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Sinead Waters

Research Officer - Animal Genomics Molecular Biology

Research Interests

Leading a research programme in the application of genomics technologies to address key issues in agriculture, particularly in the role of the rumen microbiome in improving nutrient utilisation from feed and reducing greenhouse gas (GHG) emissions from ruminants (particularly enteric methane) and it’s manipulation via animal breeding and dietary supplementation. I have a special interest in the development and evaluation of a wide range of feed additives/dietary supplements to reduce enteric methane emissions from sheep, beef and dairy cattle working closely with industry partners. Ultimately data from the research will lead to a reduction in feed costs and reduce environmental footprint of agriculture enhancing both economic and environmental sustainability.

Since 2018 Adjunct Professor at the Genetics and Biotechnology Laboratory, Plant and Agri-Biosciences Research Centre (PABC), Ryan Institute, University of Galway, Ireland. 

My interests in genomics and microbiome based research also led to a focus on understanding the genetic basis for bovine respiratory disease (a major cause of morbidity and mortality in young calves). Data will contribute to understanding and breeding for resistance to BRD in the Irish herd.  

Main areas of Expertise: Rumen microbiology, methane emissions abatement strategies, animal nutrition, feed additives, bovine genetics/genomics.

Current Projects

  • Development of DNA-based biomarkers for compensatory growth in beef cattle (2015-2020: Funded by Science Foundation Ireland: Career Development Award 13/CDA/2182
  • RumenPredict: Predicting appropriate GHG mitigation strategies based on modelling variables that contribute to ruminant environmental impact (2017-2021; Funded by DAFM through the FACCE ERA-GAS; 16/RD/ERAGAS/1)
  • BRDC-SEQ: Application of next generation sequencing for the identification of DNA based biomarkers in regulatory regions of the genome for susceptibility to bovine respiratory disease complex (2017-2021; Funded by US-Ireland R&D Partnership Call in Agriculture SFI 16/RD/US-ROI/11).
  • MASTER: Microbiome application for sustainable food systems through technologies and enterprise (WP3: The Rumen Microbiome). 2019-2023. Funded by the EU Horizon 2020 research and innovation programme (application number 818368).
  • METH-ABATEDevelopment and validation of novel technologies to reduce methane emissions from Irish pasture based systems (2019R479). Funded by DAFM Research Stimulus Fund. 2019-2023.
  • Methane-Predict: 'Development and Validation of high throughput predictors for large capacity screening of methane emitting ruminant livestock at an individual and system level (2022IRLNZ121). Ireland-New Zealand Joint call. 2023-2027.
    INTEGRITY:  Integrated crop-ruminant livestock systems as a strategy to increase nutrient circularity. EU ERA-GAS funding. 2022-2026.

    HoloRuminant: Horizon 2020 (Grant Agreement No 101000213) Understanding microbiomes of the ruminant Holobiont. Workpackage leader and Irish coordinator. 2021-2026.

Education

2008: Trinity College Dublin. Higher Diploma (Statistics). Distinction. 
2003: National University of Ireland, Maynooth. Ph.D. (Gut microbiology: Biotechnology).
1999: National University of Ireland, Galway. B.Sc. (First Class Honours, Biotechnology).

Professional Membership

  • Member (representing Ireland) of the EU Expert group on enteric methane emissions (DG_AGRI) since 2021.
  • Former Co-chair of the Livestock Research Groupof the Global Research Alliance for Climate Change working with 65 countries with the agenda to grow more food without increasing GHG emissions (2018-2023).
  • Editorial boards of Scientific Reportsand Frontiers in Microbiology.
  • Research Topic Editor “Rumen Microbiome: Interacting with Host Genetics, Dietary Nutrients Metabolism, Animal Production, and Environment” for Frontiers in Microbiology (2023).
  • Expert reviewer for Genome Canada funding agency, 'The Research Council of Norway', 'Portuguese FCT national funding agency', French National Research Agency Framework and National Science Centre
  • British Society for Animal Science (Science and Technology and Events committee)
  • Steering committee member for DAFM funded project at GMIT
  • Teagasc GHG working group member
  • Rumen Microbial Genomics Network
  • Panel member and speaker at the Collaboration Platform between the European Commission Directorate-General for Agriculture and Rural Development (DG AGRI) and the U.S. Department of Agriculture (USDA) (October 2022)

Published over 140 peer reviewed research articles. A few are selected below.

O’Donoghue, S., Earley, B., Johnston, D., McCabe, M.S., Kim, J.W., Taylor, J.F., Duffy, C., Lemon, K., McMenamy, M., Cosby, S.L., Morris, D.W., Waters, S.M.  2023.  Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge.  Frontiers in Genetics, 14, 1092877.

McLoughlin S, Spillane C, Campion FP, Claffey N, Sosa CC, McNicholas Y, Smith PE, Diskin MG, Waters SM. 2023. Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep. Sci Rep. 2023 Feb 27;13(1):3336. 

Andersen TO, Altshuler I, Vera-Ponce de León A, Walter JM, McGovern E, Keogh K, Martin C, Bernard L, Morgavi DP, Park T, Li Z, Jiang Y, Firkins JL, Yu Z, Hvidsten TR, Waters SM, Popova M, Arntzen MØ, Hagen LH, Pope PB. 2023. Metabolic influence of core ciliates within the rumen microbiome..ISME J. 17(7):1128-1140. 

