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

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

  • Gruninger RJ*, Nguyen TTM, Reid I, Yanke LJ, Wang P, Abbott DW Tsang AT, McAllister TA*.(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 9:1581 *corresponding authors

  • Huws SA, Creevey C, See all  Boniface Oyama L , Mizrahi I, Denman SE, Popova M, Munoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan S, Yanez-Ruiz DR, Belanche A, Guan LL, Gruninger RJ, McAllister TA, Newbold J, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart E, Kingston-Smith A,  Scollan N, Do Prado RM, Pilau E, Mantovani HC, Attwood GT, Edwards JE, McEwan N, Morrison S, Mayorga O, Elliott C and Morgavi DP. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future. Frontiers in Microbiology, 9:2161.

  • Terry SA, Ribeiro GO, Gruninger RJ, Hunerberg M, Sheng P, Chaves AV, Beauchemin KA, McAllister TA. (2018) The effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions and rumen microbiota in beef heifers. J Animal Science 96:3863-3877

  • Azad E, Derakhshani H, Forster R, Gruninger RJ, Acharya S, McAllister TA, Khafipour E. (2018), Characterization of the rumen microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat preventive strategies. Sci Rep. In press.

  • Gruninger RJ, Riberio G, McAllister TA. (2018). Strategies for improving digestion of forages in ruminants. Cornell Nutrition Conference. 10-18.

  • Gruninger RJ*, Forster J, McAllister TA*. (2018) Isolation of high quality RNA for metatranscriptomic analysis of lignocellulose digestion in the rumen. Methods Mol Biol. 1775:75-82  *corresponding authors

  • Sesheda R, Sinead LA, Hungate 1000 Project Collaborators*, William Kelly. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology 36(4):359-367 *I am a project collaborator

  • Cameron A, Klima CL, Ha R, Gruninger RJ, Zaheer R, McAllister TA. (2018) A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens.. 3(1). pii: e00568-17.

  • Ribeiro GO, Oss DB, He Z, Gruninger RJ, Elekwachi C, Forster RJ, Yang W, Beauchemin KA, McAllister TA. (2017) Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle. Sci Rep 7(1):1276

  • Brudner L, Gruninger RJ, Cleland CP, Mosimann SC. (2017) Bacterial protein tyrosine phosphatase-like myo-inositol phosphatases, PhyA, in complex with the Ins (1, 3, 4, 5) P4 and Ins (1, 4, 5) P3 second messengers. J. Biol. Chem 292(42):17302-17311

  • Jones DR*, Uddin MS*, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW. (2017) Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl-substrates. J Biol Chem 292(30):12606-12620

  • Gruninger RJ*, Reid I, Forster RJ, Tsang AT, McAllister TA. (2017) Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics. Methods Mol Biol. 2017;1588:279-298. *Corresponding author

  • Gruninger RJ*, Tsang AT, McAllister TA (2017) Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry. Methods Mol Biol;1588:299-308.  *Corresponding author

  • Gruninger RJ*, McAllister TA, Forster RJ (2016) Bacterial and Archaeal diversity in the gastrointestinal tract of the North American Beaver (Castor Canadensis). PLoS One 11(5): e0156457 *Corresponding author

  • Ribero G, Gruninger RJ, Badhan A, McAllister TA. (2016). Mining the rumen for fibrolytic feed enzymes. Invited Review. Animal Frontiers 6(2):20-26

  • Gruninger RJ*, Cote C, McAllister TA. Abbott DW*. (2016) Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases. Biochemical J. 473:839-849 *co-corresponding author

  • Sobhanifar S*, Worrall LJ*, Gruninger RJ, Wasney G, Blaukopf M, Baumann L, Lameignere E, Solomonson M, Brown ED, Withers SG, Strynadka NC. (2015) An intimate look at the structure and mechanism of a Staphylococcus aureus wall teichoic acid α-glycosyltransferase. Proceedings of the National Academy of Science. 112:E576-85 *equal contributions

