Luke Thompson

Research Highlights

January 23, 2024

A Collaborative Effort Investigates the Biological Carbon Pump, Deploying Sediment Traps Hundreds of Meters Below

May 23, 2022

New study highlights major step forward in monitoring ocean health

January 12, 2022

Environmental DNA Sampling Gets an Upgrade and Transitions to New Open-Source Technology

Luke Thompson, Ph.D.

Research Scientist, Ocean Chemistry and Ecosystems Division

305.361.4553

Luke.Thompson@noaa.gov

Luke_Thompson

4301 Rickenbacker Causeway
Miami, Florida 33149

About

Dr. Luke Thompson is a microbial ecologist and bioinformatician with diverse experience in the field and laboratory. He is a lead author of publications in Nature, PNAS, and The ISME Journal, among others.

Current Work & CV

Current Work

Principal Investigator for the AOML ‘Omics program

Download Full CV

Education

2003 – 2010, Ph.D. Microbiology, Massachusetts Institute of Technology, Cambridge, MA

1998 – 2003, B.S. Biological Sciences, Stanford University, Stanford, CA

Publications

Gold, Z., R.P. Kelly, A.O. Shelton, A.R. Thompson, K.D. Goodwin, R. Gallego, K.M. Parsons, L.R. Thompson, D. Kacev, and P.H. Barber. Archived DNA reveals marine heatwave-associated shifts in fish assemblages. Environmental DNA, 6:e400, https://doi.org/10.1002/edn3.400 2024
Ref. 4248
Lim, S.J., L.R. Thompson, and K.D. Goodwin. Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data. Frontiers in Marine Science, 9:1067482, https://doi.org/10.3389/fmars.2022.1067482 2023
Ref. 4218
Park, H., S.J. Lim, J. Cosme, K. O'Connell, J. Sandeep, F. Gayanilo, G.R. Cutter, E. Montes, C. Nitikitpaiboon, S. Fisher, H. Moustahfid, and L.R. Thompson. Investigation of machine learning algorithms for taxonomic classification of marine metagenomes. Microbiology Spectrum, 11(5):e5237-22, https://doi.org/10.1128/spectrum.05237-22 2023
Ref. 4324

