Publications: Spencer Nyholm
2024
- Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods.
Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV
Applied and environmental microbiology (2024) 90(3):e0099023 PMC6386654 10.1073/pnas.1817322116 - Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes.
Rogers TF, Yalçın G, Briseno J, Vijayan N, Nyholm SV, Simakov O
Scientific data (2024) 11(1):40 PMC6857279 10.1016/S0022-2836(05)80360-2 2023
- Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid.
Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O
iScience (2023) 26(7):107091 PMC6324079 10.1002/wdev.265 - Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology.
Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB
Integrative and comparative biology (2023) 63(6):1226-1239 PMC9699675 10.1101/pdb.ip77 - "Failure To Launch": Development of a Reproductive Organ Linked to Symbiotic Bacteria.
McAnulty SJ, Kerwin AH, Koch E, Nuttall B, Suria AM, Collins AJ, Schleicher TR, Rader BA, Nyholm SV
mBio (2023) 14(1):e0213122 PMC3156573 10.1038/nmeth.f.303 2022
- Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization.
Schmidbaur H, Kawaguchi A, Clarence T, Fu X, Hoang OP, Zimmermann B, Ritschard EA, Weissenbacher A, Foster JS, Nyholm SV, Bates PA, Albertin CB, Tanaka E, Simakov O
Nature communications (2022) 13(1):2172 PMC5360930 10.1002/bies.201100001 - Publisher Correction: A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner.
Nyholm SV, McFall-Ngai MJ
Nature reviews. Microbiology (2022) 20(5):315 10.1038/s41579-022-00723-y 2021
- Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, .
Kerwin AH, McAnulty SJ, Nyholm SV
The Biological bulletin (2021) 240(3):205-218 10.1086/713965 - A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner.
Nyholm SV, McFall-Ngai MJ
Nature reviews. Microbiology (2021) 19(10):666-679 PMC8440403 10.1038/s41579-021-00557-0 2020
- In the beginning: egg-microbe interactions and consequences for animal hosts.
Nyholm SV
Philosophical transactions of the Royal Society of London. Series B, Biological sciences (2020) 375(1808):20190593 PMC7435154 10.1098/rstb.2019.0593 - Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D'.
Suria AM, Tan KC, Kerwin AH, Gitzel L, Abini-Agbomson L, Bertenshaw JM, Sewell J, Nyholm SV, Balunas MJ
mSphere (2020) 5(4): PMC7333567 10.1128/mSphere.00166-20 2019
- Shielding the Next Generation: Symbiotic Bacteria from a Reproductive Organ Protect Bobtail Squid Eggs from Fungal Fouling.
Kerwin AH, Gromek SM, Suria AM, Samples RM, Deoss DJ, O'Donnell K, Frasca S, Sutton DA, Wiederhold NP, Balunas MJ, Nyholm SV
mBio (2019) 10(5): PMC6819662 10.1128/mBio.02376-19 - Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment.
Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA
eLife (2019) 8: PMC6773444 10.7554/eLife.47606 - Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis.
Lynch JB, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG
Journal of bacteriology (2019) 201(20): PMC6755730 10.1128/JB.00319-19 - Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis.
Rader B, McAnulty SJ, Nyholm SV
MicrobiologyOpen (2019) 8(10):e858 PMC6813443 10.1002/mbo3.858 - Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.
Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV
Proceedings of the National Academy of Sciences of the United States of America (2019) 116(8):3030-3035 PMC6386654 10.1073/pnas.1817322116 2018
- Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of from Oahu, Hawaii.
Kerwin AH, Nyholm SV
mSphere (2018) 3(2): (PMC5874440) 10.1128/mSphere.00531-17 2017
- The Role of Hemocytes in the Hawaiian Bobtail Squid, : A Model Organism for Studying Beneficial Host-Microbe Interactions.
McAnulty SJ, Nyholm SV
Front Microbiol (2017) 7:2013 (PMC5216023) 10.3389/fmicb.2016.02013 - Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs.
Kerwin AH, Nyholm SV
Environ. Microbiol. (2017) 19(4):1463-1475 10.1111/1462-2920.13665 2016
- Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.
Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV, Balunas MJ
Front Microbiol (2016) 7:1342 (PMC5014874) 10.3389/fmicb.2016.01342 2015
- Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts.
Beinart RA, Nyholm SV, Dubilier N, Girguis PR
Environ Microbiol Rep (2015) 6(6):656-64 - Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.
Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV
Front Microbiol (2015) 6:123 (PMC4337385) 10.3389/fmicb.2015.00123 2014
- Colonization state influences the hemocyte proteome in a beneficial squid-Vibrio symbiosis.
Schleicher TR, VerBerkmoes NC, Shah M, Nyholm SV
Mol. Cell Proteomics (2014) 13(10):2673-86 (PMC4188995) 10.1074/mcp.M113.037259 2013
- Cephalopod genomics: A plan of strategies and organization.
Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, da Fonseca RR, Di Cristo C, Dilkes BP, Edsinger-Gonzales E, Freeman RM, Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A, Pungor JR, Rosenthal JJ, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW
Stand Genomic Sci (2013) 7(1):175-88 (PMC3570802) 10.4056/sigs.3136559 2012
- Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses.
Nyholm SV, Graf J
Nat. Rev. Microbiol. (2012) 10(12):815-27 (PMC3870473) 10.1038/nrmicro2894 - Host/microbe interactions revealed through "omics" in the symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri.
Rader BA, Nyholm SV
Biol. Bull. (2012) 223(1):103-11 10.1086/BBLv223n1p103 - Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae.
Nyholm SV, Song P, Dang J, Bunce C, Girguis PR
PLoS ONE (2012) 7(6):e38267 (PMC3372519) 10.1371/journal.pone.0038267 - Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early stage of squid colonization.
Fidopiastis PM, Rader BA, Gerling DG, Gutierrez NA, Watkins KH, Frey MW, Nyholm SV, Whistler CA
J. Bacteriol. (2012) 194(15):3995-4002 (PMC3416539) 10.1128/JB.00108-12 - Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics.
Collins AJ, Schleicher TR, Rader BA, Nyholm SV
Front Immunol (2012) 3:91 (PMC3349304) 10.3389/fimmu.2012.00091 - Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes.
Collins AJ, LaBarre BA, Won BS, Shah MV, Heng S, Choudhury MH, Haydar SA, Santiago J, Nyholm SV
Appl. Environ. Microbiol. (2012) 78(12):4200-8 (PMC3370523) 10.1128/AEM.07437-11 2011
- Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri.
Schleicher TR, Nyholm SV
PLoS ONE (2011) 6(10):e25649 (PMC3187790) 10.1371/journal.pone.0025649 - Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.
Collins AJ, Nyholm SV
J. Bacteriol. (2011) 193(13):3397-8 (PMC3133266) 10.1128/JB.05139-11 2010
- Obtaining hemocytes from the Hawaiian bobtail squid Euprymna scolopes and observing their adherence to symbiotic and non-symbiotic bacteria.
Collins AJ, Nyholm SV
J Vis Exp (2010) (36): (PMC2830252) 10.3791/1714 - Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis.
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
Proc. Natl. Acad. Sci. U.S.A. (2010) 107(5):2259-64 (PMC2836665) 10.1073/pnas.0909712107 2009
- The role of the immune system in the initiation and persistence of the Euprymna scolopes--Vibrio fischeri symbiosis.
McFall-Ngai M, Nyholm SV, Castillo MG
Semin. Immunol. (2009) 22(1):48-53 (PMC3992935) 10.1016/j.smim.2009.11.003 - Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes.
Nyholm SV, Stewart JJ, Ruby EG, McFall-Ngai MJ
Environ. Microbiol. (2009) 11(2):483-93 (PMC2652691) 10.1111/j.1462-2920.2008.01788.x - Peptidoglycan monomer release and Vibrio fischeri.
Nyholm SV
J. Bacteriol. (2009) 191(7):1997-9 (PMC2655520) 10.1128/JB.01801-08 2008
- Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae.
Nyholm SV, Robidart J, Girguis PR
Biol. Bull. (2008) 214(3):255-65 10.2307/25470667 - THE EVOLUTIONARY ECOLOGY OF A SEPIOLID SQUID-VIBRIO ASSOCIATION: FROM CELL TO ENVIRONMENT.
Nyholm SV, Nishiguchi MK
Vie Milieu (2008) 58(2):175-184 (PMC2857784) 2006
- fester, A candidate allorecognition receptor from a primitive chordate.
Nyholm SV, Passegue E, Ludington WB, Voskoboynik A, Mitchel K, Weissman IL, De Tomaso AW
Immunity (2006) 25(1):163-73 10.1016/j.immuni.2006.04.011 2005
- Isolation and characterization of a protochordate histocompatibility locus.
De Tomaso AW, Nyholm SV, Palmeri KJ, Ishizuka KJ, Ludington WB, Mitchel K, Weissman IL
Nature (2005) 438(7067):454-9 (PMC1401502) 10.1038/nature04150 2004
- The winnowing: establishing the squid-vibrio symbiosis.
Nyholm SV, McFall-Ngai MJ
Nat. Rev. Microbiol. (2004) 2(8):632-42 10.1038/nrmicro957 2003
- Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity.
Nyholm SV, McFall-Ngai MJ
Appl. Environ. Microbiol. (2003) 69(7):3932-7 (PMC165210) 10.1128/aem.69.7.3932-3937.2003 2002
- Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ.
Nyholm SV, Deplancke B, Gaskins HR, Apicella MA, McFall-Ngai MJ
Appl. Environ. Microbiol. (2002) 68(10):5113-22 (PMC126412) 10.1128/aem.68.10.5113-5122.2002 2000
- Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment.
Nyholm SV, Stabb EV, Ruby EG, McFall-Ngai MJ
Proc. Natl. Acad. Sci. U.S.A. (2000) 97(18):10231-5 (PMC27829) 10.1073/pnas.97.18.10231