Jack A Gilbert B.Sc. Ph.D.http://gilbertlab.com

Microbial EcologistGroup LeaderArgonne National Laboratory9700, S Cass Avenue, Lemont, IL, 60439Office: (630)-252-7489Email: gilbertjack@anl.govWeb page: http://www.bio.anl.gov/PI/gilbert.html

Associate ProfessorThe University of Chicago Department of Ecology and Evolution, 5640 South Ellis Avenue, Chicago, IL 60637-1234Office: (630)-915-2383Email: gilbertjack@uchicago.edu Web page: http://pondside.uchicago.edu/ecol-evol/people/gilbert.html

Senior ScientistAdjunctThe Bay Paul CenterMarine Biological LaboratoryWoods Hole, MA.

ACADEMIC APPOINTMENTS 1998-1999 Research Assistant, Natural History Museum, London2000 Chief Science Officer, ANARE station Davis, Antarctica.2005-2010 Molecular Ecologist, Senior Scientist

Plymouth Marine Laboratory, Plymouth, UK2010-2014 Environmental Microbiologist, Argonne National Laboratory, USA2010-2013 Assistant Professor, Dept Ecology and Evolution, University of Chicago,

USA2013-Present Associate Professor, Dept. Ecology and Evolution, University of Chicago,

USA2014-Present Microbial Ecologist, Group Leader, Argonne National Laboratory, USA2014-Present Adjunct Senior Scientist, The Marine Biological Laboratory, USA.

Ph.D. COMMITTEE, PROGRAM, INSTITUTE AND CENTRE APPOINTMENTS Committee on Genetic, Genomics and Systems Biology, University of ChicagoCommittee on Evolutionary BiologyCommittee on BiophysicsMarine Biological Laboratory-UChicago Faculty Advisory Committee.EU-US Bioinformatics Committee.Senior Fellow, Institute for Genomic and Systems BiologySenior Fellow, Computing and Environmental Life Sciences

ACADEMIC TRAINING

1995-1998 Kings College, University of LondonBSc with First Class Honours in Biological Sciences with specialization in Marine Biology

1999-2002 University of Nottingham / Unilever Colworth Laboratories – Ph.D.‘Cold Adaptation and Biodiversity of Antarctic Lake Bacteria’PhD Life and Environmental Science/Food Microbiology

2002-2005 Post-Doctoral Fellowship - BiochemistryDepartment of Biochemistry, Queen’s University, Ontario, Canada

SCHOLARSHIPPeer-reviewed publications in the primary literature, exclusive of abstracts:

2014

1. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. Vol. 345 no. 6200 pp. 1048-1052. DOI: 10.1126/science.1254529

2. Gilbert JA, Jansson JK, and Knight R. 2014. The Earth Microbiome project: successes and aspirations. BMC Biology, 12:69  doi:10.1186/s12915-014-0069-1

3. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong X-Z, Ehrlich DS, Fraser C, Gibbs R, Gilbert JA, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee J-S, Li W-J, Juncai M, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K-i, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou Y-G, Field D, Whitman WB, Garrity GM, Klenk H-P. 2014. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biology. 12:8, e1001920. DOI: 10.1371/journal.pbio.1001920.

4. Larsen PE, Scott N, Post, AF, Field D, Knight R, Hamada Y, Gilbert JA. 2014. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME Journal. Advanced Online Publication July 29th 2014. doi: 10.1038/ismej.2014.107

5. Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. (2014). Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio 5:4 e01371-14. doi: 10.1128/mBio.01371-14

6. Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA, Hartsel J, Kennedy S, Gibbons S. (2014) Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome. PLoS ONE 9(6): e99641. doi:10.1371/journal.pone.0099641

7. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou H, Knight R, Caporaso JG. (2014) Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2:e545 http://dx.doi.org/10.7717/peerj.545

8. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA. (2014) Human and Environmental Impacts on River Sediment Microbial Communities. PLoS ONE 9(5): e97435. doi:10.1371/journal.pone.0097435

9. Nielsen S, Minchin T, Kimber S, van Zwieten L, Gilbert JA, Munroe P, Joseph S, Thomas T. 2014. Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilizers. Agriculture, Ecosystems and the Environment. DOI:10.1016/j.agee.2014.04.006

10. Kumar A, Dames JF, Gupta A, Sharma S, Gilbert JA, and Ahmad P. 2014. Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation: a biotechnological perspective. Crit Rev Biotechnol, Early Online: 1–14. DOI: 10.3109/07388551.2014.899964

11. Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B, Mellilo D, Meuller MG, Natale L, Zucchetti I, De Santis R, Pinto MR, Litman GW, Gilbert JA. (2014) The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota. PLoS ONE 9(4): e93386. doi:10.1371/journal.pone.0093386

12. Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA. 2014. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Frontiers in Microbiolology, 25 March 2014 | doi: 10.3389/fmicb.2014.00108

13. Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE and Banfield JF. 2014. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental Microbiology. DOI: 10.1111/1462-2920.12467

14. Hamada Y, Gilbert JA, Larsen PE, Norgaard MJ. 2014. Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing. Photogrammetric Engineering & Remote Sensing 80 (4), 311-321

15. Handley KM, Bartels D, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonoploulos D, Kemner KM, Meyer F. 2014. The complete genome sequence for putative H2-and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environmental Microbiology, DOI: 10.1111/1462-2920.12453.

16. Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, Gilbert JA, Chu H. 2014. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbial Ecology. 10.1111/1574-6941.12289

17. Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D. 2014. Saliva from Obese individuals suppresses the released of aroma compounds from wine. PLoS ONE 9(1): e85611. doi:10.1371/journal.pone.0085611.

18. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicus D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. 2014. Metagenomics reveals sediment microbial community response to the Deepwater Horizon oil spill. ISME Journal. 23rd Jan 2014. doi:10.1038/ismej.2013.254

19. Peer X, Gilbert JA, An GC. 2014. Examining the Microbial Ecological Dynamics of Clostridium difficile Infections and the Efficacy of Fecal Microbiome Transplant (FMT) using an Agent-based Model. Journal of Surgical Research 186 (2), 689.

20. Gilbert JA, van der Lelie D, Zarraonaindia I. 2014. Microbial terroir for wine grapes. PNAS. 111 (1), 5-6.

201321. Gilbert JA, Krajmalnik-Brown R, Porazinska DL, Weiss SJ, Knight R. 2013. Toward

Effective Probiotics for Autism and Other Neurodevelopmental Disorders. Cell. 155(7) 1446-1448.

22. Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert JA, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Čapek P, Šantrůčková H, Gentsch N, Shibistova O,

Guggenberger G, Richter A, Torsvik VL, Schleper C and Urich T. 2013. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J. Advanced online publication. doi:10.1038/ismej.2013.219

23. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. 2013. Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science. 342, 621-624.

24. Gilbert JA. 2013. Biological Oceanography: Some Phytoplankton Like it Hot. Nature Climate Change. 3, 954-955.

25. Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. 2013. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12115.

26. Dennis KL, Wang Y, Blatner NR, Wang S, Saadalla A, Trudeau E, Roers A, Weaver CT, Lee JJ, Gilbert JA, Chang EB, Khazaie K. 2013. Adenomatous Polyps Are Driven by Microbe-Instigated Focal Inflammation and Are Controlled by IL-10-Producing T Cells. Cancer Research. 1;73(19):5905-13. doi: 10.1158/0008-5472.CAN-13-1511.

27. Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Khurana JP, Gilbert JA and Lal R. 2013. Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data. ISME J. 8(2):398-408 doi:10.1038/ismej.2013.153

28. Laverock B, Kitidis V, Tait K, Gilbert JA, Osborn AM, Widdicombe S. 2013. Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification. Philosophical Transactions of the Royal Society B: Biological Sciences. 368: 1627.

29. U Riebesell, JP Gattuso, TF Thingstad, JJ Middelburg, J Czerny, K von Bröckel, T Boxhammer, J Büdenbender, M Deckelnick, M Fischer, D Hoffmann, SA Krug, U Lentz, A Ludwig, R Muche, KG Schulz, RGJ Bellerby, CPD Brussaard, A Engel, S Koch-Klavsen, S Lischka, M Meyerhöfer, G Nondal, A Silyakova, A Stuhr, AAM Noordeloos, H Witte, MCJ Collenteur, K Schulz, C Borchard, J Piontek, R Bellerby, AS Roy, SM Gibbons, H Schunck, S Owens, JG Caporaso, M Sperling, JI Nissimov, S Romac, L Bittner, M Mühling, J LaRoche, JA Gilbert, R Zhang, X Xia, SCK Lau, C Motegi, MG Weinbauer, N Jiao, G Gerdts, A Wichels, J La Roche, JA Gilbert, T Tanaka, N Aberle, AM Malzahn, B Niehoff, T Schmithüsen, N Knüppel, M Daase, E Leu, T De Lange, A Ludvig, A de Kluijver, K Soetaert, S Alliouane, RGB Bellerby, K Nachtigall, SD Archer, SA Kimmance, JA Stephens, FE Hopkins. 2013. Arctic ocean acidification: pelagic ecosystem and biogeochemical responses during a mesocosm study. Biogeosciences, 10: 5619-5626.

30. Rubin BER, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA. (2013) Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples. PLoS ONE 8(7): e70460. doi:10.1371/journal.pone.0070460

31. Bourlat SJ, Borja A, Gilbert JA, Taylor MI, Davies N, Weisberg SB, Griffith JF, Lettieri T, Field D, Benzie J, Glockner FO, Rodriguez-Ezpeleta N, Faith DP, Bean TP, Obst M. 2013. Genomics in marine monitoring: New opportunities for assessing marine health status. Marine Pollution Bulletin. In press.

32. Kelley ST, Gilbert JA. 2013. Studying the microbiology of the indoor environment. Genome Biology. 14(2), 1-9.

33. Larsen P, Gilbert JA (2013) Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology. PLoS ONE 8(3): e58119. doi:10.1371/journal.pone.0058119

34. Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA. 2013. Evidence for a persistent microbial seed bank throughout the global ocean. PNAS. 110 (12); 4651-4655

35. Roy A-S, Gibbons, SM, Shunck H, Owens S, Caporaso JG, Sperling M, Nissimov, JI, Romac, S, Bittner L, Muhling M, Riebesell U, LaRoche J, Gilbert JA. 2013. Ocean

acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences Discussions. 10, 555-566.

36. Zarraonaindia I, Smith D, Gilbert JA. 2013. Beyond the genome: community-level analysis of the microbial world. Biology & Philosophy. 10.1007/s10539-012-9357-8

201237. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA,

Wall DH, Caporaso JG. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS. 109 (52), 21390-21395.

38. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Anand S, Malhortra J, Jindal S, Nigam A, Lai D, Dua A, Saxena A, Garg N, Verma M, Kaur J, Mukherjee U, Gilbert JA, Dowd SE, Raman R, Khurana P, Khurana JP, Lal R. 2012 Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels. PLoS ONE 7(9): e46219. doi:10.1371/journal.pone.0046219

39. Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert JA, Meyer F. 2012. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC bioinformatics 13 (1), 183

40. Sperling M, Piontek J, Gerdts G, Wichels A, Schunck H, Roy AS, La Roche J, Gilbert JA, Bittner L, Romac S, Riebesell U, Engel A. 2012. Effect of elevated CO2 on the dynamics of particle attached and free living bacterioplankton communities in an Arctic fjord. Biogeosciences Discuss, 9, 10725-10755

41. Olivas AD, Shogan BD, Valuckaite V, Zaborin A, Belogortseva N, Musch M, Meyer F, Trimble WL, An G, Gilbert JA, Zaborina O, Alverdy JC. 2012. Intestinal Tissues Induce an SNP Mutation in Pseudomonas aeruginosa That Enhances Its Virulence: Possible Role in Anastomotic Leak. PLoS ONE 7(8): e44326. doi:10.1371/journal.pone.0044326

42. Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, Bicak M, Rocca-Serra P, Sansone S-A, Willis K, Field D. 2012. A Call for an International Network of Genomic Observatories (GOs). GigaScience. 1(1) 5.

43. Larsen, P, Gibbons S, Gilbert JA. 2012. Bacterial diversity and function across time and space: modeling microbial community structure. FEMS Microbiology Letters. Volume 332, Issue 2, pages 91–98,

44. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman J, Hugenholtz P, Meyer F, Stevens R, Bailey M, Gordon JI, Kowalchuk G, Gilbert JA. 2012. Designing Better Metagenomic Surveys: The role of experimental design and metadata capture in making useful metagenomic datasets for ecology and biotechnology. Nature Biotechnology. 30 (6), 513–520

45. Larsen PE, Field D, Gilbert JA. 2012. Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods. 9 621-625 doi:10.1038/nmeth.1975

46. Gilbert JA, Catlett C, Desai, N, Field D, Knight R, White O, Robbins R, Sankaran R, Meyer F. 2012. White Paper: Conceptualizing a Genomics Software Institute (GSI). Standards in Genomic Science. 6:1.

47. Larsen PE, Hamada Y, Gilbert JA. Modeling Microbial Communities. Journal of Biotechnology. 160 (1–2) 17–24.

48. Willetts A, Joint I, Gilbert JA, Trimble W, Muhling M. Isolation and initial characterization of a novel type of Baeyer-Villiger monooxygenase activity from a marine microorganism. Microbial Biotechnology. 5(4) 549-559.

49. Thomas T, Gilbert JA, Meyer F. 2012. Metagenomics – a guide from sampling to data analysis. Microbial Informatics and Experimentation. 2:3; doi:10.1186/2042-5783-2-3.

50. Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM. 2012. Structure, Fluctuation and Magnitude of a Natural Prairie Soil Metagenome. ISME J. 6(9):1677-87.

51. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624.

52. Gilbert JA, Meyer F. 2012. Modeling the Earth’s Microbiome: A real world deliverable for microbial ecology. ASM Microbe Magazine. 7 (2), 64

53. Desai N, Antonopoulos D, Gilbert JA, Glass E, and Meyer F. 2012. From genomics to metagenomics. Current Opinions in Biotechnology. 23(1): 72-6.

54. Sansone S-A, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman L, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert JA, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I & Hide W. 2012. Toward interoperable bioscience data. Nature Genetics 44, 121–126 (2012) doi:10.1038/ng.1054.

55. Gilbert JA, Steele J, Caporaso JG, Steinbruck L, Somerfield PJ, Reeder J, Temperton B, Huse S, Joint I, McHardy AC, Knight R, Fuhrman JA, Field D. 2012. Defining seasonal marine microbial community dynamics. ISME J. 6, 298-308.

