Mills Laboratory > Nickolas A. Bokulich

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Nickolas A. Bokulich

Nicks picGraduate Student Researcher

Food Science Graduate Group

One Shields Ave

Department of Viticulture and Enology

University of California

Davis, CA

EM:  nbokulich@ucdavis.edu

 

 

Education

B.A. Microbiology and Zymurgy, Hampshire College, 2008

M.S. Viticulture and Enology, UC Davis, 2011

 

Research Interests

  • Microbiology of Fermented Foods. Fermented foods represent the world’s oldest and most stable delivery system for beneficial bacteria in the human diet. My primary interests are concerned with the microbial ecology of fermented foods and beverages, and linking community data to functional genetics and fermentation process phenomena. I apply combined molecular techniques including terminal restriction fragment length polymorphism and high-throughput sequencing (HTS) technologies to reveal the deep community structure and genetic expression patterns underlying a range of mixed-microbial food systems and systems-level interactions with product quality. This has the additional function of bioprospecting for microbes with potential health-positive and/or functional roles in fermented foods.
  • Human Gut Microbiome. I also study the downstream impact of consumption of functional foods, the interface between beneficial food-borne microbes and the human host. I apply the same molecular approaches to study community dynamics in the gut and how probiotic/prebiotic supplementation alters both microbial content and health status of infants.
  • Molecular/Bioinformatic Tools. The third aspect of my research involves developing tools for high-throughput analysis of microbial communities. This has involved optimizing NGS protocols for studying both bacterial and fungal communities in these environments, and developing complementary, clade-specific tools for observing species-level community dynamics. I am currently collaborating with Rob Knight (University of Colorado, Boulder) and Gregory Caporaso (Northern Arizona University) to optimize computational filtration settings of NGS data in their open-source bioinformatics pipeline, QIIME, and to better understand how error rates and sequence quality impact microbial community assessments. These projects are developing guidelines for more efficient generation and analysis of microbial community data using NGS tools.

 

Publications

  • Bokulich, N. A., J. H. Thorngate, P. M. Richardson and D. A. Mills. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.  Proceedings of the National Academy of Sciences 111:E139-148.
  • Underwood, M. A., K. M. Kalanetra, N. A. Bokulich, M. Mirmiran, D. Barile, D. J. Tancredi, J. B. German, C. B. Lebrilla and D. A. Mills.  2014. Prebiotic oligosaccharides in premature infants.   Journal of Pediatric Gastroenterology & Nutrition 58:352-360.
  • Underwood, M., K. Kalanetra, N. Bokulich, Z. T. Lewis, M. Mirmiran, D. Tancredi and D. A. Mills.  2013. A comparison of two probiotic strains of bifidobacteria in premature infants.  Journal of Pediatrics 163:1585-1591.
  • Bokulich, N. A. and D. A. Mills. 2013. House microbiome drives microbial landscapes of artisan cheesemaking plants.  Applied and Environmental Microbiology 79:5214-5223.
  • Bokulich, N. A., D. A. Mills and M. Underwood.  2013.  Surface microbes in the neonatal intensive care unit: Changes with routine cleaning and over time. Journal of Clinical Microbiology 51:2617-2624.
  • Bokulich, N. A., M. Ohta, P. M. Richardson and D. A. Mills.  2013. Monitoring seasonal changes in winery-resident microbiota.  PLoS One 8:e66437.
  • Ellis, C. L., N. A. Bokulich, K. M. Kalanetra, M. Mirmiran, J. Elumalai, L. Haapanen, T. Schegg, J. C. Rutledge, G. Raff, D. A. Mills, M. A. Underwood. 2013.  Probiotic administration in congenital heart disease: A pilot study.  Journal of Perinatology 33:691-697.
  • Bokulich, N.A. and Bamforth, C.W. 2013. The microbiology of malting and brewing. Microbiology and Molecular Biology Reviews 77:157-172.
  • Bokulich, N. A. and D. A. Mills.  2013. Improved internal transcribed spacer primer selection enables quantitative, ultra-high-throughput fungal community profiling.  Applied and Environmental Microbiology 79:2519-2526.
  • Lewis, Z. T., N. A. Bokulich, K. M. Kalanetra, S. Ruiz-Moyano, M. A Underwood and D. A Mills.  2013. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.  Anaerobe 19:62-69.
  • Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, J. G. Caporaso.  2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10:57-59.
  • Bokulich, N.A., and D.A. Mills. 2012. Differentiation of mixed lactic acid bacteria communities in beverage fermentations using targeted terminal restriction fragment length polymorphism. Food Microbiol. 31: 126-132.
  • Bokulich, N., C.F. Hwang, S. Liu, K. Boundy-Mills, and D.A. Mills. 2012. Profiling the yeast communities of wine using terminal restriction fragment length polymorphism analysis. Am. J. Enol. Vitic. . 63:185-194.
  • Bokulich, N. A., C. W. Bamforth and D. A. Mills. 2012. A review of molecular methods for microbial community profiling of beer and wine.  Journal of the American Society for Brewing Chemists 70:150-162.
  • Bokulich, N.A, C. Bamforth, and D.A. Mills. 2012. Brewhouse-resident microbiota responsible for fermentation of American coolship ale. PLoS One. 7(4): e35507.
  • Bokulich, N.A., C.M.L. Joseph, G. Allen, A. Benson, and D.A. Mills. 2012. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One. 7(5): e36357
  • Bokulich, N, and D. A. Mills. 2012. Next-generation approaches to the microbial ecology of food fermentations.  Journal of Biochemistry and Molecular Biology 45:377-389.
  • Ma, B. W., N. A. Bokulich, P. A. Castillo, A. Kananurak, M. A. Underwood, D. A. Mills, C. L. Bevins. 2012. Routine habitat change: A source of unrecognized transient alteration of intestinal microbiota in laboratory mice.  PLoS One 7(10): e47416.