View all Related Publications

Gold, Z., R.P. Kelly, A.O. Shelton, A.R. Thompson, K.D. Goodwin, R. Gallego, K.M. Parsons, L.R. Thompson, D. Kacev, and P.H. Barber. Archived DNA reveals marine heatwave-associated shifts in fish assemblages. Environmental DNA, 6:e400, https://doi.org/10.1002/edn3.400 2024
Ref. 4248
Lim, S.J., L.R. Thompson, and K.D. Goodwin. Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data. Frontiers in Marine Science, 9:1067482, https://doi.org/10.3389/fmars.2022.1067482 2023
Ref. 4218
Park, H., S.J. Lim, J. Cosme, K. O'Connell, J. Sandeep, F. Gayanilo, G.R. Cutter, E. Montes, C. Nitikitpaiboon, S. Fisher, H. Moustahfid, and L.R. Thompson. Investigation of machine learning algorithms for taxonomic classification of marine metagenomes. Microbiology Spectrum, 11(5):e5237-22, https://doi.org/10.1128/spectrum.05237-22 2023
Ref. 4324
Thompson, L.R., and P. Thielen. Decoding dissolved information: Environmental DNA sequencing at global scale to monitor a changing ocean. Current Opinion in Biotechnology, 81:102936, https://doi.org/10.1016/j.copbio.2023.102936 2023
Ref. 4252
Anderson, S.R., and L.R. Thompson. Optimizing an enclosed bead beating extraction method for microbial and fish environmental DNA. Environmental DNA, 4(2):291-303, https://doi.org/10.1002/edn3.251 2022
Ref. 4014
Clayton, S., H. Alexander, J.R. Graff, N.J. Poulton, L.R. Thompson, H. Benway, E. Boss, and A. Martiny. Bio-GO-SHIP: The time is right to establish global repeat sections of ocean biology. Frontiers in Marine Science, 8:767443, https://doi.org/10.3389/fmars.2021.767443 2022
Ref. 4058
Den Uyl, P.A., L.R. Thompson, R.M. Errera, J.M. Birch, C.M. Preston, B. Ussler III, C.E. Yancey, S. Rao Chaganti, S.A. Ruberg, G.J. Doucette, G.J. Dick, C.A. Scholin, and K.D. Goodwin. Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms. Frontiers in Marine Science, 9:1021952, https://doi.org/10.3389/fmars.2022.1021952 2022
Ref. 4170
Jorge, F., J.C. Brealey, P.J. Brindley, M. Buysse, C. Cantacessi, O. Duron, R. Fichorova, C.R. Fitzpatrick, M. Hahn, C. Hunter, V. Herve, L.J. Knoll, K.D. Kohl, M. Lalle, J. Lukes, J. Martinez-Martinez, S.L. Perkins, R. Poulin, K. Rosario, A.C. Schneider, L.M. Schriml, L.R. Thompson, R.L. Walls, and N.M. Dheilly. MIxS-SA: A MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms. ISME Communications, 2:9, https://doi.org/10.1038/s43705-022-00092-w 2022
Ref. 4069
Lim, S.J., L.R. Thompson, C.M. Young, T. Gaasterland, and K.D. Goodwin. Dominance of Sulfurospirillum in metagenomes associated with the methane ice worm (Sirsoe methanicola). Applied and Environmental Microbiology, 88(15):e00290-22, https://doi.org/10.1128/aem.00290-22 2022
Ref. 4125
Shaffer, J.P., L.-F. Nothias, L.R. Thompson, J.G. Sanders, R.A. Salido, S.P. Couvillion, A.D. Brejnrod, F. Lejzerowicz, N. Haiminen, S. Huang, H.L. Lutz, Q. Zhu, C. Martino, J.T. Morton, S. Karthikeyan, M. Nothias-Esposito, K. Duhrkop, S. Bocker, H.W. Kim, A.A. Aksenov, W. Bittremieux, J.J. Minich, C. Marotz, M.M. Bryant, K. Sanders, T. Schwartz, G. Humphrey, Y. Vazquez-Baeza, A. Tripathi, L. Parida, A.P. Carrieri, K.L. Beck, P. Das, A. Gonzalez, D. McDonald, J. Ladau, S.M. Karst, M. Albertsen, G. Ackermann, J. DeReus, T. Thomas, D. Petras, A. Shade, J. Stegen, S.J. Song, T.O. Metz, A.D. Swafford, P.C. Dorrestein, J.K. Jansson, J.A. Gilbert, R. Knight and Earth Microbiome Project 500 (EMP500) Consortium. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology, 7:2128-2150, https://doi.org/10.1038/s41564-022-01266-x 2022
