D. Wade Abbott, Ph. D.

Research Scientist

Agricultural Glycomics

Functional Genomics of Carbohydrate Utilization

Intestinal Microbiomes

Carbohydrate Active Enzymes

Agriculture and Agri-Food Canada

5403-1st Avenue South, Lethbridge, Alberta

Current research and/or projects

Principle Investigator. Abbott, DW (PI), Title: “New value streams for Canadian pea proteins and co-products.” SCAP Agriscience Clusters - Bioproducts (AAFC)
Principal Investigator. Abbott DW (PI). Title: “Workshop and Relationship building with the Tla-o-qui-aht First Nation.” AAFC-Indigenous Agriculture Science Partnership Program
Co-Applicant. Master, E (PI), Brumer, H, Abbott, DW, Title: “Enzymatic upgrading of biorefinery side-streams.” SCAP Agriscience Clusters - Bioproducts (AAFC)
Principle Investigator. Abbott, DW (PI), Terry, S (Co-PI), Alexander, TW, Challis, J. Title: “Impact of indigenous plants on bovine-associated microbial communities and climate performance of cattle.” Annual Call (AAFC)
Co-Applicant. Gruninger, RJ (PI), Petri, R (Co-PI), Abbott, DW, McAllister, TA, Ortega Polo, R, Terry, S. Title: “Application of culturomics and in-silico inhibitor design to identify next-generation methane inhibitors that will reduce the environmental footprint of beef and dairy production in Canada.” Annual Call (AAFC)
Co-Applicant. Bainard, J (PI), Bainard, L (Co-PI), Abbott, DW, Alemu, A., Elsigner, M, Ensing, D., Fressanges, S, Gagne, D, Gorzelak, M., Hannam, K, Hannam, K, Iwaasa, A, Leewis, M-C, Messiga, A, Riendeau, G, Royer, I, Savard, T, Thomas, B, Wallace, R. Title: “SCAP-ASC-01 Beef Cluster Activity 10: Grazing management across western Canada: uncovering the role of the microbiome and implications for forage productivity, carbon sequestration and greenhouse gas emissions.” Beef and Cattle Research Council Agriscience Cluster Projects (AAFC)
Co-Applicant. Terry, S (PI), Abbott, DW, Coates, T, Gruninger, R, McAllister, T. Title: “SCAP-ASC-01 Beef Cluster Activity 14A: Potential for the up-cycling and reduction of food waste in feedlot cattle.” Beef and Cattle Research Council Agriscience Cluster Projects (AAFC)
Co-Principle Investigator. Alexander, TW (PI), Abbott DW (Co-PI), Malmuthuge, N. Title: “SCAP-ASC-01 Beef Cluster Activity 9A - Application of glycomics to enhance resilience against bovine respiratory disease.’ Beef and Cattle Research Council Agriscience Cluster Projects (AAFC)
Co-Applicant. Mupondwa, E (PI), Soolanayakanahally, R (Co-PI), Dumonceaux, T, Abbott, DW. Title: “Biomass and thermochemical conversion technologies for renewable fuels and value-added pathways with potential application in Northern, Indigenous, and remote communities of Canada.” Program of Energy Research and Development (PERD)
Co-Applicant. McAllister, TA (PI), Guan, LL (Co-PI), Abbott, DW. Title: “Meta-transcriptomics to better understand and enhance the digestion of forages in the diets of dairy cows.” Agriculture Funding Consortium, Alberta Milk
Principal Investigator. Abbott DW (PI). Title: “Spatial and structural characterization of Canadian seaweeds cultivated by Indigenous communities for cattle health.” 2022 Prize for Outstanding Achievement in Science, Agriculture and Agri-Food Canada
Co-PI. Singer, S (PI), Abbott DW (Co-PI) , Poudel, H. “Characterization of abiotic stress tolerant alfalfa genotypes for beef and dairy production in a changing climate.” RDAR-Agricultural Funding Consortium
Co-Applicant. Gorzelak, M (PI), Yanni, S (Co-PI), Pacheco, A, Theriault, G, Krobel, R, Pogue, S, St. Luce, M, McAllister, TA, Zhang, H, Abbott, DW, Phillips, B, McComb, M, Stephens, E, Donohue, M, Chau, H. Title: “Maximizing agricultural climate solutions through integration of beneficial management practices.” Partner Organizations include: Food Water Wellness Foundation and The Resilience Institute. AAFC-Agricultural Climate Solutions, “Living Labs”

Research and/or project statements

Agricultural Glycomics: Developing methods to study carbohdyrate structure in complex samples, including: animal gut, plants, fungi, seaweeds, and environment.

Carbohydrate active enzyme discovery from sequence datasets and functional characterization of enzyme activity using MultiOMICs and bioinformatics (SACCHARIS).

Fluorescent Polysaccharides (FLA-PS): a glyco-enabling tool to visualize carbohdyrate interactions, study selective metabolism, and sort cells into enriched metagenomes for functional analysis.

Indigenous partnships and student training; weaving traditional and scientific knowledges to explore solutions for the impacts of climate change in agriculture.

Professional activities / interests

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).

