Glowing Squid

Ruby Lab: Current Members

Research Publications

  • Lynch JB, James N, McFall-Ngai M, Ruby EG, Shin S, Takagi D (2022) Transitioning to confined spaces impacts bacterial swimming and escape response. Biophysical journal : · Pubmed · DOI

  • Bongrand C, Koch E, Mende D, Romano A, Lawhorn S, McFall-Ngai M, DeLong EF, Ruby EG (2022) Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host. Frontiers in microbiology 13:854355 PMC8922018 · Pubmed · DOI

  • Lynch JB, Bennett BD, Merrill BD, Ruby EG, Hryckowian AJ (2022) Independent host- and bacterium-based determinants protect a model symbiosis from phage predation. Cell reports 38((7)):110376 PMC8983117 · Pubmed · DOI

  • McFall-Ngai M, Ruby E (2021) Getting the Message Out: the Many Modes of Host-Symbiont Communication during Early-Stage Establishment of the Squid-Vibrio Partnership. mSystems 6((5)):e0086721 PMC8547416 · Pubmed · DOI

  • Visick KL, Stabb EV, Ruby EG (2021) A lasting symbiosis: how Vibrio fischeri finds a squid partner and persists within its natural host. Nature reviews. Microbiology 19((10)):654-665 PMC8529645 · Pubmed · DOI

  • Moriano-Gutierrez S, Ruby EG, McFall-Ngai MJ (2021) MicroRNA-Mediated Regulation of Initial Host Responses in a Symbiotic Organ. mSystems 6((3)): PMC8125070 · Pubmed · DOI

  • Vroom MM, Rodriguez-Ocasio Y, Lynch JB, Ruby EG, Foster JS (2021) Modeled microgravity alters lipopolysaccharide and outer membrane vesicle production of the beneficial symbiont Vibrio fischeri. NPJ microgravity 7((1)):8 PMC7940393 · Pubmed · DOI

  • Moriano-Gutierrez S, Bongrand C, Essock-Burns T, Wu L, McFall-Ngai MJ, Ruby EG (2020) The noncoding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses. PLoS biology 18((11)):e3000934 PMC7665748 · Pubmed · DOI

  • Aschtgen MS, Brennan CA, Nikolakakis K, Cohen S, McFall-Ngai M, Ruby EG (2020) Insights into flagellar function and mechanism from the squid-vibrio symbiosis. NPJ biofilms and microbiomes 5((1)):32 · Pubmed

  • Koch EJ, Bongrand C, Bennett BD, Lawhorn S, Moriano-Gutierrez S, Pende M, Vadiwala K, Dodt HU, Raible F, Goldman W, Ruby EG, McFall-Ngai M (2020) The cytokine MIF controls daily rhythms of symbiont nutrition in an animal-bacterial association. Proceedings of the National Academy of Sciences of the United States of America 117((44)):27578-27586 PMC7959500 · Pubmed · DOI

  • Ruby E (2020) Getting to know our microbial friends by dropping into their neighbourhood. Environmental microbiology reports 13((1)):27-30 · Pubmed · DOI

  • Bennett BD, Essock-Burns T, Ruby EG (2020) HbtR, a Heterofunctional Homolog of the Virulence Regulator TcpP, Facilitates the Transition between Symbiotic and Planktonic Lifestyles in Vibrio fischeri. mBio 11((5)): PMC7468203 · Pubmed · DOI

  • Koch EJ, Moriano-Gutierrez S, Ruby EG, McFall-Ngai M, Liebeke M (2020) The impact of persistent colonization by on the metabolome of the host squid . The Journal of experimental biology 223((Pt 16)): PMC7473655 · Pubmed · DOI

  • Bennett, BD, T Essock-Burns and EG Ruby (2020) HbtR, a heterofunctional homolog of the virulence regulator TcpP, facilitates the transition between symbiotic and planktonic lifestyles in Vibrio fischeri. mBio (in press): · DOI

  • Essock-Burns T, Bongrand C, Goldman WE, Ruby EG, McFall-Ngai MJ (2020) Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis. mBio 11((3)): PMC7251207 · Pubmed · DOI

  • Cohen SK, Aschtgen MS, Lynch JB, Koehler S, Chen F, Escrig S, Daraspe J, Ruby EG, Meibom A, McFall-Ngai M (2020) Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging. Cellular microbiology 22((4)):e13177 PMC7765731 · Pubmed · DOI

