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Jack Gilbert

Title(s)Professor, Pediatrics
SchoolHealth Sciences
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. Quantifying and Understanding Well-to-Well Contamination in Microbiome Research. mSystems. 2019 Jun 25; 4(4). PMID: 31239396.
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    2. Gupta N, Skinner KA, Summers ZM, Edirisinghe JN, Faria JP, Marshall CW, Sharma A, Gottel NR, Gilbert JA, Henry CS, O'Loughlin EJ. Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium. Microbiol Resour Announc. 2019 Jun 20; 8(25). PMID: 31221646.
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    3. Richardson M, Gottel N, Gilbert JA, Gordon J, Gandhi P, Reboulet R, Hampton-Marcell JT. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area. Microbiome. 2019 Jun 03; 7(1):82. PMID: 31159879.
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    4. Gilbert JA, Lynch SV. Community ecology as a framework for human microbiome research. Nat Med. 2019 06; 25(6):884-889. PMID: 31133693.
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    5. Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R. Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. Biotechniques. 2019 May 24. PMID: 31124709.
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    6. Dodiya HB, Kuntz T, Shaik SM, Baufeld C, Leibowitz J, Zhang X, Gottel N, Zhang X, Butovsky O, Gilbert JA, Sisodia SS. Sex-specific effects of microbiome perturbations on cerebral Aß amyloidosis and microglia phenotypes. J Exp Med. 2019 Jul 01; 216(7):1542-1560. PMID: 31097468.
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    7. Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems. 2019 May 14; 4(4). PMID: 31120031.
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    8. Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA, Mark Welch JL. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems. 2019 Jul-Aug; 4(4). PMID: 31098396.
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    9. Hu J, Ben Maamar S, Glawe AJ, Gottel N, Gilbert JA, Hartmann EM. Impacts of indoor surface finishes on bacterial viability. Indoor Air. 2019 Jul; 29(4):551-562. PMID: 30980566.
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    10. Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. Early-Career Scientists Shaping the World. mSystems. 2019 May 07; 4(3). PMID: 31219787.
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    11. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. PMID: 31048484.
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    12. Sharma A, Richardson M, Cralle L, Stamper CE, Maestre JP, Stearns-Yoder KA, Postolache TT, Bates KL, Kinney KA, Brenner LA, Lowry CA, Gilbert JA, Hoisington AJ. Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets. Microbiome. 2019 May 02; 7(1):70. PMID: 31046835.
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    13. Lax S, Cardona C, Zhao D, Winton VJ, Goodney G, Gao P, Gottel N, Hartmann EM, Henry C, Thomas PM, Kelley ST, Stephens B, Gilbert JA. Microbial and metabolic succession on common building materials under high humidity conditions. Nat Commun. 2019 04 16; 10(1):1767. PMID: 30992445.
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    14. Sharma A, Buschmann MM, Gilbert JA. Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response? Clin Pharmacol Ther. 2019 Apr 02. PMID: 30937887.
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    15. Urbaniak C, van Dam P, Zaborin A, Zaborina O, Gilbert JA, Torok T, Wang CCC, Venkateswaran K. Genomic Characterization and Virulence Potential of Two Fusarium oxysporum Isolates Cultured from the International Space Station. mSystems. 2019 Mar-Apr; 4(2). PMID: 30944876.
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    16. Yee AL, Miller E, Dishaw LJ, Gordon JM, Ji M, Dutra S, Ho TTB, Gilbert JA, Groer M. Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants. mSystems. 2019 Jan-Feb; 4(1). PMID: 30834328.
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    17. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. PMID: 30679363.
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    18. Sharma A, Schmidt M, Kiesel B, Mahato NK, Cralle L, Singh Y, Richnow HH, Gilbert JA, Arnold W, Lal R. Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes. Front Microbiol. 2018; 9:3095. PMID: 30619174.
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    19. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K. GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019 Mar; 4(3):396-403. PMID: 30531975.
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    20. Navarro G, Sharma A, Dugas LR, Forrester T, Gilbert JA, Layden BT. Gut microbial features can predict host phenotype response to protein deficiency. Physiol Rep. 2018 Dec; 6(23):e13932. PMID: 30516001.
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    21. Dugas LR, Bernabé BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X, Dong Q, Sun J, Kliethermes S, Gottel N, Luke A, Gilbert JA, Layden BT. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Sci Rep. 2018 Nov 20; 8(1):17135. PMID: 30459320.
