SWAGÊÓƵ

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

• Professor. May 2020 – present. Western University of Health Sciences, College of Veterinary Medicine, Pomona, CA.
• Interim Director of Year 3 Curriculum, October 2018- June 2020.Western University of Health Sciences, College of Veterinary Medicine, Pomona, CA.
• 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 & MENTORING EXPERIENCE

• Course Leader. 2014-present. Western University of Health Sciences, College of Veterinary Medicine, 3rd year Food & Feed Safety course.
• Research Mentor & Supervisor for DVM students (12), Post-Doctoral fellows (3), Ph.D. students (2), Master's students (4),undergraduates (2) and high school students (2).
• 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.
• 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 >250 middle school students from 1995 - present.

• CVM 7060 Food & Feed Safety - Course Leader (2014-present). Required course in 3rd year DVM curriculum.
• CVM 5120 Veterinary Basic and Medical Sciences - Problem based learning (PBL) & Basic Science Lab (BSL) facilitator.
• CVM 6120 Veterinary Basic and Medical Sciences - Problem based learning (PBL) & Basic Science Lab (BSL)facilitator.
• CVM 5130 Molecular and Cellular Biology lecturer

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. The standard toolkit in my lab combines field work with classical microbiology, microscopy, quantitative PCR, high-throughput 16S rRNA sequencing, metagenomics, and associated bioinformatics. My research is currently funded through several extramural grants, intramural mechanisms supporting student research, and industry partnerships.

• Phi Zeta Veterinary Honor Society. Honorary membership for research contributions to the field of Veterinary Medicine. Western University of Health Sciences Alpha Epsilon chapter of Phi Zeta. 2019.
• Independent Researcher of the Year Award. Western University of Health Sciences, College of Veterinary Medicine. 2019.
• Zoetis Award for Veterinary Research Excellence. 2018.
• Association of American Veterinary Medical Colleges (AAVMC) Leadership Academy - 2017-2018.
• Invited visiting Faculty, University of Lille, France. February 2018.
• International Probiotics Congress, Budapest, Hungary. Invited speaker and Animal Health Session Chair. June 2017.
• OIE, Paris, France. Invited speaker and expert panelist for the 2nd International Symposium on Alternatives to Antibiotics in Agriculture. December 2016.
• USDA NIFA, Washington, DC. Competitive Grant Review Panelist.
• National Science Foundation, Arlington, VA. Review Panelist.
• Academic Editor, PLoS ONE

1. Tegzes J, B Oakley, and G Brennan. 2019. Comparison of Mycotoxin Concentrations in Grain versus Grain-Free Dry and Wet Commercial Dog Foods. Toxicology Communications. 3(1): 61-66.
2. *Kumar S, P Adhikari, B Oakley, and W Kim. 2019. Changes in cecum microbial community in response to total sulfur amino acid (TSAA: DL-methionine) in antibiotic-free and supplemented poultry birds. Poultry Science, epub ahead of print. doi:10.3382/ps/pez380.
3. Park B, MB Eady, B Oakley, SC Yoon, KC Lawrence, and GR Gamble. 2019. Hyperspectral microscope imaging methods for multiplex detection of Campylobacter. Journal of Spectral Imaging. 8(a6).
4. *Vasconcelos EJR, SA Billeter, LA Jett, RJ Meinersmann, MC Barr, P Diniz, and BB Oakley. 2018. Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing. Vector-Borne and Zoonotic Diseases. 18(9): p. 491-499.
5. Shang Y, S Kumar, B Oakley, and W Kim. 2018. Chicken Gut Microbiota: Importance and Detection Technology. Frontiers in Veterinary Science. Vol 5(254).
6. *Oakley B, E Vasconcelos, P Diniz, K Calloway, E Richardson, R Meinersmann, N Cox, and M Berrang. 2018. The cecal microbiome of commercial broiler chickens varies significantly by season. Poultry Science. 97(10): p. 3635-3644.