  • Bongrand C, Moriano-Gutierrez S, Arevalo P, McFall-Ngai M, Visick KL, Polz M, Ruby EG (2020) Using Colonization Assays and Comparative Genomics To Discover Symbiosis Behaviors and Factors in Vibrio fischeri. mBio 11((2)): PMC7064787 · Pubmed · DOI

  • Koch EJ, Moriano-Gutierrez S, Ruby EG, McFall-Ngai M, Liebeke M (2020) The impact of persistent colonization by Vibrio fischeri on the metabolome of the host squid Euprymna scolopes. The Journal of experimental biology : · Pubmed · DOI

  • Aschtgen MS, Brennan CA, Nikolakakis K, Cohen S, McFall-Ngai M, Ruby EG (2019) Insights into flagellar function and mechanism from the squid-vibrio symbiosis. NPJ biofilms and microbiomes 5((1)):32 PMC6814793 · Pubmed

  • Bongrand C, Ruby EG (2019) The impact of Vibrio fischeri strain variation on host colonization. Current opinion in microbiology 50:15-19 PMC6899189 · Pubmed

  • Bongrand, C and EG Ruby (2019) The impact of Vibrio fischeri strain variation on host colonization. Current Opinion in Microbiology 50:15-19 · DOI

  • 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. Journal of Bacteriology : · DOI

  • Schwartzman JA, Lynch JB, Flores Ramos S, Zhou L, Apicella MA, Yew JY, Ruby EG (2019) Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria-animal mutualism. Molecular microbiology 112((4)):1326-1338 PMC6823639 · Pubmed

  • 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 Molecular Microbiology 112(4):1326-1338 · DOI

  • Lynch JB, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG (2019) Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. Journal of bacteriology 201((20)): PMC6755730 · Pubmed

  • Moriano-Gutierrez S, Koch EJ, Bussan H, Romano K, Belcaid M, Rey FE, Ruby EG, McFall-Ngai MJ (2019) Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proceedings of the National Academy of Sciences of the United States of America 116((16)):7990-7999 PMC6475425 · Pubmed

  • Bongrand C, Ruby EG (2018) Achieving a multi-strain symbiosis: strain behavior and infection dynamics. The ISME journal 13((3)):698-706 PMC6461934 · Pubmed

  • Kremer N, Koch EJ, El Filali A, Zhou L, Heath-Heckman EAC, Ruby EG, McFall-Ngai MJ (2018) Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis. mSystems 3((5)):e00165-18 PMC6172772 · Pubmed · DOI

  • Koehler S, Gaedeke R, Thompson C, Bongrand C, Visick KL, Ruby E, McFall-Ngai M (2018) The model squid-vibrio symbiosis provides a window into the impact of strain- and species-level differences during the initial stages of symbiont engagement. Environmental microbiology : PMC6386636 · Pubmed

  • Nawroth JC, Guo H, Koch E, Heath-Heckman EAC, Hermanson JC, Ruby EG, Dabiri JO, Kanso E, McFall-Ngai M (2017) Motile cilia create fluid-mechanical microhabitats for the active recruitment of the host microbiome. Proceedings of the National Academy of Sciences of the United States of America 114((36)):9510-9516 PMC5594677 · Pubmed · DOI

  • Pan S, Nikolakakis K, Adamczyk PA, Pan M, Ruby EG, Reed JL (2017) Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium . The Journal of biological chemistry 292((24)):10250-10261 PMC5473228 · Pubmed

  • Chen F, Krasity BC, Peyer SM, Koehler S, Ruby EG, Zhang X, McFall-Ngai MJ (2017) Bactericidal Permeability-Increasing Proteins Shape Host-Microbe Interactions. mBio 8((2)): PMC5380838 · Pubmed

  • Thompson LR, Nikolakakis K, Pan S, Reed J, Knight R, Ruby EG (2017) Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. Environmental microbiology 19((5)):1845-1856 PMC5409853 · Pubmed · DOI

  • Aschtgen MS, Lynch JB, Koch E, Schwartzman J, McFall-Ngai M, Ruby E (2016) Rotation of Vibrio fischeri Flagella Produces Outer Membrane Vesicles That Induce Host Development. Journal of bacteriology 198((16)):2156-65 PMC4966437 · Pubmed

  • Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG (2016) A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. The ISME journal 10((12)):2907-2917 PMC5148191 · Pubmed · DOI

  • Aschtgen M-S, Wetzel K, Goldman W, McFall-Ngai MJ, Ruby EG (2016) Vibrio fischeri-derived outer membrane vesicles trigger host development. Cellul Microbiol 18(4):488-499 4803540 · Pubmed · DOI