  • Nkema VN, Gilroyed B, Yanke J, Gruninger RJ, Vedres D, McAllister TA, Hao X. (2015) Bioaugmentation with anaerobic fungi in a two-stage process for biohydrogen and biogas productions using corn silage and cattail. Bioresourc Technol 185:79-88

  • Badhan A, Wang YX, Gruninger R, Patton D, Powlowski J, Tsang A, McAllister T. (2015) Improvement in saccharification yield from rumen mixed enzymes by identification of recalcitrant cell wall constituents using enzyme fingerprinting. Special issue of Biomed Res Int2015:562952

  • Gruninger RJ, Puniya A, Callaghan T, Edwards J, Youssef N, Dagar S, Fliegerová K, Griffith G, Forster R, Tsang A, McAllister Tim, Elshahed M. (2014) Anaerobic Fungi (Phylum Neocallimastigomycota): Advances in understanding of their taxonomy, life cycle, ecology, role, and biotechnological potential. Invited Review. FEMS Microbiol Ecol. 90: 1-17

  • Badhan A, Wang A, Gruninger R, Patton D, Powlowski J, Tsang A, McAllister T (2014) Formulation of enzyme blends to maximize the hydrolysis of alkaline peroxide pretreated alfalfa hay and barley straw by rumen enzymes and commercial cellulases. BMC Biotechnology 14(1): 31

  • Gruninger RJ, Thibault J, Capeness MJ, Till R, Selinger B, Sockett R, Mosimann SC, Lovering AL. (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.

  • Gruninger RJ, Paterson L, McAllister TA, Forster RJ (2014) Diversity of rumen bacteria in wild Canadian Ruminants. PLoS ONE. 9(2): e89682.

  • Gruninger RJ, Gong X, Forster RJ, McAllister TA (2013) Biochemical and kinetic characterization of the multifunctional b-Glucosidase/b-xylosidase/a-arabinosidase, Bgxa1. Appl. Microbiol. Biotechnol. 98(7): 3003-12

  • Solomonson M, Wasney GA, Watanabe N, Gruinger RJ, Prehna G, Strynadka NC. (2013) Structure of the mycosin-1 protease from the mycobacterial ESX-1 type VII secretion system. J Biol Chem. 288(24): 17782-90

  • Gong X, Gruninger RJ, Qi M, Paterson M, Forster RJ, Teather RM, McAllister TA. (2012) Cloning and identification of novel hydrolase genes from a dairy cow rumen metagenomic library and characterization of a cellulase gene BMC Research Notes, 5:566

  • King DK, Worrall LJ, Gruninger RJ, Strynadka NC. (2012) New Delhi Metallo-b-Lactamase: Structural Insights into b-Lactam Recognition and Inhibition. J. Am. Chem. Soc. 134(28): 11362-11365

  • Gong X*, Gruninger RJ*, Forster RJ, Teather RM, McAllister TA. (2012) Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen derived metagenomic library. Appl Microbiol. Biotechnol. 97(6): 2423-31 Equal contribution

  • Gruninger RJ, Dobing S, Smith AD, Bruder LM, Selinger LB, Wieden HJ, Mosimann SC. (2012) Substrate binding in protein tyrosine phosphatase-like inositol polyphosphatases. J. Biol Chem. 287(13): 9722-30

  • Capyk JK, Casabon I, Gruninger RJ, Strynadka NC, Eltis DL. (2011) Specificity of KshAB indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. J Biol Chem. 286(47): 40717-24

  • Gruninger RJ, Selinger LB, Mosimann SC. (2009) Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase. J. Mol. Biol. 392:75–86.

  • Gruninger RJ, Selinger LB, Mosimann SC. (2008) Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase like phytase, PhyAsr. FEBS J. 275:3783–3792.