56. Foster J, Bunge J, Gilbert JA, Moore J. 2012. Measuring the Microbiome: perspective on advances in exploring microbial life. Briefings in Bioinformatics. 13(4):420-9

57. Davies N, Field D, Meyer C, Gilbert JA et al 2012. Sequencing data: A genomic network to monitor Earth. Nature. 481, 145.

58. Caporaso JG, Field D, Paszkiewicz K, Knight R, Gilbert JA. 2012. Evidence for a persistent microbial community in the Western English Channel. ISME J. 6, 1089–1093.

59. Jansson J, Neufeld J, Moran MA, Gilbert JA. 2012. Omics for Understanding Microbial Functional Dynamics. Environmental Microbiology: Special Issue: OMICS Driven Microbial Ecology. 14(1), 1-3.

201160. Jeffries TC, Seymour JR, Gilbert JA, Dinsdale E, Newton K, Leterne SSC, Roudnew B,

Smith RJ, Seuront L, Mitchell JG. Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS ONE 6(9): e25173. doi:10.1371/journal.pone.0025173 PMID: 21966446

61. Gilbert JA. 2011. The Smallest Champions in the World. Marine Scientist. 34:16-1962. Kulakova AN, Simthen M, Pavlov E, Gilbert JA, Quinn JP, McGrath JW. Direct

quantification of inorganic polyphosphate in microbial cells using 4’-6-diamidino-2-phenylindole (DAPI). Environmental Science and Technology. 45(18):7799-803. doi: 10.1021/es201123r.

63. Gilbert JA, O’Dor R, King N, Vogel T. 2011. The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial Informatics and Experimentation,1:5

64. Larsen PE, Collart F, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA. 2011. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microbial Informatics and Experimentation. 1:4

65. White J, Gilbert JA, Hill G, Hill E, Huse SM, Weightman AJ, and Mahenthiralingam E. 2011. Culture-independent analysis of bacterial fuel contamination provides insights into the level of concordance with the standard industry practice of aerobic cultivation. Applied and Environmental Microbiology 77:13, 4527-4538.

66. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk H-P, Knight R, Kottmann R, Kyrpides

N, Meyer F, San Gil I, Sansone S-A, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J. 2011. The Genomic Standards Consortium. PLoS Biology 9(6): e1001088.

67. Best A, DeJongh M, DevoidS, Gilbert JA, Glass E, Henry CS,  Larsen P, Meyer F, Overbeek R, Stevens RL, Vonstein V, Wilke A, Wilkening J, Xia F. 2011. Connecting Genotype to Phenotype in the Era of High-Throuhgput Sequencing. Biochimica et Biophysica Acta General Subjects. 1810(10): 967-977

68. Laverock B, Gilbert JA, Tait K, Osborn AM, Widdicombe S. 2011. Bioturbation: impact on the marine nitrogen cycle. Biochem Soc Trans. 39(1):315-20.

69. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA et al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29, 415-420.

70. Cooley NA, Kulakova AN, Villareal-Chiu JF, Gilbert JA, McGrath JW, Quinn JP. 2011. Phosphonoacetate Biosynthesis: In vitro Detection of a Novel NADP+ Dependent Phosphonoacetaldehyde Oxidizing Activity in Cell Extracts of a Marine Roseobacter. Microbiology, 80(3), 335-340.

71. Turk K, Pereira N, Swift P, Shelley R, Zehr J, Lohan M, Woodward EMS, Rees A, Gilbert JA. 2011. Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. ISME J. 5, 1201-1212 doi:10.1038/ismej.2010.205

72. Gilbert JA, Meyer F and Bailey M. 2011. The Future of microbial metagenomics (or is ignorance bliss?). ISME J. 5, 777-779 doi:10.1038/ismej.2010.178

73. Temperton B, Gilbert JA, Quinn JP, McGrath JW (2011) Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments. PLoS ONE 6(1): e16499. doi:10.1371/journal.pone.0016499

74. Gilbert JA and Dupont C. 2011. Marine Metagenomics. Annual Review of Marine Science. Volume 3: 347-371.

75. Gilbert JA, O’Dor R, Vogel T. 2011. Survey studies are still vital to science. Nature. 469, 162.

2010

76. Gilbert JA, Field D, Swift P, Thomas S, Cummings D, et al. (2010) The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation. PLoS ONE 5(11): e15545. doi:10.1371/journal.pone.0015545.

77. Mitra S, Rupek P, Urich T, Gilbert JA, Meyer F, Huson DH. 2010. Functional analysis of meta-genomes and –transcriptomes using SEED and KEGG. BMC Bioinformatics. 12(Suppl 1):S12+.

78. Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM. 2010. Metagenomics: A foundling finds its feet. Standards in Genomic Science. Vol 3 (2).

79. Heidelberg KB, Gilbert JA and Joint I. 2010. Mini Review: Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microbial Biotechnology. 3(5), 531–543

80. Laverock B., Widdicombe S, Tait K, Smith C, Osborn M, Gilbert JA. 2010. The impact of burrowing shrimp on bacterial diversity in temperate coastal sediments. ISME J. 4, 1531–1544.

81. Gilbert JA. 2010. Beyond the Infinite – tracking bacterial gene expression. Microbiology Today. 37:2; 82-85.

82. Mitra S, Gilbert JA, Field D & Huson DH. 2010. Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME J. 4, 1236-1242

83. Craft J., Gilbert JA, Temperton B., Dempsey KA, Ashelford K, Tiwari B, Hutchinson T & Chipman K. 2010. The mussel transcriptome: analysis using pyrosequencing. PLoS One 5(1): e8875.

84. Thomas S, Burdett H, Temperton B, Wick R, Snelling D, Woodward M, McGrath J, Quinn J, Munn C and Gilbert JA. 2010. The diversity of phnA gene homologues in temperature-stressed Cnidarian-associated Bacteria. ISME J. 4, 459-461 doi:10.1038/ismej.2009.129

2009

85. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield P, Huse S, Joint I. 2009. Seasonal succession of microbial communities in the Western English Channel using 16S rDNA-tag pyrosequencing. Environmental Microbiology. 11(12), 3132–3139

86. Temperton B, Field D, Oliver A, Tiwari B, Joint I and Gilbert JA. 2009. Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J 3: 792-96.

87. Quinn J, Kulakova A, Kulakov L, Villarreal-Chiu J, Gilbert JA, McGrath J. 2009. Expression of the Phosphonoalanine Degradative Gene Cluster from Variovorax sp. Pal2 is induced by Growth on Phosphonoalanine and Phosphonopyruvate. FEMS Microbiology Letters. 292(1):100-6.

88. Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I. 2009. Potential for Phosphonate utilisation by marine bacteria in temperate coastal waters. Environmental microbiology. 11(1):111-25

2008

89. Rees AP, Gilbert JA, Kelly-Gerreyn BA. 2008. Evidence of Nitrogen fixation in a temperate coastal sea (western English Channel). Marine Ecology Progress Series Vol. 374: 7–12

90. Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE 3(8): e3042. doi:10.1371/journal.pone.0003042

91. Gilbert JA, Muhling M & Joint I. 2008. A SAR11 fosmid clone with coding sequences not present in the “Candidatus Pelagibacter ubique” genome. ISME J. 2(7):790-3

92. Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Jack Gilbert, et al. 2008. The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies?". OMICS. 12(2):143-9.