  • Beeby M, Ribardo DA, CBrennan CA, Ruby EG, Jensen GJ, Hendrixson DR (2016) Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold Proc Natl Acad Sci USA 113:e1917-1926 · Pubmed

  • Schwartzman JA, Ruby EG (2016) Stress as a Normal Cue in the Symbiotic Environment. Trends in microbiology 24((5)):414-424 PMC4841697 · Pubmed

  • Beeby M, Ribardo DA, Brennan CA, Ruby EG, Jensen GJ, Hendrixson DR (2016) Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold. Proceedings of the National Academy of Sciences of the United States of America 113((13)):E1917-26 PMC4822576 · Pubmed

  • Schwartzman JA, Ruby EG (2016) A conserved chemical dialog of mutualism: Lessons from squid and vibrio. Microbes Infect 18(1):1-10 PMC4715918 · Pubmed · DOI

  • Julie S. Biteen, Paul C. Blainey, Zoe G. Cardon, Miyoung Chun, George M. Church, Pieter C. Dorrestein, Scott E. Fraser, Jack A. Gilbert, Janet K. Jansson, Rob Knight, Jeff F. Miller, Aydogan Ozcan, Kimberly A. Prather, Stephen R. Quake, Edward G. Ruby, Pamela A. Silver, Sharif Taha, Ger van den Engh, Paul S. Weiss, Gerard C. L. Wong, Aaron T. Wright, and Thomas D. Young (2016) Tools for the microbiome: Nano and beyond ACS Nano 10(1):6-37 · DOI

  • Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA, (2015) MICROBIOME. A unified initiative to harness Earth's microbiomes. Science (New York, N.Y.) 350((6260)):507-8 · Pubmed · DOI

  • Nikolakakis K, Lehner EM, McFall-Ngai MJ, Ruby EG (2015) Use of hybridization chain reaction-fluorescent in situ hybridization (HCR-FISH) to track gene expression by both partners during initiation of symbiosis. Appl Environ Microbiol 81(14):4728-4735 (PMC4010582) · Pubmed · DOI

  • Miyashiro T, Oehlert D, Ray VA, Visick KL, Ruby EG (2014) The putative oligosaccharide translocase SypK connects biofilm formation with quorum signaling in Vibrio fischeri. Microbiologyopen : · Pubmed

  • Studer SV, Schwartzman JA, Ho JS, Geske GD, Blackwell HE, Ruby EG (2014) Non-native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability. Environ. Microbiol. 16(8):2623-34 (PMC4010582) · Pubmed

  • Kremer N, Schwartzman J, Augustin R, Zhou L, Ruby EG, Hourdez S, McFall-Ngai MJ (2014) The dual nature of haemocyanin in the establishment and persistence of the squid-vibrio symbiosis. Proc. Biol. Sci. 281(1785):20140504 (PMC4024306) · Pubmed

  • Koch EJ, Miyashiro T, McFall-Ngai MJ, Ruby EG (2014) Features governing symbiont persistence in the squid-vibrio association. Mol. Ecol. 23(6):1624-34 (PMC3907463) · Pubmed

  • Brennan CA, Hunt JR, Kremer N, Krasity BC, Apicella MA, McFall-Ngai MJ, Ruby EG (2014) A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide. Elife 3:e01579 (PMC3941163) · Pubmed

  • Brennan CA, Mandel MJ, Gyllborg MC, Thomasgard KA, Ruby EG (2013) Genetic determinants of swimming motility in the squid light-organ symbiont Vibrio fischeri. Microbiologyopen 2(4):576-94 (PMC3948606) · Pubmed

  • Kremer N, Philipp EE, Carpentier MC, Brennan CA, Kraemer L, Altura MA, Augustin R, Häsler R, Heath-Heckman EA, Peyer SM, Schwartzman J, Rader BA, Ruby EG, Rosenstiel P, McFall-Ngai MJ (2013) Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization. Cell Host Microbe 14(2):183-94 (PMC3928804) · Pubmed

  • Altura MA, Heath-Heckman EA, Gillette A, Kremer N, Krachler AM, Brennan C, Ruby EG, Orth K, McFall-Ngai MJ (2013) The first engagement of partners in the Euprymna scolopes-Vibrio fischeri symbiosis is a two-step process initiated by a few environmental symbiont cells. Environ. Microbiol. : (PMC3937295) · Pubmed

  • McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110(9):3229-36 (PMC3587249) · Pubmed

