Jack A Gilbert B.Sc. Ph.D.

ProfessorDepartment of SurgeryThe University of Chicago 5841 S Maryland AveChicago, IL 60637-1234Office: (630)-915-2383Email: gilbertjack@uchicago.edu Web page: http://surgeryresearch.uchicago.edu/jack-gilbert

DirectorThe Microbiome CenterUniversity of ChicagoChicago, IL 60637-1234Office: (630)-915-2383Email: gilbertjack@uchicago.edu

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

Senior ScientistAdjunctThe Josephine Bay Paul CenterMarine Biological Laboratory7 MBL StreetWoods Hole, MA 02543Tel: 508-548-3705

Associate DirectorInstitute for Genomic and Systems BiologyKnapp Center for Biological DiscoveryRoom 10152University of Chicago900 East 57th Street, Chicago, IL 606037Tel: (773) 834-3913Web: http://www.igsb.org/people/jack-gilbert

Research AssociateField Museum of Natural History1400 S Lake Shore Dr, Chicago, IL 60605

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,

USA2013-2015 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.2014-Present Associate Director, IGSB, University of Chicago, ANL, MBL.2015-Present Research Associate, Field Museum of Natural History.2016-Present Professor, Dept. of Surgery, University of Chicago, 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, Computing and Environmental Life Sciences

AWARDSCrain’s Business Chicago – 2014 40 under 40.Business Insider – 50 Scientists Changing the World 2015 Business Insider –Top 10 Scientists in Biomedical Science 2015 Popular Science – Brilliant 10 2015American Association for Clinical Chemistry – 2015 Outstanding Speaker Award.Altemeier Lecture Prize – Surgical Infection Society, 2016WH Pierce Prize – Society for Applied Microbiology 2016.

ACADEMIC TRAINING 1995-1998 Kings College, University of London

BSc 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:

2016

1. Rachel I Adams, Seema Bhangar, Karen C Dannemiller, Jonathan A Eisen, Noah Fierer, Jack A Gilbert, Jessica L Green, Linsey C Marr, Shelly L Miller, Jeffrey A Siegel, Brent Stephens, Michael S Waring, Kyle Bibby. 2016. Ten questions concerning the microbiomes

of buildings. Building and Environment. http://dx.doi.org/10.1016/j.buildenv.2016.09.0012. Ruibo Sun, Melissa Dsouza, Jack A Gilbert, Xisheng Guo, Daozhong Wang, Zhibin Guo,

Yingying Ni, Haiyan Chu. 2016. Fungal community composition in soils subjected to long‐term chemical fertilization is most influenced by the type of organic matter. Environmental Microbiology. DOI: 10.1111/1462-2920.13512.

3. Embriette R Hyde, Jose A Navas-Molina, Se Jin Song, Jordan G Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R Mendelson, Valerie J McKenzie, Jack A Gilbert, Rob Knight. 2016. The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems Journal. 1; 4 e00046-16

4. Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, dos Santos MM, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI. 2016. Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. N Engl J Med 2016; 375:411-421

5. Hang Wang, Naseer Sangwan, Hong-Yi Li, Jian-Qiang Su, Wei-Yin Oyang, Zhi-Jian Zhang, Jack A Gilbert, Yong-Guan Zhu, Fan Ping, Han-Luo Zhang. 2016. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome. ISME J. (26 July 2016) | doi:10.1038/ismej.2016.103

6. Yee A & Gilbert JA. 2016. Is Triclosan Harming Your Microbiome? Science, 353, (6297), 348-349.

7. Vipin Gupta, Shazia Haider, Utkarsh Sood, Gilbert JA, Meenakshi Ramjee, Ken Forbes, Yogendra Singh, Bruno S Lopes, Rup Lal. 2016. Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach. Scientific Reports. 6, 29043. doi:10.1038/srep29043

8. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature, 535, 94–103 doi:10.1038/nature18850

9. Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FS-M, Medeiros JD, Assis Geraldo J, Gilbert JA, Volpini AC, Rocha Fernandes G. (2016) ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms. PLoS Negl Trop Dis 10(6): e0004817. doi:10.1371/journal.pntd.0004817

10. Torsten Thomas, Lucas Moitinho-Silva, Miguel Lurgi, Johannes R. Björk, Cole Easson, Carmen Astudillo-García, Julie B. Olson, Patrick M. Erwin, Susanna López-Legentil, Heidi Luter, Andia Chaves-Fonnegra, Rodrigo Costa, Peter J. Schupp, Laura Steindler, Dirk Erpenbeck, Jack A. Gilbert, Rob Knight, Gail Ackermann, Jose Victor Lopez, Michael W. Taylor, Robert W. Thacker, Jose M. Montoya, Ute Hentschel & Nicole S. Webster. 2016. Diversity, structure and convergent evolution of the global sponge microbiome. Nature Communications. 7, 11870 doi:10.1038/ncomms11870.

