College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, 91766
Short Biography(5-10 sentences):
Dr. Oakley’s graduate and post-doctoral training combined classical and microbial ecology at the University of Washington in Seattle, the Fred Hutchinson Cancer Research Center also in Seattle, and the University of Warwick in the U.K. Prior to joining the faculty of Western University in 2014, Dr. Oakley was a research microbiologist with the USDA Agricultural Research Service’s Poultry Microbiology Safety Research Unit in Athens, GA. Dr. Oakley has published over 50 peer-reviewed articles and regularly serves as a peer reviewer for various journals, and as a review panelist for the National Science Foundation and USDA NIFA competitive grants programs. He has an extensive track record in the microbiome and comparative genomics fields with over 35 relevant publications in the last seven years.
Current Research: Dr. Oakley’s ongoing research program embraces a new paradigm in agriculture in which the GI microbiome of food animals is considered as a critical element of productivity and food safety. Dr. Oakley’s research applies the tools and techniques of microbial ecology to various questions, often focused on commercial poultry production to understand the poultry GI microbiome and its relationships to food safety, infectious disease, and nutrition. Recent examples include a farm-to-fork census of poultry-associated microbial communities, validation of specific and sensitive assays for poultry-associated pathogens such as Campylobacter, and the first sequencing-based documentation of the composition of healthy gut communities in commercial broiler chickens. The standard toolkit in Dr. Oakley’s lab combines classical microbiology, microscopy, quantitative PCR, high-throughput amplicon sequencing, metagenomics, genomics, and associated bioinformatics. Dr. Oakley’s research is currently funded through several intramural mechanisms, extramural grants, and industry partnerships.
- Oakley BB, Kogut MH: Spatial and temporal changes in the broiler chicken cecal and fecal microbiomes and correlations of bacterial taxa with cytokine gene expression. Frontiers in Veterinary Science 2016, 3:11. doi: 10.3389/fvets.2016.00011
- Day JM, Oakley BB, Seal BS, Zsak L: Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms. PLoS One 2015, 10(1).
- Oakley BB, Buhr R, Ritz CW, Kiepper BH, Berrang ME, Seal BS, Cox NA: Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives. BMC Vet Res 2014, 10(1):282.
- Oakley BB, Lillehoj HS, Kogut MH, Kim WK, Maurer JJ, Pedroso A, Lee MD, Collett SR, Johnson TJ, Cox NA: The chicken gastrointestinal microbiome. FEMS Microbiology Letters 2014, 360(2):100-112. Invited mini-review.
- Oakley, B.B., et al., The poultry-associated microbiome: Network analysis and farm-to-fork characterizations. PloS One, 2013. 8(2): p. e57190.
- Oakley, B.B., C.A. Morales, J.E. Line, B.S. Seal, and K.L. Hiett, Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen campylobacter. FEMS Microbiology Ecology, 2012. 79(2): p. 327-36.
- Oakley, B.B., J.E. Line, M.E. Berrang, J.M. Johnson, R.J. Buhr, N.A. Cox, K.L. Hiett, and B.S. Seal, Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection. Diagnostic Microbiology and Infectious Disease, 2012. 72(2): p. 131-8.
- Oakley, B.B., E. Talundzic, C.A. Morales, K.L. Hiett, G.R. Siragusa, N.V. Volozhantsev, and B.S. Seal, Comparative genomics of four closely related clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential. BMC Genomics, 2011. 12(1): p. 282.
- Oakley, B.B., S.E. Dowd, and K.J. Purdy, Thermophyl: A software tool for selecting phylogenetically optimized conventional and quantitative-pcr taxon-targeted assays for use with complex samples. FEMS Microbiology Ecology, 2011. 77(1): p. 17-27.
- Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23): p. 7537-41.