93. Field D, Joint I, Gilbert JA et al. 2008. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology. 26(5):541-7.

94. Garnham C.P.†, Gilbert JA*, Hartman C†, Campbell RL†, Laybourn-Parry J.‡ and Davies PL. 2008. Ca2+-dependent bacterial antifreeze protein domain has a novel beta-helical ice-binding fold. Biochemistry Journal. 411, 171-180

2007

95. Booth T, Gilbert JA, Neufeld JD, Ball J, Thurston M, Chipman K Joint I & Field D. 2007. Handlebar: a flexible, web-based inventory manager for handling barcoded samples. Biotechniques. 42(3):300-02

2006

96. Scotter AJ, Marshall CB, Graham LA, Gilbert JA, Garnham CP, Davies PL. (2006). The basis for hyperactivity of antifreeze proteins. Cryobiology. 53(2). 229-239.

2005

97. Gilbert, J. A.; Davies, P.L.; Laybourn-Parry, J. (2005). A hyperactive, Ca2+-dependent antifreeze protein in an Antarctic bacterium. FEMS Microbiology Letters. 245(1), 67-72.

2004

98. Gilbert, J. A.; Hill, P. J.; Dodd, C. E. R. and Laybourn-Parry, J. (2004). Demonstration of antifreeze protein activity in Antarctic lake bacteria. Microbiology, 150, 171-180.

2003

99. Tomczak, M. M.; Marshall, C. B.; Gilbert, J. A. and Davies, P. L. (2003). A facile method for determining ice recrystallisation inhibition by antifreeze proteins. Biochemical and Biophysical Research Communications, 311 (4), 1041-1046.

Book chapters:2014

2013100. Owens S, Wilkening J, Fessler J, Gilbert JA. 2014. Metagenomics: Biofouling Methods.

Wiley and Sons. 101. Hampton-Marcell JT, Moormann SM, Owens SM, Gilbert JA. 2013. Preparation and

metatranscriptomic analyses of host-microbe systems. Methods Enzymol. 2013;531:169-85. doi: 10.1016/B978-0-12-407863-5.00009-5. PMID: 24060121

102. Lopez, J., Cuvelier, M., Gilbert, J. A., Larsen, P., Willoughby, D., Wu, Y., ... & Thurber, V. R. (2013, April). Synergistic Effects of Crude Oil and Corexit Dispersant on a Sponge Holobiont System. In INTEGRATIVE AND COMPARATIVE BIOLOGY (Vol. 53, pp. E130-E130). JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA: OXFORD UNIV PRESS INC.

2012103. Gilbert JA, Li L-L, Taghavi S, McCorkle SM, Tringe S, van der Lelie N. 2012.

Bioprospecting metagenomics for new glycoside hydrolases. In: Methods in Molecular Biology Vol. 908 – Biomass Conversion. Ed. Himmel, Michael E. Humana Press. ISBN 978-1-61779-955-6

2011104. Gilbert J.A. and Hughes M. 2011. Gene Expression Profiling: Metatranscriptomics. In:

Methods in Molecular Biology, Vol 733: High-throughput Sequencing: Applications to Microbiology. Kwon, Young Min; Ricke, Steven C. (Eds.) Springer. ISBN: 978-1-61779-088-1.

105. Gilbert J.A., Laverock B, Temperton B, Thomas S, Mühling M and Hughes M. Metagenomic protocols. 2011. In: Methods in Molecular Biology, Vol 733: High-throughput Sequencing: Applications to Microbiology. Kwon, Young Min; Ricke, Steven C. (Eds.) Springer. ISBN: 978-1-61779-088-1.

2010106. Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. 2010. Detection of Large

Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. In Volume 2 of “Handbook of Molecular Microbial Ecology II:

Metagenomics in Different Habitats” edited by Frans J. de Bruijn. John Wiley & Sons, Inc.107. Gilbert JA, Zhang K & Neufeld J. 2010. Multiple Displacement Amplification. In:

HANDBOOK OF HYDROCARBON AND LIPID MICROBIOLOGY. Ed. Timmis, K. Springer-Verlag Berlin Heidelberg. 10.1007/978-3-540-77587-4_333. 4255-4263

108. Gilbert JA. 2010. Aquatic metagenome library (archive; expression) generation and analysis. In: HANDBOOK OF HYDROCARBON AND LIPID MICROBIOLOGY. Ed. Timmis, K. . Springer-Verlag Berlin Heidelberg.10.1007/978-3-540-77587-4_340. 4347-4352

Peer Reviewed Community Reports:

2014109. Shogan Benjamin D., An Gary C., Schardey Hans M., Matthews Jeffrey B., Umanskiy

Konstantin, Fleshman James W. Jr., Hoeppner Jens, Fry Donald E., Garcia-Granereo Eduardo, Jeekel Hans, van Goor Harry, Dellinger E. Patchen, Konda Vani, Gilbert Jack A., Auner Gregory W., and Alverdy John C. 2014. Proceedings of the First International Summit on Intestinal Anastomotic Leak, Chicago, Illinois, October 4–5, 2012. Surgical Infections. doi:10.1089/sur.2013.114.

110. Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen E, Mackey KRM, DeLong EF. 2014. Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013). Standards in Genomic Science. 2014 9:3. doi:10.4056/sigs.5749944

111. Neil Davies, Dawn Field, Linda Amaral-Zettler, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, Alexei Drummond, Jack A Gilbert, Frank Oliver Glöckner, Renzo Kottmann, Chris Meyer, Norman Morrison, Matthias Obst, Robert Robbins, Lynn Schriml, Peter Sterk, Steven Stones-Havas. 2014. Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. Standards in Genomic Sciences, 9(3).

112. Neil Davies, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, Jonathan Geller, Jack A. Gilbert, Frank Oliver Glöckner, Penny Hirsch, Jo-Ann Leong, Chris Meyer, Matthias Obst, Serge Planes, Chris Scholin, Alfried P Vogler, Ruth D Gates, Rob Toonen, Véronique Berteaux-Lecellier, Michèle Barbier, Katherine Barker, Stefan Bertilsson, Mesude Bicak, Matthew J Bietz, Jason Bobe, Levente Bodrossy, Angel Borja, Jonathan Coddington, Jed Fuhrman et al. 2014. The founding charter of the Genomic Observatories Network. GigaScience 2014, 3:2 doi:10.1186/2047-217X-3-2

113. Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Neil Davies, Peter Dawyndt, George M. Garrity, Gilbert JA, Frank Oliver Glöckner, Lynette Hirschman, Hans-Peter Klenk, Rob Knight, Nikos Kyrpides, Folker Meyer, Ilene Karsch-Mizrachi, Norman Morrison, Robert Robbins, Inigo San Gil, Susanna Sansone, Lynn Schriml, Tatiana Tatusova, Dave Ussery, Pelin Yilmaz, Owen White, John Wooley, Gregory Caporaso. 2014. Genomic Standards Consortium Projects. Stand. Genomic Sci. 2014 9:3

114. John Alverdy, Jack A. Gilbert, Jennifer R DeFazio, Michael J Sadowsky, Eugene B Chang, Michael J Morowitz, Daniel H Teitelbaum. 2014. Proceedings of the ASPEN-Sponsored Workshop The Interface Between Nutrition and the Gut Microbiome: Implications and Applications for Human Health. Journal of Parenteral and Enteral Nutrition. Published online before print December 30, 2013, doi: 10.1177/0148607113517904.