11. Hu Li, Xiaoru Yang, Bosen Weng, Jianqiang Su, San’an Nie, Jack A Gilbert, Yong-Guan Zhu. 2016. The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil. Soil Biology and Biochemistry. 100; 59-65.

12. Kuntz T, Gilbert JA. 2016. Does the Brain Listen to the Gut? eLife. 5: e17052.13. Sangwan N, Zarraonaindia I, Hampton-Marcel JT, Ssegane H, Eshoo TW, Rijal G, Negri

MC, Gilbert JA. 2016. Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter populations. mSystems. DOI: 10.1128/mSystems.00003-16

14. Sharma A, Gilbert JA, Lal R. 2016. (Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans. Scientific Reports. 6; 25527.

15. Cardona C, Weisenhorn P, Henry C, Gilbert JA. 2016. Network-based metabolic analysis and microbial community modeling. Current Opinions in Microbiology. 31, 124-131.

16. Sangwan N, Xia FF, Gilbert JA. 2016. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 4:8 DOI: 10.1186/s40168-016-0154-5

17. De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D. 2016. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Scientific reports. 6:21871.

18. O'Brien SL, Gibbons SM, Owens SM, Hampton‐Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. 2016. Spatial scale drives patterns in soil bacterial diversity. Environmental Microbiology. DOI: 10.1111/1462-2920.13231

19. Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, Brookes PC, Xu J, Gilbert JA. 2016. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. doi:10.1038/ismej.2015.261

20. Burstein D, Amaro F, Zusman T, Lifshitz Z, Cohem O, Gilbert JA, Pupko T, Shuman HA, Segal G. 2016. Genomic analysis of 38 Legionella species identified large and diverse effector repertoires. Nature Genetics. doi:10.1038/ng.3481

21. Dugas LR, Fuller M, Gilbert JA, Layden BT. 2016. The obese gut microbiome across the epidemiologic transition. Emerging Themes in Epidemiology. 13 (1) 1.

22. Gilbert JA, Alverdy JA. 2016. Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? Gut 65 (1), 1-2. doi:10.1136/gutjnl-2015-310043.

23. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song, SJ, Amir A, Larsen P, Sangwan N, Harman D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Busheli SR, Carter DO, Knight R. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 351 (6269) 158-162 DOI:10.1126/science.aad2646

2015

24. Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J and Gilbert JA. 2015. A simple novel device for air sampling by electrokinetic capture. Microbiome. 3:79; DOI: 10.1186/s40168-015-0141-2

25. Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight B. 2015. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1(1):e00009-15. doi:10.1128/ mSystems.00009-15.

26. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Frazer SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. 2015. Tools for the Microbiome: Nano and Beyond. ACS Nano. DOI: 10.1021/acsnano.5b07826

27. Maya Britstein, Giulia Devescovi, Kim M Handley, Assaf Malik, Markus Haber, Kumar Saurav, Roberta Teta, Valeria Costantino, Ilia Burgsdorf, Jack A Gilbert, Noa Sher, Vittorio Venturi, Laura Steindler. 2015. A new N-acyl homoserine lactone synthase in an uncultured symbiont of the red sea sponge Theonella swinhoei. Applied and Environmental Microbiology. 03111-15

28. Teng Yang, Pamela Weisenhorn, Jack A Gilbert, Yingying Ni, Ruibo Sun, Yu Shi, Haiyan Chu. 2015. Carbon constrains fungal endophyte assemblages along the timberline. Environmental Microbiology. 2015/12/1

29. Gibbons SM and Gilbert JA. 2015. Microbial Diversity – exploration of natural ecosystems and microbiomes. Current Opinion in Genetics and Development. 35, 66-72

30. Ying S, Zeng D-N, Chi L, Tan Y, Galzote C, Cardona C, Lax S. Gilbert JA, Quan Z-X. 2015. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban

and Rural Human Populations. PLoS ONE 10(10): e0141842. doi:10.1371/journal.pone.0141842

31. Alivisatos AP, MJ Blaser, EL Brodie, M Chun, JL Dangl, TJ Donohue, PC Dorrestein, JA Gilbert, JL Green, JK Jansson, R Knight, ME Maxon, MJ McFall-Ngai, JF Miller, KS Pollard, EG Ruby, SA Taha, Unified Microbiome Initiative Consortium. 2015. A unified initiative to harness Earth’s microbiomes. Science. 350 (6260): 507-508.

32. Denner DR, N Sangwan, JB Becker, DK Hogarth, J Oldham, J Castillo, AI Sperling, J Solway, ET Naureckas, C Ober, JA Gilbert, and SR White. 2015. Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways. Journal of Allergy and Clinical Immunology. S0091-6749(15)01563-8. doi: 10.1016/j.jaci.2015.10.017..