Ref. 4199
Thompson, L.R., S.R. Anderson, P.A. Den Uyl, N.V. Patin, G. Sanderson, and K.D. Goodwin. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. GigaScience, 11(1):giac066, https://doi.org/10.1093/gigascience/giac066 2022
Ref. 4130
Truelove, N.K., N.V. Patin, M. Min, K.J. Pitz, C.M. Preston, K.M. Yamahara, Y. Zhang, B.Y. Raanan, B. Kieft, B. Hobson, L.R. Thompson, K.D. Goodwin, and F.P. Chavez. Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling. Environmental DNA, 4(4):972-984, https://doi.org/10.1002/edn3.299 2022
Ref. 4111
Formel, N., I.C. Enochs, C. Sinigalliano, S.R. Anderson, and L.R. Thompson. Subsurface Automated Samplers for eDNA (SASe) for biological monitoring and research. HardwareX, 10:e00239, https://doi.org/10.1016/j.ohx.2021.e00239 2021
Ref. 4031
Lim, S.J., and LR. Thompson. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA, 3(4):706-715, https://doi.org/10.1002/edn3.187 2021
Ref. 3929
Vangay, P., J. Burgin, A. Johnston, K.L. Beck, D.C. Berrios, K. Blumberg, S. Canon, P. Chain, J.-M. Chandonia, D. Christianson, S.V. Costes, J. Damerow, W.D. Duncan, J.P. Dundore-Arias, K. Fagnan, J.M. Galazka, S.M. Gibbons, D. Hays, J. Hervey, B. Hu, B.L. Hurwitz, P. Jaiswal, M.P. Joachimiak, L. Kinkel, J. Ladau, S.L. Martin, L.A. McCue, K. Miller, N. Mouncey, C. Mungall, E. Pafilis, T.B.K. Reddy, L. Richardson, S. Roux, J.P. Shaffer, J.C. Sundaramurthi, L.R. Thompson, R.E. Timme, J. Zheng, E.M. Wood-Charlson, and E.A. Eloe-Fadrosh. Microbiome metadata standards: Report of the National Microbiome Data Collaborative’s Workshop and follow-on activities. mSystems, 6(1):e01194-20, https://doi.org/10.1128/mSystems.01194-20 2021
Ref. 3934
Lavrinienko, A., E. Tukalenko, T.A. Mousseau, L.R. Thompson, R. Knight, T. Mappes, and P.C. Watts. Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota. Scientific Data, 7:312, https://doi.org/10.1038/s41597-020-00656-2 2020
Ref. 3858
Bolyen, E., J.-R. Rideout, M.R. Dillon, N.A. Bokulich, C.C. Abnet, G.A. Al-Ghalith, H. Alexander, E.J. Alm, M. Arumugam, F. Asnicar, Y. Bai, J.E. Bisanz, K. Bittinger, A. Brejnrod, C.J. Brislawn, C.T. Brown, B.J. Callahan, A.M. Caraballo-Rodríguez, J. Chase, E.K. Cope, R. Da Silva, C. Diener, P.C. Dorrestein, G.M. Douglas, D.M. Durall, C. Duvallet, C.F. Edwardson, M. Ernst, M. Estaki, J. Fouquier, J.M. Gauglitz, S.M. Gibbons, D.L. Gibson, A. Gonzalez, K. Gorlick, J. Guo, B. Hillmann, S. Holmes, H. Holste, C. Huttenhower, G.A. Huttley, S. Janssen, A.K. Jarmusch, L. Jiang, B.D. Kaehler, K.B. Kang, C.R. Keefe, P. Keim, S.T. Kelley, D. Knights, I. Koester, T. Kosciolek, J. Kreps, M.G.I. Langille, J. Lee, R. Ley, Y.-X. Liu, E. Loftfield, C. Lozupone, M. Maher, C. Marotz, B.D. Martin, D. McDonald, L.J. McIver, A.V. Melnik, J.L. Metcalf, S.C. Morgan, J.T. Morton, A.T. Naimey, J.A. Navas-Molina, L.F. Nothias, S.B. Orchanian, T. Pearson, S.L. Peoples, D. Petras, M.L. Preuss, E. Pruesse, L.B. Rasmussen, A. Rivers, M.S. Robeson, P. Rosenthal, N. Segata, M. Shaffer, A. Shiffer, R. Sinha, S.J. Song, J.R. Spear, A.D. Swafford, L.R. Thompson, P.J. Torres, P. Trinh, A. Tripathi, P.J. Turnbaugh, S. Ul-Hasan, J.J.J. van der Hooft, F. Vargas, Y. Vázquez-Baeza, E. Vogtmann, M. von Hippel, W. Walters, Y. Wan, M. Wang, J. Warren, K.C. Weber, C.H.D. Williamson, A.D. Willis, Z.Z. Xu, J.R. Zaneveld, Y. Zhang, Q. Zhu, R. Knight, J.G. Caporaso. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8):852-857, https://doi.org/10.1038/s41587-019-0209-9 2019