  • Mandel MJ, Schaefer AL, Brennan CA, Heath-Heckman EA, Deloney-Marino CR, McFall-Ngai MJ, Ruby EG (2012) Squid-derived chitin oligosaccharides are a chemotactic signal during colonization by Vibrio fischeri. Appl. Environ. Microbiol. 78(13):4620-6 (PMC3370474) · Pubmed

  • Miyashiro T, Ruby EG (2012) Shedding light on bioluminescence regulation in Vibrio fischeri. Mol. Microbiol. 84(5):795-806 (PMC3359415) · Pubmed

  • Post DM, Yu L, Krasity BC, Choudhury B, Mandel MJ, Brennan CA, Ruby EG, McFall-Ngai MJ, Gibson BW, Apicella MA (2012) O-antigen and core carbohydrate of Vibrio fischeri lipopolysaccharide: composition and analysis of their role in Euprymna scolopes light organ colonization. J. Biol. Chem. 287(11):8515-30 (PMC3318738) · Pubmed

  • Wollenberg MS, Preheim SP, Polz MF, Ruby EG (2012) Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion. Environ. Microbiol. 14(3):655-68 · Pubmed

  • Wollenberg MS, Ruby EG (2012) Phylogeny and fitness of Vibrio fischeri from the light organs of Euprymna scolopes in two Oahu, Hawaii populations. ISME J 6(2):352-62 (PMC3260510) · Pubmed

  • McFall-Ngai MJ, Ruby EG (2012) Deciphering the language of diplomacy: give and take in the study of the squid-vibrio symbiosis. :173-80

  • Cao X, Studer SV, Wassarman K, Zhang Y, Ruby EG, Miyashiro T (2012) The novel sigma factor-like regulator RpoQ controls luminescence, chitinase activity, and motility in Vibrio fischeri. MBio 3(1): (PMC3252764) · Pubmed

  • Miyashiro T, Klein W, Oehlert D, Cao X, Schwartzman J, Ruby EG (2011) The N-acetyl-D-glucosamine repressor NagC of Vibrio fischeri facilitates colonization of Euprymna scolopes. Mol. Microbiol. 82(4):894-903 (PMC3212624) · Pubmed

  • Septer AN, Wang Y, Ruby EG, Stabb EV, Dunn AK (2011) The haem-uptake gene cluster in Vibrio fischeri is regulated by Fur and contributes to symbiotic colonization. Environ. Microbiol. 13(11):2855-64 · Pubmed

  • Wang Y, Ruby EG (2011) The roles of NO in microbial symbioses. Cell. Microbiol. 13(4):518-26 · Pubmed

  • Wang Y, Dunn AK, Wilneff J, McFall-Ngai MJ, Spiro S, Ruby EG (2010) Vibrio fischeri flavohaemoglobin protects against nitric oxide during initiation of the squid-Vibrio symbiosis. Mol. Microbiol. 78(4):903-15 (PMC2978254) · Pubmed

  • Miyashiro T, Wollenberg MS, Cao X, Oehlert D, Ruby EG (2010) A single qrr gene is necessary and sufficient for LuxO-mediated regulation in Vibrio fischeri. Mol. Microbiol. 77(6):1556-67 (PMC2947852) · Pubmed

  • Pollack-Berti A, Wollenberg MS, Ruby EG (2010) Natural transformation of Vibrio fischeri requires tfoX and tfoY. Environ. Microbiol. 12(8):2302-11 (PMC3034104) · Pubmed

  • Dunn AK, Karr EA, Wang Y, Batton AR, Ruby EG, Stabb EV (2010) The alternative oxidase (AOX) gene in Vibrio fischeri is controlled by NsrR and upregulated in response to nitric oxide. Mol. Microbiol. 77(1):44-55 · Pubmed

  • Wang Y, Dufour YS, Carlson HK, Donohue TJ, Marletta MA, Ruby EG (2010) H-NOX-mediated nitric oxide sensing modulates symbiotic colonization by Vibrio fischeri. Proc. Natl. Acad. Sci. U.S.A. 107(18):8375-80 (PMC2889544) · Pubmed

  • Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Natl. Acad. Sci. U.S.A. 107(5):2259-64 (PMC2836665) · Pubmed

  • Mandel MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 458(7235):215-8 (PMC2713604) · Pubmed

  • Nyholm SV, Stewart JJ, Ruby EG, McFall-Ngai MJ (2009) Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 11(2):483-93 (PMC2652691) · Pubmed

  • Wollenberg MS, Ruby EG (2009) Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from Two Oahu (Hawaii) populations. Appl. Environ. Microbiol. 75(1):193-202 (PMC2612210) · Pubmed

