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Home  /  People  /  Ned (Edward) Ruby

Ned (Edward) Ruby

Faculty Associate in Biology and Biological Engineering
Research Summary
Dr. Ruby has worked for 40 years on beneficial bacterial-host interactions. His doctoral training was at the Scripps Institution of Oceanography, UC San Diego, where he worked on luminescent bacteria isolated from the light organs of fishes, and on the discovery of microbial quorum signaling. He did postdoctoral work at Harvard University, Woods Hole Oceanographic Institution, and UCLA before becoming a faculty member at the University of Southern California, and entering into a collaboration with Dr. Margaret McFall-Ngai to develop the Vibrio fischeri-sepiolid squid light-organ association as a model for beneficial bacteria-host interactions. He was hired into the Symbiosis Cluster at the University of Wisconsin-Madison in 2004, where he held the Steenbock Chair of Microbiological Sciences, and was Vice-Chair and Acting-Chair of the Department of Medical Microbiology & Immunology. He has served on the Board of Governors of the American Academy of Microbiology, and been a visiting professor at HuaZhong U, China, and a EU/Marie Curie ITN Researcher at the Max-Planck Institute, Bremen, Germany. He was also a Moore Scholar at Caltech, and Chair of the American Academy of Microbiology Awards Board. In 2015, Dr. Ruby moved his lab to the University of Hawaii, where the squid-vibrio system is endemic, and in 2022 brought his lab to the Caltech campus. His current research uses (i) a broad-based approach to analyze how sequential signaling cascades and nutrient manipulation produce rhythmic patterns of bacterial metabolism that underlie the association’s persistence, (ii) new analytical and imaging approaches to discover novel pathways of signaling between the symbiont and its host, and (iii) comparative and functional genomics to discover principles controlling population-level interactions among symbionts.

Publications

Yang, L, S Lawhorn, C Bongrand, JC Kosmopoulos, J Kuwabara, M VanNieuwenhze, MJ Mandel, M McFall-Ngai, and E Ruby. 2024. Bacterial growth dynamics in a rhythmic symbiosis. Mol Bio Cell 35: doi: 10.1091/mbc.E24-01-0044 (PMC11238090)

Bongrand, C, E Koch, D Mende, A Romano, S Lawhorn, M McFall-Ngai, EF DeLong, and EG Ruby.  2022. Evidence of genomic diversification in a natural symbiotic population within its host. Front Microbiol 13:854355 (PMC8922018)

Essock-Burns, T, BD Bennett, D Arencibia, S Moriano-Gutierrez, M Medeiros, MJ McFall-Ngai and EG Ruby. 2021. Bacterial quorum sensing induces morphological change in a key host tissue during the Euprymna scolopes‒Vibrio fischeri symbiosis. mBio doi: 10.1128/mBio.02402-21(PMC8546586).

Moriano-Gutierrez, S, EG Ruby and MJ McFall-Ngai. 2021. MicroRNA-mediated regulation of initial host responses in a symbiotic organ. mSystems doi: 10.1128/mSystems.00081-21. (PMC8125070)  *Selected by the journal as ‘Editor's Pick'.

Moriano-Gutierrez, S, C Bongrand, T Essock-Burns, L Wu, MJ McFall-Ngai and EG Ruby. 2020. The non-coding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses.

PLoS Biol 18: doi: 10.1371/journal.pbio.3000934 (PMC7665748). *Selected by the journal as "one of the most exciting papers of 2020". 

Bongrand, C, S Moriano-Gutierrez, P Arevalo, MJ McFall-Ngai, KL Visick, M Polz and EG   Ruby. 2020. Using colonization assays and comparative genomics to discover symbiosis behaviors and factors in Vibrio fischeri. mBio 11: doi: 10.1128/mBio.03407-19 (PMC7064787)

Schwartzman, JA, JB Lynch, S Flores Ramos, L Zhou, MA Apicella, JY Yew and EG Ruby. 2019. Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria-animal mutualism. Mol Microbiol 112:1326-1338 (PMC6823639)

Lynch, JB, JA Schwartzman, BD Bennett, SJ McAnulty, M Knop, SV Nyholm and EG Ruby 2019. Ambient pH alters protein content of outer membrane vesicles, driving host development in a beneficial symbiosis. J Bacteriol 201: doi:10.1128/JB.00319-19 (PMC6755730)

Moriano-Gutierrez, S, EJ Koch, H Bussan, K Romano, M Belcaid, FE Rey, E Ruby and M McFall-Ngai. 2019. Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proc Natl Acad Sci USA 116:7990-7999 (PMC6475425)