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Brian Oakley, M.S., Ph.D.

Associate Professor

College of Veterinary Medicine

E-Mail: boakley@westernu.edu

Phone: 5524

Join year: 2014

Education

  • Ph.D. (2003) University of Washington, Seattle, WA.
  • M.S. (1997)  University of Washington, Seattle, WA.
  • B.A. (1990)  University of Vermont, Burlington, VT  

Professional Experience

  • Associate Professor.  September 2014 – present.  Western University of Health Sciences, College of Veterinary Medicine, Pomona, CA.
  • Research Microbiologist.  September 2010 – August 2014.  USDA Agricultural Research Service, Athens, GA.
  • European Union Marie Curie Senior Researcher.  April 2007 – May 2010.  University of Warwick, Department of Biological Sciences, Microbiology Research Group.  U.K.
  • Post-Doctoral Associate.  September 2006 – March 2007.  Fred Hutchinson Cancer Research Center, Infectious Disease Division.  Seattle, WA.
  • Post-Doctoral Associate.  2003-2006. University of Washington School of Medicine, Microbiology Department.  Seattle, WA.
  • Field Ecologist & Field Crew Leader.  1995-2001.  USDA Forest Service.  H.J. Andrews Experimental Forest, Blue River, OR, Eldorado National Forest, Placerville, CA, Teakettle Experimental Forest, Fresno CA.
  • English Teacher.  1991–1993.  Japan Exchange & Teaching (JET) program sponsored by Japanese Ministry of Education.  Hokkaido, Japan. 

Teaching Experience

TEACHING & MENTORING EXPERIENCE

  • Course Leader.  2014-present.  Western University of Health Sciences, College of Veterinary Medicine, 3rd year Food & Feed Safety course.
  • Mentor for Fulbright Scholar visiting research group at USDA ARS. 2013. Supervised poultry microbiology projects and developed ongoing collaborations with Dr. Raja Chalghoumi, Assistant Professor, Department of Animal Science, University of Carthage, Tunisia.
  • Mentor & Supervisor for post-doctoral associate (1), Ph.D. students (2), DVM summer research students (3), undergraduate students (5), and high school research trainee (1), variously at University of Washington Department of Microbiology, University of Warwick, Western University of Health Sciences.
  • Part-time faculty.  2001-2002.  Shoreline Community College and Green River Community College, Seattle, WA.  Instructor for Biology and Ecology courses.
  • Graduate Teaching Assistant.  1998-2001. University of Washington, Seattle, WA.
  • English Teacher.  1991–1993.  Japanese Ministry of Education & Shimizu Town Board of Education.  Hokkaido, Japan.  
  • Co-founder of sister-city relationship between Shimizu,  Japan and Chelsea, Michigan.  Annual exchanges of middle school students from 1995 - present.

Courses

  • Course Leader.  Food & Feed Safety course - required course in 3rd year DVM curriculum.  
  • Problem based learning (PBL) facilitator.
  • Basic Science Labs (BSL).

Research Interest

I am a microbial ecologist interested in tackling important problems at the interface of basic and applied research.  The revolution in high-throughput DNA sequencing has conclusively demonstrated the importance of microbial communities for life on earth.  Microbial ecology cuts across many fields and I have applied the tools and techniques of microbial ecology to disciplines ranging from oceanography to human and animal health.  My graduate training combined classical and microbial ecology but I only considered myself a microbiologist after working in the Microbiology Department of the University of Washington, the Fred Hutchinson Cancer Research Center, and the University of Warwick.  Four years as a research microbiologist with the USDA Agricultural Research Service gave me first-hand knowledge of the poultry industry and a chance to apply the tools and techniques of microbial ecology to veterinary microbiology.  Most of the current focus of my research is on the poultry microbiome and its relationships to food safety, infectious disease, and poultry nutrition.  Our standard toolkit combines field work with classical microbiology, microscopy, quantitative PCR, high-throughput 16S rRNA sequencing, metagenomics, and associated bioinformatics.  We are currently funded through several intramural mechanisms, extramural grants, and industry partnerships.

Publication

2016

Bradshaw JK, Snyder BJ, Oladeinde A, Spidle D, Berrang ME, Meinersmann RJ, Oakley B, Sidle RC, Sullivan K, Molina M: Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed. Water Research 2016, In Press.

