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Jack A. Gilbert

Joint Appointment

Professor Gilbert is the Group Leader for Microbial Ecology at Argonne National Laboratory.


Professor Jack A Gilbert earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada. From 2005-2010 he was a senior scientist at Plymouth Marine Laboratory, UK; and from 2010-2018 he was a Professor of Surgery and Director of The Microbiome Center at University of Chicago.

In 2019 he moved to University of California San Diego, where he is a Professor in Pediatrics and the Scripps Institution of Oceanography. He is also Group Leader for Microbial Ecology at Argonne National Laboratory, and the Yeoh Ghim Seng Visiting Professorship in Surgery at the National University of Singapore.

Dr. Gilbert uses molecular analysis to test fundamental hypotheses in microbial ecology. He cofounded the Earth Microbiome Project and American Gut Project. He has authored more than 250 peer reviewed publications and book chapters on microbial ecology. He is the founding Editor in Chief of mSystems journal.

In 2014 he was recognized on Crain’s Business Chicago’s 40 Under 40 List, and in 2015 he was listed as one of the 50 most influential scientists by Business Insider, and in the Brilliant Ten by Popular Scientist. In 2016 he won the Altemeier Prize from the Surgical Infection Society, and the WH Pierce Prize from the Society for Applied Microbiology for research excellence. He also co-authored Dirt is Good” published in 2017, a popular science guide to the microbiome and children’s health.


To download free pdfs of each article see our personal site: http://​gilbert​lab​.com


1.     James S Griffin, Nanxi Lu, Naseer Sangwan, Angang Li, Melissa Dsouza, Andrew J Stumpf, Tiffany Sevilla, Alessandro Culotti, Laura L Keefer, John J Kelly, Jack A Gilbert, George F Wells, Aaron I Packman. 2017. Microbial diversity in an intensively managed landscape is structured by landscape connectivity. FEMS Microbiology Ecology; https://​doi​.org/​10​.​1093​/​f​e​m​s​e​c​/​f​ix120

2.     Thompson TR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Kopylova E, Vázquez-Baeza Y, Janssen S, Morton JT, Mirarab S, Zech Xu Z, Haroon MF, Kanbar J, Zhu Q, Gonzalez A, Song SJ, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey CJ, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK*, Gilbert JA*, Knight R*. 2017. The Earth Microbiome Project. Nature. In Press. *senior co-corresponding authors. DOI 10.1038/nature24621

3.     Marshall CW, Ross DE, Handley KM, Weisenhorn PB, Edirisinghe JN, Henry CS, Gilbert JA, May HD, Norman RS. 2017. Metabolic reconstruction and modeling microbial electrosynthesis. Scientific Reports. 7, 8391, doi:10.1038/s41598-017-08877-z

4.     Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, \Adam R Rivers, Emiley A Eloe-Fadrosh, Susannah G Tringe, Natalia N Ivanova, Alex Copeland, Alicia Clum, Eric D Becraft, Rex R Malmstrom, Bruce Birren, Mircea Podar, Peer Bork, George M Weinstock, George M Garrity,Frank O Glöckner, Jack A Gilbert, William C Nelson, Steven J Hallam, Sean P Jungbluth, Thijs J G Ettema, Scott Tighe, Konstantinos T Konstantinidis, Wen-Tso Liu, Brett J Baker, Thomas Rattei, Jonathan A Eisen, Brian Hedlund, Katherine D McMahon, Noah Fierer, Rob Knight, Rob Finn, Guy Cochrane, & Tanja Woyke. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35,725731

5.     Noronha MF, Junior GVL, Gilbert JA, de Oliviera VM. 2017. Taxonomic and functional patterns across soil microbial communities of global biomes. Science of the Total Environment. 609, 1064-1074.

6.     Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. 2017. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon Oil Spill. The ISME Journal.

7.     Kunkun Fan, Cesar Cardona, Yuntao Li, Yu Shi, Xingjia Xiang, Congcong Shen, Hongfei Wang, Jack A Gilbert, Haiyan Chu. 2017. Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. Soil Biology and Biochemistry. Volume 113, 275284

8.     Stephen A Wood, Jack A Gilbert, Jonathan W Leff, Noah Fierer, Heather D’Angelo, Carling Bateman, Seren M Gedallovich, Caitlyn M Gillikin, Mary R Gradoville, Patahayah Mansor, Audrey Massmann, Nina Yang, Benjamin L Turner, Francis Q Brearley, Krista L McGuire. 2017. Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure. Soil Biology and Biochemistry. 112. 258-268.