Additional links

https://scholar.google.ca/citations?user=ZuZ0rZoAAAAJ&hl=en

Key publications

TBD
2024 - View publication details
Reintjes, G., Klassen, L., Abbott, D.W. (2023). Visualization of Carbohydrate Uptake Using Fluorescent Polysaccharides. Methods in Molecular Biology (Clifton, N.J.), [online] 2657 241-249. http://dx.doi.org/10.1007/978-1-0716-3151-5_18
2023 - View publication details
Holman, D.B., Kommadath, A., Tingley, J.P., Abbott, D.W. (2022). Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes. Microbiology Spectrum, [online] 10(4), http://dx.doi.org/10.1128/spectrum.02380-22
2022 - View publication details
Tingley, J.P., Low, K.E., Xing, X., Abbott, D.W. (2021). Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues, 14(1), http://dx.doi.org/10.1186/s13068-020-01869-8
2021 - View publication details
Klassen, L., Reintjes, G., Tingley, J.P., Jones, D.R., Hehemann, J.H., Smith, A.D., Schwinghamer, T.D., Arnosti, C., Jin, L., Alexander, T.W., Amundsen, C., Thomas, D., Amann, R., McAllister, T.A., Abbott, D.W. (2021). Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. Microbiome, [online] 9(1), http://dx.doi.org/10.1186/s40168-020-00975-x
2021 - View publication details
Douglas Inglis, G., Wright, B.D., Sheppard, S.A., Wade Abbott, D., Oryschak, M.A., Montina, T. (2021). Expeller-pressed canola (Brassica napus) meal modulates the structure and function of the cecal microbiota, and alters the metabolome of the pancreas, liver, and breast muscle of broiler chickens. Animals, [online] 11(2), 1-23. http://dx.doi.org/10.3390/ani11020577
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
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
Pluvinage, B., Grondin, J.M., Amundsen, C., Klassen, L., Moote, P.E., Xiao, Y., Thomas, D., Pudlo, N.A., Anele, A., Martens, E.C., Inglis, G.D., Uwiera, R.E.R., Boraston, A.B., Abbott, D.W. (2018). Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont. Nature Communications, [online] 9(1), http://dx.doi.org/10.1038/s41467-018-03366-x
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
Brown, K., Abbott, D.W., Uwiera, R.R.E., Inglis, G.D. (2018). Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice. Gut Microbes, [online] 9(3), 218-235. http://dx.doi.org/10.1080/19490976.2017.1408763
2018 - View publication details
Jones, D.R., Thomas, D., Alger, N., Ghavidel, A., Douglas Inglis, G., Wade Abbott, D. (2018). SACCHARIS: An automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets. Biotechnology for Biofuels, [online] 11(1), http://dx.doi.org/10.1186/s13068-018-1027-x
2018 - View publication details
Luis, A.S., Briggs, J., Zhang, X., Farnell, B., Ndeh, D., Labourel, A., Baslé, A., Cartmell, A., Terrapon, N., Stott, K., Lowe, E.C., McLean, R., Shearer, K., Schückel, J., Venditto, I., Ralet, M.C., Henrissat, B., Martens, E.C., Mosimann, S.C., Abbott, D.W., Gilbert, H.J. (2018). Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nature Microbiology, [online] 3(2), 210-219. http://dx.doi.org/10.1038/s41564-017-0079-1
2018 - View publication details
Grondin, J.M., Tamura, K., Déjean, G., Abbott, D.W., Brumer, H. (2017). Polysaccharide utilization loci: Fueling microbial communities, 199(15), http://dx.doi.org/10.1128/JB.00860-16
2017 - View publication details
Jiminez, J.A., Uwiera, T.C., Wade Abbott, D., Uwiera, R.R.E., Inglis, G.D. (2017). Butyrate supplementation at high concentrations alters enteric bacterial communities and reduces intestinal inflammation in mice infected with Citrobacter rodentium. mSphere, [online] 2(4), http://dx.doi.org/10.1128/mSphere.00243-17
2017 - View publication details
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., Taboada, E.N. (2017). A genome-wide association study to identify diagnostic markers for human pathogenic campylobacter jejuni strains, 8(JUN), http://dx.doi.org/10.3389/fmicb.2017.01224
2017 - View publication details
Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Baslé, A., Gray, J., Venditto, I., Briggs, J., Zhang, X., Labourel, A., Terrapon, N., Buffetto, F., Nepogodiev, S., Xiao, Y., Field, R.A., Zhu, Y., O'Neill, M.A., Urbanowicz, B.R., York, W.S., Davies, G.J., Abbott, D.W., Ralet, M.-C., Martens, E.C., Henrissat, B., Gilbert, H.J. (2017). Complex pectin metabolism by gut bacteria reveals novel catalytic functions, 544(7648), 65-70. http://dx.doi.org/10.1038/nature21725
2017 - View publication details
Holman, D.B., Timsit, E., Amat, S., Abbott, D.W., Buret, A.G., Alexander, T.W. (2017). The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot. BMC Microbiology, [online] 17(1), http://dx.doi.org/10.1186/s12866-017-0978-6
2017 - View publication details
Jiminez, J.A., Uwiera, T.C., Abbott, D.W., Uwiera, R.R.E., Inglis, G.D. (2016). Impacts of resistant starch and wheat bran consumption on enteric inflammation in relation to colonic bacterial community structures and short-chain fatty acid concentrations in mice. Gut Pathogens, [online] 8(1), http://dx.doi.org/10.1186/s13099-016-0149-6
2016 - View publication details
Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W., Boraston, A.B. (2016). KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate. Proceedings of the National Academy of Sciences of the United States of America, [online] 113(22), 6188-6193. http://dx.doi.org/10.1073/pnas.1524214113
2016 - View publication details