  • Ruby EG (2008) Symbiotic conversations are revealed under genetic interrogation. Nat. Rev. Microbiol. 6(10):752-62 · Pubmed

  • Studer SV, Mandel MJ, Ruby EG (2008) AinS quorum sensing regulates the Vibrio fischeri acetate switch. J. Bacteriol. 190(17):5915-23 (PMC2519518) · Pubmed

  • Chun CK, Troll JV, Koroleva I, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F, Casavant TL, Soares MB, Ruby EG, McFall-Ngai MJ (2008) Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association. Proc. Natl. Acad. Sci. U.S.A. 105(32):11323-8 (PMC2516268) · Pubmed

  • Mandel MJ, Stabb EV, Ruby EG (2008) Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. BMC Genomics 9:138 (PMC2330054) · Pubmed

  • Adin DM, Phillips NJ, Gibson BW, Apicella MA, Ruby EG, McFall-Ngai MJ, Hall DB, Stabb EV (2008) Characterization of htrB and msbB mutants of the light organ symbiont Vibrio fischeri. Appl. Environ. Microbiol. 74(3):633-44 (PMC2227739) · Pubmed

  • Antunes LC, Schaefer AL, Ferreira RB, Qin N, Stevens AM, Ruby EG, Greenberg EP (2007) Transcriptome analysis of the Vibrio fischeri LuxR-LuxI regulon. J. Bacteriol. 189(22):8387-91 (PMC2168698) · Pubmed

  • Hussa EA, O'Shea TM, Darnell CL, Ruby EG, Visick KL (2007) Two-component response regulators of Vibrio fischeri: identification, mutagenesis, and characterization. J. Bacteriol. 189(16):5825-38 (PMC1952042) · Pubmed

  • Nelson EJ, Tunsjø HS, Fidopiastis PM, Sørum H, Ruby EG (2007) A novel lux operon in the cryptically bioluminescent fish pathogen Vibrio salmonicida is associated with virulence. Appl. Environ. Microbiol. 73(6):1825-33 (PMC1828807) · Pubmed

  • Whistler CA, Koropatnick TA, Pollack A, McFall-Ngai MJ, Ruby EG (2007) The GacA global regulator of Vibrio fischeri is required for normal host tissue responses that limit subsequent bacterial colonization. Cell. Microbiol. 9(3):766-78 · Pubmed

  • Stabb EV, Schaefer A, Bose J, Ruby EG (2007) Quorum signaling and symbiosis in the marine luminous bacterium Vibrio fischeri. :233-50

  • Visick KL, Ruby EG (2006) Vibrio fischeri and its host: it takes two to tango. Curr. Opin. Microbiol. 9(6):632-8 · Pubmed

  • Sycuro LK, Ruby EG, McFall-Ngai MJ (2006) Confocal microscopy of the light organ crypts in juvenile Euprymna scolopes reveals their morphological complexity and dynamic function in symbiosis. J. Morphol. 267(5):555-68 · Pubmed

  • Lupp C, Ruby EG (2005) Vibrio fischeri uses two quorum-sensing systems for the regulation of early and late colonization factors. J. Bacteriol. 187(11):3620-9 (PMC1112064) · Pubmed

  • Ruby EG, Urbanowski M, Campbell J, Dunn A, Faini M, Gunsalus R, Lostroh P, Lupp C, McCann J, Millikan D, Schaefer A, Stabb E, Stevens A, Visick K, Whistler C, Greenberg EP (2005) Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc. Natl. Acad. Sci. U.S.A. 102(8):3004-9 (PMC549501) · Pubmed

  • McFall-Ngai MJ, Henderson B, Ruby EG (2005) The Influence of Cooperative Bacteria on Animal Host Biology. :

  • Millikan DS, Ruby EG (2004) Vibrio fischeri flagellin A is essential for normal motility and for symbiotic competence during initial squid light organ colonization. J. Bacteriol. 186(13):4315-25 (PMC421587) · Pubmed

  • Lupp C, Ruby EG (2004) Vibrio fischeri LuxS and AinS: comparative study of two signal synthases. J. Bacteriol. 186(12):3873-81 (PMC419941) · Pubmed

  • Ruby EG, Henderson B, McFall-Ngai MJ (2004) We Get By with a Little Help from Our (Little) Friends. Science 303(5662):1305-7

  • Whistler CA, Ruby EG (2003) GacA regulates symbiotic colonization traits of Vibrio fischeri and facilitates a beneficial association with an animal host. J. Bacteriol. 185(24):7202-12 (PMC296250) · Pubmed

