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Aspen Reese


Host-associated microbes shape the evolution and ecology both of their own communities and the organisms they inhabit. The microbiota can be crucial for physiological processes such as nutrient and waste processing, signaling, and immunity. But these functions can be in conflict with one another, and some microbes—most notably pathogens—can more explicitly undercut host fitness. Understanding the biology of host organisms, therefore, requires jointly considering the microbiota’s diverse functions and their tradeoffs.

We study host and microbial responses to changing environments and how ecological or evolutionary microbial responses impact host fitness. We do this work with a variety of experimental and observational techniques in a range of animal systems. Current areas of focus include the impact of domestication on the mammalian gut microbiota and its implications for laboratory models and agriculture; how captive breeding alters the microbiota, potentially affecting animal conservation; and the historic and future responses of the microbiota to human pressures.

Select Publications

  • Frederickson, M.E. and A.T. Reese. 2021. Microbial ecology and evolution are essential for understanding pandemics. mBio 12:e02144-21. PubMed PMID:34579579.
  • Kuthyar, S. and A.T. Reese. 2021. Variation in microbial exposure at the human-animal interface and the implications for microbiome-mediated health outcomes. mSystems 6: e00567-21. PubMed PMID: 34342530.
  • Carmody, R.N., A. Sarkar, and A.T. Reese. 2021. Gut microbiota through an evolutionary lens. Science, 372:462-463. PubMed PMID: 33926939
  • Reese, A.T., K.S. Chadaideh, C.E. Diggins, M. Beckel, P. Callahan, R. Ryan, M.E. Thompson, R.N. Carmody. 2021. Effects of domestication on the gut microbiota parallel those of human industrialization. eLife 10: e60197. PMID: 33755015
  • Reese, A.T., S.R. Phillips, L.A. Owens, E.M. Venable, K.E. Langergraber, Z.P. Machanda, J.C. Mitani, M.N. Muller, D.P. Watts, R.W. Wrangham, T.L. Goldberg, M. Emery Thompson, R.N. Carmody. 2021. Age patterning in wild chimpanzee gut microbiota diversity reveals differences from humans in early life. Curr Bio 31: 613-620. PMID: 33232664
  • Reese, A.T., A.A. Madden, M. Joossens, G. Lacaze, R.R. Dunn. 2020. Influences of ingredients and bakers on the bacteria and fungi in sourdough starters and bread. mSphere 5(1): e00950-19. PMID: 31941818
  • Reese, A.T.*, T.R. Kartzinel*, B.L. Petrone, P.J. Turnbaugh, R.M. Pringle, and L.A. David. 2019. Using DNA metabarcoding to evaluate the plant component of human diets: a proof of concept. mSystems 4:e00458-19. PMID: 31594830
  • Reese, A.T. and S.M. Kearney. 2019. Incorporating functional trade-offs into studies of the gut microbiota. Current Opinion in Microbiology 50:20-27. PMID: 31593869
  • Reese, A.T. and R.N. Carmody. 2019. Thinking outside the cereal box: non-carbohydrate routes for dietary manipulation of the gut microbiota. Applied and Environmental Microbiology 85:e02246-18.
  • Reese, A.T., F.C. Pereira, A. Schintlmeister, D. Berry, M. Wagner, L.P. Hale, A. Wu, S. Jiang, H.K. Durand, X. Zhou, R. Premont, A.M. Diehl, T.M. O’Connell, S.C. Alberts, T.R. Kartzinel, R.M. Pringle, R.R. Dunn, J.P. Wright, and L.A. David. 2018. Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology 3:1441-1450. PMID: 30374168
  • Reese, A.T., R.R. Dunn. 2018. Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. mBio 9: e01294-18. PMID: 30065092
  • Reese, A.T., E.H. Cho, B. Klitzman, S.P. Nichols, N.A. Wisniewski, M.M. Villa, H.K. Durand, F.S. Midani, S. Nimmagadda, T.M. O’Connell, J.P. Wright, M.A. Deshusses, L.A. David. 2018. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLife 7: e35987. PMID: 29916366
  • Reese, A.T., K. Lulow, L.A. David, J.P. Wright. 2018. Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms. Ecology and Evolution 8: 1196-1205. PMID: 29375790
  • Reese, A.T., A. Savage, E. Youngsteadt, K.L. McGuire, A. Koling, O. Watkins, S.D. Frank, and R.R. Dunn. 2016. Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan. The ISME Journal. 10: 751-760. PMID: 26394011


Aspen completed her Ph.D. at Duke University where her research explored the ecological dynamics of gut and soil microbial communities. During that time, she was awarded an NSF Graduate Research Fellowship and a Doctoral Dissertation Improvement Grant. Following graduate school, Aspen was a Junior Fellow at the Harvard Society of Fellows, conducting research funded by the Harvard Milton Fund and the Star Family Challenge for Promising Scientific Research. Aspen joined the UCSD faculty in 2020.

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