7. Geiger J, BA Morton, EJR Vasconcelos, M Tngrian, M Kachani, EA Barron, CM Gavidia, RH Gilman, NP Angulo, R Lerner, T Scott, NH Mirrashed, B Oakley, and P Diniz. 2018. Molecular Characterization of Tandem Repeat Protein 36 Gene of Ehrlichia canis Detected in Naturally Infected Dogs from Peru. The American Journal of Tropical Medicine and Hygiene. 99(2): p. 297-302.
8. Chan D, J Geiger, E Vasconcelos, B Oakley, and P Diniz. 2018. Bartonella rochalimae detection by a sensitive and specific PCR platform. The American Journal of Tropical Medicine and Hygiene. Vol 99(4): p. 840-843.
9. King H, T Khera-Butler, J James, B Oakley, G Erenso, A Aseffa, R Knight, E Wellington, and O Courtenay. 2017. Environmental reservoirs of pathogenic Mycobacteria across the Ethiopian biogeographical landscape. PLoS ONE. 12(3): p. e0173811.
10. Wong K, T Shaw, A Oladeinde, T Glenn, B Oakley, and M Molina. 2016. Rapid microbiome changes in freshly deposited cow feces under field conditions. Frontiers in Microbiology. 7(500).
11. *Kogut MH and BB Oakley. 2016. 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. 3(11).
12. Bradshaw J, B Snyder, A Oladeinde, D Spidle, M Berrang, R Meinersmann, B Oakley, R Sidle, K Sullivan, and M Molina. 2016. 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. 101: p. 498-509.
13. Berrang ME, SR Ladely, RJ Meinersmann, JE Line, BB Oakley, and NA Cox. 2016. Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media. Journal of Food Protection. 79(11): p. 1986-1989.
14. Berrang M, R Meinersmann, and B Oakley. 2016. Detection of Campylobacter on the outer surface of retail broiler chicken meat packages and from product within. Food Protection Trends. 36(3): p. 176-182.
15. Swift S, B Seal, J Garrish, B Oakley, K Hiett, H-Y Yeh, R Woolsey, K Schegg, J Line, and D Donovan. 2015. A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens-Specific Cell Wall Binding Domain Creates an Anti-Clostridium Antimicrobial with Improved Thermostability. Viruses. 7(6): p. 3019-3034.
16. *Oakley BB, N Gonzalez-Escalona, and M Molina. 2015. Molecular Typing and Differentiation, in: Compendium of Methods for the Microbiological Examination of Foods. American Public Health Association: Washington, DC.
17. Meinersmann R, J Bono, R Lindsey, L Genzlinger, V Loparev, and B Oakley. 2015. Genome sequence of a urease-positive Campylobacter lari strain. Genome Announcements 3(5).
18. Day JM, BB Oakley, BS Seal, and L Zsak. 2015. Comparative metagenomic analysis of the enteric viromes from sentinel birds placed on selected broiler chicken farms. PLoS ONE. 10(1).
19. Berrang M, N Cox, R Meinersmann, B Oakley, and J Line. 2015. Detection of Campylobacter in 100 commercial flocks - Evaluation of plating media and filtration method. Journal of Applied Poultry Research 24(2): p. 240-245.
20. *Oakley BB, HS Lillehoj, MH Kogut, WK Kim, JJ Maurer, A Pedroso, MD Lee, SR Collett, TJ Johnson, and NA Cox. 2014. The chicken gastrointestinal microbiome. FEMS Microbiology Letters. 360(2): p. 100-112. >170 CITATIONS
21. *Oakley BB, RJ Buhr, CW Ritz, BH Kiepper, ME Berrang, BS Seal, and NA Cox. 2014. Successional changes in poultry cecal microbiome during 42d of growth independent of organic acid feed additives. BMC Veterinary Research. 10(1): p. e282.