  • Puhl AA*, Gruninger RJ*, Greiner R, Janzen TW, Mosimann SC, Selinger LB. (2007) Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase. Protein Sci. 16:1368–1378. Equal contribution

  • Gruninger RJ*, Nguyen TTM, Reid I, Yanke LJ, Wang P, Abbott DW Tsang AT, McAllister TA*.(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 9:1581 *corresponding authors

  • Huws SA, Creevey C, See all  Boniface Oyama L , Mizrahi I, Denman SE, Popova M, Munoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan S, Yanez-Ruiz DR, Belanche A, Guan LL, Gruninger RJ, McAllister TA, Newbold J, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart E, Kingston-Smith A,  Scollan N, Do Prado RM, Pilau E, Mantovani HC, Attwood GT, Edwards JE, McEwan N, Morrison S, Mayorga O, Elliott C and Morgavi DP. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future. Frontiers in Microbiology, 9:2161.

  • Terry SA, Ribeiro GO, Gruninger RJ, Hunerberg M, Sheng P, Chaves AV, Beauchemin KA, McAllister TA. (2018) The effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions and rumen microbiota in beef heifers. J Animal Science 96:3863-3877

  • Azad E, Derakhshani H, Forster R, Gruninger RJ, Acharya S, McAllister TA, Khafipour E. (2018), Characterization of the rumen microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat preventive strategies. Sci Rep. In press.

  • Gruninger RJ, Riberio G, McAllister TA. (2018). Strategies for improving digestion of forages in ruminants. Cornell Nutrition Conference. 10-18.

  • Gruninger RJ*, Forster J, McAllister TA*. (2018) Isolation of high quality RNA for metatranscriptomic analysis of lignocellulose digestion in the rumen. Methods Mol Biol. 1775:75-82  *corresponding authors

  • Sesheda R, Sinead LA, Hungate 1000 Project Collaborators*, William Kelly. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology 36(4):359-367 *I am a project collaborator

  • Cameron A, Klima CL, Ha R, Gruninger RJ, Zaheer R, McAllister TA. (2018) A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens.. 3(1). pii: e00568-17.

  • Ribeiro GO, Oss DB, He Z, Gruninger RJ, Elekwachi C, Forster RJ, Yang W, Beauchemin KA, McAllister TA. (2017) Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle. Sci Rep 7(1):1276

  • Brudner L, Gruninger RJ, Cleland CP, Mosimann SC. (2017) Bacterial protein tyrosine phosphatase-like myo-inositol phosphatases, PhyA, in complex with the Ins (1, 3, 4, 5) P4 and Ins (1, 4, 5) P3 second messengers. J. Biol. Chem 292(42):17302-17311

  • Jones DR*, Uddin MS*, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW. (2017) Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl-substrates. J Biol Chem 292(30):12606-12620

  • Gruninger RJ*, Reid I, Forster RJ, Tsang AT, McAllister TA. (2017) Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics. Methods Mol Biol. 2017;1588:279-298. *Corresponding author

  • Gruninger RJ*, Tsang AT, McAllister TA (2017) Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry. Methods Mol Biol;1588:299-308.  *Corresponding author

  • Gruninger RJ*, McAllister TA, Forster RJ (2016) Bacterial and Archaeal diversity in the gastrointestinal tract of the North American Beaver (Castor Canadensis). PLoS One 11(5): e0156457 *Corresponding author

  • Ribero G, Gruninger RJ, Badhan A, McAllister TA. (2016). Mining the rumen for fibrolytic feed enzymes. Invited Review. Animal Frontiers 6(2):20-26

  • Gruninger RJ*, Cote C, McAllister TA. Abbott DW*. (2016) Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases. Biochemical J. 473:839-849 *co-corresponding author

  • Sobhanifar S*, Worrall LJ*, Gruninger RJ, Wasney G, Blaukopf M, Baumann L, Lameignere E, Solomonson M, Brown ED, Withers SG, Strynadka NC. (2015) An intimate look at the structure and mechanism of a Staphylococcus aureus wall teichoic acid α-glycosyltransferase. Proceedings of the National Academy of Science. 112:E576-85 *equal contributions