Wong K, Shaw T, Oladeinde A, Glenn T, Oakley BB, Molina M: Rapid microbiome changes in freshly deposited cow feces under field conditions. Frontiers in Microbiology 2016, 7:500. doi:10.3389/fmicb.2016.00500

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

Berrang MJ, Meinersmann RJ, Oakley BB:  Detection of Campylobacter on the Outer Surface of Retail Broiler Chicken Meat Packages and from Product Within.  Food Protection Trends 2015 36(3): 176-182.

 

2015

Swift SM, Seal BS, Garrish JK, Oakley BB, Hiett K, Yeh H-Y, Woolsey R, Schegg KM, Line JE, Donovan DM: A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens-Specific Cell Wall Binding Domain Creates an Anti-Clostridium Antimicrobial with Improved Thermostability. Viruses 2015, 7(6):3019-3034.

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).

Berrang ME, Cox NA, Meinersmann RJ, Oakley BB, Line JE: Detection of Campylobacter in 100 commercial flocks-Evaluation of plating media and filtration method. J Appl Poultry Res 2015, 24(2):240-245.

Meinersmann RJ, Bono JL, Lindsey RL, Genzlinger LL, Loparev VN, Oakley BB: Genome Sequence of a Urease-Positive Campylobacter lari Strain. Genome Announcements 2015, 3(5).

 

2014

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.

Carbonero, F., B.B. Oakley, and K.J. Purdy,  Metabolic flexibility as a major predictor of spatial distribution in microbial communities. PLoS One, 2014 9(1): e85105.

Oakley, B.B., N. Gonzalez-Escalona, and M. Molina, Molecular typing and differentiation, In Compendium of methods for the microbiological examination of foods, 5th Edition. In press, American Public Health Association: Washington, DC.  Invited chapter.

Berrang, M.E., N.A. Cox, and B.B. Oakley, Sampling by sponge wipe or skin excision for recovery of inoculated Salmonella and Campylobacter from defeathered broiler carcasses. Journal of Food Protection, 2014. 77(5): 824-827.

 

2013

Pedroso, A.A., A.L. Hurley-Bacon, A.S. Zedek, T.W. Kwan, A.P.O. Jordan, G. Avellaneda, C.L. Hofacre, B.B. Oakley, S.R. Collett, J.J. Maurer, and M.D. Lee, Can probiotics improve the environmental microbiome and resistome of commercial poultry production? International Journal of Environmental Research and Public Health, 2013. 10(10): p. 4534-4559.

Yeh, H.Y., K.L. Hiett, J.E. Line, B.B. Oakley, and B.S. Seal, Construction, expression, purification and antigenicity of recombinant Campylobacter jejuni flagellar proteins. Microbiological Research, 2013. 168(4): p. 192-8.

Pontiroli, A., et al., Prospecting environmental mycobacteria: Combined molecular approaches reveal unprecedented diversity. PLoS One, 2013. 8(7).

Oakley, B.B., et al., The poultry-associated microbiome: Network analysis and farm-to-fork characterizations. PloS One, 2013. 8(2): p. e57190.

Meinersmann, R.J., R.L. Lindsey, J.L. Bono, T.P. Smith, and B.B. Oakley, Proposed model for the high rate of rearrangement and rapid migration observed in some inca/c plasmid lineages. Applied and Environmental Microbiology, 2013. 79(16): p. 4806-4814.

Line, J.E., B.B. Oakley, and N.J. Stern, Comparison of cumulative drip sampling with whole carcass rinses for estimation of campylobacter species and quality indicator organisms associated with processed broiler chickens. Poultry Science, 2013. 92(1): p. 218-24.

 

2012

Volozhantsev, N.V., et al., Molecular characterization of podoviral bacteriophages virulent for clostridium perfringens and their comparison with members of the picovirinae. PloS One, 2012. 7(5): p. e38283.

Tillman, G.E., J.L. Wasilenko, M. Simmons, T.A. Lauze, J. Minnicozzi, B. Oakley, N. Narang, P. Fratamico, and W.C. Cray, Isolation of shiga-toxin producing escherichia coli serogroups o26, o45, o103, o111, o121 and o145 from ground beef using modified rainbow agar and post-immunomagnetic separation acid treatment. Journal of Food Protection, 2012. 75(9): p. 1548-1554.