Ref. 3700
Cao, L., A. Gurevich, K.L. Alexander, C.B. Naman, T. Leao, E. Glukov, T. Luzzatto-Knaan, F. Vargas, R. Quinn, A. Bouslimani, L.F. Nothias, N.K. Singh, J.G. Sanders, R.A.S. Benitez, L.R. Thompson, M.-N. Hamid, J.T. Morton, A. Mikheenko, A. Shlemov, A. Korobeynikov, I. Friedberg, R. Knight, K. Ventkateswaran, W.H. Gerwick, L. Gerwick, P.C. Dorrestein, P.A. Pezvner, and H. Mohimani. MetaMiner: A scalable peptidogenomics approach for discovery of ribosomal peptide natural products with blind modifications from microbial communities. Cell Systems, 9(6):600-608e4, https://doi.org/10.1016/j.cels.2019.09.004 2019
Ref. 3859
Dheilly, N.M., J. Martinez Martinez, K. Rosario, P.J. Brindley, R.N. Fichorova, J.Z. Kaye, K.D. Kohl, L.J. Knoll, J. Lukes, S.L. Perkins, R. Poulin, L. Schrimi, and L.R. Thompson. Parasite microbiome project: Grand challenges. PLoS Pathogens, 15(10):e1008028, https://doi.org/10.1371/journal.ppat.1008028 2019
Ref. 3738
Martino, C., J.T. Morton, C.A. Marotz, L.R. Thompson, A. Tripathi, and R. Knight. A novel sparse compositional technique reveals microbial perturbations. mSystems, 4(1):e00016-19, https://doi.org/10.1128/mSystems.00016-19 2019
Ref. 3633
Thompson, L.R., M.F. Haroon, A.A. Shibl, M.J. Cahill, D.K. Ngugi, G.J. Williams, J.T. Morton, R. Knight, K.D. Goodwin, and U. Stingl. Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes. Applied and Environmental Microbiology, 85(13):e00369-19, https://doi.org/10.1128/AEM.00369-19 2019
Ref. 3673
Franzosa, E.A., L.J. McIver, G. Rahnavard, L.R. Thompson, M. Schirmer, G. Weingart, K. Schwarzberg-Lipson, R. Knight, J.G. Caporaso, N. Segata, and C. Huttenhower. Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods, 15(11):962-968, https://doi.org/10.1038/s41592-018-0176-y 2018
Ref. 3614
Kharbush, J.J., L.R. Thompson, M.F. Haroon, R. Knight, and L.I. Aluwihare. Hopanoid-producing bacteria in the Red Sea include the major marine nitrite-oxidizers. FEMS Microbiology Ecology, 94(6):fiy063, https://doi.org/10.1093/femsec/fiy063 2018
Ref. 3521
Knight, R., A. Vrbanac, B.C. Taylor, A. Aksenov, C. Callewaert, J. Debelius, A. Gonzalez, T. Kosciolek, L.-I. McCall, D. McDonald, A.V. Melnik, J.T. Morton, J. Navas, R.A. Quinn, J.G. Sanders, A.D. Swafford, L.R. Thompson, A. Tripathi, Z.Z. Xu, J.R. Zaneveld, Q. Zhu, J.G. Caporaso, and P.C. Dorrestein. Best practices for analyzing microbiomes. Nature Reviews Microbiology, 16(7):410-422, https://doi.org/10.1038/s41579-018-0029-9 2018
Ref. 3541
Lavrinienko, A., T. Mappes, E. Tukalenko, T.A. Mousseau, A.P. Møller, R. Knight, J.T. Morton, L.R. Thompson, and P.C. Watts. Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. The ISME Journal, 12(11):2801-2806, https://doi.org/10.1038/s41396-018-0214-x 2018
Ref. 3560
