Devin Holman, Ph.D.

Research Scientist

Livestock Microbiology

Agriculture and Agri-Food Canada

Lacombe, Alberta

Current research and/or projects

Understanding the dynamics of the swine gut microbiome in response to perturbations and weaning.
Sow milk microbiome and resistome
Nasopharyngeal microbiome of beef cattle and the development of bovine respiratory disease.
Developing antimicrobial alternatives for use in swine production.

Education and awards

Ph.D., Microbiology, McGill University

M.Sc., Food Microbiololgy, Dalhousie University

B.Sc. (Hons.), Environmental Biology, Nova Scotia Agricultural College (Dalhousie University)

International experience and/or work

ORISE Postdoctoral Fellow, United States Department of Agriculture, National Animal Disease Center, Ames, IA, USA, 2016-17.

Key publications

Peer-reviewed publications

Hooker, K., Forwood, D.L., Caro, E., Huo, Y., Holman, D.B., Chaves, A.V., Meale, S.J. 2019. Microbial characterization and fermentative characteristics of crop maize ensiled with unsalable vegetables. Sci. Rep. In press.

Amat, S., Holman, D.B., Timsit, E., Schwinghamer, T.D., Alexander, T.W. 2019. Evaluation of the nasopharyngeal microbiota in beef cattle transported to a feedlot, with a focus on lactic acid-producing bacteria. Front Microbiol. doi: doi.org/10.3389/fmicb.2019.01988

Mou, K.T., Allen, H.K., Alt, D.P., Trachsel, J., Hau, S.J., Coetzee, J.F., Holman, D.B., Kellner, S., Loving, C.L., Brockmeier, S.L. 2019. Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administration. doi: doi.org/10.1016/j.vetmic.2019.108386

Teoh, R., Caro, E., Holman, D.B., Joseph, S., Meale, S.J., Chaves, A.V. 2019. Effects of hardwood biochar on methane production, fermentation characteristics, and the rumen microbiota using rumen simulation. Front Microbiol. 10:1534. doi: doi.org/10.3389/fmicb.2019.01534.

Amat, Samat, Holman, D.B., Timsit, E., Gzyl, K.E., Alexander, T.W. 2019. Draft genome sequences of 14 Lactobacillus, Enterococcus and Staphylococcus isolates from the nasopharynx of healthy feedlot cattle. Microbiol. Resour. Announ. 8(34): e00534-19. doi.org/10.1128/MRA.00534-19

Holman, D.B., Yang, W., Alexander, T.W. 2019. Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota. Microbiome. 7:86. doi.org/10.1186/s40168-019-0696-4.

Holman, D.B., Gzyl, K.E. 2019. A meta-analysis of the bovine gastrointestinal tract microbiota. FEMS Microbiol. Ecol. fiz072. doi: 10.1093/femsec/fiz072.

Holman, D.B., Bearson, B.L., Allen, H.K., Shippy, D.C., Loving, C.L., Kerr, B.J., Bearson, S.M.D., Brunelle, B.W. 2019. Chlortetracycline enhances tonsil colonization and fecal shedding of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 in pigs. Appl. Environ. Microbiol. 85(4). doi: 10.1128/AEM.02354-18.

Klima, C.L., Holman, D.B., Ralston, B.J., Stanford, K., Zaheer, R., Alexander, T.W., McAllister, T.A. 2019. Lower respiratory tract microbiome and resistome of bovine respiratory disease mortalities. Microb. Ecol. doi:10.1007/s00248-019-01361-3.

Holman, D.B., Timsit, E., Booker, C.W., Alexander, T.W. 2018. Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance. Vet. Microbiol.214:140-147.

Holman, D.B., Brunelle, B.W., Bearson, B.L., Bearson, S.M.D. 2018. Chlortetracycline and florfenicol induce expression of genes associated with pathogenicity in multidrug-resistant Salmonella enterica serovar Typhimurium Gut Pathog. 10:10. doi: 10.1186/s13099-018-0236-y.