Thompson L, Rowntree J, Windisch W, Waters SM, Shalloo L, Manzano P. 2023. Ecosystem management using livestock: embracing diversity and respecting ecological principles. Anim Front. 13(2):28-34.

Roskam E., Kirwan SF, Kenny DA, O'Flaherty V, O'Donnell, C., Waters SM. 2022. Effect of brown and green seaweeds on diet digestibility, ruminal fermentation patterns and enteric methane emissions using the rumen simulation technique. Frontiers in Animal Science. 10.3389.

Smith PE, Kelly AK, Kenny DA, Waters SM. 2022. Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions. Front Microbiol. 13:855565.

Smith PE, Waters SM, Kenny DA, Kirwan SF, Conroy S, Kelly AK. 2021. Effect of divergence in residual methane emissions on feed intake and efficiency, growth and carcass performance, and indices of rumen fermentation and methane emissions in finishing beef cattle.  J Anim Sci. 2021 Oct 1:skab275.

Mancia A, Chadwick DR, Waters SM, Krol DJ. 2022. Uncertainties in direct N2O emissions from grazing ruminant excreta (EF3PRP) in national greenhouse gas inventories. Sci Total Environ. 803:149935.

Keogh K, Carthy TR, McClure MC, Waters SM, Kenny DA. 2021. Genome-wide association study of economically important traits in Charolais and Limousin beef cows.  Animal. 15(1):100011

Keogh K, McKenna C, Porter RK, Waters SM, Kenny DA. 2021. Effect of dietary restriction and subsequent realimentation on hepatic oxidative phosphorylation in cattle.  Animal.15(1):100009.

Johnston D, Kim J, Taylor JF, Earley B, McCabe MS, Lemon K, Duffy C, McMenamy M, Cosby SL, Waters SM. ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus. 

2021. BMC Genomics. 22(1):14.

McGovern E, McGee M, Byrne CJ, Kenny DA, Kelly AK, Waters SM. 2020. Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed. Sci Rep. 10(1):15317.

Smith PE, Enriquez-Hidalgo D, Hennessy D, McCabe MS, Kenny DA, Kelly AK, Waters SM. 2020. Sward type alters the relative abundance of members of the rumen microbial ecosystem in dairy cows. Sci Rep. 10(1):9317.

McLoughlin S, Spillane C, Claffey N, Smith PE, O'Rourke T, Diskin MG, Waters SM. 2020. Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency. Front Microbiol.;11:1981.

O'Hara E, Kenny DA, McGovern E, Byrne CJ, McCabe MS, Guan LL, Waters SM. 2020. Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life. 2020. FEMS Microbiol Ecol. 96(2):fiz203.

Mullins Y, Keogh K, Kenny DA, Kelly A, O' Boyle P, Waters SM. Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth. 2020. Sci Rep. 2020 Feb 13;10(1):2613. doi: 10.1038/s41598-020-59412-6.

Keogh K, Kenny DA, Waters SM. 2019. Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle. Sci Rep. 9(1):6093.

Johnston D, Earley B, McCabe MS, Lemon K, Duffy C, McMenamy M, Cosby SL, Kim J, Blackshields G, Taylor JF, Waters SM. 2019. Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response. Sci Rep 9(1):14736.

Higgins MG, Fitzsimons C, McClure MC, McKenna C, Conroy S, Kenny DA, McGee M, *Waters SM, *Morris DW. 2018. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Sci Rep. 2018 Sep 24;8(1):14301. (*shared senior authorship).

Surlis C, Earley B, McGee M, Keogh K, Cormican P, Blackshields G, Tiernan K, Dunn A, Morrison S, Arguello A, Waters SM. 2018. Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age. Sci Rep.;8(1):15461.

McGovern E, Kenny DA, McCabe MS, Fitzsimons C, McGee M, Kelly AK, Waters SM. 2018. 16S rRNA Sequencing Reveals Relationship Between Potent Cellulolytic Genera and Feed Efficiency in the Rumen of Bulls. Front Microbiol. 9:1842.

Popova M, McGovern E, McCabe MS, Martin C, Doreau M, Arbre M, Meale SJ, Morgavi DP, Waters SM. 2017. The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate. Front Microbiol. 24;8:937.

Book Chapters/Reviews:

Smith PE, Kelly AK, Kenny DA, Waters SM. 2022. Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems. Front Vet Sci. 9:958340.

J. Patton, M. Dineen and T.W.J. Keady McGee, M, Waters SM. 2022. Developments in nutrition for pasture-based cattle and sheep systems in Ireland. Irish Journal of Agricultural and Food Research. DOI: 10.15212/ijafr-2020-0148

Waters, SM, Kenny DA, Smith PE. 2020. Role of the rumen microbiome in pasture-fed ruminant production systems. In: Improving rumen function. Eds: McSweeney CS and Mackie RI. Burleigh Dodds Science Publishing. Pp 591-634.

David A. Kenny, Claire Fitzsimons, Sinead M. Waters and Mark McGee. 2017. Improving feed efficiency of beef cattle; current state of the art and future challenges. Animal. Invited Review, 12(9) 1815-1826.

Fitzsimons C, McGee M, Keogh K, Waters SM and Kenny DA. 2017. Molecular Physiology of Feed Efficiency in Beef Cattle (Chapter 6). In: The Biology of Domestic Animals. C.G. Scanes and R.A. Hill (Eds). CRC Press. Boca Raton.

Sabine Scully

Emily Roskam

Steven McLoughlin

Stephanie O’Donoghue