9.     Julia W. Neilson, Katy Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L. Josephson, Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, Raina M. Maier. 2017. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems J. DOI10.1128/mSystems.00195-16

10Linwei Wu, Yunfeng Yang, Shiping Wang, Haowei Yue, Qiaoyan Lin, Yigang Hu, Zhili He, Joy D Van Nostrand, Lauren Hale, Xiangzhen Li, Jack A Gilbert, Jizhong Zhou. 2017. Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling. ISME J. 10.1038/ismej.2017.7

11Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N Shakarad, Ram Krishan Negi, Yogendra Singh, JP Khurana, Jack A Gilbert, Rup Lal. 2017. Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium. mSystems. 2 (3); e00020-17

12Simon Lax, Naseer Sangwan, Daniel Smith, Peter Larsen, Kim M. Handley, Miles Richardson, Kristina Guyton, Monika Krezalek, Benjamin D. Shogan, Jennifer Defazio, Irma Flemming, Baddr Shakhsheer, Stephen Weber, Emily Landon, Sylvia Garcia-Houchins, Jeffrey Siegel, John Alverdy, Rob Knight, Brent Stephens, Jack A. Gilbert. 2017. Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine. Vol. 9, Issue 391, eaah6500. DOI: 10.1126/scitranslmed.aah6500

13John C Alverdy, Neil Hyman, Jack Gilbert, James N Luo, Monika Krezalek. 2017. Preparing the Bowel for Surgery: Learning from the Past and Planning for the Future. Journal of the American College of Surgeons. https://​doi​.org/​10​.​1016​/​j​.​j​a​m​c​o​l​l​s​u​r​g​.​2017​.​05.005

14Joshua Schaeffer, Stephen J. Reynolds, Sheryl Magzamen, Amanda VanDyke, Neil Gottel, Jack Gilbert, Sarah Owens, Jarrad T. Hampton-Marcell, and John Volckens. 2017. Size, Composition, and Source Profiles of Inhalable Bioaerosols from Colorado Dairies. Environ. Sci. Technol. DOI10.1021/acs.est.7b00882

15Alfredo Franco-Obregón, Jack A. Gilbert. 2017. The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals. mSystems. DOI10.1128/mSystems.00018-17

16JN Luo, J Gilbert, O Zaborina, JC Alverdy. 2017. Optimum Operating Room Environment for the Prevention of Surgical Site Infections. Surgical Infections. doi:10.1089/sur.2017.020.

17Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter. 2017. Celebrating Parasites. Nature Genetics. 49 (4). 483-484.

18Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA. 2017. Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. mSystems. https://​doi​.org/​10​.​1128​/​m​S​y​s​t​e​m​s​.​00178-16

19Highfield A, Joint I, Gilbert JA, Crawfurd KJ, Schroeder DC. 2017. Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment. Viruses, 9, 41; doi:10.3390/v9030041

20Hampton-Marcell JT, Lopez JV, Gilbert JA. 2017. The human microbiome: an emerging tool in forensics. Microbial Biotechnology. 10 (2) 228-230.

21Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge LM Rodrigues, Jack A Gilbert, Philip C Brookes, Jianming Xu. 2017. Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China. mSystems. DOI10.1128/mSystems.00174-16

22Thomas M Kuntz, Jack A Gilbert. 2017. Introducing the Microbiome into Precision Medicine. Trends in Pharmacological Sciences. http://​dx​.doi​.org/​10​.​1016​/​j​.​t​i​p​s​.​2016​.​10.001

23Alverdy JC, Hyoju SK, Weigerinck M, JA Gilbert. 2017. The gut microbiome and the mechanism of surgical infection. British Journal of Surgery. DOI10.1002/bjs.10405.

24Hang 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. 2017. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome. ISME J. doi:10.1038/ismej.2016.103


1.     Jackrel SL, Owens SM, Gilbert JA, Pfister CA. 2016. Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12645

2.     Gibbons SM, Scholtz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML. 2016. Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System. mBio. doi: 10.1128/mBio.01372-16

3.     Brewer T, Handley KM, Carini P, Gilbert JA, Fierer N. 2016. Genome reduction in an abundant and ubiquitous soil bacterium Candidatus Udaeobacter copiosus’. Nature Microbiology 2;16198. doi:10.1038/nmicrobiol.2016.198

4.     Jack A Gilbert. 2016. How do we make indoor environments and healthcare settings healthier? Microbial Biotechnology. DOI: 10.1111/1751-7915.12430

5.     Nathaniel Charles Wardrip, Melissa Dsouza, Meltem Urgun-Demirtas, Seth W Snyder, Jack A. Gilbert, and Christopher J. Arnusch. 2016. Printing-Assisted Surface Modifications of Patterned Ultrafiltration Membranes. ACS Appl. Mater. Interfaces. DOI: 10.1021/acsami.6b11331

6.     Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R. 2016. Migraines are correlated with higher levels of nitrate-, nitrite-, and nitric oxide-reducing oral microbes in the American Gut Project Cohort. mSystems 1(5):e00105-16. doi:10.1128/mSystems.00105-16.

