Jonathan Lynch, Ph.D.

Assistant Professor

Website

Description of Research

Animals are intimately associated with communities of microorganisms collectively referred to as the microbiota. The bacteria, archaea, fungi, and viruses that make up the animal microbiota profoundly shape the physiology of their host, altering host metabolism, immune function, and development. This powerfully positions the microbiota as a tool that we can use to influence host biology in meaningful ways.

However, the microbiota is incredibly complex, making it difficult to properly describe, let alone to intentionally manipulate. This is especially true with the gastrointestinal/gut microbiota, where hundreds of poorly characterized microbial species that vary across hosts collectively shape host physiology at multiple levels. Still, the foundations of these complex relationships are shared across different hosts and different contexts, so it is often possible to generalize specific mechanisms across unique microbiotas.

The lab of Host-Microbe Dynamics works to define the fundamental principles of symbiotic relationships between animals and their microbiota. We focus on how the microbiota senses, responds to, and interacts with host lipid metabolism, neurotransmitters, and physical parameters. Ultimately, our goal is to better define the host-microbe relationship and to understand how we can exploit the microbiota to improve host health.

Lab Members

  • Grace Heiting, research technologist, Department of Biological Chemistry
  • Tanae Lewis, graduate student, GPBC
  • Kamal Kaur, undergraduate student
  • Sarah Rosental, undergraduate student

Publications

§=corresponding, *=these authors contributed equally

  • 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 https://www.biorxiv.org/content/10.1101/2022.06.27.497673v2.
  • 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 https://www.biorxiv.org/content/10.1101/2021.09.15.460467v1.
  • Jonathan B. Lynch, Bennett BD, Merrill BD, Ruby EG, Hryckowian AJ. A model symbiosis reveals host- and symbiont-derived phage protection mechanisms. Cell Reports 38(7), 2022. bioRxiv https://www.biorxiv.org/content/10.1101/2021.07.09.451802v1.
  • Vroom M, Rodruiguez-Ocasio Y, Jonathan B. Lynch, Ruby E, Foster J. Modeled microgravity alters lipopolysaccharide and outer membrane vesicle production of the beneficial symbiont Vibrio fischeri. npj Microgravity 7(8), 2021.
  • Cohen SK, Aschtgen M‐S, Jonathan B. Lynch, Koehler S, Chen F, Escrig S, Daraspe J, Ruby EG, Meibom A, McFall-Ngai M. Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging. Cellular Microbiology 22, 2020.
  • Jonathan B. Lynch§, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science, (365)6460, 2019. –Highlighted in Faculty Opinions, 2020
  • Schwartzman JA*, Jonathan B. Lynch*, Flores Ramos S, Zhou L, Apicella MA, Yew JY, Ruby EG. Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria–animal mutualism. Molecular Microbiology, 112(4), 2019.
  • 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.
  • Jonathan B. Lynch§ and Alegado RA§. Spheres of hope, packets of doom: the good and bad of Outer Membrane Vesicles (OMVs) in interspecies and ecological dynamics. Journal of Bacteriology, 199(15), 2017.
  • Aschtgen MS, Jonathan B. Lynch, Koch E, Schwartzman J, McFall-Ngai M, Ruby E. Rotation of Vibrio fischeri flagella produces outer membrane vesicles that induce host development. Journal of Bacteriology 198(16), 2016.
  • Ng KM, Ferreyra JA, Higginbottom SK, Jonathan B. Lynch, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, Sonnenburg JL. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502(7469), 2013.
  • Jonathan B. Lynch and Sonnenburg JL. Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Molecular Microbiology 85(3), 2012.
  • Harrison JE, Jonathan B. Lynch, Sierra LJ, Blackburn LA, Ray N, Collman RG, Doms RW. Baseline resistance of primary human immunodeficiency virus type 1 strains to the CXCR4 inhibitor AMD3100. Journal of Virology 82(23), 2008.