Aaron Walsh
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Affiliation(s): Trinity College Dublin, Teagasc
Research Interests:
- Vaginal Microbiome
- Host–Microbe Interactions
- Within-host Evolution of Commensal and Pathogenic Bacteria
Dr Aaron Walsh is a Research Officer in bioinformatics at Teagasc and a Visiting Research Fellow at Trinity College Dublin. He holds a PhD in Microbiology from University College Cork and has previously held research positions at Trinity College Dublin, the Harvard T.H. Chan School of Public Health and Teagasc.
His research uses microbial genomics and metagenomics to study how microbial populations vary between individuals and change within their hosts over time. His current work includes the strain-level analysis of longitudinal vaginal metagenomes collected during pregnancy and postpartum, with a particular interest in microbiome stability, strain persistence and replacement, mixed-strain colonisation, and within-host bacterial evolution. He is interested in developing integrated studies that examine how changes in the vaginal microbiome relate to host immune and transcriptional responses.
His wider research spans human, animal and food microbiomes, with a particular focus on translating bioinformatic analyses into biologically and clinically meaningful insights.
Publications:
Walsh AM, Roycroft E, Hinchion K, et al. (2025). Genomic characterisation of recurrent Mycobacterium avium isolates from chronically infected patients reveals patterns of within-host evolution. Genome Medicine, 17, 120. https://doi.org/10.1186/s13073-025-01549-y
Brown K, Walsh AM, Yennemadi AS, et al. (2026). HIV inhibits Warburg metabolism in human macrophages infected with Mycobacterium tuberculosis. Scientific Reports. https://doi.org/10.1038/s41598-026-50059-3
McDermott G*, Walsh AM*, Crispie F, et al. (2024). Insights into the adolescent cystic fibrosis airway microbiome using shotgun metagenomics. International Journal of Molecular Sciences, 25, 3893. https://doi.org/10.3390/ijms25073893
Walsh AM*, Macori G*, Kilcawley KN, Cotter PD. (2020). Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nature Food, 1, 500–510. https://doi.org/10.1038/s43016-020-0129-3
Walsh AM, Crispie F, O’Sullivan O, et al. (2018). Species classifier choice is a key consideration when analysing low-complexity food microbiome data. Microbiome, 6, 50. https://doi.org/10.1186/s40168-018-0437-0