Simmons, M., C.A. Morales, B.B. Oakley, and B.S. Seal, Recombinant expression of a putative amidase cloned from the genome of listeria monocytogenes that lyses the bacterium and its monolayer in conjunction with a protease. Probiotics and Antimicrobial Proteins, 2012. 4(1): p. 1-10.

Seal, B., N.V. Volozhantsev, B.B. Oakley, C.A. Morales, J.K. Garrish, M. Simmons, E.A. Svetoch, and G.R. Siragusa, Bacteriophages of clostridium perfringens, In Bacteriophages, I. Kurtboke, Editor 2012, InTech Press. p. 23.

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., F. Carbonero, S.E. Dowd, R.J. Hawkins, and K.J. Purdy, Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. ISME J, 2012. 6(5): p. 905-914.  ISMEJ TOP TEN SELECTION.

Morales, C.A., B.B. Oakley, J.K. Garrish, G.R. Siragusa, M.B. Ard, and B.S. Seal, Complete genome sequence of the podoviral bacteriophage phicp24r, which is virulent for clostridium perfringens. Archives of Virology, 2012. 157(4): p. 769-72.

Fuchsman, C.A., J.T. Staley, B.B. Oakley, J.B. Kirkpatrick, and J.W. Murray, Free-living and aggregate-associated planctomycetes in the black sea. FEMS Microbiology Ecology, 2012.

 

2011

Zsak, L., J.M. Day, B.B. Oakley, and B.S. Seal, The complete genome sequence and genetic analysis of phica82 a novel uncultured microphage from the turkey gastrointestinal system. Virology Journal, 2011. 8: p. 331.

Volozhantsev, N.V., et al., The genome sequence and proteome of bacteriophage phicpv1 virulent for clostridium perfringens. Virus Research, 2011. 155(2): p. 433-9.

Tillman, G.E., G.J. Haas, M.G. Wise, B. Oakley, M.A. Smith, and G.R. Siragusa, Chicken intestine microbiota following the administration of lupulone, a hop-based antimicrobial. FEMS Microbiology Ecology, 2011.

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.  HIGHLY ACCESSED PUBLICATION.

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.

Line, J.E., N.J. Stern, B.B. Oakley, and B.S. Seal, Comparison of an automated most-probable-number technique with traditional plating methods for estimating populations of total aerobes, coliforms, and escherichia coli associated with freshly processed broiler chickens. Journal of Food Protection, 2011. 74(9): p. 1558-63.

Carbonero, F., B.B. Oakley, R.J. Hawkins, and K.J. Purdy, Genotypic distribution of a specialist model microorganism, methanosaeta, along an estuarine gradient: Does metabolic restriction limit niche differentiation potential? Microbial Ecology, 2011.

Calvo-Bado, L.A., et al., Ovine pedomics: The first study of the ovine foot 16s rrna-based microbiome. ISME J, 2011. 5(9): p. 1426-1437.

 

2010

Purdy, K.J., P.J. Hurd, J. Moya-LaraÒo, M. Trimmer, B.B. Oakley, and G. Woodward, Systems biology for ecology: From molecules to ecosystems, In Advances in ecological research, G. Woodward, Editor 2010, Academic Press. p. 87-149.

Oakley, B.B., F. Carbonero, C.J. van der Gast, R.J. Hawkins, and K.J. Purdy, Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations. ISME J, 2010. 4(4): p. 488-97.

Morris, C.E., D.C. Sands, J.L. Vanneste, J. Montarry, B. Oakley, C. Guilbaud, and C. Glaux, Inferring the evolutionary history of the plant pathogen pseudomonas syringae from its biogeography in headwaters of rivers in north america, europe, and new zealand. mBio, 2010. 1(3).

Mori, Y., K.J. Purdy, B.B. Oakley, and R. Kondo, Comprehensive detection of phototrophic sulfur bacteria using pcr primers that target reverse dissimilatory sulfite reductase gene. Microbes and Environments, 2010. 25(3): p. 190-6.

Ma, S., A. Concilio, B. Oakley, M. North, and J. Chen, Spatial variability in microclimate in a mixed-conifer forest before and after thinning and burning treatments. Forest Ecology and Management, 2010. 259(5): p. 904-915.

Carbonero, F., B.B. Oakley, and K.J. Purdy, Improving the isolation of anaerobes on solid media: The example of the fastidious methanosaeta. J Microbiol Methods, 2010. 80(2): p. 203-5.