2013115. Benjamin D. Shogan, Daniel P. Smith, Aaron I. Packman, Scott T. Kelley, Emily M

Landon, Seema Bhangar, Gary J. Vora, Rachael M. Jones, Kevin Keegan, Brent Stephens , Tiffanie Ramos, Benjamin C. Kirkup, Jr., Hal Levin, Mariana Rosenthal, Betsy Foxman, Eugene B. Chang, Jeffrey Siegel, Sarah Cobey, Gary An, John C. Alverdy, Paula J. Olsiewski, Mark O. Martin, Rachel Marrs, Mark Hernandez, Scott Christley, Michael

Morowitz, Stephen Weber, Jack Gilbert. 2013. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project, Chicago, USA, January 15th, 2013. Standards in Genomic Science. 8:3.

116. Lynn Schriml, Ilene Mizrachi, Peter Sterl, Dawn Field, Lynette Hirschman, Tatiana Tatusova, Susanna Sansone, Jack Gilbert, David Schindel, Neil Davies, Chris Meyer, Folker Meyer, George Garrity, Lite Proctor, Marnix Medema, Yemin Lan, Anna Klindworth, Frank Oliver Glöckner, Tonia Korves, Antonia Gonzalez, Peter Dwayndt, Markus Göker, Anjette Johnston, Evangelos Pafilis, Susanne Schneider, Katherine Baker, Cynthia Parr, Granger Sutton, Heather Creasy, Nikos Kyrpides, K Eric Wommack, Patricia L Whetzel, Daniel Nasko, Hilmar Lapp, Takamoto Fujisawa, Adam M Phillippy, Renzo Kottman, Judith A Blake, Junhua Li, Elizabeth M Glass, Petra ten Hoopen, Rob Knight, Susan Holmes, Curtis Huttenhower, Steven L Salzberg, Bing Ma, Owen White. 2013. The 15th Genomic Standards Consortium Meeting. Standards in Genomic Sciences. 8; 1.

117. Smith D, Alverdy J, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley S, Kirkup B, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert JA. 2013. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Standards in Genomic Science. 8:1.

2012118. Robbins R, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA,

Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EO, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J. 2012. RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta) Genomics, March 2011. Standards in Genomic Sciences 7 (1)

119. Gilbert JA, Bao Y, Wang H, Sansone, S-A, Edmunds, SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith D, Mizrachi I, Moreau C. 2012. Report of the 13th Genomic Standards Consortium Meeting, Shenzhen China, March 4-7th 2012. Standards in Genomic Science. 6(2): 276–286.

120. Amaro F, Gilbert JA, Owens S, Trimble W, Shuman HA. 2012. Whole-genome sequence of the human pathogen Legionella pneumophila Serotype 12 strain 570-CO-H. Journal of Bacteriology. 194 (6), 1613-1614

2011121. Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, Hu B, Jansson J, Knight R,

Kowalchuk GA, Kyrpides NC, Meyer F, Stevens R. 2011. The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011. Standards in Genomic Science. 5(2).

122. O’Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F. 2011. Meeting Report: The 2nd Annual Argonne Soils Workshop, Argonne National Laboratory, Chicago USA, October 6-8, 2010. Standards in Genomic Science. 5(2)

123. Amanda Birmingham, Jose C Clemente, Narayan Desai, Jack A. Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B Leontis, Craig Zirbel, Rob Knight, Alain Laederach. 2011. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Science, 4:2.

2010124. Hirschman L., Sterk P., Field D., Wooley J., Cochrane G., Gilbert JA., Kolker E.,

Kyrpides N., Meyer F., Mizrachi I., Nakamura Y., Sansone S., Schriml L., Tatusova T., White O. and Yilmaz P. 2010. Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Standards in Genomic Sciences, Vol 2, No 3

125. Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity G, Cochrane G, Wooley J, and Gilbert J.A. 2010. Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Special Interest Group at ISMB 2009. Standards in Genomic Science. Vol 1, No 3.

126. Gilbert JA, Meyer F, Knight R, Field D, Kyrpides N, Yilmaz P, Wooley J. 2010. Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA, August 22-27th 2010. Standards in Genomic Science. 3:3

127. Gilbert JA, Meyer F, Antonoploulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Feng W, Huson D, Jasson J, Knight R, Knight J, Kolker E, Kostantindis K, Kostka J, Kyrpides, N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2010. Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Science. 3:3.

128. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glockner F-O, Klenk H-P, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. 2010. The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 th 2010. Standards in Genomic Science. 3:3.

129. Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottman R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O , Wooley J. 2010. Meeting report from the Genomics Satndards Consortium (GSC) workshop 10. Standards in Genomic Science 3:3.

130. Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert JA, Glöckner F-O, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J. 2010. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Standards in Genomic Science. 3:3.

Genome Reports:2014131. Erik R Hawley, Stephanie A Malfatti, Ioanna Pagani, Marcel Huntemann, Amy Chen,

Brian Foster, Alexander Copeland, Tijana Glavina del Rio, Amrita Pati, Janet R Jansson, Jack A Gilbert, Susannah Green Tringe, Thomas D Lorenson, Matthias Hess. 2014. Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Marine Genomics. DOI: 10.1016/j.margen.2014.06.003.

132. Erik R Hawley, Hailan Piao, Nicole M Scott, Stephanie Malfatti, Ioanna Pagani, Marcel Huntemann, Amy Chen, Tijana Glavina del Rio, Brian Foster, Alex Copeland, Janet Jansson, Amrita Pati, Jack A Gilbert, Susannah Tringe, Thomas D Lorenson, Matthias Hess. 2014. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Standards in Genomic Science, 9;3.

2013133. Choudhari S, Smith S, Owens S, Gilbert JA, Shain DH, Dial RJ, Grigoriev A. 2013.

Metagenome Sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska. Genome Announcements, 1 (2).

2012134. Trimble WL, Phung LT, Meyer F, Gilbert JA, Silver S. 2012. Draft Genome Sequence

of Agrobacterium albertimagni Strain AOL15. Journal of Bacteriology. 194 (24) 6986-6987.

135. Trimble WL, Phung LT, Meyer F, Silver S, Gilbert JA. 2012. Draft Genome Sequence of Achromobacter piechaudii Strain HLE. Journal of Bacteriology 194 (22), 6355-6355.

136. Phung LT, Trimble WL, Meyer F, Gilbert JA, Silver S. 2012. Draft Genome Sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071). Journal of Bacteriology 194 (18), 5153-5153

137. Phung L, Silver S, Trimble W, Gilbert JA. 2012. Draft genome of Halomonas strain

GFAJ-1 (ATCC BAA-2256). Journal of Bacteriology. 194 (7), 1835-1836.2011138. Temperton B, Thomas S, Tait K, Parry H, Emery M, Allen M, Quinn J, McGrath J,

Gilbert JA. 2011. Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Standards in Genomic Science. 4:2

2010139. Gilbert JA, Meyer F, Joint I, Mühling M, Field D. 2010. Short Metagenome Report:

Metagenomes and metatranscriptomes from the L4 long term coastal monitoring station in the Western English Channel. Standards in Genomic Science. Vol 3 (2).