33. Miles Fuller, Medha Priyadarshini, Sean M Gibbons, Anthony R Angueira, Michael Brodsky, M. Geoffrey Hayes, Petia Kovatcheva-Datchary, Fredrik Backhed, Jack A Gilbert, William L. Lowe, Brian T. Layden. 2015. The Short Chain Fatty Acid Receptor, FFA2, contributes to gestational glucose homeostasis. American Journal of Physiology - Endocrinology and Metabolism DOI: 10.1152/ajpendo.00171.2015

34. Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA and Nagler CR. 2015. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J. doi:10.1038/ismej.2015.151

35. Perisin M, Vetter M, Gilbert JA, and Bergelson J. 2015. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME J. doi:10.1038/ismej.2015.161

36. Wang H, Li H, Gilbert JA, Li H, Wu L, Liu M, Wang L, Zhou Q, Yuan J, Zhang Z. 2015. Housefly Larvae Vermicomposting efficiently attenuates Antibiotic Resistant Genes in Swine Manure Coupled with distinct bacterial population change. Applied and Environmental Microbiology, 01367-15

37. Karim H Lüchmann, Melody S Clark, Afonso CD Bainy, Jack A Gilbert, John A Craft, J Kevin Chipman, Michael AS Thorne, Jacó J Mattos, Marília N Siebert, Declan C Schroeder. 2015. Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana. Aquatic Toxicology. doi:10.1016/j.aquatox.2015.06.012

38. Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT. 2015. Athletic equipment microbiota are shaped by interactions with human skin. Microbiome. 3:25  doi:10.1186/s40168-015-0088-3

39. Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. 2015. Lifestyle evolution in cyanobacterial symbionts of sponges. mBio 6(3):e00391-15. doi:10.1128/mBio.00391-15.

40. Van Bonn W, LaPointe A, Gibbons SM, Frazier A, Hampton-Marcel J, Gilbert JA. 2015. Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management. Zoo Biology. DOI: 10.1002/zoo.21220

41. Lin X, Handley KM, Gilbert JA, Kostka JE. 2015. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J. doi:10.1038/ismej.2015.77

42. Gilbert JA. 2015. Our Unique Microbial Identity. Genome Biology. 16:97 doi:10.1186/s13059-015-0664-7

43. Lax S, Hampton-Marcell TJ, Gibbons S, Colares G, Smith D, Eisen AJ, Gilbert JA. 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome. 3:21  doi:10.1186/s40168-015-0082-9

44. Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. 2015. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel

predator-prey genotypes. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12297

45. Shogun BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers, R, Hancock LE, Gilbert JA, Zborina O, Alverdy JC. 2015. Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak, Science Translational Medicine. Vol. 7, Issue 286, p. 286ra68. DOI: 10.1126/scitranslmed.3010658

46. Lax S and Gilbert JA. 2015. Hospital-associated microbiota and implications for nosocomial infections. Trends in Molecular Medicine. DOI: http://dx.doi.org/10.1016/j.molmed.2015.03.005

47. Leone V, Gibbons SM, Martinez K, Hutchinson AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpali A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB. 2015. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host & Microbe. http://dx.doi.org/10.1016/j.chom.2015.03.006

48. Dedesko S, Stephens B, Gilbert JA, Siegel JA. 2015. Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms. Building and Environment. doi:10.1016/j.buildenv.2015.03.029

49. Canani RB, Gilbert JA, Nagler CR. 2015. The role of the commensal microbiota in the regulation of tolerance to dietary allergens. Curr Opin Allergy Clin Immunol. 15. Online.

50. Gilbert JA. 2015. Metagenomics: Social behavior and the microbiome. eLife 2015;4:e0732251. Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich

NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA. 2015. The soil microbiome influences grapevine-associated microbiota. mBio 6(2):e02527-14. doi:10.1128/mBio.02527-14.

52. Daniel McDonald, Mady Hornig, Catherine Lozupone, Justine Debelius, Jack A Gilbert, Rob Knight. 2015. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microbial Ecology in Health & Disease 2015, 26: 26555 - http://dx.doi.org/10.3402/mehd.v26.26555

53. Huang EY, Inoue T, Leone V, Dalal S, Touw K, Wang Y, Musch M, Theriault B, Higuchi K, Donovan S, Gilbert JA, Chang E. 2015. Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases. Inflammatory Bowel Diseases. 21(5):963-72 10.1097/MIB.0000000000000332

54. Lax S, Nagler CR. Gilbert JA. 2015. Our interface with the built environment: immunity and the indoor microbiota. Trends in Immunology. http://dx.doi.org/10.1016/j.it.2015.01.001

55. Gilbert JA and Henry C. 2015. Predicting ecosystem emergent properties at multiple scales. Environmental Microbiology. DOI: 10.1111/1758-2229.12258