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    22. Gilbert JA, Stephens B. Microbiology of the built environment. Nat Rev Microbiol. 2018 Nov; 16(11):661-670. PMID: 30127345.
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    23. Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H. Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. mSystems. 2018 Sep-Oct; 3(5). PMID: 30374458.
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    24. Li HY, Wang H, Wang HT, Xin PY, Xu XH, Ma Y, Liu WP, Teng CY, Jiang CL, Lou LP, Arnold W, Cralle L, Zhu YG, Chu JF, Gilbert JA, Zhang ZJ. The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome. 2018 10 19; 6(1):187. PMID: 30340631.
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    25. Bello MGD, Knight R, Gilbert JA, Blaser MJ. Preserving microbial diversity. Science. 2018 Oct 05; 362(6410):33-34. PMID: 30287652.
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    26. Ho TTB, Groer MW, Kane B, Yee AL, Torres BA, Gilbert JA, Maheshwari A. Dichotomous development of the gut microbiome in preterm infants. Microbiome. 2018 09 12; 6(1):157. PMID: 30208950.
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    27. Sharma A, Gilbert JA. Microbial exposure and human health. Curr Opin Microbiol. 2018 08; 44:79-87. PMID: 30195150.
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    28. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 07 06; 36(7):660. PMID: 29979671.
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    29. Kayani MUR, Doyle SM, Sangwan N, Wang G, Gilbert JA, Christner BC, Zhu TF. Metagenomic analysis of basal ice from an Alaskan glacier. Microbiome. 2018 07 05; 6(1):123. PMID: 29976249.
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    30. Cardona C, Lax S, Larsen P, Stephens B, Hampton-Marcell J, Edwardson CF, Henry C, Van Bonn B, Gilbert JA. Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics. mSystems. 2018 May-Jun; 3(3). PMID: 29854953.
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    31. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). PMID: 29795809.
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    32. Gilbert JA, Jansson JK, Knight R. Earth Microbiome Project and Global Systems Biology. mSystems. 2018 May-Jun; 3(3). PMID: 29657969.
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    33. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018 Apr 10; 24(4):392-400. PMID: 29634682.
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    34. Gilbert JA. Early-Career Systems Microbiology Scientists. mSystems. 2018 Mar-Apr; 3(2). PMID: 29556547.
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    35. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. Correction: A microbial survey of the International Space Station (ISS). PeerJ. 2018; 5. PMID: 29498380.
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    36. Peñalver Bernabé B, Cralle L, Gilbert JA. Systems biology of the human microbiome. Curr Opin Biotechnol. 2018 06; 51:146-153. PMID: 29453029.
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    37. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2018 02 06; 36(2):196. PMID: 29406516.
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    38. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA. A microbial survey of the International Space Station (ISS). PeerJ. 2017; 5:e4029. PMID: 29492330.
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    39. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, 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. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. 2017 11 23; 551(7681):457-463. PMID: 29088705.
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    40. Griffin JS, Lu N, Sangwan N, Li A, Dsouza M, Stumpf AJ, Sevilla T, Culotti A, Keefer LL, Kelly JJ, Gilbert JA, Wells GF, Packman AI. Microbial diversity in an intensively managed landscape is structured by landscape connectivity. FEMS Microbiol Ecol. 2017 10 01; 93(10). PMID: 28961974.
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    41. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 08; 35(8):725-731. PMID: 28787424.
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    42. Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. ISME J. 2017 11; 11(11):2569-2583. PMID: 28777379.
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    43. Noronha MF, Lacerda Júnior GV, Gilbert JA, de Oliveira VM. Taxonomic and functional patterns across soil microbial communities of global biomes. Sci Total Environ. 2017 Dec 31; 609:1064-1074. PMID: 28787780.
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    44. Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD. Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes". mSphere. 2017 Jul-Aug; 2(4). PMID: 28744483.
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    45. Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. mSphere. 2017 May-Jun; 2(3). PMID: 28680968.
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    46. Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, Knight R, Gilbert JA, Quade J, Caporaso JG, Maier RM. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems. 2017 May-Jun; 2(3). PMID: 28593197.
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    47. Schaeffer JW, Reynolds S, Magzamen S, VanDyke A, Gottel NR, Gilbert JA, Owens SM, Hampton-Marcell JT, Volckens J. Size, Composition, and Source Profiles of Inhalable Bioaerosols from Colorado Dairies. Environ Sci Technol. 2017 Jun 06; 51(11):6430-6440. PMID: 28492313.