FUNDING

Past:1. PI: J A Gilbert. My Role: PI. Arthur P Sloan Foundation (2011-6-05). Total Direct Costs:

$145k. Title: “How personal is your home microbiome? Unraveling the relationship between human-associated and home-associated microbial signatures”. Annual Salary recovery or effort: 20%. Period: 01/08/11-30/09/12.

2. PI: J A Gilbert. My Role: PI. Doe Travel Award GSC13. Total Direct Costs: $15k. Title: Travel award for the Genomic Standards Consortium’s 13 th annual meeting. Annual salary recovery or effort: 0%. Period: 01/02/12-30/09/12.

3. PI: J A Gilbert. My Role: PI. U.S. Dept. of Energy (DE-AC02-06CH11357) – Total Direct costs: $1.8M. Title “Simultaneous ecological assessment and characterization of novel proteins from a soil microbial community”. Annual salary recovery or effort: 100%. Projected period 01/08/10-30/07/13

4. PI: J A Gilbert. My Role: PI. DDRCC-Gilbert. Total Direct Costs: $20k. Title: “A Metagenomic Understanding of the Causes of Acute Appendicitis”. Annual Salary Recovery or Effort: 0%. Period. 01/06/11-30/05/13.

5. PI: J A Gilbert. My Role: PI. Arthur P Sloan Foundation (2012-3-25). Total Direct Costs: $17.5k. Title “Convening a working group to design a sampling scheme, and building metadata acquisition, to characterize the source and succession of microbial and viral communities in a new hospital”. Annual salary recovery or effort: 0%. Projected Period: 01/06/12-30/08/13.

Current:6. PI: J A Gilbert. My Role: PI. U.S. Dept. of Energy (2012-016-N0). Total Direct Costs:

$300k. Title “Knowledge discovery in microbial community composition and metabolite turnover using satellite remote sensing data”. Annual Salary recovery or effort: 10%. Project Period 01/10/11-30/09/14.

7. PI: Folker Meyer. My Role: Co-PI. Gordon and Betty Moore Foundation. Total Direct Costs: $450,000. Title: “METAZen”. Annual salary recovery or effort: 0%. Projected Period: 01/03/12-28/02/15.

8. PI: J A Gilbert. My Role: PI. Arthur P Sloan Foundation (2012-11-01). Total Direct Costs $850,000. Title “The Hospital Microbiome Project”. Annual salary recovery or effort: 10%. Project Period: 01/11/12-31/10/14.

9. PI: J A Gilbert. My Role: PI. Gulf of Mexico Research Institute. Total Direct Costs: $266,000. Title “Creating a Predictive Model of Microbially Mediated Carbon Remediation in the Gulf of Mexico”. Annual salary recovery or effort: 10%. Project Period: 01/01/13-31/12/14.

10. PI: Cristina Negri. My Role: Co-PI. Municipal Water Research Division. Total Direct Costs: $1.98M. Title “Creating a predictive model of microbial dynamics in the Chicago

water ways. Annual Salary Recovery 10%. Project Period: 04/01/13-03/31/19.11. PI: Rob Knight. My Role: Co:PI. Keck Foundation. Total Direct Costs: $1M. Title “The

Earth Microbiome Project”. Annual Salary Recovery 0%. Project Period. 07/01/13-06/30/15.

12. PI: Jack A Gilbert. My Role: PI. UChicago-Argonne Coordination Program. Total Direct Costs: $200,000. Title “Inference for pathogen interactions”. Annual Salary Recovery 0%. Project Period. 11/01/13-10/31/15.

13. PI: Meltem Urgun-Demirtas. My Role: CoPI. UChicago-Argonne-BenGurion Collaboration on Water Research. Total Direct costs: $350k. Title: “Membrane-biofilm nexus: Advanced membrane autopsy as a tool for revealing membrane biofouling and development of new membranes materials and structures”. Annual Salary Recovery 0%. Project Period. 12/01/13-11/30/15.

14. PI: Flynn Picardl (U Indiana). My Role: Co-PI. NSF. Total Direct Costs $140,000. Title Collaborative Research: Biogenic Methanogenesis and Biodegradation of Organic Matter in Coals. Annual Salary Recovery 2.5%. Project Period 01/01/15-12/31/16.

15. PI: Pam Solstis (U Florida). My Role: Co-PI. NSF. Total Direct Costs $400,000. Title: Dimensions US-China: Collaborative Research: How historical constraints, local adaptation, and species interactions shape biodiversity across an ancient floristic disjunction. Annual Salary Recovery 5%. Project Period. 01/01/15-12/31/19.

MANAGEMENT TRAINING2007 Basic Management – matrix management (Plymouth Marine Laboratory)2008 Group Management Strategies (Plymouth Marine Laboratory)2009 Advanced Management Practice (Plymouth Marine Laboratory)2012 Strategic Laboratory Leadership program (Chicago Booth School of

Business)

EDUCATIONThe College (B.A., B.S.):2011-2011 BIOS 13129, " Environmental Science: a Microbiology Toolkit for the

Modern Age ", Spring Quarter, 20 lecturers, no discussion sections or laboratories, ~40 students

2011-2011 BIOS 20150, “Introductory Biology”, Spring Quarter, 1 lecture, 300 students

Graduate programs (Ph.D.):2009 Masters in Bioinformatics, 5 lectures, Oxford University, Zoology

Department, 24 students.2010 Masters in Bioinformatics, 3 lectures, Oxford University, Zoology

Department, 19 students.2012 Ph.D. graduate course on bioinformatics and manuscript writing, 20

lectures, University of Chicago, Ecology and Evolution, 8 students.2013 PhD. Graduate course on bioinformatics and manuscript writing, 20

lectures, University of Chicago, Ecology and Evolution, 8 students

Research trainees:Graduate (Ph.D.)2006-2009 Principal supervisor for Bonnie Laverock, PhD 2010. Currently:

Postdoctoral Associate, University of Western Australia.2006-2009 Principal supervisor for Simon Thomas, PhD 2010. Currently Senior

Principle Researcher, Plymouth Marine Laboratory, UK.

2007-2010 Principal supervisor for Ben Temperton, PhD 2011. Currently: Postdoctoral Associate, Oregon State University, USA.

2011 Principle supervisor for Sean Gibbons, Biophysical program, University of Chicago. Still in program.

2012 Principle supervisor for Simon Lax, Ecology and Evolution, University of Chicago. Still in program.

2009-2012 Ph.D. Committee member for Anna Klindworth (MPI Bremen), Jacobs University, Germany. PhD. 2012.

2011-2014 Ph.D. Committee member for Matthew Perisin, Ecology and Evolution, University of Chicago. Still in Program.

2012-2014 Ph.D. Committee member for Benjamin Rubin. The Field Museum. Still in Program.

2011-2014 Ph.D. Committee member for Orissa Moulton. Department of Ecology and Evolution, University of Chicago. Still in Program.

Postdoctoral Fellows.2010-2013 Daniel Smith (PhD Oregon State University, USA). Currently at Baylor

College of Medicine with Joe Petrisano.2011-2014 Iratxe Zarraonaindia (PhD University of the Basque Country, Spain).

Currently at University of the Basque Country, Spain.2012 Nicole Scott (Ph.D. University of Chicago). Project to be completed in

2015.2013 Kim Handley (Ph.D. University of California, Berkeley). Project to be

completed in 2015.2013 Chris Marshall (Ph.D. University of Southern Carolina). Project to be

completed in 2015.