56. Ramos T, Dedesko S, Siegel JA, Gilbert JA, Stephens B (2015) Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building. PLoS ONE 10(3): e0118207. doi:10.1371/journal.pone.0118207

57. Stephen A Wood, Mark A Bradford, Gilbert JA, Krista L McGuire, Cheryl A Palm, Katherine L Tully, Jizhong Zhou, Shahid Naeem. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. Journal of Applied Ecology. DOI: 10.1111/1365-2664.12416

58. Haowei Yue, Mengmeng Wang, Shiping Wang, Gilbert JA, Xin Sun, Linwei Wu, Qiaoyan Lin, Yigang Hu, Xiangzhen Li, Zhili He, Jizhong Zhou, Yunfeng Yang. 2015. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME Journal. 17 February 2015; doi:10.1038/ismej.2015.19

59. Shade A, Gilbert JA. 2015. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends in Microbiology. doi:10.1016/j.tim.2015.01.007

60. Amaro F, Wang W, Gilbert JA, Anderson OR, Shuman HA. 2015. Diverse protist grazers select for virulence-related traits in Legionella. ISME Journal. 2015/1/9.

61. Vitaglione P, Mennella I, Ferracane R, Rivellese AA, Giacco R, Ercolini D, Gibbons SM, La Storia A, Gilbert JA, Jonnalagadda A, Thielecke F, Gallo MA, Scalfi L, Fogliano V. 2015. Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber. The American Journal of Clinical Nutrition. ajcn. 088120

62. Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. 2015. Ecological succession and viability of human-associated microbiota on restroom surfaces. Applied and Environmental Microbiology. 81(2), 765-773.

63. Xiao-Ru Yang, Hu Li, San-An Nie, Jian-Qiang Su, Bo-Sen Weng, Gui-Bing Zhu, Huai-Ying Yao, Gilbert JA and Yong-Guan Zhu. 2015. The potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Applied and Environmental Microbiology. 81 (3), 938-947.

2014

64. Gilbert JA, Neufeld JD (2014) Life in a World without Microbes. PLoS Biol 12(12): e1002020. doi:10.1371/journal.pbio.1002020

65. Helianthous Verma, Roshan Kumar, Phoebe Oldach, Naseer Sangwan, Jitendra P Khurana, Jack A Gilbert, Rup Lal. 2014. Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics, 15:1014  doi:10.1186/1471-2164-15-1014

66. Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. 2014. Development of the preterm infant gut microbiome: a research priority. Microbiome 2014, 2:38  doi:10.1186/2049-2618-2-38

67. Pfister CA, Gilbert JA, Gibbons SM. (2014) The role of macrobiota in structuring microbial communities along rocky shores. PeerJ 2:e631 http://dx.doi.org/10.7717/peerj.631

68. LaBelle EV, Marshall CW, Gilbert JA, May HD (2014) Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome. PLoS ONE 9(10): e109935. doi:10.1371/journal.pone.0109935

69. Gilbert JA. 2014. Science is innate! Genome Biology. 15:477.70. Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J,

Gilbert JA, Zaborina O, Alverdy JC. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. mBio 5(5):e01361-14. doi:10.1128/mBio.01361-14.

71. Rubin BER, Sanders JG, Hampton-Marcell J, Owens SM, Gilbert JA, and Moreau CS. 2014. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. Microbiology Open. Article first published online: 26 SEP 2014. DOI: 10.1002/mbo3.216

72. Shogan BD, Smith DP, Christley S, Gilbert JA, Zaborina O, and Alverdy JC. 2014. Intestinal anastomotic injury alters spatially defined microbiome composition and function. Microbiome 2014, 2:35  doi:10.1186/2049-2618-2-35

73. 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

74. 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

75. 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.

76. 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

77. 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

78. 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

79. 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

80. 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

81. 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

82. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA and Knight R (2014) Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front. Microbiol. 5:298. doi: 10.3389/fmicb.2014.00298

83. 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

84. 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

85. O’Malley MA, Brigandt I, Love AC, Crawford JA, Gilbert JA, Knight R. Mitchell SD, Rohwer F. 2014. Multilevel research strategies and biological systems. Philosophy of Science. 81(5) 811-828.

86. 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, 5:108. doi: 10.3389/fmicb.2014.00108

87. 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

88. 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

89. 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.

90. 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

91. 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.

92. 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. 8, 1464–1475; doi:10.1038/ismej.2013.254

93. 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.

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

2013

95. 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.

96. 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

97. 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.

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

99. 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.

100. 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.

101. 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

102. 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.

103. 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.

104. 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

105. 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. Volume 74, Issue 1, 15 September 2013, Pages 19–31

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

107. 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

108. 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

109. 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.

110. 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

2012

111. 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.

112. 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

113. 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

114. 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

115. 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

116. 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.