McDonald, D., E.R. Hyde, J.W. Debelius, J.T. Morton, A. Gonzalez, G. Ackermann, A.A. Aksenov, B. Behsaz, C. Brennan, Y. Chen, L. DeRight Goldasich, P.C. Dorrestein, R.R. Dunn, A.K. Fahimipour, J. Gaffney, J.A. Gilbert, G. Gogul, J.L. Green, P. Hugenholtz, G. Humphrey, C. Huttenhower, M.A. Jackson, S. Janssen, D.V. Jeste, L. Jiang, S.T. Kelley, D. Knights, T. Kosciolek, J. Ladau, J. Leach, C. Marotz, D. Meleshko, A.V. Melnik, J.L. Metcalf, H. Mohimani, E. Montassier, J. Navas-Molina, T.T. Nguyen, S. Peddada, P. Pevzner, K.S. Pollard, G. Rahnavard, A. Robbins-Pianka, N. Sangwan, J. Shorenstein, L. Smarr, S.-J. Song, T. Spector, A.D. Swafford, V.G. Thackray, L.R. Thompson, A. Tripathi, Y. Vazquez-Baeza, A. Vrbanac, P. Wischmeyer, E. Wolfe, Q. Zhu, and R. Knight. American Gut: An open platform for citizen-science microbiome research. mSystems, 3(3):e00031.18, https://doi.org/10.1128/mSystems.00031.18 2018
Ref. 3533
Michaud, J.M., L.R. Thompson, D. Kaul, J.L. Espinoza, R.A. Richter, Z.Z. Xu, C. Lee, K.M. Pham, C.M. Beall, F. Malfatti, F. Azam, R. Knight, M.D. Burkart, C.L. Dupont, and K.A. Prather. Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nature Communications, 9(1):2017, https://doi.org/10.1038/s41467-018-04409-z 2018
Ref. 3537
Shibl, A.A., D.K. Ngugi, A. Talarmin, L.R. Thompson, J. Blom, and U. Stingl. The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis. FEMS Microbiology Ecology, 94(12):fiy182, https://doi.org/10.1093/femsec/fiy182 2018
Ref. 3914
Goodwin, K.D., L.R. Thompson, B. Duarte, T. Kahlke, A.R. Thompson, J.C. Marques, and I. Cacador. DNA sequencing as a tool to monitor marine ecological status. Frontiers in Marine Science, 4:107, https://doi.org/10.3389/fmars.2017.00107 2017
Ref. 3401
Thompson, L.R., J.G. Sanders, D. McDonald, A. Amir, J. Ladau, K.J. Locey, R.J. Prill, A. Tripathi, S.M. Gibbons, G. Ackermann, J.A. Navas-Molina, S. Janssen, E. Kopylova, Y. Vázquez-Baeza, A. Gonzalez, J.T. Morton, S. Mirarab, Z.Z. Xu, L. Jiang, M.F. Haroon, J. Kanbar, Q. Zhu, S.J. Song, T. Kosciolek, N.A. Bokulich, J. Lefler, C.J. Brislawn, G. Humphrey, S.M. Owens, J. Hampton-Marcell, D. Berg-Lyons, V. McKenzie, N. Fierer, J.A. Fuhrman, A. Clauset, R.L. Stevens, A. Shade, K.S. Pollard, K.D. Goodwin, J.K. Jansson, J.A. Gilbert, R. Knight, and the Earth Microbiome Project Consortium. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681):457-463, https://doi.org/10.1038/nature24621 2017
Ref. 3471

Awards

Scripps Institution of Oceanography Graduate Teaching Award, 2019

For efforts to teach Scripps students about data science using the Python programming language.

NOAA Outstanding Paper Award, 2018

For pre-eminent science published through rigorous peer-review:
Thompson, L.R., J.G. Sanders, D. McDonald, A. Amir, J. Ladau, K.J. Locey, R.J. Prill, A. Tripathi, S.M. Gibbons, G. Ackermann, J.A. Navas-Molina, S. Janssen, E. Kopylova, Y. Vázquez-Baeza, A. Gonzalez, J.T. Morton, S. Mirarab, Z.Z. Xu, L. Jiang, M.F. Haroon, J. Kanbar, Q. Zhu, S.J. Song, T. Kosciolek, N.A. Bokulich, J. Lefler, C.J. Brislawn, G. Humphrey, S.M. Owens, J. Hampton-Marcell, D. Berg-Lyons, V. McKenzie, N. Fierer, J.A. Fuhrman, A. Clauset, R.L. Stevens, A. Shade, K.S. Pollard, K.D. Goodwin, et al., 2017: A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681):457-463.