22. Carbonero F, BB Oakley, and KJ Purdy. 2014. Metabolic flexibility as a major predictor of spatial distribution in microbial communities. PLoS ONE. 9(1): p. e85105.
23. Berrang ME, NA Cox, and BB Oakley. 2014. Sampling by sponge wipe or skin excision for recovery of inoculated Salmonella and Campylobacter from defeathered broiler carcasses. Journal of Food Protection. 77(5): p. 824-827.
24. Yeh HY, KL Hiett, JE Line, BB Oakley, and BS Seal. 2013. Construction, expression, purification and antigenicity of recombinant Campylobacter jejuni flagellar proteins. Microbiological Research. 168(4): p. 192-8.
25. Pontiroli A, TT Khera, BB Oakley, S Mason, SE Dowd, ER Travis, G Erenso, A Aseffa, O Courtenay, and EMH Wellington. 2013. Prospecting environmental Mycobacteria: combined molecular approaches reveal unprecedented diversity. PLoS ONE. 8(7): p. e68648.
26. Pedroso AA, AL Hurley-Bacon, AS Zedek, TW Kwan, APO Jordan, G Avellaneda, CL Hofacre, BB Oakley, SR Collett, JJ Maurer, and MD Lee. 2013. Can probiotics improve the environmental microbiome and resistome of commercial poultry production? International Journal of Environmental Research and Public Health. 10(10): p. 4534-4559.
27. *Oakley BB, CA Morales, J Line, ME Berrang, RJ Meinersmann, GE Tillman, MG Wise, GR Siragusa, KL Hiett, and BS Seal. 2013. The poultry-associated microbiome: network analysis and farm-to-fork characterizations. PLoS ONE. 8(2): p. e57190.
28. Meinersmann RJ, RL Lindsey, JL Bono, TP Smith, and BB Oakley. 2013. Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages. Applied and Environmental Microbiology. 79(16): p. 4806-4814.
29. Line JE, BB Oakley, and NJ Stern. 2013. 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. 92(1): p. 218-24.
30. Volozhantsev NV, BB Oakley, CA Morales, VV Verevkin, VA Bannov, VM Krasilnikova, AV Popova, EL Zhilenkov, JK Garrish, KM Schegg, R Woolsey, DR Quilici, JE Line, KL Hiett, GR Siragusa, EA Svetoch, and BS Seal. 2012. Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae. PLoS ONE. 7(5): p. e38283.
31. Tillman GE, JL Wasilenko, M Simmons, TA Lauze, J Minnicozzi, B Oakley, N Narang, P Fratamico, and WC Cray. 2012. 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. 75(9): p. 1548-1554.
32. Simmons M, CA Morales, BB Oakley, and BS Seal. 2012. 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. 4(1): p. 1-10.
33. Seal B, NV Volozhantsev, BB Oakley, CA Morales, JK Garrish, M Simmons, EA Svetoch, and GR Siragusa. 2012. Bacteriophages of Clostridium perfringens, in: Bacteriophages, I. Kurtboke, Editor. InTech Press. p. 23.
34. *Oakley BB, CA Morales, JE Line, BS Seal, and KL Hiett. 2012. Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen Campylobacter. FEMS Microbiology Ecology. 79(2): p. 327-36.
35. *Oakley BB, JE Line, ME Berrang, JM Johnson, RJ Buhr, NA Cox, KL Hiett, and BS Seal. 2012. 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. 72(2): p. 131-8.
36. *Oakley BB, F Carbonero, SE Dowd, RJ Hawkins, and KJ Purdy. 2012. Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. ISME Journal. 6(5): p. 905-914. ISMEJ TOP TEN SELECTION
37. Morales CA, BB Oakley, JK Garrish, GR Siragusa, MB Ard, and BS Seal. 2012. Complete genome sequence of the podoviral bacteriophage PhiCP24R, which is virulent for Clostridium perfringens. Archives of Virology. 157(4): p. 769-72.
