Image of Jonathan Lynch

Jonathan Lynch

Assistant Professor


725 N. Wolfe Street
WBSB 509

Biological Chemistry

Animals, including humans, have stable relationships with communities of microorganisms collectively referred to as the microbiota. These communities profoundly influence the biology of their hosts, impacting host features such as immune function, metabolism, and even so-called “higher” traits such as cognition and social behavior. Due to the wide range of microbiota-associated effects on host biology, understanding host-microbe relationships is not only important for understanding the normal physiology of the host, but may also allow us to use the microbiota to intentionally shape host health. We focus on several areas of host-microbe symbiosis, ranging from the fundamental features that govern these relationships to the translational prospects of using the microbiota to improve human health. This includes roles of intestinal bacteria in shaping host lipid and cholesterol metabolism, interactions between the microbiota and neurotransmitters, and the biophysical drivers of microbial colonization. We employ diverse techniques from molecular biology, biochemistry, and a variety of -omics platforms to explore our interactions with our microbial partners.

Lynch JB*, Hsiao EY. Toward understanding links between the microbiome and neurotransmitters. Ann N Y Acad Sci. 2023 Apr 5. doi: 10.1111/nyas.14993. Epub ahead of print. PMID: 37017112.

Lynch JB*, James N, McFall-Ngai M, Ruby EG, Shin S, Takagi D. Transitioning to confined spaces impacts bacterial swimming and escape response. Biophys J. 2022 Jul 5;121(13):2653-2662. doi: 10.1016/j.bpj.2022.04.008. Epub 2022 Apr 6. PMID: 35398019; PMCID: PMC9300662.

Vroom MM, Rodriguez-Ocasio Y, Lynch JB, Ruby EG, Foster JS. Modeled microgravity alters lipopolysaccharide and outer membrane vesicle production of the beneficial symbiont Vibrio fischeri. NPJ Microgravity. 2021 Mar 8;7(1):8. doi: 10.1038/s41526-021-00138-8. PMID: 33686090; PMCID: PMC7940393.

Cohen SK, Aschtgen MS, Lynch JB, 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. Cell Microbiol. 2020 Apr;22(4):e13177. doi: 10.1111/cmi.13177. PMID: 32185893; PMCID: PMC7765731.

Lynch JB, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science. 2019 Sep 27;365(6460):1405-1409. doi: 10.1126/science.aay0240. PMID: 31604267.

Schwartzman JA, Lynch JB*, Flores Ramos S, Zhou L, Apicella MA, Yew JY, Ruby EG. Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria-animal mutualism. Mol Microbiol. 2019 Oct;112(4):1326-1338. doi: 10.1111/mmi.14365. Epub 2019 Aug 27. PMID: 31400167; PMCID: PMC6823639.

Lynch JB, 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. J Bacteriol. 2019 Sep 20;201(20):e00319-19. doi: 10.1128/JB.00319-19. PMID: 31331976; PMCID: PMC6755730.

Lynch JB*, Alegado RA. Spheres of Hope, Packets of Doom: the Good and Bad of Outer Membrane Vesicles in Interspecies and Ecological Dynamics. J Bacteriol. 2017 Jul 11;199(15):e00012-17. doi: 10.1128/JB.00012-17. PMID: 28416709; PMCID: PMC5512217.

Aschtgen MS, Lynch JB, Koch E, Schwartzman J, McFall-Ngai M, Ruby E. Rotation of Vibrio fischeri Flagella Produces Outer Membrane Vesicles That Induce Host Development. J Bacteriol. 2016 Jul 28;198(16):2156-65. doi: 10.1128/JB.00101-16. PMID: 27246572; PMCID: PMC4966437.

Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, 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. 2013 Oct 3;502(7469):96-9. doi: 10.1038/nature12503. Epub 2013 Sep 1. PMID: 23995682; PMCID: PMC3825626.

Lynch JB, Sonnenburg JL. Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Mol Microbiol. 2012 Aug;85(3):478-91. doi: 10.1111/j.1365-2958.2012.08123.x. Epub 2012 Jul 5. PMID: 22686399; PMCID: PMC3404733.

Harrison JE, Lynch JB, 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. J Virol. 2008 Dec;82(23):11695-704. doi: 10.1128/JVI.01303-08. Epub 2008 Sep 17. PMID: 18799588; PMCID: PMC2583649.



Jonathan B. Lynch, Gonzalez EL, Choy K, Faull KF, Jewell T, Arellano A, Liang J, Yu KB, Paramo J, Hsiao EY. Turicibacter strains differentially modify bile acids and host lipids. In revision. biorXiv