Title
Professor of the Graduate School

Department
Dept of Plant and Microbial Biology


Faculty URL
http://plantandmicrobiology.berkeley.edu/profile/taylor

Research Group
http://taylorlab.berkeley.edu/

Email
jtaylor@berkeley.edu

Phone
(510) 642-5366

Fax
(510) 642-4995


Search UC Berkeley Directory





Research Expertise and Interest
evolution, fungi, phylogenomics, mycology, population genomics, ecology

Research Description
Some recent publications from the lab:
Valley Fever or coccidioidomycosis
Taylor, J. W., & Barker, B. M. (2019). The endozoan, small-mammal reservoir hypothesis and the life cycle of?Coccidioides?species.?Medical mycology,?57(Supplement_1), S16-S20.?https://doi.org/10.1093/mmy/myy039
Taylor, J.W., Hann-Soden, C., Branco, S., Sylvain, I., Ellison, C.E.? 2015. Clonal reproduction in fungi. Proceedings of the National Academy of Science 112(29): 8901-8908.?https://doi.org/10.1073/pnas.1503159112
Whiston, E. and J. W. Taylor. 2016. Comparative phylogenomics of pathogenic and non-pathogenic species. G3: Genes, Genomes, Genetics 6:235-244??https://doi.org/10.1534/g3.115.022806
Taylor, J. W. 2015. Evolutionary perspectives on human fungal pathogens. Pp 23-40, In: Casadevall, A., Mitchell, A., Berman, J., Kwon-Chung, K., Perfect, J., Heitman, J. (eds), Human Fungal Pathogens, Cold Spring Harbor Perspectives in Medicine, CSHL Press, Cold Spring Harbor, NY. DOI:?10.1101/cshperspect.a019588
Thompson, G. R., Stevens, D. A., Clemons, K. V, Fierer, Johnson, R. H., Sykes, J. Rutherford, M. Peterson, J. W. Taylor and V. Chaturvedi (2015). "Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease." Mycopathologia 179: 1-9.?https://doi.org/10.1007/s11046-014-9816-7
Whiston, E., Taylor, J.W., 2014. Genomics in?Coccidioides: Insights into evolution, ecology, and pathogenesis. Medical Mycology. 52, 149-155.?https://doi.org/10.1093/mmy/myt001
Wise, H-Z, Hung, C-Y, Whiston, E, Taylor, JW, Cole GT. 2013. Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease. Microbial Pathogenesis 59-60: 19-28.?https://doi.org/10.1016/j.micpath.2013.04.003
Whiston, E., Wise, H.-Z., Jui, G., Sharpton, T. J., Cole, G. T., J. W. Taylor. 2012. Comparative transcriptomics of the saprobic and parasitic growth phases in?Coccidioides?spp. PLoS One 7: e41034.?https://doi.org/10.1371/journal.pone.0041034
Neafsey, D. E., B. M. Barker, Sharpton, T.J., Stajich, J. E., Park, D. J., Whiston, E. Taylor, J.W., Rounsley, S. D. (2010). Population genomic sequencing of?Coccidioides?fungi reveals recent hybridization and a novel form of transposon control. Genome Research 20:938-946.?10.1101/gr.103911.109
Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C-Y, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, and JW Taylor. 2009. Comparative genomic analyses of the human fungal pathogens?Coccidioides?and their relatives. Genome Research 19 1722-1731.?10.1101/gr.087551.108
Johannesson, H. Kasuga, T., Schaller, R.A, Good, B. Gardner, M.J., Townsend, J.P., Cole, G.T., and J. W. Taylor. 2006. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus,?Coccidioides posadasii.?Fungal Genetics and Biology 43:545-559.?https://doi.org/10.1016/j.fgb.2006.02.003
Johannesson, H., Townsend, J.P., Hung, C.-Y., Cole, G.T., and J.W. Taylor. 2005.? Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi?Coccidioides immitis?and?C. posadasii.? Genetics 171: 109-117.?10.1534/genetics.105.040923
Johannesson, H., Vidal, P., Guarro, J., Herr, R.A., Cole, G.T., and J. W. Taylor. 2004. Positive directional selection in the proline-rich-antigen (PRA) gene among the human pathogenic fungi?Coccidioides immitis,?Coccidioides posadasii?and their closest relatives. Molecular Biology and Evolution 21:1134-1145.?https://doi.org/10.1534/genetics.105.040923
Fisher, M.C., Ranalla, B., Chaturvedi, V. and J. W. Taylor. 2002. Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human?Coccidioides?infections.? Proc. Natl. Acad. Sci. (USA) 99:9067-9071.?https://doi.org/10.1073/pnas.132178099
Fisher, M. C., Koenig, G. L., White, T. J., and J. W. Taylor. 2002. Molecular and phenotypic description of?Coccidioides posadasii?sp. nov., previously recognized as the non-California population of?Coccidioides immitis.??Mycologia 94:73-84.?https://doi.org/10.1080/15572536.2003.11833250
Koufopanou, V., Burt, A., Szaro, T., and Taylor, J. W. 2001. Gene Genealogies, Cryptic Species, and Molecular Evolution in the Human Pathogen?Coccidioides immitis?and Relatives (Ascomycota, Onygenales). Molecular Biology and Evolution 18: 1246-1258.?https://doi.org/10.1093/oxfordjournals.molbev.a003910
Fisher, M. C., Koenig, G. L., White, T. J., San-Blas, G., Negroni, R., Gutierrez Alvarez, I., Wanke, B., and J. W. Taylor. 2001. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc. Natl. Acad. Sci. (USA) 98:4558-4562.?https://doi.org/10.1073/pnas.071406098
