2023. Global variability and controls on the accumulation of fallout radionuclides in cryoconite. Science of the Total Environment, 894, p.164902.

Gadhia, N.A., Smyrnakis, M., Liu, P.Y., Blake, D., Hay, M., Nguyen, A., Xia, D., Krishna, R. and Richards, D., 2023, September. Formulating a method to analyse the differential expression of co-occurrence networks for small-sampled microbiome data. In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 1-6).

Edwards, A., Cameron, K.A., Cook, J.M., Debbonaire, A.R., Furness, E., Hay, M.C. and Rassner, S.M., 2020. Microbial genomics amidst the Arctic crisis. Microbial genomics, 6(5), p.e000375.

 

 

Researcher Association Committee

  • UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) One Health Poultry Hub

    With integrated streams of social, economic, biological, mathematical and policy-led research, we are co-producing detailed knowledge on the biological, structural and socio-economic factors that shape networks of chicken production and distribution. The RVC-led UKRI GCRF One Health Poultry Hub brings together leading laboratory, clinical, veterinary and social scientists, as well as skilled communications experts, programme support staff and external stakeholders.  

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