Dr. Robert J Gruninger

Research Scientist

Application of a multi -omics approach to the gut microbiome in cattle, rumen microbiology, and functional genomics of rumen microbes

Current research and/or projects

A microbiome is a community of microbes that inhabits a particular environment. These communities can be complex and consist of many different types of microbes including bacteria, archaea, fungi, protozoa and viruses. The microbial community that inhabits the gut is highly diverse and plays and essential role in digestion and heath. Ruminants (cows, goats, sheep, deer, etc) have a speciallized chamber in their gastrointestinal tract called a rumen that functions in the digestion of ingested plant material. The rumen microbiome is responsible for the efficient digestion of plant carbohydrates and the conversion of these sugars into volatile fatty acids which serve as the animal's energy source. The microbes in the rumen are also the primary source of protein used by ruminants for growth. My research is focused on applying state of the art genomic techniques, classical microbiology, and protein biochemistry to understand how the microbes in gastrointestinal tract of cattle influence the health and efficiency of the animal. Ultimately the goal is to improve the health and efficiency of cattle.

Research and/or project statements

  • Development of pretreatment technology to improve the digestion of crop by-products.
  • Impact of diet on the gut microbiome in ruminants.
  • Impact of in-feed methane inhibitors on the function of the rumen microbiome.
  • Discovery and characterization of novel carbohydrate degrading enzymes in rumen microbes.
  • Role of the gut microbiome in animal health.

Education and awards

  • PhD Biochemistry, University of Lethbridge, 2009.
  • BSc (Hons.) Biochemistry, University of Lethbridge, 2005.

Awards and Honours:

  • Mentee in the Beef Cattle Research Council Mentorship program (2017-2018).
  • NSERC Government lab visiting fellowship (2014-2016).
  • Michael Smith Foundation for Health Research Fellowship (2009-2012).
  • NSERC Canadian Graduate Doctoral Award (2006-2009).
  • NSERC Canadian Graduate Masters Award (2005-2006).
  • Alberta Ingenuity Graduate Studies Award (2005-2009).
  • Top Biochemistry Graduate Award, University of Lethbridge (2005).

Key publications

  1. Zhang, X.M., Smith, M.L., Gruninger, R.J., Kung, L., Vyas, D., McGinn, S.M., Kindermann, M., Wang, M., Tan, Z.L., Beauchemin, K.A. (2021). Combined effects of 3-nitrooxypropanol and canola oil supplementation on methane emissions, rumen fermentation and biohydrogenation, and total tract digestibility in beef cattle, 99(4), http://dx.doi.org/10.1093/jas/skab081

    2021 - View publication details

  2. Abbott, D.W., Aasen, I.M., Beauchemin, K.A., Grondahl, F., Gruninger, R., Hayes, M., Huws, S., Kenny, D.A., Krizsan, S.J., Kirwan, S.F., Lind, V., Meyer, U., Ramin, M., Theodoridou, K., Soosten, D.V., Walsh, P.J., Waters, S., Xing, X. (2020). Seaweed and seaweed bioactives for mitigation of enteric methane: Challenges and opportunities, 10(12), 1-28. http://dx.doi.org/10.3390/ani10122432

    2020 - View publication details

  3. Gruninger, R.J., Ribeiro, G.O., Cameron, A., McAllister, T.A. (2019). Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants, 13(9), 1843-1854. http://dx.doi.org/10.1017/S1751731119000752

    2019 - View publication details

  4. Huws, S.A., Creevey, C.J., Oyama, L.B., Mizrahi, I., Denman, S.E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S.M., Hess, M., Tapio, I., Smidt, H., Krizsan, S.J., Yáñez-Ruiz, D.R., Belanche, A., Guan, L., Gruninger, R.J., McAllister, T.A., Newbold, C.J., Roehe, R., Dewhurst, R.J., Snelling, T.J., Watson, M., Suen, G., Hart, E.H., Kingston-Smith, A.H., Scollan, N.D., Do Prado, R.M., Pilau, E.J., Mantovani, H.C., Attwood, G.T., Edwards, J.E., McEwan, N.R., Morrisson, S., Mayorga, O.L., Elliott, C., Morgavi, D.P. (2018). Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future, 9(SEP), http://dx.doi.org/10.3389/fmicb.2018.02161

