Rodrigo Ortega Polo

Image Rodrigo Ortega Polo
Biology Study Leader - Bioinformatics

I am the head of the Bioinformatics Research Support Unit at the Lethbridge Research and Development Centre. Our unit designs, develops and conducts collaborative science activities in genomics, bioinformatics and big data applications in support of research programs. I lead technology adoption in science programs, and I help to developing training programs for staff. I also collect, compile, analyse, and interpret research data from research studies.

Agriculture and Agri-Food Canada
5403 1st Avenue South, Lethbridge, Alberta

Current research and/or projects

Grants Held – Principal Investigator

Grants Held – Co-investigator

Collaborations

  • Old plots, new hypotheses: Toward a revitalized AAFC long-term agroecosystem experiment (LTAE) network. AAFC A-base. PIs: Charles Geddes & Mervin St. Luce.
  • Increasing photosynthetic efficiency. AAFC A-base. PI: Stacy Singer
  • Phenomics and digital imaging. AAFC A-base. PI: Anne Smith
  • Pan-genome of tan spot (Pyrenophora tritici-repentis). PI: Reem Abboukhaddour
  • Multi-omics strategy to investigate liver abscess development in beef cattle. BCRC. PI: Robert Gruninger.
  • STEC in Cattle and Clinical Infections. BCRC. PI: Tim McAllister
  • Rumen adaptation to seaweed consumption. AAFC A-base. PI: D. Wade Abbott
  • Bacterial therapeutic administration. BCRC. PI: Trevor Alexander

Building bioinformatics capacity in AAFC as member of the Bioinformatics and Big Data Research Support Network (BSRN) and in Alberta as member of BioNet Alberta.

Professional activities / interests

  • Bioinformatics education and training
  • Metagenomics and microbiome profiles in agricultural systems
  • Genomics of bacteria, fungal plant pathogens, and cereal crops
  • Data portals
  • Workflow management systems (e.g. Nextflow/nf-core, Snakemake)
  • High performance computing
  • Mining of publicly available data

Education and awards

  • Master of Science, University of Lethbridge
  • Bachelor of Science, University of Lethbridge

International experience and/or work

Attended the workshop Managing a Bioinformatics Core Facility at the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK (June, 2019)

Member of the organizing committee of the Bioinfo-Core Community of Special Interest. Co-chaired the Bioinfo-Core session in the ISMB 2020 virtual conference.

Additional links

BioNet Alberta

Bioinfo-Core

Key publications

  1. K.D. Singh, S.D. Noble, P. Ravichandran, K. Halcro, R. Soolanayakanahally, J. Sangha, E. Brauer, K.T. Nilsen, O. Molina, H.S. Randhawa, R. Ortega Polo, C. Workman, S. Pahari, “Unmanned Ground Vehicle for High-throughput Phenotyping to Quantify Field Crops Characteristics”, NAPPN Annual Conference, West Lafayette, Indiana, USA, February, 2024 (Hybrid); https://doi.org/10.22541/essoar.170008912.21420303/v1

    2024 - View publication details

  2. Cunningham MM, Deckers T, Ho J, Wizenberg SB, Lansing L, Tran L, Zorz J, Pepinelli M, French S, Conflitti IM, Ortega Polo R, Hoover S, Currie R, Pernal SF, Giovenazzo P, Zayed A, Foster LJ, Jabbari H, Guarna MM (2023) Sub-lethal pesticide exposure in field trials may alter microbial composition of the honey bee gut microbiome. 48th International Apimondia Congress, p. 222, 4-8 Sep 2024, Santiago, Chile. (Poster) https://apimondia2023.com/docs/abstract-book.pdf

    2023 - View publication details

  3. Guarna MM, Cunningham MM, Tran L, Ortega Polo R, Pernal SF, Griffiths JS, Murcia-Morales M, Fernández-Alba AR, Bilodeau GJ, Rott ME (2023) Bee-mediated monitoring of pesticides, pathogens, and emerging threats. 48th International Apimondia Congress, p. 49, 4-8 Sep 2024, Santiago, Chile.
    https://apimondia2023.com/docs/abstract-book.pdf

    2023 - View publication details

  4. Liu, X.; Floate, K.D.; Gorzelak, M.A.; Holman, D.B.; Hrycauk, S.; Kubota, H.; Lupwayi, N.; Neilson, J.A.D.; Ortega Polo, R.; Petri, R.M.; Tran, L.; Wang, H.; Wilches, D.; Yang, X.; Zorz, J.; Guarna, M.M. Prairie Agroecosystems: Interconnected Microbiomes of Livestock, Soil and Insects. Agriculture 2023, 13, 326. https://doi.org/10.3390/agriculture13020326

    2023 - View publication details

  5. Raičević J , Cunningham M, Griffiths JS, Wu L, Pernal, SF, Deckers T, Tran L, Ortega Polo, Zorz J, Clarke K, Newman T, Lansing L, Rott ME, Bilodeau GJ, Bishop C, Jabbari H, Guarna MM (2022) Honey bees as biomonitors of plant pathogens, pesticides, and antimicrobial resistance. EurBee 9 – 9th European Congress of Apidology Proceedings, p. 352, 20-22 September 2022, Belgrade, Serbia. (Poster) https://zenodo.org/record/7239012#.Y4BgMnbMKUk

    2022 - View publication details

  6. Vishwakarma S, Mesina L, Lam K, Ryabov M, Lansing L, Chen G, Guarna MM, Ortega Polo R. BeeBiome.info: a portal for increasing the accessibility of bee microbiome data. North America Bee Research Conference – virtual; Jan 13 – 14, 2022.