38. Fuchsman CA, JT Staley, BB Oakley, JB Kirkpatrick, and JW Murray. 2012. Free-living and aggregate-associated Planctomycetes in the Black Sea. FEMS Microbiology Ecology. 80: p. 402-416.
39. Zsak L, JM Day, BB Oakley, and BS Seal. 2011. The complete genome sequence and genetic analysis of PhiCA82 a novel uncultured microphage from the turkey gastrointestinal system. Virology Journal. 8: p. 331.
40. Volozhantsev NV, VV Verevkin, VA Bannov, VM Krasilnikova, VP Myakinina, EL Zhilenkov, EA Svetoch, NJ Stern, BB Oakley, and BS Seal. 2011. The genome sequence and proteome of bacteriophage PhiCPV1 virulent for Clostridium perfringens. Virus Research. 155(2): p. 433-9.
41. Tillman GE, GJ Haas, MG Wise, B Oakley, MA Smith, and GR Siragusa. 2011. Chicken intestine microbiota following the administration of lupulone, a hop-based antimicrobial. FEMS Microbiology Ecology. 77(2): p. 395-403.
42. *Oakley BB, E Talundzic, CA Morales, KL Hiett, GR Siragusa, NV Volozhantsev, and BS Seal. 2011. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential. BMC Genomics. 12(1): p. 282.
43. *Oakley BB, SE Dowd, and KJ Purdy. 2011. ThermoPhyl: a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples. FEMS Microbiology Ecology. 77(1): p. 17-27.
44. Line JE, NJ Stern, BB Oakley, and BS Seal. 2011. 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. 74(9): p. 1558-63.
45. Carbonero F, BB Oakley, RJ Hawkins, and KJ Purdy. 2011. Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: Does metabolic restriction limit niche differentiation potential? Microbial Ecology. 63(4): p. 856-864.
46. Calvo-Bado LA, BB Oakley, SE Dowd, LE Green, GF Medley, A Ul-Hassan, V Bateman, W Gaze, L Witcomb, R Grogono-Thomas, J Kaler, CL Russell, and EMH Wellington. 2011. Ovine pedomics: The first study of the ovine foot 16S rRNA-based microbiome. ISME Journal. 5(9): p. 1426-1437.
47. Purdy KJ, PJ Hurd, J Moya-LaraÃ’o, M Trimmer, BB Oakley, and G Woodward. 2010. Systems Biology for Ecology: From Molecules to Ecosystems, in: Advances in Ecological Research, G. Woodward, Editor. Academic Press. p. 63.
48. *Oakley BB, F Carbonero, CJ van der Gast, RJ Hawkins, and KJ Purdy. 2010. Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations. ISME Journal. 4(4): p. 488-97.
49. Morris CE, DC Sands, JL Vanneste, J Montarry, B Oakley, C Guilbaud, and C Glaux. 2010. 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. 1(3): p. e00107-10.
50. Mori Y, KJ Purdy, BB Oakley, and R Kondo. 2010. Comprehensive detection of phototrophic sulfur bacteria using PCR primers that target reverse dissimilatory sulfite reductase gene. Microbes and Environments. 25(3): p. 190-6.
51. Ma S, A Concilio, B Oakley, M North, and J Chen. 2010. Spatial variability in microclimate in a mixed-conifer forest before and after thinning and burning treatments. Forest Ecology and Management. 259(5): p. 904-915.
52. Carbonero F, BB Oakley, and KJ Purdy. 2010. Improving the isolation of anaerobes on solid media: the example of the fastidious Methanosaeta. Journal of Microbiological Methods. 80(2): p. 203-5.
53. Schloss PD, SL Westcott, T Ryabin, JR Hall, M Hartmann, EB Hollister, RA Lesniewski, BB Oakley, DH Parks, CJ Robinson, JW Sahl, B Stres, GG Thallinger, DJ Van Horn, and CF Weber. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 75(23): p. 7537-41. >10,000 CITATIONS; most cited paper of all time in Applied and Environmental Microbiology
54. Doty SL, B Oakley, G Xin, JW Kang, G Singleton, Z Khan, A Vajzovic, and JT Staley. 2009. Diazotrophic endophytes of native black cottonwood and willow. Symbiosis. 47(1): p. 23-33.