117. 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,

118. 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. Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology. 30 (6), 513–520

119. 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

120. 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.

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

122. 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.

123. 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.

124. 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.

125. 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.

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

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

128. 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.

129. 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.

130. 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

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

132. 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.

133. 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.

2011

134. 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

135. Gilbert JA. 2011. The Smallest Champions in the World. Marine Scientist. 34:16-19136. 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.

137. 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

138. 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

139. 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.

140. 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.

141. 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

142. 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.

143. 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.

144. 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.

145. 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

146. 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

147. 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

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

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

2010

150. 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.

151. 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+.

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

153. 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

154. 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.

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

156. 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

157. 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.

158. 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

159. 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

160. 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.

161. 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.

162. 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

163. 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

164. 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

165. 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

166. 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.

167. 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.

168. 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

169. 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

170. 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

171. 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

172. 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

173. 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

174. Hampton-Marcell JT, Frazier A, Moormann SM, Owens SM, Gilbert JA. 2014. Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems. Humana Press, Totowa, NJ. In T.J.McGenity et al., (eds.) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocol Handbooks. DOI: 10.1007/8623_2014_5

175. Gilbert, J.A. and Scott, N.M. (2014) Introduction to Genetic, Genomic, and System Analyses for Communities. Humana Press, Totowa, NJ. In T.J.McGenity et al., (eds.) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocol Handbooks. DOI: 10.1007/8623_2014_5

176. Owens S, Wilkening J, Fessler J, Gilbert JA. 2014. Metagenomics: Biofouling Methods. Wiley and Sons.

2013

177. 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

178. 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.

2012

179. 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

2011

180. 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.

181. 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.

2010

182. 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.

183. 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

184. 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:

2015185. Anna Kopf, Mesude Bicak, Renzo Kottmann, Julia Schnetzer, Ivaylo Kostadinov, Katja

Lehmann, Antonio Fernandez-Guerra, Christian Jeanthon, Eyal Rahav, Matthias Ullrich, Antje Wichels, Gunnar Gerdts, Paraskevi Polymenakou, Giorgos Kotoulas, Rania Siam, Rehab Z Abdallah, Eva C Sonnenschein, Thierry Cariou, Fergal O’Gara, Stephen Jackson, Sandi Orlic, Michael Steinke, Julia Busch, Bernardo Duarte, Isabel Caçador, João Canning-Clode, Oleksandra Bobrova, Viggo Marteinsson, Eyjolfur Reynisson, Clara Magalhães Loureiro, Gian Marco Luna, Grazia Marina Quero, Carolin R Löscher, Anke Kremp, Marie E DeLorenzo, Lise Øvreås, Jennifer Tolman, Julie LaRoche, Antonella Penna, Marc Frischer, Timothy Davis, Barker Katherine, Christopher P Meyer, Sandra Ramos, Catarina Magalhães, Florence Jude-Lemeilleur, Ma Leopoldina Aguirre-Macedo, Shiao Wang, Nicole Poulton, Scott Jones, Rachel Collin, Jed A Fuhrman, Pascal Conan, Cecilia Alonso, Noga Stambler, Kelly Goodwin, Michael M Yakimov, Federico Baltar, Levente Bodrossy, Jodie Van De Kamp, Dion MF Frampton, Martin Ostrowski, Paul Van Ruth, Paul Malthouse, Simon Claus, Klaas Deneudt, Jonas Mortelmans, Sophie Pitois, David Wallom, Ian Salter, Rodrigo Costa, Declan C Schroeder, Mahrous M Kandil, Valentina Amaral, Florencia Biancalana, Rafael Santana, Maria Luiza Pedrotti, Takashi Yoshida, Hiroyuki Ogata, Tim Ingleton, Kate Munnik, Naiara Rodriguez-Ezpeleta, Veronique Berteaux-Lecellier, Patricia Wecker, Ibon Cancio, Daniel Vaulot, Christina Bienhold, Hassan Ghazal, Bouchra Chaouni, Soumya Essayeh, Sara Ettamimi, El Houcine Zaid, Noureddine Boukhatem, Abderrahim Bouali, Rajaa Chahboune, Said Barrijal, Mohammed Timinouni, Fatima El Otmani, Mohamed Bennani, Marianna Mea, Nadezhda Todorova, Ventzislav Karamfilov, Petra ten Hoopen, Guy Cochrane, Stephane L’Haridon, Kemal Can Bizsel, Alessandro Vezzi, Federico M Lauro, Patrick Martin, Rachelle M Jensen, Jamie Hinks, Susan Gebbels, Riccardo Rosselli, Fabio De Pascale, Riccardo Schiavon, Antonina dos Santos, Emilie Villar, Stéphane Pesant, Bruno Cataletto, Francesca Malfatti, Ranjith Edirisinghe, Jorge A Herrera Silveira, Michele Barbier, Valentina Turk, Tinkara Tinta, Wayne J Fuller, Ilkay Salihoglu, Nedime Serakinci, Mahmut Cerkez Ergoren, Eileen Bresnan, Juan Iriberri, Paul Anders Fronth Nyhus, Edvardsen Bente, Hans Erik Karlsen, Peter N Golyshin, Josep M Gasol, Snejana Moncheva, Nina Dzhembekova, Zackary Johnson, Christopher David Sinigalliano, Maribeth Louise Gidley, Adriana Zingone, Roberto Danovaro, George Tsiamis, Melody S Clark, Ana Cristina Costa, Monia El Bour, Ana M Martins, R Eric Collins, Anne-Lise Ducluzeau, Jonathan Martinez,