    2018 - View publication details

  5. Gruninger, R.J., Nguyen, T.T.M., Reid, I.D., Yanke, J.L., Wang, P., Abbott, D.W., Tsang, A., McAllister, T. (2018). Application of transcriptomics to compare the carbohydrate active enzymes that are expressed by diverse genera of anaerobic fungi to degrade plant cell wall carbohydrates, 9(JUL), http://dx.doi.org/10.3389/fmicb.2018.01581

    2018 - View publication details

  6. Seshadri, R., Leahy, S.C., Attwood, G.T., Teh, K.H., Lambie, S.C., Cookson, A.L., Eloe-Fadrosh, E.A., Pavlopoulos, G.A., Hadjithomas, M., Varghese, N.J., Paez-Espino, D., Perry, R., Henderson, G., Creevey, C.J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N.C., Henrissat, B., Woyke, T., Ivanova, N.N., Kelly, W.J., Palevic, N., Janssen, P.H., Ronimus, R.S., Noel, S., Soni, P., Reilly, K., Atherly, T., Ziemer, C., Wright, A., Ishaq, S., Cotta, S., Thompson, S., Crosley, K., McKain, S., Wallace, R.J., Flint, H.J., Martin, J.C., Forster, R.J., Gruninger, R.J., McAllister, T., Gilbert, R., Ouwerkerk, R.J., Klieve, R.J., Jassim, R.A., Denman, S., McSweeney, C., Rosewarne, S., Koike, S., Kobayashi, Y., Mitsumori, M., Shinkai, T., Cravero, S., Cerón Cucchi, T. (2018). Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection, 36(4), 359-367. http://dx.doi.org/10.1038/nbt.4110

    2018 - View publication details

  7. Nkemka, V.N., Gilroyed, B., Yanke, J., Gruninger, R., Vedres, D., McAllister, T., Hao, X. (2015). Bioaugmentation with an anaerobic fungus in a two-stage process for biohydrogen and biogas production using corn silage and cattail, 185 79-88. http://dx.doi.org/10.1016/j.biortech.2015.02.100

    2015 - View publication details

  8. Badhan, A., Wang, Y.X., Gruninger, R., Patton, D., Powlowski, J., Tsang, A., McAllister, T.A. (2015). Improvement in saccharification yield of mixed rumen enzymes by identification of recalcitrant cell wall constituents using enzyme fingerprinting, 2015 http://dx.doi.org/10.1155/2015/562952

    2015 - View publication details

  9. Gruninger, R.J., Thibault, J.-N., Capeness, M.J., Till, R., Mosimann, S.C., Sockett, R.E., Selinger, L.B., and Lovering, A.L. (2014). "Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.", PLoS ONE, 9(4: e94403). doi : 10.1371/journal.pone.0094403

    2014 - View publication details

  10. Gruninger, R.J., Sensen, C.W., McAllister, T.A., Forster, R.J. (2014). Diversity of rumen bacteria in Canadian cervids, 9(2), http://dx.doi.org/10.1371/journal.pone.0089682

    2014 - View publication details

  11. Gruninger, R.J., Gong, X., Forster, R.J., McAllister, T.A. (2014). Biochemical and kinetic characterization of the multifunctional β-glucosidase/β-xylosidase/α-arabinosidase, Bgxa1, 98(7), 3003-3012. http://dx.doi.org/10.1007/s00253-013-5191-4

    2014 - View publication details

  12. Gruninger, R.J., Puniya, A.K., Callaghan, T.M., Edwards, J.E., Youssef, N., Dagar, S.S., Fliegerova, K., Griffith, G.W., Forster, R., Tsang, A., Mcallister, T., Elshahed, M.S. (2014). Anaerobic fungi (phylum Neocallimastigomycota): Advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential, 90(1), 1-17. http://dx.doi.org/10.1111/1574-6941.12383

    2014 - View publication details

  13. Gong, X., Gruniniger, R.J., Forster, R.J., Teather, R.M., McAllister, T.A. (2013). Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen-derived metagenomic library, 97(6), 2423-2431. http://dx.doi.org/10.1007/s00253-012-4088-y

    2013 - View publication details

  14. Gong, X., Gruninger, R.J., Qi, M., Paterson, L., Forster, R.J., Teather, R.M., McAllister, T.A. (2012). Cloning and identification of novel hydrolase genes from a dairy cow rumen metagenomic library and characterization of a cellulase gene, 5 http://dx.doi.org/10.1186/1756-0500-5-566

    2012 - View publication details