Jonathan B. Lynch, Ph.D.

Headshot of Jonathan B. Lynch
  • Assistant Professor of Biological Chemistry

Research Interests

Host-microbe interactions, microbiota, bacterial influences on host lipids and neurotransmitters more


Dr. Lynch received his BA in biology and psychology from the University of Pennsylvania, where he studied HIV drug resistance in the lab of Dr. Bob Doms. He then moved to Stanford University, where he began his love of host-microbe interactions while pursuing his Ph.D. in Microbiology and Immunology in the lab of Dr. Justin Sonnenburg. His thesis work identified the molecular regulation of nutrient consumption hierarchies by a gut bacterium, describing how these bacteria "chose" which sugars to metabolize in the intestine. He then moved to the lab of Dr. Ned Ruby at the University of Hawaii-Manoa for a postdoctoral fellowship, where he used the model squid-Vibrio symbiosis to characterize fundamental aspects of animal-bacteria symbiosis. His research there included bacterial physiological responses to symbiosis, symbiosis-dependent bacteriophage resistance, and biophysical determinants of symbiotic motility. He concluded his postdoctoral training in the lab of Dr. Elaine Hsiao at UCLA, where he returned to the gut microbiota to apply his host-microbe expertise to exploring understudied bacteria from the genus Turicibacter. He identified genes these bacteria use to influence host lipids, cholesterol, and serotonin production, potentially positioning these bacteria at the center of several important host processes.

Dr. Lynch's current research focuses on the determinants of host-microbe symbiosis, from fundamental molecular processes that bind animals and bacteria to the applied uses of the microbiota to treat lipid and neurological disorders. His research group emphasizes creative approaches to difficult problems and training scientists from all backgrounds to be leaders in their future fields. more


  • Assistant Professor of Biological Chemistry

Departments / Divisions



  • Ph.D.; Stanford University (California) (2014)
  • B.A.; University of Pennsylvania (Pennsylvania) (2008)

Research & Publications

Research Summary

We explore how symbiotic bacteria sense, respond to, and shape host physiology, from molecular mechanisms to translational applications.


Lab Website: Host-Microbe Dynamics

Selected Publications

View all on PubMed

Jonathan B. Lynch, Gonzalez EL, Choy K, Faull KF, Jewell T, Arrellano A, Liang J, Yu KB, Paramo J, Hsiao EY. Gut microbiota Turicibacter strains differentially modify bile acids and host lipids. Nature Communications 14(3669), 2023. bioRxiv

Jonathan B. Lynch, Hsiao EY. Toward understanding links between the microbiome and neurotransmitters. Annals of the New York Academy of Sciences 1-7, 2023. -Highlighted in H1 Connect, 2023

Jonathan B. Lynch, James NG, McFall-Ngai M, Ruby EG, Shin S, Takagi D. Transitioning to confined spaces impacts bacterial swimming and escape response. Biophysical Journal 121(13), 2022. bioRxiv

Jonathan B. Lynch, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science, (365)6460, 2019. Highlighted in Faculty Opinions, 2020

Jonathan B. Lynch, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG. Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. Journal of Bacteriology, 201(20), 2019

Academic Affiliations & Courses

Graduate Program Affiliation

Biological Chemistry

Biochemistry, Cellular, and Molecular Biology (BCMB)

Activities & Honors


  • Graduate Research Fellowship, National Science Foundation
  • F32 Postdoctoral Fellowship, National Institutes of Health
  • Postdoctoral Fellowship, Ford Foundation/NASEM
  • Intersections Fellowship, ISFS
  • Leadership in Diversity Award, Stanford Biosciences Office of Graduate Education and Diversity

Patient Ratings & Comments

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