Mark J Costello, Linda A Amaral-Zettler, Jack A Gilbert, Neil Davies, Dawn Field, Frank Oliver Glöckner. 2015. The ocean sampling day consortium. Giga Science. 4, 1, 1-5.

2014

186. Jack Westwood, Matthew Burnett, David Spratt, Michael Ball, Daniel J Wilson, Sally Wellsteed, David Cleary, Andy Green, Emma Hutley, Anna Cichowska, Susan Hopkins, Mark Wilcox, Anthony Kessel, Ghada Zoubiane, Lara Bethke, Derrick W Crook, Jimmy Walker, Mark Sutton, Philip Marsh, Ginny Moore, Peter Wilson, Alison Holmes, Peter Hoffman, Chris Smith, Beryl Oppenheim, Julian Parkhill, Neil Woodford, Julie Robotham, Claire Kidgell, Martin Anyim, Gabriella Gilkes, Dawn Field, Josh Quick, Tony Pickering, Benjamin C Kirkup, Jack A. Gilbert. 2014. The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013. Standards in genomic Science. 9(1), 12; http://www.standardsingenomics.com/content/9/1/12

187. Jack A Gilbert, Madeleine Ball, Paul Blainey, Martin J Blaser, Brendan JM Bohannan, Ashley Bateman, John Bunge, Maria G Dominguez-Bello, Slava Epstein, Noah Fierer, Dirk Gevers, Tracy Grikscheit, Leila J Hamdan, James Harvey, Curtis Huttenhower, Benjamin Kirkup, Heidi H Kong, Christian Lauber, Katherine P Lemon, Susan V Lynch, Lance Martin, Charlene Mello, Joseph Palma, Roy Parker, Joseph Petrosino, Julia A Segre, Leslie Vosshall, Rui Yi, Rob Knight. 2014. Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012. Standards in Genomic Science. 9(1); 13. http://www.standardsingenomics.com/content/9/1/13

188. 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.

189. O'Malley, Maureen A. and Brigandt, Ingo and Love, Alan C. and Crawford, John W. and Gilbert, Jack A. and Knight, Rob and Mitchell, Sandra D. and Rohwer, Forest (2014) Multilevel Research Strategies and Biological Systems. In: [2012] Philosophy of Science Assoc. 23rd Biennial Mtg (San Diego, CA) > PSA 2012 Symposia

190. 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

191. 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).

192. 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

193. 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

194. 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.

2013

195. 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.

196. 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.

197. 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.

2012

198. 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)

199. 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.

200. 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

2011

201. 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).

202. 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)

203. 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.

2010

204. 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

205. 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.

206. 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

207. 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.

208. 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.

209. 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.

210. 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:

2014

211. 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.

212. 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.

2013

213. 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).

2012

214. 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.

215. 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.

216. 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

217. 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.

2011

218. 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

2010

219. 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).

Editorial:

2016

220. Arturo Casadevall, Stefano Bertuzzi, Michael J Buchmeier, Roger J Davis, Harold Drake, Ferric C Fang, Jack Gilbert, Barbara M Goldman, Michael J Imperiale, Philip Matsumura, Alexander J McAdam, Marcela F Pasetti, Rozanne M Sandri-Goldin, Thomas Silhavy, Louis

Rice, Jo-Anne H Young, Thomas Shenk. 2016. ASM Journals Eliminate Impact Factor Information from Journal Websites. mBio/mSystems/etc. DOI: 10.1128/mSystems.00088-16

221. Gilbert JA, Klyczek KK, Elliott SL. 2016. Introducing the JMBE Themed Issue on Scientific Citizenship. Journal of Microbiology and Biology Education. 17(1). DOI: http://dx.doi.org/10.1128/jmbe.v17i1.1114.

2015

222. Gilbert JA. 2015. mSystems: learning to love systems. mSystems 1(1):e00015-15. doi: 10.1128/mSystems.00015-15.

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.

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: 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.

8. 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.