PRESENTATIONSI have given >35 Keynote lectures and >110 invited seminars, 40 offered talks, 10 television interviews, >30 radio interviews over the last 5 years, including: David A. Relman, Jack A. Gilbert, Rob Knight. 2014. The promise of the microbiome:

Function and dysfunction in humans and beyond. Science 11 July 2014: Vol. 345 no. 6193 p. 226. DOI: 10.1126/science.345.6193.226-c

Consortium for Foreign Relations, DC, May 2014 Institute for the Future, Keynote, May 2014 AgriBio GRDC Key note, April 2014. AAAS Built Environment Microbiome Meeting, March 2014 AAAS Congressional Symposium, March 2014 Exxon Mobil Science of the Future Lecture Series Invited speaker, March 2014 Invited Speaker, ASLO 2014 Invited Speaker, Lausanne Genomic Days, February 2014 Invited Speaker – Field Museums A Watson Armour III Research Seminar, Feb 5 th 2014 Rotary Club of Naperville Special Guest Speaker, January 2014 Invited Speaker, Monsanto Microbiome Symposium, January 2014 Invited Speaker, AGU, December, 2013 Invited Speaker, University of Colorado at Boulder, December 2013 Invited Speaker, Illumina Microbiology Experts Meetings, November 2013 Invited Speaker, Hope College, MI., October 2013 A.S.P.E.N. Los Angeles, Keynote Speaker October 2013. Keynote Speaker, Brazilian Microbiome Association, September 2013.

Invited speaker at ICG Americas 2 meeting, Sacramento, USA, Sept 2013. Keynote speaker at International Environmental Omics Synthesis symposium, UK, Sept

2013. Keynote speaker at the Gordon Research Conference on Applied and Environmental

Microbiology, July 2013. Keynote speaker at Ningbo and Hangzhou symposia on microbial ecology, Chinese Academy

of Sciences. July 2013. Keynote speaker at University of Chicago center in Beijing’s international conference on

surgical microbiology. May 2013. Invited speaker at Alfred P Sloan Foundation Symposium on the built Environment, May

2013. Invited speaker and session organizer, American Society for Microbiology, May 2013. Keynote speaker at Join PI meeting for Terrestrial Ecosystems Science and Subsurface

Biogeochemistry DOE, May 2013. Invited speaker at SMBE satellite meeting, April 2013. Keynote speaker at the Genomic Standards Consortium’s 15th meeting, DC April 2013. Invited speaker at Michigan State University, April 2013 Invited speaker at Northwestern University, April 2013. Invited speaker at University of Oslo, March 2013 Invited speaker at EMBL Heidelberg, March 2013 Invited speaker at University of Minnesota, March 2013 Keynote speaker at Nanjing Soil Microbiology Conference, Chinese Academy of Sciences,

February 2013. Invited Speaker at EU-US Microbial Community Dynamics Workshop, November 2012 Invited Speaker at Loyola University, Chicago, IL, October 2012 Invited Speaker at the SLOAN workshop, Boulder, Co, October 2012 Invited Speaker at the Max Planck Institute, Bremen, Germany, October 2012 Invited Speaker at University of Chicago, Gleecher Center, October 2012 Invited Speaker at the GSC14, Oxford, UK, September 2012 Invited Speaker at the Microbiota Conference, Basel, Switzerland, September 2012 Invited Speaker at the SGM Conference, University of Warwick, UK, September 2012 Invited Speaker at ISME14, Denmark, Copenhagen, August 2012 Invited Speaker at MBL STAMPS Workshop, Falmouth, Ma, August 2012 Invited Speaker at the Gordon Research Conference, Naples, Italy, June 2012 Invited Speaker at the IOM forum on Microbial Threats, Washington, DC, June 2012 Invited Speaker at KAUST, Jeddah, Saudi Arabia, June 2012 Invited Speaker at the Research Triangle Institute, Raleigh NC, May 2012 Invited Speaker at the Frontiers in Metagenomics Symposium, Columbia, Mo, May 2012 Invited Speaker at the Bio Vision Alexandria, Alexandria, Egypt, April 2012 Invited Speaker at the EMBRC workshop, Heidelberg, Germany, March 2012 GSC13, Shenzhen China, March 2012 Panel participant at the AAAS Annual Meeting, February 2012 Invited Speaker at the BPC Seminar, December 2011 Invited Speaker at the International Congress of Genomics, Shenzhen, China, November

2011 Invited Speaker at Roche, New Delhi, India, November 2011 Invited Speaker at GSC12, September 2011 Invited Speaker at Max Planck Institute for Marine Microbiology, Bremen, September 2011 Invited Speaker at CeBiTec Conference in Bielefeld University, July 2011 Invited Speaker at ICiS Conference in Utah, July 2011.

Invited Seminar for the 1st International EMP Conference, June 2011 Plenery Lecture for Biogeography at ASM2011, April 2011 Invited lecture for Oregon State University expert series, April 2011 Special session, Waterloo University, Canada, April 2011 GSC11, Wellcome Trust Campus, Cambridge, UK, March 2011 CAMERA Inspirational Lecture Series – UCSD, January 2011 BIOTA10 – Sao Paolo, Brazil, December 2010 Soil Metagenomics 2010 – Braunschweig Germany, December 2010 ICG V Shenzhen China, November 2010 Departmental Seminar Miami University, Ohio, October 2010 Departmental Seminar Colorado University Boulder, October 2010 GSC10 – ANL, October 2010 US-EU Special Taskforce meeting, Washington DC, October 2010 Challenger Conference, UK – Invited Talk, September 2010. ISME 13 – Chair of Roundtable and Invited talk, August 2010 Cambridge Next Generation Sequencing Bioinformatics Meeting, March 2010 Metatranscriptomics for Microbes, REAL meeting, IGB Berlin, January 2010 Genomic standards on microbial ecology, PSB10, January 2010 2nd Next Generation Sequencing Retreat 14th– Metagenomics, December 2009 BBC Panorama – Britain’s Dirty Beaches, August 31st 2009 AIMS Seminar Series, August 22nd 2009 INTERCOL-10 – Genes in the Night, August 20th 2009 BBC “Bang Goes the Theory” Science show http://www.bbc.co.uk/bang/ - Dr. Venter in UK

Waters, June 2009 ICoMM meeting – Microbial biodiversity using pyrosequencing, April 2009 “Using 16S rDNA pyrosequencing tag technology to investigate bacterial diversity changes

over one year in the Western English Channel” offered speaker – ASLO, 2009. “Metagenomics and Metatranscriptomics in real world experiments” – invited speaker,

Metagenomics, 2008 “Metatranscriptomics and Ocean Acidification” – invited speaker, ISME, 2008 “Phosphonate utilization in marine bacteria” – invited speaker, SGM, 2008

INVITED, ELECTED, OR APPOINTED EXTRAMURAL SERVICE2009 – Invited to write an article for Annual Reviews in Marine Science2010 – Editorial Board for ISME Journal: Marine Drugs2010 – Invited Academic Editor for PLoS ONE2010 – Invited to editorial board of Frontiers in Marine Science2011 – Editorial Board for Marine Genomics, BMC: Microbial Informatics and Experimentation2011 – Editor for Special Issue of Environmental Microbiology2012 – Senior Editor for ISME Journal2012 – Invited to Faculty of 10002013 – Senior Section Editor for PLoS ONE.2013 – Senior Editor for Environmental Microbiology, Environmental Microbiology ReportsVarious – Reviewer for Science, Nature, African Journal of Microbiology, Applied and

Environmental Microbiology, Applied Soil Ecology, Briefing in Bioinformatics, Environmental Microbiology, Genome Biology, GigaScience, ISME Journal, Journal of Applied Microbiology, Journal of Bacteriology, Journal of Microbial Methods, Limnology and Oceanography, Letters in Applied Microbiology, Microbial Ecology, Molecular Biology and Evolution, Molecular Ecological Resources, Nature Climate Change, Nature Methods, Nature Reviews

Microbiology, Nature Science Reports, Nucleic Acids Research, PloS ONE, PNAS, Standards in Genomic Science, Trends in Microbiology, Water Research.