Holman, D.B., Brunelle, B.W., Trachsel, J., Allen, H.K. 2017. Meta-analysis to define a core microbiota in the swine gut. mSystems. 2(3) e00004. doi: 110.1128/mSystems.00004-17.

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 Microbiol. 17(1):70. doi: 10.1186/s12866-017-0978-6.

Holman, D.B., Hao, X., Topp, E., Yang, H.E., Alexander, T.W. 2016. Effect of co-composting cattle manure with construction and demolition waste on the archaeal, bacterial, and fungal Microbiota, and on antimicrobial resistance determinants. PLoS One. 11(6):e0157539. doi: 10.1371/journal.pone.0157539.

Holman, D.B., Timsit, E., Alexander, T.W. 2015. The nasopharyngeal microbiota of feedlot cattle. Sci Rep. 5:15557. doi: 10.1038/srep15557.

Conference abstracts

Holman, D.B., Jones, T.H., Zaheer, R., McAllister, T.A. Antimicrobial resistance and genomic analysis of Enterococcus spp. collected along the production line within a beef processing plant and at retail. ASM Microbe. San Francisco, CA. June 20-24, 2019.

Holman, D.B., Jones, T.H., Zaheer, R., McAllister, T.A. Comparative genomic analysis and antimicrobial resistance of Enterococcus spp. isolated from a beef processing plant and retail meat. 69th Annual Conference of the Canadian Society of Microbiologists. Sherbrooke, QC. June 10-13, 2019.

Holman, D.B., James-Gzyl, K. 2018. A meta-analysis of the bovine ruminal and gastrointestinal microbiota. Focused Meeting 2018: Microbiomes Underpinning Agriculture. Cork, Ireland. October 1-2, 2018.

Holman, D.B., Klima, C.L., Ralston, B.J., Stanford, K., Alexander, T.W., McAllister, T.A. 2018. The lung microbiome and antimicrobial resistome of bovine respiratory disease mortalities. 68th Annual Conference of the Canadian Society of Microbiologists. Winnipeg, MB. June 18-21, 2018.

Holman, D.B., Yang, W., Alexander, T.W. 2018. The dynamics of the fecal and nasopharyngeal microbiome of feedlot cattle administered oxytetracycline and tulathromycin. 2018. 68th Annual Conference of the Canadian Society of Microbiologists. Winnipeg, MB. June 18-21, 2018.

Klima, C.L., Holman, D.B., Zaheer, R., Cook, S.R., Ralston, B.J., Anholt, R.M., Niu, Y.D., Stanford, K., Hannon, S.J., Booker, C., Read, R.R., McAllister, T.A. 2018. Multidrug resistance in Pasteurellaceae contributing to fatal bovine respiratory disease cases in North American feedlots between 2011 and 2016. 68th Annual Conference of the Canadian Society of Microbiologists. Winnipeg, MB. June 18-21, 2018.

Holman, D.B., Bearson, S.M., Bearson, B.L., Allen, H.K., Shippy, D.C., Brunelle, B.W. The effect of therapeutic chlortetracycline administration on colonization and shedding of multidrug-resistant Salmonella Typhimurium and on the gut microbiota in post-weaned piglets. ASM Microbe 2017. New Orleans, LA. June 1-5, 2017.

Holman, D.B., Brunelle, B.W., Trachsel, J., Allen, H.K. 2016. A meta-analysis of the swine gut microbiota: identifying core members. 76th annual meeting for the North Central Branch of the American Society for Microbiology. Ames, IA. October 21-22, 2016.

Holman, D.B, Bearson, S.M.D., Bearson, B.L., Brunelle, B.W. 2016. Chlortetracycline and florfenicol induce expression of genes involved in type III secretion systems and attachment in multidrug-resistant Salmonella Typhimurium. 5th American Society for Microbiology Conference on Salmonella. Potsdam, Germany. August 29-September 1, 2016.