9. Title:  Hospital Microbiome Project; Source:  Alfred P. Sloan Foundation; Total Award Amount: $856,900; Award Period: 11/01/12 – 10/31/15. Location of Project: University of Chicago. Persons-Months Per Year Calendar 1.2. Major Goals: To determine the influence of population demographics, how the demographic interfaces with a space, and the building materials used to create that space, on the community succession, and rate of colonization by potential pathogens in two hospitals.

Current:

(1) Title” Membrane biofouling and development of new membranes materials and structures. Source: Ben-Gurion University- Argonne National Laboratory- University of Chicago. Total Award Amount: $150,000. Award Period: 12/01/13-11/30/15. Location of Project: University of Chicago. Persons-Months Per Year: Calendar 0. Major Goals: To develop tools to evaluate and understand microbial community structure in biofilms formed on water treatnent membrane materials, as well as the functional interaction between these communities and the membrane surface.

(2) Title: Collaborative Research: Biogenic Methanogenesis and Biodegradation of Organic Matter in Coals. Source: NSF. Total Award Amount: $74,597. Award Period: 08/01/14-07/31/16. Location of Project: University of Chicago. Persons-Months Per Year: Calendar 0.30. Major Goals: To understand the substrates that sustain microbial transformations of organic matter in coal beds, the nature of involved chemical pathways, and the role of these processes in the generation of coalbed methane.

(3) Title: Dimensions US-China: Collaborative Research: How historical constraints, local adaptation, and species interactions shape biodiversity across an ancient floristic disjunction. Source: NSF. Total Award Amount: $399,376. Award Period: 01/01/15-12/31/19. Location of Project: University of Chicago. Persons-Months Per Year: Calendar 0.60. Major Goals: To explore biodiversity across spatial and temporal scales in the deciduous forests of eastern Asia and eastern North America to discover those factors that shape biodiversity through space and time.

(4) Title: Modeling Mechanisms of Microbial Succession in the Built Environment. Source: Alfred P. Sloan Foundation. Total Award Amount: $881,666. Award Period:  06/01/15 – 05/31/18. Location of Project: University of Chicago. Persons-Months Per Year: Calendar 1.2. Major Goals: To determine how different building surface materials, under variable temperature and humidity, influence microbial growth, evolution and survival, and to develop a mechanistic model that can predict the succession and metabolism of microbial communities on surfaces.

(5) (Gilbert, Co-PI). 08/15/13-09/30/19. 5%. Metropolitan Water Reclamation. $1.925M Cost. District of Greater Chicago Collaborative Research:  Chicago Area Waterway System Microbiome Research. The major goal of this project is to provide a more complete understanding of the role of different sources of microbial contributions to the Chicago Area Waterway System (CAWS).  The outcome of this project will guide actions and provide insights into the most effective remediation and management options to support primary contact recreation uses of the CAWS.

(6) (Gilbert, PI). 10/1/14-09/30/19. 20%. Marine Biological Laboratory. $168,792 Direct Cost. Joint Appointment with Marine Biological Laboratory. The goal of this project is to develop programs associated with the intersection between microbial ecology at Chicago and Argonne and the MBL. In addition, to work at expanding specific relationships, building funding initiatives, and developing collaborative projects.

(7) (Gilbert, Co-I). 04/01/15-03/31/20. 15%. NIH. $2.15M Annual Direct Cost. The Preterm Infant Microbiome:  Biological, Behavioral and Health Outcomes at 2 and 4 years of Age. The goal of this project is a prospective study of a cohort of VLBW infants initially studied in an R21 grant, with measures of human milk intake, milk immunobiology, fecal calprotectin levels and early health outcomes. Now we propose to study the microbiomes of these infants in the 6 weeks of preserved stool samples while they were admitted to the Neonatal Intensive Care Unit. We will follow these infants through 4 years of age, studying the succession of the microbiome, and the relationships of microbiome to early and later health outcomes.

(8) Title: Early Career Workshop on the Microbiology of the Built Environment. PI – Gilbert. Source: Alfred P. Sloan Foundation. Total Award Amount: $80,000. Award Period:

08/01/15-07/31/16. Location of Project: University of Chicago. Persons-Months Per Year. Calendar 0. Major Goals: To convene a workshop focused on the microbiology of the built environment for early career researchers.

(9) Title: A predictive knowledgebase linking microbial signatures to human lifestyle characteristics. PI – Gilbert. Source: National Institute of Justice. Total Award Amount: $563,735. Award Period: 01/01/16-12/31/17. Location of Project: University of Chicago. Person Months per Year: Calander 1.8. Main Goal: To develop a data base associated with microbial signatures left behind at crime scenes.