  • Nkema VN, Gilroyed B, Yanke J, Gruninger RJ, Vedres D, McAllister TA, Hao X. (2015) Bioaugmentation with anaerobic fungi in a two-stage process for biohydrogen and biogas productions using corn silage and cattail. Bioresourc Technol 185:79-88

  • Badhan A, Wang YX, Gruninger R, Patton D, Powlowski J, Tsang A, McAllister T. (2015) Improvement in saccharification yield from rumen mixed enzymes by identification of recalcitrant cell wall constituents using enzyme fingerprinting. Special issue of Biomed Res Int2015:562952

  • Gruninger RJ, Puniya A, Callaghan T, Edwards J, Youssef N, Dagar S, Fliegerová K, Griffith G, Forster R, Tsang A, McAllister Tim, Elshahed M. (2014) Anaerobic Fungi (Phylum Neocallimastigomycota): Advances in understanding of their taxonomy, life cycle, ecology, role, and biotechnological potential. Invited Review. FEMS Microbiol Ecol. 90: 1-17

  • Badhan A, Wang A, Gruninger R, Patton D, Powlowski J, Tsang A, McAllister T (2014) Formulation of enzyme blends to maximize the hydrolysis of alkaline peroxide pretreated alfalfa hay and barley straw by rumen enzymes and commercial cellulases. BMC Biotechnology 14(1): 31

  • Gruninger RJ, Thibault J, Capeness MJ, Till R, Selinger B, Sockett R, Mosimann SC, Lovering AL. (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.

  • Gruninger RJ, Paterson L, McAllister TA, Forster RJ (2014) Diversity of rumen bacteria in wild Canadian Ruminants. PLoS ONE. 9(2): e89682.

  • Gruninger RJ, Gong X, Forster RJ, McAllister TA (2013) Biochemical and kinetic characterization of the multifunctional b-Glucosidase/b-xylosidase/a-arabinosidase, Bgxa1. Appl. Microbiol. Biotechnol. 98(7): 3003-12

  • Solomonson M, Wasney GA, Watanabe N, Gruinger RJ, Prehna G, Strynadka NC. (2013) Structure of the mycosin-1 protease from the mycobacterial ESX-1 type VII secretion system. J Biol Chem. 288(24): 17782-90

  • Gong X, Gruninger RJ, Qi M, Paterson M, Forster RJ, Teather RM, McAllister TA. (2012) Cloning and identification of novel hydrolase genes from a dairy cow rumen metagenomic library and characterization of a cellulase gene BMC Research Notes, 5:566

  • King DK, Worrall LJ, Gruninger RJ, Strynadka NC. (2012) New Delhi Metallo-b-Lactamase: Structural Insights into b-Lactam Recognition and Inhibition. J. Am. Chem. Soc. 134(28): 11362-11365

  • Gong X*, Gruninger RJ*, Forster RJ, Teather RM, McAllister TA. (2012) Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen derived metagenomic library. Appl Microbiol. Biotechnol. 97(6): 2423-31 Equal contribution

  • Gruninger RJ, Dobing S, Smith AD, Bruder LM, Selinger LB, Wieden HJ, Mosimann SC. (2012) Substrate binding in protein tyrosine phosphatase-like inositol polyphosphatases. J. Biol Chem. 287(13): 9722-30

  • Capyk JK, Casabon I, Gruninger RJ, Strynadka NC, Eltis DL. (2011) Specificity of KshAB indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. J Biol Chem. 286(47): 40717-24

  • Gruninger RJ, Selinger LB, Mosimann SC. (2009) Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase. J. Mol. Biol. 392:75–86.

  • Gruninger RJ, Selinger LB, Mosimann SC. (2008) Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase like phytase, PhyAsr. FEBS J. 275:3783–3792.

  • Puhl AA*, Gruninger RJ*, Greiner R, Janzen TW, Mosimann SC, Selinger LB. (2007) Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase. Protein Sci. 16:1368–1378. Equal contribution