    2022 - View publication details

  7. Cunningham MM, Tran L, McKee CG, Ortega-Polo R, Newman T, Lansing L, Griffiths JS, Bilodeau GJ, Rott M, Guarna MM. Bee-based environmental biomonitoring of pesticides, pollutants, and pathogens. North America Bee Research Conference. Virtual, Jan 13-14, 2022

    2022 - View publication details

  8. Cunningham, M.M., Tran, L., McKee, C.G., Ortega Polo, R., Newman, T., Lansing, L., Griffiths, J.S., Bilodeau, G.J., Rott, M., Marta Guarna, M. (2022). Honey bees as biomonitors of environmental contaminants, pathogens, and climate change, 134 http://dx.doi.org/10.1016/j.ecolind.2021.108457

    2022 - View publication details

  9. Tran L, Newman T, Cunningham M M, Lansing L, Gregoris A, Ortega Polo R, Guarna MM (2021) DNA sequencing approaches for gut microbiome analyses of highbush blueberry-pollinating honey bees (Apis mellifera). Entomology 2021, 69th Annual Meeting of the Entomological Society of America, 31 Oct - 03 Nov, Denver, CO, hybrid meeting proceedings

    2021 - View publication details

  10. Tran, L., Newman, T., Lansing, L., Gregoris, A., Ortega Polo, R., Guarna, M.M. Analysis of sample types and sequencing methods for optimal characterization of the honey bee (Apis mellifera) gut microbiome. Intelligent Systems for Molecular Biology, 25-30 July 2021 (virtual meeting)

    2021 - View publication details

  11. Tran, L., Medici de Mattos, I., Ortega Polo, R., Cunningham, M., Simko, E., Guarna, M.M. Gut microbiome response to protective treatments against Nosema sp. Infection in the honey bee (Apis mellifera) gut microbiome. World Microbe Forum, 20-24 June 2021 (virtual meeting)

    2021 - View publication details

  12. Moote, P.E., Bescucci, D.M., Polo, R.O., Uwiera, R.R.E., Inglis, G.D. (2021). Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine. Applied and Environmental Microbiology, [online] 87(9), 1-23. http://dx.doi.org/10.1128/AEM.00088-21

    2021 - View publication details

  13. Ortega-Polo R, Vishwakarma S, Tran L, Gregoris A, Guarna MM (2020) A reproducible workflow for amplicon-based microbial community analysis using the drake R package. Bioinformatics Community Conference. 19-21 July 2020, virtual meeting. https://bcc2020.github.io/

    2020 - View publication details

  14. Ortega Polo, R., Gregoris, A., Tran, L., Vishwakarma, S. & Guarna, M. M. Evaluation of the impact of sequencing depth and choice of bioinformatics methods in the taxonomic and functional profiling of the honeybee (Apis mellifera) microbiome. 28th Conference on Intelligent Systems for Molecular Biology. Virtual conference. July 13-16, 2020

    2020 - View publication details

  15. Ragupathy R, Larsen JR, Frick M, Cattani DJ, Miller J, Elwood J, Zezula A, OrtegaPolo R, Soto-Cerda BJ, Laroche A. 2020. Genomic prediction of heading date in intermediate wheatgrass (Thinopyrum intermedium). PAG XXVIII Conference PE0510

    2020 - View publication details

  16. Bescucci, D.M., Moote, P.E., Polo, R.O., Uwiera, R.R.E., Inglis, G.D. (2020). Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine. Applied and Environmental Microbiology, [online] 86(21), http://dx.doi.org/10.1128/AEM.01569-20

    2020 - View publication details

  17. Zaheer, R., Lakin, S.M., Polo, R.O., Cook, S.R., Larney, F.J., Morley, P.S., Booker, C.W., Hannon, S.J., Van Domselaar, G., Read, R.R., McAllister, T.A. (2019). Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent. BMC Microbiology, [online] 19(1), http://dx.doi.org/10.1186/s12866-019-1548-x

    2019 - View publication details

  18. Inglis, G.D., Duke, G.M., Goettel, M.S., Kabaluk, J.T., Ortega-Polo, R. (2019). Biogeography and genotypic diversity of metarhizium brunneum and metarhizium robertsii in northwestern North American soils. Canadian Journal of Microbiology, [online] 65(4), 261-281. http://dx.doi.org/10.1139/cjm-2018-0297

    2019 - View publication details

Contact

Research facility

Lethbridge Research and Development Centre
5403 1st Avenue South
Lethbridge, AB T1J 4B1
Canada

Expertise

Agriculture›Bioinformatics
Information Technology›Big Data›Genomics

Affiliations

  • Member of the International Society for Computational Biology (ISCB)
  • Member of the Bioinformatics Network Alberta (BioNet Alberta)
  • Member of the Canadian Society of Microbiologists (CSM)
  • Member of the Bee Microbiome Consortium (BeeBiome)
  • Member of the Prevention of Honey Bee Colony Losses International Honey Bee Research Association (COLOSS)
  • AAFC Bioinformatics Research Support Network. Former Science & Technology co-chair and deputy co-chair.
  • Member of the AAFC Bioinformatics Directors Group (STB liaison)

Language

English
French

Other languages

Spanish