  • McCann J, Stabb EV, Millikan DS, Ruby EG (2003) Population dynamics of Vibrio fischeri during infection of Euprymna scolopes. Appl. Environ. Microbiol. 69(10):5928-34 (PMC201191) · Pubmed

  • Lupp C, Urbanowski M, Greenberg EP, Ruby EG (2003) The Vibrio fischeri quorum-sensing systems ain and lux sequentially induce luminescence gene expression and are important for persistence in the squid host. Mol. Microbiol. 50(1):319-31 · Pubmed

  • Millikan DS, Ruby EG (2003) FlrA, a sigma54-dependent transcriptional activator in Vibrio fischeri, is required for motility and symbiotic light-organ colonization. J. Bacteriol. 185(12):3547-57 (PMC156232) · Pubmed

  • Miyamoto CM, Dunlap PV, Ruby EG, Meighen EA (2003) LuxO controls luxR expression in Vibrio harveyi: evidence for a common regulatory mechanism in Vibrio. Mol. Microbiol. 48(2):537-48 · Pubmed

  • Stabb EV, Ruby EG (2003) Contribution of pilA to competitive colonization of the squid Euprymna scolopes by Vibrio fischeri. Appl. Environ. Microbiol. 69(2):820-6 (PMC143614) · Pubmed

  • Stabb EV, Ruby EG (2002) RP4-based plasmids for conjugation between Escherichia coli and members of the Vibrionaceae. Meth. Enzymol. 358:413-26 · Pubmed

  • Lupp C, Hancock RE, Ruby EG (2002) The Vibrio fischeri sapABCDF locus is required for normal growth, both in culture and in symbiosis. Arch. Microbiol. 179(1):57-65 · Pubmed

  • Fidopiastis PM, Miyamoto CM, Jobling MG, Meighen EA, Ruby EG (2002) LitR, a new transcriptional activator in Vibrio fischeri, regulates luminescence and symbiotic light organ colonization. Mol. Microbiol. 45(1):131-43 · Pubmed

  • Millikan DS, Ruby EG (2002) Alterations in Vibrio fischeri motility correlate with a delay in symbiosis initiation and are associated with additional symbiotic colonization defects. Appl. Environ. Microbiol. 68(5):2519-28 (PMC127559) · Pubmed

  • Aeckersberg F, Lupp C, Feliciano B, Ruby EG (2001) Vibrio fischeri outer membrane protein OmpU plays a role in normal symbiotic colonization. J. Bacteriol. 183(22):6590-7 (PMC95490) · Pubmed

  • Stabb EV, Reich KA, Ruby EG (2001) Vibrio fischeri genes hvnA and hvnB encode secreted NAD(+)-glycohydrolases. J. Bacteriol. 183(1):309-17 (PMC94880) · Pubmed

  • Stabb EV, Visick DS, Millikan AA, Corcoran L, Gilson SV, Nyholm MJ, McFall-Ngai MJ, Ruby EG (2001) The Vibrio fischeri-Euprymna scolopes symbiosis: A model marine animal-bacteria interaction. :269-77

  • McFall-Ngai MJ, Ruby EG (2000) Developmental biology in marine invertebrate symbioses. Curr. Opin. Microbiol. 3(6):603-7 · Pubmed

  • Nyholm SV, Stabb EV, Ruby EG, McFall-Ngai MJ (2000) Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment. Proc. Natl. Acad. Sci. U.S.A. 97(18):10231-5 (PMC27829) · Pubmed

  • Visick KL, Foster J, Doino J, McFall-Ngai MJ, Ruby EG (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J. Bacteriol. 182(16):4578-86 (PMC94630) · Pubmed

  • Graf J, Ruby EG (2000) Novel effects of a transposon insertion in the Vibrio fischeri glnD gene: defects in iron uptake and symbiotic persistence in addition to nitrogen utilization. Mol. Microbiol. 37(1):168-79 · Pubmed

  • Ruby EG, McFall-Ngai MJ (1999) Oxygen-utilizing reactions and symbiotic colonization of the squid light organ by Vibrio fischeri. Trends Microbiol. 7(10):414-20 · Pubmed

  • Ruby EG (1999) The Euprymna scolopes-Vibrio fischeri symbiosis: a biomedical model for the study of bacterial colonization of animal tissue. J. Mol. Microbiol. Biotechnol. 1(1):13-21 · Pubmed

  • Fidopiastis PM, Sørum H, Ruby EG (1999) Cryptic luminescence in the cold-water fish pathogen Vibrio salmonicida. Arch. Microbiol. 171(3):205-9 · Pubmed