55. *Oakley BB, TL Fiedler, JM Marrazzo, and DN Fredricks. 2008. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Applied and Environmental Microbiology. 74(15): p. 4898-4909. >250 CITATIONS
56. Yee B, FF Lafi, B Oakley, JT Staley, and JA Fuerst. 2007. A canonical FtsZ protein in Verrucomicrobium spinosum, a member of the Bacterial phylum Verrucomicrobia that also includes tubulin-producing Prosthecobacter species. BMC Evolutionary Biology. 7(37).
57. *Oakley BB, CA Francis, KJ Roberts, CA Fuchsman, S Srinivasan, and JT Staley. 2007. Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone. Environmental Microbiology. 9(1): p. 118-130.
58. Fredricks DN, TL Fiedler, KK Thomas, BB Oakley, and JM Marrazzo. 2007. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. Journal of Clinical Microbiology. 45(10): p. 3270-6. >350 CITATIONS
59. *Oakley BB, MP North, and JF Franklin. 2006. Facilitative and competitive effects of a N-fixing shrub on white fir saplings. Forest Ecology and Management. 233(1): p. 100-107.
60. Kirkpatrick J, B Oakley, C Fuchsman, S Srinivasan, JT Staley, and JW Murray. 2006. Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea. Applied and Environmental Microbiology. 72(4): p. 3079-3083.
61. North M, B Oakley, R Fiegener, A Gray, and M Barbour. 2005. Influence of light and soil moisture on Sierran mixed-conifer understory communities. Plant Ecology. 177(1): p. 13-24.
62. Ma S, J Chen, JR Butnor, M North, ES Euskirchen, and B Oakley. 2005. Biophysical controls on soil respiration in the dominant patch types of an old-growth, mixed-conifer forest. Forest Science. 51(3): p. 221-232.
63. Francis CA, KJ Roberts, JM Beman, AE Santoro, and BB Oakley. 2005. 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. 102(41): p. 14683-8. FACULTY OF 1000 SELECTION, >1700 CITATIONS.
64. Bjerrum L, K Pedersen, and RM Engberg. 2005. The influence of whole wheat feeding on Salmonella infection and gut flora composition in broilers. Avian Diseases. 49(1): p. 9-15.
65. *Oakley B, M North, JF Franklin, BP Hedlund, and JT Staley. 2004. Diversity and distribution of Frankia strains symbiotic with Ceanothus in California. Applied and Environmental Microbiology. 70(11): p. 6444-52.
66. North M, J Chen, B Oakley, B Song, M Rudnicki, A Gray, and J Innes. 2004. Forest stand structure and pattern of old-growth western hemlock/Douglas-fir and mixed-conifer forests. Forest Science. 50(3): p. 299-311.
67. *Oakley BB, MP North, and JF Franklin. 2003. The effects of fire on soil nitrogen associated with patches of the actinorhizal shrub Ceanothus cordulatus. Plant and Soil. 254(1): p. 35-46.
68. North M, B Oakley, J Chen, H Erickson, A Gray, A Izzo, D Johnson, S Ma, J Marra, M Meyer, K Purcell, T Rambo, D Rizzo, B Roath, and T Schowalter. 2002. Vegetation and Ecological Characteristics of Mixed-Conifer and Red Fir Forests at the Teakettle Experimental Forest. USDA Forest Service General Technical Report. Albany, CA: USDA Forest Service PSW Research Station. 52 p.
69. *Oakley B and JF Franklin. 1998. Bitter cherry (Prunus emarginata) distribution, successional dynamics, and implications for the role of the seed bank. Canadian Journal of Botany. 76(10): p. 1725-1732.