D. Wade Abbott, PhD

Image Wade Abbott
Research Scientist

Agricultural Glycomics

Functional Genomics of Carbohydrate Utilization

Agriculture and Agri-Food Canada
Lethbridge Research and Development Centre

Current research and/or projects

  1. Principal Investigator. Abbott DW, Alexander, T, Thomas, D. Title: “Evidence-based prebiotic-probiotic solutions for improving gut health and feed efficiency in cattle.” Beef and Cattle Research Council. Requested: Apr 2018-Mar 2023.

  2. Principal Investigator. Abbott DW, Inglis GD, Slominski B.  Title: “Discovery pipeline for rapid development of tailored fibrolytic enzymes that improve the digestibility of canola meal for monogastric livestock” Agriculture Funding Consortium. Apr 2018-Mar 2020.

  3. Principal Investigator. Abbott DW, Thomas, D. Title: “Discovery of novel carbohydrate active enzymes for generating novel bioproducts from agricultural residues using whole genome and microbiome sequence datasets.” Abase-AAFC. Apr 2018-Mar2021.

  4. Co-Applicant. Brumer, H (PI), Inglis, GD (Co-PI), Abbott DW, Uwiera, RRE. Title: “Glyco-Cage.” GlycoNet. Jul 2017-Jun 2019.

  5. Principal Investigator. Abbott DW, Larsen, J, Thomas, D. Title: “Cell-wall deconstruction and degrading enzymes.” CleanTech-AAFC. Apr 2017-Mar2020.

  6. Principal Investigator. Abbott DW, Inglis, GD (Co-PI), Thomas, D. Boraston, AB, Kastelic, K, Koegler, D, Martens, E, Metz, G, Selinger, B, Uwiera, R, Uwiera, T. Title: “Non-antimicrobial alternatives for improving innate immune health, colonization resistance, and environmental performance of swine.” Abase-AAFC. Apr 2016-Mar 2019.

  7. Co-Applicant. Inglis, GD, Abbott DW, Thomas, D, Taboada, E, Carrillo, C, Amoak, K, Waddington, L, Uwiera, R, Selinger, B, Boras, V, Suttorp, V, Uwiera, T. Title: “Novel Innovations to Mitigate Relevant Campylobacter jejuni Subtypes in the Poultry Supply Chain.” Abase-AAFC. Apr 2016-Mar 2019.

Research and/or project statements

Agricultural glycomics

Functional genomics of complex carbohydrate utilization

Structural biology of carbohydrate active enzymes

Bioengineering of Bacteroides spp.

Enzyme discovery

Alternatives to antibiotics for livestock production

Education and awards

PhD, Biochemistry University of Victoria (2005). PhD thesis awarded the University of Victoria Governor General’s Gold Medal (2006) and Nominated for NSERC Silver Medal (2006)

BSc (Great Distinction), BIology (Major), Geography (Concentration), Trinity Western University (2000).

Key publications

For a complete list of publications, please visit: AAFC Online

  1. Gruninger, R.J., Nguyen, T.T.M., Reid, I., Yanke, L.J., Wang, P., Abbott, D.W., Tsang, A., McAllister, T.A. (2018) Comparison of the transcriptomes and Carbohydrate active Enzymes expressed by four anaerobic fungi: Neocallimastix frontalis, Piromyces rhizinflatus, Orpinomyces joyonii, and Anaeromyces mucronatus (Accepted: Frontiers).

  2. Badhan A., Huang, J., Wang, Y., Abbott, D.W., Di Falco, M., Tsang, A., McAllister, T.A. (2018). Characterization of multi enzyme complexes of the secretome from aerobic fungi. New Biotechnology 25:1-6. doi: 10.1016/j.nbt.2018.05.003. PMID: 29803771.
  3. Badhan, A., Riberio, G., Jones, D., Wang, Y., Abbott, D.W., Di Felco, M., Tsang, A., McAllister, T.A. (2018). Identification of novel enzymes to enhance the ruminal digestion of barley straw. Bioresource Technology 260:76-84.doi: 10.1016/j.biortech.2018.03.086.PMID: 29621684

  4. Pluvinage, B.§, Grondin, J.M.§, Amundsen, C., Klassen, L., Moote, P.E., Xiao, P., Thomas, D., Pudlo, N., Anele, A., Martens, E.C., Inglis, G.D., Uwiera, R.E.E., Boraston, A.B.†, Abbott, D.W.†. (2018) Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont. Nature Comm 9. Mar 13, 2018 doi:10.1038/s41467-018-03366-x .§These authors contributed equally. †Co-corresponding author.