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    48. Lax S, Sangwan N, Smith D, Larsen P, Handley KM, Richardson M, Guyton K, Krezalek M, Shogan BD, Defazio J, Flemming I, Shakhsheer B, Weber S, Landon E, Garcia-Houchins S, Siegel J, Alverdy J, Knight R, Stephens B, Gilbert JA. Bacterial colonization and succession in a newly opened hospital. Sci Transl Med. 2017 05 24; 9(391). PMID: 28539477.
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    49. Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad MN, Negi RK, Singh Y, Khurana JP, Gilbert JA, Lal R. Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium. mSystems. 2017 May-Jun; 2(3). PMID: 28567447.
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    50. Wu L, Yang Y, Wang S, Yue H, Lin Q, Hu Y, He Z, Van Nostrand JD, Hale L, Li X, Gilbert JA, Zhou J. Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling. ISME J. 2017 09; 11(9):2102-2111. PMID: 28534876.
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    51. Franco-Obregón A, Gilbert JA. The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals. mSystems. 2017 May-Jun; 2(3). PMID: 28497122.
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    52. Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R. Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort". mSystems. 2017 Mar-Apr; 2(2). PMID: 28428981.
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    53. Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA. Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. mSystems. 2017 Mar-Apr; 2(2). PMID: 28289729.
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    54. Hampton-Marcell JT, Lopez JV, Gilbert JA. The human microbiome: an emerging tool in forensics. Microb Biotechnol. 2017 03; 10(2):228-230. PMID: 28244273.
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    55. Ma B, Dai Z, Wang H, Dsouza M, Liu X, He Y, Wu J, Rodrigues JL, Gilbert JA, Brookes PC, Xu J. Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China. mSystems. 2017 Jan-Feb; 2(1). PMID: 28191504.
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    56. Jackrel SL, Owens SM, Gilbert JA, Pfister CA. Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery. Mol Ecol Resour. 2017 Sep; 17(5):931-942. PMID: 27997751.
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    57. Gibbons SM, Scholz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML. Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System. MBio. 2016 12 20; 7(6). PMID: 27999158.
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    58. Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'. Nat Microbiol. 2016 Oct 31; 2:16198. PMID: 27798560.
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    59. Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R. Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort. mSystems. 2016 Sep-Oct; 1(5). PMID: 27822557.
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    60. Sun R, Dsouza M, Gilbert JA, Guo X, Wang D, Guo Z, Ni Y, Chu H. Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter. Environ Microbiol. 2016 12; 18(12):5137-5150. PMID: 27581342.
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    61. Hyde ER, Navas-Molina JA, Song SJ, Kueneman JG, Ackermann G, Cardona C, Humphrey G, Boyer D, Weaver T, Mendelson JR, McKenzie VJ, Gilbert JA, Knight R. The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems. 2016 Jul-Aug; 1(4). PMID: 27822543.
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    62. Wang H, Sangwan N, Li HY, Su JQ, Oyang WY, Zhang ZJ, Gilbert JA, Zhu YG, Ping F, Zhang HL. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome. ISME J. 2017 01; 11(1):100-111. PMID: 27458785.
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    63. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016 07 07; 535(7610):94-103. PMID: 27383984.
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    64. Sangwan N, Zarraonaindia I, Hampton-Marcell JT, Ssegane H, Eshoo TW, Rijal G, Negri MC, Gilbert JA. Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations. mSystems. 2016 May-Jun; 1(3). PMID: 27822527.
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    65. Sharma A, Gilbert JA, Lal R. (Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans. Sci Rep. 2016 05 06; 6:25527. PMID: 27151933.
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    66. Cardona C, Weisenhorn P, Henry C, Gilbert JA. Network-based metabolic analysis and microbial community modeling. Curr Opin Microbiol. 2016 06; 31:124-131. PMID: 27060776.
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    67. O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol. 2016 06; 18(6):2039-51. PMID: 26914164.
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    68. Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 2016 Mar 08; 4:8. PMID: 26951112.
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    69. Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, Brookes PC, Xu J, Gilbert JA. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016 08; 10(8):1891-901. PMID: 26771927.
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    70. Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J, Gilbert JA. A simple novel device for air sampling by electrokinetic capture. Microbiome. 2015 Dec 27; 3:79. PMID: 26715467.
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    71. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser 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 GC, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS Nano. 2016 Jan 26; 10(1):6-37. PMID: 26695070.
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    72. Gilbert JA. mSystems: Learning To Love Systems. mSystems. 2016 Jan-Feb; 1(1). PMID: 27822517.