McEwen, J.G., Taylor, J.W., Carter, D., Xu J., Felipe, M.S.S., Vilgalys, R., Mitchell, T.G., Kasuga, T., White, T. and C.M.S. Soares. 2000. Molecular typing of pathogenic fungi. Medical Mycology 38 (Supplement 1): 189-97.?https://doi.org/10.1080/mmy.38.s1.189.197
Burt, A., Koufopanou, V., Taylor, J.W. 2000. Population genetics of human-pathogenic fungi.? Pp. 229-244 In:?Molecular Epidemiology of Infectious Diseases, R.C.A. Thompson (ed.). Arnold, London.
Fisher, M.C., Koenig, G., White, T.W., Taylor, J.W. 2000. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus?Coccidioides immitis.? Molec. Biol. Evol. 17:1164-1174.?https://doi.org/10.1093/oxfordjournals.molbev.a026399
Fisher, M.C., Koenig, G.L., White, T.J. and J.W. Taylor.? 2000.? Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen?Coccidioides immitis.? J. Clin. Microbiol. 38:807-813.?https://jcm.asm.org/content/38/2/807
Greene, D. R. and Taylor, J. W. 2000.? Soil isolation and molecular identification of?Coccidioides?immitis.? Mycologia 92: 406-410.?https://doi.org/10.1080/00275514.2000.12061175
Drought, fungi and Sorghum
Gao, Cheng, Liliam Montoya, Ling Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Vasanth Singan, John Vogel, Robert B. Hutmacher, Jeffery A. Dahlberg, Devin Coleman-Derr, Peggy G. Lemaux, John W. Taylor. 2020. Fungal community assembly in drought stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nature Communications (in press).
Nelle Varoquaux,?Benjamin Cole,?Cheng Gao,?Grady Pierroz,?Christopher R. Baker,?Dhruv Patel,?Mary Madera,?Tim Jeffers,?Joy Hollingsworth,?Julie Sievert,?Yuko Yoshinaga,?Judith A. Owiti,?Vasanth R. Singan,?Stephanie DeGraaf,?Ling Xu,?Matthew J. Blow,?Maria J. Harrison,?Axel Visel,?Christer Jansson,?Krishna K. Niyogi,?Robert Hutmacher,?Devin Coleman-Derr,?Ronan C. O’Malley,?John W. Taylor,?Jeffery Dahlberg,?John P. Vogel,?Peggy G. Lemaux, and?Elizabeth Purdom. 2019. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc Natl Acad Sci USA?first published December 5, 2019.?https://doi.org/10.1073/pnas.1907500116
Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Purdom, E., Hutmacher, R.B., Dahlberg, J.A., Coleman-Derr, D., Lemaux, P.G. and Taylor, J.W., 2019. Strong succession in arbuscular mycorrhizal fungal communities.?The ISME journal,?13:214-226?https://doi.org/10.1038/s41396-018-0264-0
Ling Xu, Dan Naylor, Zhaobin Dong, Tuesday Simmons, Grady Pierroz, Kim K. Hixson, Young-Mo Kim, Erika M. Zink, Kristin M. Engbrecht, Yi Wang, Cheng Gao, Stephanie DeGraaf, Mary A. Madera, Julie A. Sievert, Joy Hollingsworth, Devon Birdseye, Henrik V. Scheller, Robert Hutmacher, Jeffery Dahlberg, Christer Jansson, John W. Taylor, Peggy G. Lemaux, and Devin Coleman-Derr (2018). Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences, 115(18), E4284-E4293.?https://doi.org/10.1073/pnas.1717308115
Indoor air, fungi and water intrusion
Sylvain?IA, Adams?RI, Taylor?JW (2019)?A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building. PLOS ONE 14(3): e0213355.?https://doi.org/10.1371/journal.pone.0213355
Adams, R. I., Lymperopoulou, D. S., Misztal, P. K., Pessotti, R. D., Behie, S. W., Tian, Y. L., Goldstein, A. H., Lindow, S. E., Nazaroff, W. W., Taylor, J. W., Traxler, M. F., Bruns, T. D., 2017. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces. Microbiome. 5, Article number 128,?https://doi.org/10.1186/s40168-017-0347-6
Adams, Rachel I.,? Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyv?rinen, Martin T?ubel. 2015. Passive dust collectors for assessing airborne microbial material. Microbiome 3(1):46.?https://doi.org/10.1186/s40168-015-0112-7.
Adams, Rachel I.,? Seema Bhangar, Wilmer Pasut, Edward A. Arens , John W. Taylor, Steven E. Lindow, William W. Nazaroff, Thomas D. Bruns. 2015. Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS ONE 10(5):e0128022.?https://doi.org/10.1371/journal.pone.0128022
Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., Bruns, T. D., 2013b. Airborne bacterial communities in residences: Similarities and differences with fungi. Plos One. 9: e91283.?https://doi.org/10.1371/journal.pone.0091283
Adams, R. I., Miletto, M., Taylor, J. W., Bruns, T. D., 2013b. The Diversity and Distribution of Fungi on Residential Surfaces. Plos One. 8(11) e78866.?https://doi.org/10.1371/journal.pone.0078866
Adams, R.I., Amend, A.S., Taylor, J.W., Bruns, T.D. 2013. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: A case study of fungi in indoor dust. Microbial. Ecol. 66:735-741?https://doi.org/10.1007/s00248-013-0266-4.
Adams RI, Miletto M, Taylor JW, Bruns TD. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7:1262-1273, 21?February?2013;?https://doi.org/10.1038/ismej.2013.28