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UC Davis Thesis-Related Publications by Dr. Nick Bokulich

Publications by Dr. Nick Bokulich from his MS in Viticulture and Enology (2009-2011) and PhD in Food Science (2011-2014) at UC Davis

UC Davis Thesis-Related Publications by Dr. Nick Bokulich

This list is the publications involving Nick Bokulich during his time as a Masters and PhD student in Departments of Food Science & Technology and Viticulture & Enology at UC Davis.   For a full list of Nick's publications please check out his Google Scholar page.   An amazing amount of impact for graduate degree. Congratulations Nick!

Publications during PhD Thesis in Department of Food Science & Technology (Food Science Graduate Group; 2011-2014).

28.  Burns,K. A., N. A Bokulich, D. Cantu, R. F. Greenhut, D. A. Kluepfel, A. T. O'Geen, S. L. Strauss, K. L. Steenwerth. 2017.  Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management.  Soil Biology and Biochemistry  103:337-348.

27. Bokulich, N. A., C. Masarweh, T. S. Collins, G. Allen, H. Heymann, S. E. Ebeler and D. A. Mills. 2016. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio 7:e00631-16.

26. Walker, G. A., A. Hjelmeland, N. A. Bokulich, D. A. Mills1, S. E. Ebeler and L. F. Bisson. 2016.  Impact of the [GAR+] prion on fermentation progression and bacterial population composition with Saccharomyces cerevisiae strain UCD932.  American Journal of Enology and Viticulture. .

25. Bokulich, N. A., Z. T. Lewis, K. L Boundy-Mills, D. A. Mills.  2016.  A new perspective on microbial landscapes within food production. Current Opinion in Biotechnology. 37:182–189.

24. Zarraonaindia, I., S. M. Owens, K. West, J. Hampton-Marcell, S.Lax, N. A. Bokulich, D. A. Mills, G Martin, S. Taghavid, D. van der Lelie and J. A. Gilbert.  2015.  The soil microbiome influences grapevine-associated microbiota. mBio 6:e02527-14.

23. Burns,K. N., D. A. Kluepfel, S. L. Strauss, N. A. Bokulich, D. Cantu, K. L. Steenwerth. 2015. Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by geographic features.  Soil Biology and Biochemistry 91, 232-247.

22. Bokulich, N. A., J. Bergsveinson, B. Ziola, D. A. Mills. 2015. Mapping microbial ecosystems and spoilage-gene flow in brewery environments highlights patterns of contamination and resistance. Elife 4:e04634.

21. Bokulich, N. A., L. Amiranashvili, K. Chitchyan, N. Ghazanchyan, K. Darbinyan, N. Gagelidze, T. Sadunishvili, V. Goginyan, G. Kvesitadze, T. Torok and D. A. Mills. 2015. Microbial biogeography of the transnational fermented milk Matsoni. Food Microbiology 50:12–19.

20. Bokulich, N. A., M. Swadener, K. Sakamoto, D. A. Mills and Linda F. Bisson. 2015. Sulphur dioxide treatment alters wine microbial diversity and fermentation progression in a dose-dependent fashion. American Journal of Enology and Viticulture. 66:73-79.

19. Bokulich, N. A., M. Ohta, M. Lee and D. A. Mills. 2014. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Applied and Environmental Microbiology 80:5522-5529.

18. 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.

17. 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.

16. 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.

15. 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.

14. Bokulich, N. A. and D. A. Mills. 2013. House microbiome drives microbial landscapes of artisan cheesemaking plants.  Applied and Environmental Microbiology 79:5214-5223.

13. 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.

12. Bokulich, N.A. and Bamforth, C.W. 2013. The microbiology of malting and brewing. Microbiology and Molecular Biology Reviews 77:157-172.

11. Bokulich, N. A., M. Ohta, P. M. Richardson and D. A. Mills.  2013. Monitoring seasonal changes in winery-resident microbiota.  PLoS One8:e66437.

10. 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.

9. 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.

8. 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.

7. 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.

6. 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.

5. 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.

4. 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 Microbiology 31:126-131.


Publications during MS Thesis in Department of Viticulture and Enology (Viticulture and Enology Graduate Group; 2009-2011)


3. Bokulich, N. A., C. M. L. Joseph, G. Allen, A. K. Benson and D. A. Mills. 2012. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One 7:e36357.

2. Bokulich, N. A., C. Bamforth, and D. A. Mills. 2012. Brewhouse-resident microbiota responsible for fermentation of American coolship ale. PLoS One 7:e35507.

1. Bokulich, N., C. H. Hwang, L. Shuwen, K. Boundy-Mills and D. A. Mills.  2012. Profiling the yeast ecology of wine using terminal restriction fragment length polymorphism analysis.  American Journal of Enology and Viticulture 63:185-194. (AJEV best Paper award).

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Cell paper profiled Apr 17, 2016
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Wine microbiome work profiled by Nature Plants Nov 24, 2015
Liver Cancer-Gut Microbiome work profiled by Synthesis May 04, 2015
Bokulich interviewed on eLife brewery paper Apr 25, 2015
Zachery Lewis's paper in Microbiome Profiled by NPR and UC Davis Apr 11, 2015
Dr. Mills Elected Fellow in American Academy of Microbiology Feb 25, 2015
Milk Bioactives Group profiled by UC Davis Office of Research Dec 11, 2014
NIH Grant Success on Milk Bioactives!! Nov 26, 2014
UC Davis Milk Bioactives Group Profiled in Science Sep 26, 2014
Steve Frese honored by European Probiotics Association Sep 07, 2014
Nick Bokulich garners 2013-14 Kinsella Thesis award Sep 07, 2014
Bangladesh infant cohort paper profiled Jul 26, 2014
Milk Bioactives Program Profiled in Davis Enterprise Jul 26, 2014
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Gates project profiled Apr 03, 2014