  5. Jones, D.R., Thomas, D., Alger, N., Ghavidel, A. Inglis, G.D., Abbott, D.W.† (2018) SACCHARIS:An automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets. Biotechnol Biofuels 11:27. doi: 10.1186/s13068-018-1027-x. †Corresponding author. PMID: 29441125

  6. Luis, A.S.* Briggs, J.*, Zhang, X.*, Farnell, B., Ndeh, D., Labourel, A., Basle, A, McLean, R., Terrapon, N., Shearer, K., Ralet, M.-C., Henrissat, B., Martens, E.C., Mosimann, S.C., Abbott, D.W.†, and Gilbert, H.J.† (2018) A dynamic system of enzyme pathways are required to deconstruct the pectic network presented to the human gut microbiota. Nat Micro doi: 10.1038/s41564-017-0079-1 *Contributed equally.  †Co-corresponding author. PMID: 29255254

  7. CAZypedia Consortium. (2017) Ten years of CAZypedia: A living encyclopedia of carbohydrate-active enzymes. Glycobiology. 10.1093/glycob/cwx089. PMID: 29040563

  8. Inglis, G.D, Jiminez, J., Uwiera, T., Abbott, D.W. and Uwiera, R.R.E. (2017) Butyrate supplementation at high concentrations alters enteric bacterial communities and reduces intestinal inflammation in mice infected with Citrobacter rodentium

  9. Buchanan C.J. Webb, A.L., Mutschall, S.K., Kruczkiewicz, P., Barker, D.O.R., Hetman, B.M., Gannon, V.P.J., Abbott, D.W., Thomas, J.E., Inglis, G.D., and Taboada, E.N. (2017). A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains. Front Micro 8:1224. PMID: 28713351

  10. Jones, D.R.§, Uddin, M.S.§, Gruninger, RJ, Thanh, MPT, Thomas, D, Boraston, A.B., Pluvinage, B., McAllister, T.A., Forster, R., Tsang A., Selinger, B., Abbott, D.W.† (2017). Discovery and characterization of glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl-substrates. JBC 292:12606-20.  †Corresponding author. PMID: 28330466. *NOTE: made ASBMB-From the journals highlights (Sept 2017).

  11. Holman, D.B., Amat, S., Abbott, D.W., Timsit, E., Klima, C., and Alexander, T.W. (2017) The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot. BMC Microbiol. 17:70. PMID: 28330466

  12. Ndeh, N.§, Rogowski, A.§, Cartmell, C.§, Luis, A.S.§, Baslé, A., Gray, J., Venditto, I., Labourel, A., Briggs, J., Zhang, X., Terrapon, N., Buffetto, F., Nepogodiev, S., Field, R.A., O’Neil, M.A., Urbanowicz, B.R.,Davies, G.J., Abbott, D.W., Ralet, M-. A., Martens, E.C., Henrissat, B., and Gilbert, H.J. (2017) Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 544:65-70. PMID: 28329766. NOTE: Comment in Nature (2017) Biochemistry: A wine-induced breakdown. doi: 10.1038/nature21901.

  13. Grondin, J.M., Tamura, K., Dejean, G., Abbott, D.W.†, Brumer, H.†. (2017) Polysaccharide Utilization Loci: Fueling microbial communities. JBAC 199: pii:e00860-16. †Co-corresponding author. PMID: 27185956

  14. Jiminez, J.A., Uwiera, T.C., Abbott, D.W., Uwiera, R.R.E, Inglis, G.D. (2016) Butyrate Ameliorates Intestinal Inflammation and Modulates Mucin Secretion in Citrobacter rodentium Infected Mice. Gut Pathogens. 8:67 doi: 10.1186/s13099-016-0149-6.  PMID: 28031748

  15. Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W., and Boraston, A.B. (2016) KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate. PNAS. 113:6188-93. PMID: 27185956

