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(* Equal contributors, § Corresponding author)

  1. 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 . Behind the Paper. Bile modifications from understudied gut bacteria (genus Turicibacter) impact host lipids, positioning these bacteria to influence large parts of host physiology.

  2. 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. Gut bacteria interact with neurotransmitters, but there is still a lot to learn about the exact mechanisms.

  3. 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. Symbiotic bacteria change the way they swim when they experience host-like physical conditions, meaning that we may need to reexamine our models of bacterial motility.

  4. 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. Host-association helps protect bacteria from being killed by bacteriophages (viruses that infect bacteria), explaining one way that symbioses can be stable in the face of abundant environmental phages.

  5. 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. Simulated microgravity change the way that bacteria release outer membrane vesicles, so bacteria in space might have different interactions with their environments than those on the ground.

  6. 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. Symbiotic animals take up materials from the external environment, including bacterial molecules that can stimulate tissue development.

  7. Jonathan B. Lynch§, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science, (365)6460, 2019. –Highlighted in Faculty Opinions, 2020. The gut microbiota influences host neurobiology, suggesting that what we consider "normal" nervous system activity is dependent on microbes.

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Before 2020

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

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