Teaching Experience

  • Instructor, UC Davis: Introduction to Beer and Brewing, Fall 2012
  • University of California Davis: Teaching assistant for Wine Microbiology Winter ’11 and Winter ’12; Teaching assistant for Practical Malting and Brewing Science, Spring ’10 and Spring ‘11; Teaching assistant for Wine Production, Fall ‘10.
  • Hampshire College: Senior Brewing Technician, Hampshire College Fermentation Science Laboratory, 07-08; Teaching Assistant for Zymurgy, Fall 07; Teaching Assistant for Kitchen Ecology, Spring 07 and Spring 08; Student Instructor for Gene Cloning, January 08.

Invited Seminars

  • "The Microbial Determinants of Wine Terroir". Mycology Reading Group, University of California, Berkeley, April 9, 2013.
  • "Regional and Varietal Patterns in Grape Microbiota: Evidence of Microbial Terroir?" Constellation Brands Technical Meeting, Monterey, CA, May 8, 2013.
  • "Microbial Terroir: Profiling Wine Quality on the Grape-to-Glass Continuum". Department of Biology, Northern Arizona University. April 25, 2013.
  • "Microbial Biogeography as a Driver of Regional Wine Quality". Invited Seminar, Lawrence Berkeley National Laboratories, January 14, 2013


Presentations

  • "Tracking Microbial Terroir Along the Grape-to-Glass Continuum." American Society of Enology and Viticulture Annual Conference. Monterey, CA, June 26, 2013.
  • "Sour Beer 102: Old World vs. New and the Art of Sour Brewing." Khyber Pass: Philly Beer Week, Philadelphia, PA, Jun 3, 2013.
  • "Sour Beer Class 102: Manufactured Beauty - European vs. American Sours." Kyhber Pass: Philly Beer Week,Philadelphia, PA, Jun 5, 2013.
  • "Exploring the Microbial Landscapes within Wineries, Dairies, and Breweries." Second Conference on the Microbiology of the Built Environment. Boulder, CO, May 24, 2013.
  • "Regional Patterns in Grape Fungal Consortia Define Wine Fermentation Communities". Society for Molecular Biology and Evolution: “Eukaryotic -Omics”. University of California, Davis, April 30, 2013.
  • "The Microbial Determinants of Terroir". VEN 290 Seminar, Department of Viticulture & Enology, UC Davis, April 9, 2013.
  • "A Novel Approach to Monitoring Winery Microbes". Recent Advances in Viticulture and Enology: Microbes of Flavor, UC Davis, March 14, 2013
  • "Microbial Terroir: Deep Insight into Site-Specific Winery and Vineyard Microbial Communities". American Society of Enology and Viticulture National Conference, Portland, OR, June 20, 2012.
  • "New Techniques for Population and Strain Profiling". Wine Flavor 101D, UC Davis, April 26, 2012
  • "Next-generation Sequencing Reveals Massive Bacterial Diversity in Botrytized Wines". Recent Advances in Viticulture and Enology: Microbes of Flavor, UC Davis, March 15, 2012
  • "Community Profiling of American Lambic-style Beers Using Terminal Restriction Fragment Length Polymorphism (TRFLP)". American Society of Brewing Chemists Annual Conference, Sanibel Harbour, FL, 2011.
  • "TRFLP: A New Addition to the Winemaker's Toolbox". VEN 290 Seminar, Department of Viticulture & Enology, UC Davis, May 30, 2011.

