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

Agriculture and Agri-Food Canada

Lethbridge, AB

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

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. Journal of Animal Science, [online] 99(4), http://dx.doi.org/10.1093/jas/skab081
2021 - View publication details
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
Zhang, X.M., Gruninger, R.J., Alemu, A.W., Wang, M., Tan, Z.L., Kindermann, M., Beauchemin, K.A. (2020). 3-Nitrooxypropanol supplementation had little effect on fiber degradation and microbial colonization of forage particles when evaluated using the in situ ruminal incubation technique. Journal of Dairy Science (JDS), [online] 103(10), 8986-8997. http://dx.doi.org/10.3168/jds.2019-18077
2020 - View publication details
Terry, S.A., Ribeiro, G.O., Conrad, C.C., Beauchemin, K.A., McAllister, T.A., Gruninger, R.J. (2020). Pretreatment of crop residues by ammonia fiber expansion (AFEX) alters the temporal colonization of feed in the rumen by rumen microbes. FEMS Microbiology Ecology, [online] 96(6), http://dx.doi.org/10.1093/femsec/fiaa074
2020 - View publication details
Ribeiro, G.O., Gruninger, R.J., Jones, D.R., Beauchemin, K.A., Yang, W.Z., Wang, Y., Abbott, D.W., Tsang, A., McAllister, T.A. (2020). Effect of ammonia fiber expansion-treated wheat straw and a recombinant fibrolytic enzyme on rumen microbiota and fermentation parameters, total tract digestibility, and performance of lambs. Journal of Animal Science, [online] 98(5), http://dx.doi.org/10.1093/jas/skaa116
2020 - View publication details
Azad, E., Derakhshani, H., Forster, R.J., Gruninger, R.J., Acharya, S., McAllister, T.A., Khafipour, E. (2019). Characterization of the rumen and fecal microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat prevention strategies. Scientific Reports, [online] 9(1), http://dx.doi.org/10.1038/s41598-019-41017-3
2019 - View publication details
Terry, S.A., Ribeiro, G.O., Gruninger, R.J., Chaves, A.V., Beauchemin, K.A., Okine, E., McAllister, T.A. (2019). A Pine Enhanced Biochar Does Not Decrease Enteric CH4 Emissions, but Alters the Rumen Microbiota. Frontiers in Veterinary Science, [online] 6 http://dx.doi.org/10.3389/fvets.2019.00308
2019 - View publication details
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
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
Terry, S.A., Ribeiro, G.d.O., Gruninger, R.J., Hunerberg, M., Ping, S., Chaves, A.V., Burlet, J., Beauchemin, K.A., McAllister, T.A. (2018). Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers. Journal of Animal Science, [online] 96(9), 3863-3877. http://dx.doi.org/10.1093/jas/sky265
2018 - View publication details
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. Frontiers in Microbiology, [online] 9(JUL), http://dx.doi.org/10.3389/fmicb.2018.01581
2018 - View publication details
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
Cameron, A., Klima, C.L., Ha, R., Gruninger, R.J., Zaheer, R., McAllister, T.A. (2018). A novel aadA aminoglycoside resistance gene in bovine and porcine pathogens. mSphere, [online] 3(1), http://dx.doi.org/10.1128/MSPHERE.00568-17
2018 - View publication details
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. Bioresource Technology, [online] 185 79-88. http://dx.doi.org/10.1016/j.biortech.2015.02.100
2015 - View publication details
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. BioMed Research International, [online] 2015 http://dx.doi.org/10.1155/2015/562952
2015 - View publication details
Gruninger, R.J., Thibault, J., Capeness, M.J., Till, R., Mosimann, S.C., Sockett, R.E., Selinger, B.L., 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, [online] 9(4), http://dx.doi.org/10.1371/journal.pone.0094403
2014 - View publication details
Gruninger, R.J., Sensen, C.W., McAllister, T.A., Forster, R.J. (2014). Diversity of rumen bacteria in Canadian cervids. PLoS ONE, [online] 9(2), http://dx.doi.org/10.1371/journal.pone.0089682
2014 - View publication details
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
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
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