  • Ruby EG (1999) Ecology of a benign “infection”: colonization of the squid luminous organ by Vibrio fischeri. :217-31

  • Nishiguchi MK, Ruby EG, McFall-Ngai MJ (1998) Competitive dominance among strains of luminous bacteria provides an unusual form of evidence for parallel evolution in Sepiolid squid-vibrio symbioses. Appl. Environ. Microbiol. 64(9):3209-13 (PMC106711) · Pubmed

  • Visick KL, Ruby EG (1998) The periplasmic, group III catalase of Vibrio fischeri is required for normal symbiotic competence and is induced both by oxidative stress and by approach to stationary phase. J. Bacteriol. 180(8):2087-92 (PMC107134) · Pubmed

  • Ruby EG, Lee KH (1998) The Vibrio fischeri-Euprymna scolopes Light Organ Association: Current Ecological Paradigms. Appl. Environ. Microbiol. 64(3):805-12 (PMC106330) · Pubmed

  • Graf J, Ruby EG (1998) Host-derived amino acids support the proliferation of symbiotic bacteria. Proc. Natl. Acad. Sci. U.S.A. 95(4):1818-22 (PMC19196) · Pubmed

  • Fidopiastis PM, von Boletzky S, Ruby EG (1998) A new niche for Vibrio logei, the predominant light organ symbiont of squids in the genus Sepiola. J. Bacteriol. 180(1):59-64 (PMC106849) · Pubmed

  • McFall-Ngai MJ, Ruby EG (1998) Sepiolids and Vibrios: When First They Meet. BioScience 48(4):257-65 · DOI

  • Ruby EG (1997) Lessons from a cooperative, bacterial-animal association: the Vibrio fischeri-Euprymna scolopes light organ symbiosis. Annu. Rev. Microbiol. 50:591-624 · Pubmed

  • Nishiguchi MK, Ruby EG, McFall-Ngai MJ (1997) Phenotypic bioluminescence as an indicator of competitive dominance in the Euprymna-Vibrio symbiosis. :123-6

  • Visick KL, Ruby EG (1997) New genetic tools for use in the marine bioluminescent bacterium Vibrio fischeri. :119-22

  • Visick KG, Ruby EG (1996) Construction and symbiotic competence of a luxA-deletion mutant of Vibrio fischeri. Gene 175(1-2):89-94 · Pubmed

  • Boettcher KJ, Ruby EG, McFall-Ngai MJ (1996) Bioluminescence in the symbiotic squid Euprymna scolopes is controlled by a daily biological rhythm. J. Comp. Physiol. 179:65-73

  • Boettcher KJ, Ruby EG (1995) Detection and quantification of Vibrio fischeri autoinducer from symbiotic squid light organs. J. Bacteriol. 177(4):1053-8 (PMC176701) · Pubmed

  • Lee K, Ruby EG (1995) Symbiotic Role of the Viable but Nonculturable State of Vibrio fischeri in Hawaiian Coastal Seawater. Appl. Environ. Microbiol. 61(1):278-83 (PMC1388331) · Pubmed

  • Graf J, Dunlap PV, Ruby EG (1994) Effect of transposon-induced motility mutations on colonization of the host light organ by Vibrio fischeri. J. Bacteriol. 176(22):6986-91 (PMC197071) · Pubmed

  • Lee KH, Ruby EG (1994) Effect of the Squid Host on the Abundance and Distribution of Symbiotic Vibrio fischeri in Nature. Appl. Environ. Microbiol. 60(5):1565-71 (PMC201518) · Pubmed

  • Lee KH, Ruby EG (1994) Competition between Vibrio fischeri strains during initiation and maintenance of a light organ symbiosis. J. Bacteriol. 176(7):1985-91 (PMC205303) · Pubmed

  • Boettcher KJ, Ruby EG (1994) Occurrence of plasmid DNA in the sepiolid squid symbiont Vibrio fischeri. Current Microbiol. 29:279-286

  • Ruby EG, Asato LM (1993) Growth and flagellation of Vibrio fischeri during initiation of the sepiolid squid light organ symbiosis. Arch. Microbiol. 159(2):160-7 · Pubmed

  • Ruby EG, McFall-Ngai MJ (1992) A squid that glows in the night: development of an animal-bacterial mutualism. J. Bacteriol. 174(15):4865-70 (PMC206296) · Pubmed