 

Poster Presentations

  • Bokulich, N.A., Ohta, M., Ryazantseva, M., Masarweh, C., Mills, D.A. 2013. A Novel Approach to Monitoring Winery Microbes. Constellation Brands Technical Meeting, Monterey, CA, May 8, 2013.
  • Bokulich, N.A., Ohta, M., Ryazantseva, M., Masarweh, C., Mills, D.A. 2013. A Novel Approach to Monitoring Winery Microbes. Recent Advances in Viticulture and Enology: Microbes of Flavor, UC Davis, March 14, 2013
  • Bokulich, N.A., C.M.L. Joseph, G. Allen, A. Benson, and D.A. Mills. 2012. Next-generation sequencing reveals massive bacterial diversity of botrytized wines. Recent Advances in Viticulture and Enology: Microbes of Flavor, UC Davis, March 15, 2012.


Honors/Awards

  • NIH NIGMS T32 Biotechnology Training Program Fellowship 2013-2014
  • Samuel Adams Scholarship Fund, American Society of Brewing Chemists 2013-2014
  • American Wine Society Education Fund Scholarship, 2012-2014
  • George F. Stewart Memorial Student Scholarship 2013
  • Brian Williams Scholarship, American Society of Brewing Chemists 2012-2013
  • American Wine Society Education Fund Scholarship, 2012-2013

  • Bernie S. and Alta Schweigert Award 2013
  • Dannon Probiotics Fellowship 2012-2013
  • Bernie S. and Alta Schweigert Award 2012
  • Cargill Malt Scholarship 2011-2012
  • Roger C. Briess Scholarship 2010-2011
  • David E. Gallo Educational Enhancement 2010-2011
  • Adolf L. & Richie C. Heck Research Fellowship 2010-2011
  • Wine Spectator Scholarship 2010-2012
  • Jastro Shields Fellowships

 

Document Actions

News
Gates project profiled Apr 03, 2014
Milk bioactives work profiled in Science News Dec 30, 2013
PNAS paper on wine microbial terroir profiled Dec 03, 2013
Bokulich garners Brewing award Oct 26, 2013
Premie probiotic paper profiled Oct 22, 2013
Bokulich beer microbiome work profiled Aug 29, 2013
Dr. Mills NIH talk online Aug 22, 2013
Dave Sela begins faculty position at University of Massachusetts-Amherst Aug 17, 2013
Chemical Engineering News article profiles milk glycan work Jul 08, 2013
Wine Microbial Terroir Work Profiled In Wines and Vines Article May 20, 2013
Mills lab alumni Daniel Garrido honored with award Apr 10, 2013
AJEV paper wins 2013 Best Enology Paper award Apr 09, 2013
Daniel Garrido begins faculty position at Pontifical Catholic University of Chile Mar 24, 2013
Nick Bokulich's Nature Methods paper profiled Dec 05, 2012
Join the American Gut project!! Nov 21, 2012
Beer and Wine Microbiome Papers profiled Nov 13, 2012
Dan Garrido's Molecular and Cellular Proteomics paper profiled Aug 20, 2012
Milk glycan work profiled in CDRF newsletter Aug 02, 2012
Dr. Mills & Foods for Health Inst. group garner RISE grant Aug 02, 2012
Bokulich receives Dannon Fellowship Jul 09, 2012
Bokulich receives American Society Brewing Chemist award May 30, 2012
Bill and Melinda Gates Foundation Award May 15, 2012
Milk Bioactives Project profiled in Discovery magazine May 11, 2012
Dr. Mills interviewed by the Scientist May 09, 2012
Bokulich receives Bernie S. and Alta Schweigert Award Mar 13, 2012
NIH-NCCAM R01 Award Mar 10, 2012
Dr. Mills in Ion Torrent video on wine microbial ecology Mar 09, 2012
Dr. Mills appointed to Shields Endowed Chair Jan 25, 2012
Raybould-Mills garner NIH-NCCAM R21 award Jul 22, 2011
Garrido receives National Milk Producers Federation Scholarship Jul 20, 2011