7.     Samantha B Joye, Sara Kleindienst, Jack A Gilbert, Kim M Handley, Pamela Weisenhorn, Will A Overholt, Joel E Kostka. 2016. Responses of microbial communities to hydrocarbon exposures. Oceanography. 29(3): 136-149.

8.     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​.​b​u​i​l​d​e​n​v​.​2016​.​09.001

9.     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.

10Embriette 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. 1; 4 e00046-16

11Stein 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

12Yee A & Gilbert JA. 2016. Is Triclosan Harming Your Microbiome? Science, 353, (6297), 348-349.

13Vipin 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

14Gilbert 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, 94103 doi:10.1038/nature18850

15Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FS-M, Medeiros JD, Assis Geraldo J, Gilbert JA, Volpini AC, Rocha Fernandes G. (2016) ZIKVCDB: 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

16Torsten 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.

17Hu 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.

18Kuntz T, Gilbert JA. 2016. Does the Brain Listen to the Gut? eLife. 5: e17052.

19Sangwan 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

20Sharma A, Gilbert JA, Lal R. 2016. (Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans. Scientific Reports. 6; 25527.

21Cardona C, Weisenhorn P, Henry C, Gilbert JA. 2016. Network-based metabolic analysis and microbial community modeling. Current Opinions in Microbiology. 31, 124-131.

22Sangwan 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

23De 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.

24O’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

25Ma 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

26Burstein 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

27Dugas LR, Fuller M, Gilbert JA, Layden BT. 2016. The obese gut microbiome across the epidemiologic transition. Emerging Themes in Epidemiology. 13 (1) 1.

28Gilbert 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.

29Metcalf 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


24Gordon 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

25Walters 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.

26Biteen 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

27Maya 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

28Teng 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

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

30Ying 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

31Alivisatos 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.

32Denner 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..

33Miles 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

34Berni 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

35Perisin 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

36Wang 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

37Karim 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

38Wood 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

39Burgsdorf 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.

40Van 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. DOI10.1002/zoo.21220

41Lin 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

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

43Lax 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

44Sangwan 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. DOI10.1111/1758-2229.12297

45Shogun 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

46Lax 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​.​m​o​l​m​e​d​.​2015​.​03.005

47Leone 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​.​c​h​o​m​.​2015​.​03.006

48Dedesko 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

49Canani 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.

50Gilbert JA. 2015. Metagenomics: Social behavior and the microbiome. eLife 2015;4:e07322

51Zarraonaindia 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.

52Daniel 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​/​m​e​h​d​.​v​26​.​26555

53Huang 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

54Lax 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​.​i​t​.​2015​.​01.001

55Gilbert JA and Henry C. 2015. Predicting ecosystem emergent properties at multiple scales. Environmental Microbiology. DOI10.1111/1758-2229.12258

56Ramos 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

57Stephen 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. DOI10.1111/1365-2664.12416

58Haowei 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

59Shade 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

60Amaro 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.

61Vitaglione 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

62Gibbons 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.

63Xiao-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.


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

65Helianthous 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

66Groer 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

67Pfister 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​/​p​e​e​r​j.631

68LaBelle 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

69Gilbert JA. 2014. Science is innate! Genome Biology. 15:477.

70Zaborin 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.

71Rubin 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. DOI10.1002/mbo3.216

72Shogan 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

73Lax 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

74Gilbert 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

75Kyrpides 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.

76Larsen 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

77Shade 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

78Winston 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

79Rideout 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​/​p​e​e​r​j.545

80Gibbons 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

81Nielsen 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

82Parfrey 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

83Kumar 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: 114. DOI: 10.3109/07388551.2014.899964

84Dishaw 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

85O’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.

86Scott 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

87Handley 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. DOI10.1111/1462-2920.12467

88Hamada 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

89Handley 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, DOI10.1111/1462-2920.12453.

90Xiong 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

91Piombino 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.

92Mason 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, 14641475; doi:10.1038/ismej.2013.254

93Peer 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.

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




95Gilbert 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.

96Gittel 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

97Fierer 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.

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

99Laverock 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. DOI10.1111/1758-2229.12115.

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 1931

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




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 9198,

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), 513520

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 (12) 1724.

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, 121126 (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, 10891093.

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.




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. 34:16-19

136.        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,

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.




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), 531543

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, 15311544.

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




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), 31323139

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




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: 712

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




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




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.




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.




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.




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:



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.




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.




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




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.




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:



185.        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.


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​.stan​dard​sin​ge​nomics​.com/​c​o​n​t​e​n​t​/​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​.stan​dard​sin​ge​nomics​.com/​c​o​n​t​e​n​t​/​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 45, 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.


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.


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): 276286.

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




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.




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 6th 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:




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.




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).




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.




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




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).





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​/​j​m​b​e​.​v​17​i​1​.1114.


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