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    73. Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems. 2016 Jan-Feb; 1(1). PMID: 27822518.
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    74. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016 Jan 08; 351(6269):158-62. PMID: 26657285.
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    75. Denner DR, Sangwan N, Becker JB, Hogarth DK, Oldham J, Castillo J, Sperling AI, Solway J, Naureckas ET, Gilbert JA, White SR. Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways. J Allergy Clin Immunol. 2016 05; 137(5):1398-1405.e3. PMID: 26627545.
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    76. Gibbons SM, Gilbert JA. Microbial diversity--exploration of natural ecosystems and microbiomes. Curr Opin Genet Dev. 2015 Dec; 35:66-72. PMID: 26598941.
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    77. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science. 2015 Oct 30; 350(6260):507-8. PMID: 26511287.
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    78. Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA, Nagler CR. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J. 2016 Mar; 10(3):742-50. PMID: 26394008.
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    79. Fuller M, Priyadarshini M, Gibbons SM, Angueira AR, Brodsky M, Hayes MG, Kovatcheva-Datchary P, Bäckhed F, Gilbert JA, Lowe WL, Layden BT. The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis. Am J Physiol Endocrinol Metab. 2015 Nov 15; 309(10):E840-51. PMID: 26394664.
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    80. Perisin M, Vetter M, Gilbert JA, Bergelson J. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME J. 2016 Apr; 10(4):1020-4. PMID: 26359911.
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    81. Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. Environ Microbiol Rep. 2015 Dec; 7(6):812-23. PMID: 25953741.
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    82. Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO. The ocean sampling day consortium. Gigascience. 2015; 4:27. PMID: 26097697.
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    83. Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT. Athletic equipment microbiota are shaped by interactions with human skin. Microbiome. 2015; 3:25. PMID: 26113975.
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    84. Berni Canani R, Gilbert JA, Nagler CR. The role of the commensal microbiota in the regulation of tolerance to dietary allergens. Curr Opin Allergy Clin Immunol. 2015 Jun; 15(3):243-9. PMID: 25827065.
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    85. Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. Forensic analysis of the microbiome of phones and shoes. Microbiome. 2015; 3:21. PMID: 25969737; PMCID: PMC4427962.
    86. Lax S, Gilbert JA. Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med. 2015 Jul; 21(7):427-32. PMID: 25907678.
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    87. Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe. 2015 May 13; 17(5):681-9. PMID: 25891358.
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    88. 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. The soil microbiome influences grapevine-associated microbiota. MBio. 2015 Mar 24; 6(2). PMID: 25805735.
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    89. McDonald D, Hornig M, Lozupone C, Debelius J, Gilbert JA, Knight R. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microb Ecol Health Dis. 2015; 26:26555. PMID: 25758371.
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    90. Lax S, Nagler CR, Gilbert JA. Our interface with the built environment: immunity and the indoor microbiota. Trends Immunol. 2015 Mar; 36(3):121-3. PMID: 25754179.
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    91. Yue H, Wang M, Wang S, Gilbert JA, Sun X, Wu L, Lin Q, Hu Y, Li X, He Z, Zhou J, Yang Y. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME J. 2015 Sep; 9(9):2012-20. PMID: 25689025.
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    92. Shade A, Gilbert JA. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends Microbiol. 2015 Jun; 23(6):335-40. PMID: 25667105.
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    93. Vitaglione P, Mennella I, Ferracane R, Rivellese AA, Giacco R, Ercolini D, Gibbons SM, La Storia A, Gilbert JA, Jonnalagadda S, Thielecke F, Gallo MA, Scalfi L, Fogliano V. 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. Am J Clin Nutr. 2015 Feb; 101(2):251-61. PMID: 25646321.
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    94. Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R. Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics. 2014 Nov 23; 15:1014. PMID: 25418849.
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    95. Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. Ecological succession and viability of human-associated microbiota on restroom surfaces. Appl Environ Microbiol. 2015 Jan; 81(2):765-73. PMID: 25398865.
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    96. Pfister CA, Gilbert JA, Gibbons SM. The role of macrobiota in structuring microbial communities along rocky shores. PeerJ. 2014; 2:e631. PMID: 25337459.
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    97. Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. Development of the preterm infant gut microbiome: a research priority. Microbiome. 2014; 2:38. PMID: 25332768.
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    98. Rubin BE, Sanders JG, Hampton-Marcell J, Owens SM, Gilbert JA, Moreau CS. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. Microbiologyopen. 2014 Dec; 3(6):910-21. PMID: 25257543; PMCID: PMC4263514.