PRESS COVERAGE, TESTIMONY, ETC.

I have been very engaged with the media for the last 5-6 years, having taken 3 courses in media relations, and how to communicate science effectively in this forum. Here is a selection of the websites that feature aspects of my research:

NPR – Indoor Microbiomehttp://hereandnow.wbur.org/2013/11/01/microbiologist-avoid-flu

BBC Naked Scientists – Stopping the Superbugshttp://www.thenakedscientists.com/HTML/podcasts/naked-scientists/show/20131020-1/

Coverage of one of my articles by Science Daily:

http://www.sciencedaily.com/releases/2010/05/100526111244.htm

Coverage of the Earth Microbiome Project:

http://www.genomeweb.com/sequencing/earth-microbiome-pilot-project-sequence-10000-microbes-en-route-200000

http://www.microbemagazine.org/index.php?option=com_content&view=article&id=4373:beyond-metagenomics-how-soil-microbes-and-climate-interact&catid=926:02-2012-current-topics&Itemid=1193

http://www.uchicago.edu/features/20120305_bacterial_frontiers_could_yield_future_cures/

http://chicagotonight.wttw.com/2012/04/10/scientific-chicago-neil-shubin

http://www.anl.gov/articles/earth-microbiome-project-catalogue-world-s-microbes

http://www.igsb.org/news/Earth-Microbiome-Project-to-catalogue-worlds-microbes/

http://www.thenakedscientists.com/HTML/content/interviews/interview/1772/

http://www.nature.com/nature/podcast/v482/n7386/nature-2012-02-23.html

Coverage of interview at the AAAS annual meeting (2012) on work I am doing in UChicago Hospitals:

Patients leave a microbial mark on hospitals. Beth Mole, NATURE. May 23rd 2013. http://www.nature.com/news/patients-leave-a-microbial-mark-on-hospitals-1.13057Sampling protocols on You Tube http://www.youtube.com/watch?v=G_oFrIBlURYHospital microbiome Project, Built Environment Research Group. http://built-envi.com/portfolio/hospital-microbiome-project/Hospital Microbiome Project, Chicago Tribune, January 2013, http://articles.chicagotribune.com/2013-01-02/news/ct-met-microbiome-20130102_1_human-microbiome-bacteria-human-lifeHospital Microbiome Project: What patients leave behind. The Advisory Board Company, May 2013. http://www.advisory.com/Daily-Briefing/2013/05/28/Hospital-Microbiome-Project-What-patients-leave-behindMicrobiologists Will Watch As Bacteria Take Over This Hospital. Business Insider. November

7th 2012. http://www.businessinsider.com/investigating-the-bacteria-that-plague-a-hospital-2012-10Bacteria Before and After: Mapping the Microbiome of a New Hospital. Science Life, Chicago. November 19th 2012. http://sciencelife.uchospitals.edu/2012/11/19/bacteria-before-and-after-mapping-the-microbiome-of-a-new-hospital/‘We are 90% bacteria,’ says researcher for Hospital Microbiome Project. LimaOhio.com. http://www.limaohio.com/lifestyle/health/article_5520f55a-5ba5-11e2-beef-001a4bcf6878.html?mode=image&photo=0; Toledo Blade http://www.toledoblade.com/Medical/2013/01/28/We-are-90-percent-bacteria-says-a-researcher-for-Hospital-Microbiome-Project.html; LifeExtension.org http://www.lef.org/news/LefDailyNews.htm?NewsID=17906&Section=Nutrition; 'We are 90% bacteria,' says researcher for Hospital Microbiome Project. Microbe World. January 5th 2013. http://www.microbeworld.org/component/jlibrary/?id=9899&view=articleThe Hospital Microbiome Project: Bacteria Colonization Tracked by Supercomputers. Wanderlistmind.com November 2012. http://wanderlustmind.com/2012/11/25/the-hospital-microbiome-project-bacteria-colonization-tracked-by-supercomputers/Microbiome Project Kicks Off with Aim of Understanding Ecology Behind Hospital-Acquired Infections. Genome Web. January 2nd 2013.http://www.genomeweb.com/sequencing/microbiome-project-kicks-aim-understanding-ecology-behind-hospital-acquired-infe http://www.telegraph.co.uk/health/healthnews/9091633/Florence- Nightingale-approach-could-help-fight-infection-in-modern-hospitals.html

http://www.guardian.co.uk/science/2012/feb/20/open-hospital-windows-stem-infections

http://www.nursingtimes.net/nursing-practice/clinical-zones/infection-control/sterile-wards-may-be-wiping-out-friendly-microbes/5041713.article

http://www.sciencenewsdaily.org/microbiology-news/cluster136687712

http://www.independent.ie/health/health-news/florence-nightingales-treatment-of-bugs-has-lessons-for-modern-medicine-3024687.html

http://topnews.us/content/246370-fresh-air-good-patients-says-jack-gilbert

http://www.timesofmalta.com/articles/view/20120227/world/How-Florence-Nightingale-had-beaten-the-bugs.408694

http://www.webmd.boots.com/nhs/news/20120222/open-hospital-windows-to-cut-risk-of-bacterial-infection

http://deskarati.com/2012/02/20/open-hospital-windows-to-stem-spread-of-infections/

Interviewed and performed analyses for BBC Panorama in the UK:

http://www.bbc.co.uk/programmes/b00mg5cg

Interview and editorial on Nature Methods paper for predicting microbial community structures in the English Channel:

http://phys.org/news/2012-04-microbial-weather.html

http://www.nature.com/nmeth/journal/v9/n6/full/nmeth.2041.html

Interacting and educating in schools:

http://www.mcs.anl.gov/news/detail.php?id=758

Interviews on Home and Hospital Microbiome Projects:

http://www.microbe.net/2012/10/24/people-behind-the-science-inverview-videos-jack-gilbert-built-environment-microbes-and-hospitals/

Work on making microbial music from ecological patterns:

http://blogs.plos.org/toothandclaw/2012/10/03/the-music-of-microbes/

Work on Western English Channel time series:

http://phylogenomics.blogspot.com/2011/08/get-to-know-jack-story-behind-paper-by.html

Interviews on the Arsenic-Life Controversy:

http://sciencelife.uchospitals.edu/2010/12/08/life-on-arsenic/

Work on the Phones and Shoes Microbiome:

http://cosmiclog.nbcnews.com/_news/2012/02/24/10499512-whats-living-on-your-smartphone?lite

Featured Speaker on a live AAAS Science Webinar:

http://webinar.sciencemag.org/webinar/archive/harnessing-power-metagenomics