  • Lee KH, Ruby EG (1992) Detection of the Light Organ Symbiont, Vibrio fischeri, in Hawaiian Seawater by Using lux Gene Probes. Appl. Environ. Microbiol. 58(3):942-7 (PMC195360) · Pubmed

  • Romo AJ, Ruby EG, Saier MH (1992) Effect of Bdellovibrio bacteriovorus infection on the phosphoenolpyruvate:sugar phosphotransferase system in Escherichia coli: evidence for activation of cytoplasmic proteolysis. Res. Microbiol. 143(1):5-14 · Pubmed

  • McFall-Ngai MJ, Ruby EG (1991) Symbiont recognition and subsequent morphogenesis as early events in an animal-bacterial mutualism. Science 254(5037):1491-4 · Pubmed

  • Gray KM, Ruby EG (1990) Prey-derived signals regulating duration of the developmental growth phase of Bdellovibrio bacteriovorus. J. Bacteriol. 172(7):4002-7 (PMC213385) · Pubmed

  • Boettcher KJ, Ruby EG (1990) Depressed light emission by symbiotic Vibrio fischeri of the sepiolid squid Euprymna scolopes. J. Bacteriol. 172(7):3701-6 (PMC213346) · Pubmed

  • Ruby EG, McFall-Ngai MJ (1990) Morphological and physiological differentiation in the luminous bacterial symbionts of Euprymna scolopes. :323-6

  • McFall-Ngai MJ, Ruby EG (1990) The changing host-tissue/symbiont relationship in the developing light organ of Euprymna scolopes (Cephalopoda: Sepiolidae). :

  • Gray KM, Ruby EG (1989) Unbalanced growth as a normal feature of development of Bdellovibrio bacteriovorus. Arch. Microbiol. 152(5):420-4 · Pubmed

  • Araki Y, Ruby EG (1988) A soluble enzyme activity that attaches free diaminopimelic acid to bdelloplast peptidoglycan. Biochemistry 27(7):2624-9 · Pubmed

  • Ruby EG, McCabe JB (1988) Metabolism of periplasmic membrane-derived oligosaccharides by the predatory bacterium Bdellovibrio bacteriovorus 109J. J. Bacteriol. 170(2):646-52 (PMC210703) · Pubmed

  • Ruby EG, Jannasch HW, Deuser WG (1987) Fractionation of Stable Carbon Isotopes during Chemoautotrophic Growth of Sulfur-Oxidizing Bacteria. Appl. Environ. Microbiol. 53(8):1940-3 (PMC204029) · Pubmed

  • Ruby EG, McCabe JB (1986) An ATP transport system in the intracellular bacterium, Bdellovibrio bacteriovorus 109J. J. Bacteriol. 167(3):1066-70 (PMC215982) · Pubmed

  • Ruby EG, McCabe JB, Barke JI (1985) Uptake of intact nucleoside monophosphates by Bdellovibrio bacteriovorus 109J. J. Bacteriol. 163(3):1087-94 (PMC219242) · Pubmed

  • Ruby EG, Greenberg EP, Hastings JW (1980) Planktonic marine luminous bacteria: species distribution in the water column. Appl. Environ. Microbiol. 39:302-6

  • Ruby EG, Nealson KH (1978) Seasonal changes in the species composition of luminous bacteria in nearshore seawater. Limnol. Oceanogr. 23:530-3

  • Ruby EG, Nealson KH (1977) A luminous bacterium that emits yellow light. Science 196:432-4

  • Ruby EG, Nealson KH (1976) Symbiotic association of Photobacterium fischeri with the marine luminous fish Monocentris japonica: a model of symbiosis based on bacterial studies. Biol. Bull. 151(3):574-86

  • Schwartzman JA, Koch E, Heath-Heckman EAC, Zhou L, Kremer N, McFall-Ngai MJ, Ruby EG (2015) The chemistry of negotiation: rhythmic, glycan-driven acidification in a symbiotic conversation. Proc Natl Acad Sci USA 112(2):566-571 (PMC4299225) · DOI

  • Pan M, Schwartzman JA, Dunn AK, Lu Z, Ruby EG (2015) A Single Host-Derived Glycan Impacts Key Regulatory Nodes of Symbiont Metabolism in a Coevolved Mutualism mBIO 6(4):e00811-15 (PMC4502230) · DOI

© 2022, All Rights Reserved.
Margaret McFall-Ngai & Edward Ruby

Designed by

McFall-Ngai Lab
Margaret McFall-Ngai
E-mail: mmcfallngai@carnegiescience.edu

Ruby Lab
Edward (Ned) Ruby
E-mail: eruby@carnegiescience.edu