(10) Title: Building a Knowledgebase for the Enzymatic and Genetic Mechanisms Associated with Microbial Degradation of Nitrogen Moieties Associated with Crude Oil. PI – Gilbert. Source: ExxonMobil. Total Award Amount: $961,459. Award Period: 04/01/15-10/31/17. Location of Project: Argonne National Laboratory. Persons-Months Per Year: Calendar 0.6. Major Goal: To explore hydrocarbon metabolism in bacteria capable of consuming nitrogen.

Private Donations: Through the Earth Microbiome Project I have been responsible for raising $400,801 between 2/2013 and 12/2015.

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)

TEACHINGThe 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

2015-2015 BIOS 15123, “The Microbiome in Human and Environmental Health”. Spring Quarter, 20 lectures, no discussion session or laboratories, ~40 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.

2011-2015 Principle supervisor for Sean Gibbons, Biophysical program, University of Chicago. Currently Postdoctoral Researcher, MIT, USA

2012-2016 Principle supervisor for Simon Lax, Ecology and Evolution, University of Chicago. Still in program.

2014-2019 Principle supervisor for Cesar Cardona, Biophysical program, University of Chicago. Still in Program.

2014-2019 Principle supervisor for Alyson Yee, MD/PHD, University of Chicago. Still in Program

2014-2019 Principle supervisor for Thomas Kuntz, Chemistry, University of Chicago. Still in Program

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

Associate, Baylor College of Medicine, TX, USA.2011-2014 Iratxe Zarraonaindia (PhD University of the Basque Country, Spain). Currently

Assistant Professor, University of the Basque Country, Spain.2012-2014 Nicole Scott (Ph.D. University of Chicago). Currently working for Biota Inc.2013-2015 Kim Handley (Ph.D. University of California, Berkeley). Currently Assistant

Professor, University of Auckland, NZ.2013-2016 Chris Marshall (Ph.D. University of Southern Carolina). Currently Senior

Research Associate, University of Pittsburg, USA.2014 Naseer Sangwan (Ph.D. University of Delhi, India). Project to be completed in

July 2017.2015 Pamela Weisenhorn (Ph.D. University of Minnesota). Project to be completed in

Jan 2018.2015 Melissa Dsouza (Ph.D. University of Auckland). Project to be completed in

March 2018.2016 Beatriz Penalver (Ph.D. Northwestern University). Project to be completed in

December 2019.2016 Holly Lutz (Ph.D. Cornell University). Project to be completed in July 2019.

PRESENTATIONSI have given >50 Keynote lectures and >200 invited and offered talks, 10 television interviews, >40 radio interviews over the last 10 years, including: University of Dundee, Annual Distinguished Lecture, April 21st 2015 NIAID, HIV and the Microbiome, April 8th 2015 Joint Genome Institute Annual Meeting Keynote, March 25th 2015 Mayo Clinic Grand Rounds, Personalized Medicine, March 9th 2015 UIUC Microbiology Special Guest Lecture, March 5th 2015 Argonne Outloud Public Lecture, December 11th 2014 American College of Rheumatology, December 14th 2014 TGAC UEA, October 8th 2014 Next Generation Genomics Helsinki University, Sept 2014 Northwestern Invited Lecture – Endocrinology and the Microbiome, August 2014 EDAME Meeting Workshop, MSU, July 2014 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 5th 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 Science

2011 – 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 Reports2015 – Founding Editor in Chief of mSystems (ASM journal).Various – 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:

Home Microbiome ProjectWashington Post http://www.washingtonpost.com/news/speaking-of-science/wp/2014/08/28/cops-could-use-bacterial-signatures-to-catch-a-murderer/Science Podcast http://www.sciencemag.org/content/345/6200/1048Newsweek http://www.newsweek.com/human-microbes-quickly-colonize-peoples-surroundings-267344National geographic – Ed Yong http://phenomena.nationalgeographic.com/2014/08/28/we-constantly-imprint-our-homes-with-our-microbes/Time http://time.com/3209387/house-germs-microbes/New Scientist http://www.newscientist.com/article/dn26119-moving-home-your-microbes-will-make-the-trip-too.html#.VABrtXRwY5sABC NEWS http://abcnews.go.com/Health/wireStory/shades-pigpen-travel-germs-25163736http://www.newsweek.com/human-microbes-quickly-colonize-peoples-surroundings-267344http://www.startribune.com/lifestyle/health/273064171.htmlhttp://www.wsvn.com/story/26396463/shades-of-pigpen-we-travel-with-our-own-germshttp://phenomena.nationalgeographic.com/2014/08/28/we-constantly-imprint-our-homes-with-our-microbes/http://www.washingtonpost.com/news/speaking-of-science/wp/2014/08/28/cops-could-use-bacterial-signatures-to-catch-a-murderer/http://www.sfgate.com/news/medical/article/Shades-of-Pigpen-We-travel-with-our-own-germs-5718814.phphttp://www.chron.com/health/article/Shades-of-Pigpen-We-travel-with-our-own-germs-

5718814.php

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