  16. Gruninger, R.J.†, Cote, C, McAllister, T.A. Abbott, D.W.† (2016) Contributions of a unique b-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases. Biochem J. 473:839-49. †Co-Corresponding author. PMID: 27026397

  17. Abbott, D.W.†, Martens, E.C.†, Gilbert, H.J.†, Cuskin, F., Lowe, E.C., Cameron, E.A. (2015) Coevolution of yeast mannan digestion: Convergence of the civilized human diet, distal gut microbiome, and host immunity. Gut Microbes (Invited Addendum). 6:334-9. †Co-corresponding author. PMID: 26440374

  18. McLean, R., Hobbs, J., Suits, M.D., Tuomivaara, S., Jones, D., Boraston, A.B., and Abbott, D.W. † Functional analyses of resurrected and contemporary enzymes illuminate an evolutionary path for the emergence of exolysis in polysaccharide lyase family two. (2015) JBC. 290:21231-43. †Corresponding author. PMID: 26160170

  19. Cuskin, F., Lowe, E.C., Temple, M.J., Zhu, Y., Thompson, A.J., Cartmell, A., Rogowski, A., Piens, K., Bracke, D., Vervecken, W., Speciale, G., Hakki, Z., Munōz-Munōz, J.L., McLean, R., Suits, M.D., Boraston, A.B., Williams, S.J., Davies, G.J., Abbott, D.W.†, Martens, E.C.†, and Gilbert, H.J.† (2015) Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature. 517:165-9. †Co-Corresponding authors. PMID: 25567280.

  20. Abbott, D.W.† (2014) Informed Carbohydrate Active Enzyme Discovery within the Human Distal Gut Microbiome. J Glycomics Lipidomics. 4:1000119. †Corresponding author.

  21. Abbott, D.W.† and Lammerts van Bueren, A. (2014) Using structure to inform carbohydrate binding module function 28C:32-40. Curr Opin Struct Biol. †Corresponding author. PMID: 25108190

  22. Thomas, D., Lone, A.G., Selinger, L.B., Taboada, E.N., Uwiera, R.R.E., Abbott, D.W., Inglis, G.D. (2014) Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts PLOS One. 9(2):e88229 PMID: 24516617

  23. Abbott, D.W. †, Thomas, D., Pluvinage, B., and Boraston, A.B. (2013) An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Bioc Biotech. 171:1911-23. †Corresponding author. PMID: 24013861

  24. Pluvinage, B., Chitayat, S., Ficko-Blean, E., Abbott, D.W., Kunjachen, J.M, Grondin, J., Spencer, H. Smith, S., and Boraston, A.B. (2013) Conformational analysis of StrH, the surface-attached exo-(beta)-D-N-acetylglucosaminidase from Streptococcus pneumoniae. J Mol Biol. 425:334-49. PMID: 23154168

  25. Boraston, A.B., and Abbott, D.W.† (2012) Crystal structure of a pectin methylesterase from Yersinia enterocolitica. Acta Crystallogr Sect F Struct Biol Cryst Commun. 68:129-33. †Corresponding author. PMID: 22297983

  26. Martens, E.C.*, Lowe, E.*, Chiang, H., Pudlo, N., Wu, M, McNulty, N., Abbott, D.W., Henrissat, B., Gilbert, H.J., Bolam, D., and Gordon, J.I. (2011). Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts. *Shared First Authorship. PLOS Biol. 9:e1001221. PMID:22205877

  27. Pluvinage, B., Higgins, M.A., Abbott, D.W., Robb, C., Dalia, A.B., Deng, L., Weiser, J.N., Parsons, T.B., Fairbanks, A.J., Vocadlo, D.J., Boraston, A.B. (2011) Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis. Structure 19:1603-14. PMID: 22078560

  28. Abbott, D.W. and Boraston, A.B. (2011) Structural analysis of a putative family 32 carbohydrate-binding module from the Streptococcus pneumoniae enzyme, EndoD. Acta Cryst F. 67:429-33. PMID:21505233 

Contact

Research facility

Lethbridge Research and Development Centre

Expertise

Food›Microbiology›Probiotics
Sciences›Biology
Technology›Microbiology

Affiliations

University of Lethbridge, Departments of Biological Sciences; and Chemistry and Biochemistry

Canadian Glycomics Network (Investigator)

Alberta Glycomics Centre (Associate Investigator)

Language

English