2009

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.  >1500 CITATIONS; 5th most cited paper of all time in AEM.

Doty, S.L., B. Oakley, G. Xin, J.W. Kang, G. Singleton, Z. Khan, A. Vajzovic, and J.T. Staley, Diazotrophic endophytes of native black cottonwood and willow. Symbiosis, 2009. 47(1): p. 23-33.

2008

Oakley, B.B., T.L. Fiedler, J.M. Marrazzo, and D.N. Fredricks, Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Applied and Environmental Microbiology, 2008. 74(15): p. 4898-4909.   >80 CITATIONS.

 

2007

Yee, B., F.F. Lafi, B. Oakley, J.T. Staley, and J.A. Fuerst, A canonical ftsz protein in verrucomicrobium spinosum, a member of the bacterial phylum verrucomicrobia that also includes tubulin-producing prosthecobacter species. BMC Evolutionary Biology, 2007. 7.

Oakley, B.B., C.A. Francis, K.J. Roberts, C.A. Fuchsman, S. Srinivasan, and J.T. Staley, Analysis of nitrite reductase (nirk and nirs) genes and cultivation reveal depauperate community of denitrifying bacteria in the black sea suboxic zone. Environmental Microbiology, 2007. 9(1): p. 118-130.

Fredricks, D.N., T.L. Fiedler, K.K. Thomas, B.B. Oakley, and J.M. Marrazzo, Targeted pcr for detection of vaginal bacteria associated with bacterial vaginosis. Journal of Clinical Microbiology, 2007. 45(10): p. 3270-6.  >90 CITATIONS.

 

2006

Oakley, B.B., M.P. North, and J.F. Franklin, Facilitative and competitive effects of a n-fixing shrub on white fir saplings. Forest Ecology and Management, 2006. 233(1): p. 100-107.

Kirkpatrick, J., B. Oakley, C. Fuchsman, S. Srinivasan, J.T. Staley, and J.W. Murray, Diversity and distribution of planctomycetes and related bacteria in the suboxic zone of the black sea. Applied and Environmental Microbiology, 2006. 72(4): p. 3079-3083.

2005

North, M., B. Oakley, R. Fiegener, A. Gray, and M. Barbour, Influence of light and soil moisture on sierran mixed-conifer understory communities. Plant Ecology, 2005. 177(1): p. 13-24.

Ma, S., J. Chen, J.R. Butnor, M. North, E.S. Euskirchen, and B. Oakley, Biophysical controls on soil respiration in the dominant patch types of an old-growth, mixed-conifer forest. Forest Science, 2005. 51(3): p. 221-232.

Francis, C.A., K.J. Roberts, J.M. Beman, A.E. Santoro, and B.B. Oakley, Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(41): p. 14683-8.  FACULTY OF 1000 SELECTION, >500 CITATIONS.

2004

Oakley, B., M. North, J.F. Franklin, B.P. Hedlund, and J.T. Staley, Diversity and distribution of Frankia strains symbiotic with Ceanothus in california. Applied and Environmental Microbiology, 2004. 70(11): p. 6444-52.

North, M., J. Chen, B. Oakley, B. Song, M. Rudnicki, A. Gray, and J. Innes, Forest stand structure and pattern of old-growth western hemlock/douglas-fir and mixed-conifer forests. Forest Science, 2004. 50(3): p. 299-311.

2003

Oakley, B.B., M.P. North, and J.F. Franklin, The effects of fire on soil nitrogen associated with patches of the actinorhizal shrub Ceanothus cordulatus. Plant and Soil, 2003. 254(1): p. 35-46.

2002

North, M., Oakley, B., Chen, J., Erickson, H., Gray, A., Izzo, A., Johnson, D., Ma, S., Marra, J., Meyer, M., Purcell, K., Rambo, T., Rizzo, D., Roath, B., Schowalter, T., Vegetation and ecological characteristics of mixed-conifer and red fir forests at the teakettle experimental forest. USDA Forest Service General Technical Report. 2002, Albany, CA: USDA Forest Service. 52 p.

1998

Oakley, B. and J.F. Franklin, Bitter cherry (Prunus emarginata) distribution, successional dynamics, and implications for the role of the seed bank. Canadian Journal of Botany, 1998. 76(10): p. 1725-1732.