    99. Shogan BD, Smith DP, Christley S, Gilbert JA, Zaborina O, Alverdy JC. Intestinal anastomotic injury alters spatially defined microbiome composition and function. Microbiome. 2014; 2:35. PMID: 25250176.
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    100. 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. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014 Aug 29; 345(6200):1048-52. PMID: 25170151.
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    101. Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014 Aug 22; 12:69. PMID: 25184604.
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    102. 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 HW, Knight R, Caporaso JG. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014; 2:e545. PMID: 25177538.
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    103. Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, Gilbert JA. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME J. 2015 Jan; 9(1):166-79. PMID: 25072414.
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    104. Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio. 2014 Jul 15; 5(4):e01371-14. PMID: 25028427.
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    105. 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, Knight R. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol. 2014; 5:298. PMID: 24995004.
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    106. Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA, Hartsel JA, Hartsel J, Kennedy SJ, Gibbons SM. Understanding cultivar-specificity and soil determinants of the cannabis microbiome. PLoS One. 2014; 9(6):e99641. PMID: 24932479.
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    107. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA. Human and environmental impacts on river sediment microbial communities. PLoS One. 2014; 9(5):e97435. PMID: 24841417.
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    108. Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE, Banfield JF. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environ Microbiol. 2015 Mar; 17(3):622-36. PMID: 24674078.
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    109. Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B, Melillo D, Mueller MG, Natale L, Zucchetti I, De Santis R, Pinto MR, Litman GW, Gilbert JA. The gut of geographically disparate Ciona intestinalis harbors a core microbiota. PLoS One. 2014; 9(4):e93386. PMID: 24695540.
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    110. Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Front Microbiol. 2014; 5:108. PMID: 24723913.
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    111. Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen E, Mackey KR, DeLong EF. Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013). Stand Genomic Sci. 2014 Jun 15; 9(3):1252-8. PMID: 25197495.
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    112. Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, Gilbert JA, Chu H. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiol Ecol. 2014 Aug; 89(2):281-92. PMID: 24476229.
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    113. Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G. Genomic standards consortium projects. Stand Genomic Sci. 2014 Jun 15; 9(3):599-601. PMID: 25197446; PMCID: PMC4148985.
    114. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 2014 Jul; 8(7):1464-75. PMID: 24451203; PMCID: PMC4069396.
    115. Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D. Saliva from obese individuals suppresses the release of aroma compounds from wine. PLoS One. 2014; 9(1):e85611. PMID: 24465618.
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    116. Hawley ER, Piao H, Scott NM, Malfatti S, Pagani I, Huntemann M, Chen A, Glavina Del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD, Hess M. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci. 2014 Jun 15; 9(3):1259-74. PMID: 25197496; PMCID: PMC4149020.
    117. Gilbert JA, Krajmalnik-Brown R, Porazinska DL, Weiss SJ, Knight R. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell. 2013 Dec 19; 155(7):1446-8. PMID: 24360269.
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    118. Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. Environ Microbiol Rep. 2014 Feb; 6(1):113-21. PMID: 24596269.
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    119. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013 Nov 01; 342(6158):621-4. PMID: 24179225.
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    120. Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Khurana JP, Gilbert JA, Lal R. Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data. ISME J. 2014 Feb; 8(2):398-408. PMID: 24030592.
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    121. Laverock B, Kitidis V, Tait K, Gilbert JA, Osborn AM, Widdicombe S. Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1627):20120441. PMID: 23980243.
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    122. Rubin BE, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA. Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS One. 2013; 8(7):e70460. PMID: 23936206.
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    123. Choudhari S, Smith S, Owens S, Gilbert JA, Shain DH, Dial RJ, Grigoriev A. Metagenome sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska. Genome Announc. 2013 Mar 21; 1(2):e0009913. PMID: 23516217.
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    124. Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA. Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A. 2013 Mar 19; 110(12):4651-5. PMID: 23487761.
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    125. Kelley ST, Gilbert JA. Studying the microbiology of the indoor environment. Genome Biol. 2013 Feb 28; 14(2):202. PMID: 23514020.
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    126. Hampton-Marcell JT, Moormann SM, Owens SM, Gilbert JA. Preparation and metatranscriptomic analyses of host-microbe systems. Methods Enzymol. 2013; 531:169-85. PMID: 24060121.
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    127. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21390-5. PMID: 23236140.
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    128. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Anand S, Malhotra J, Jindal S, Nigam A, Lal 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. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS One. 2012; 7(9):e46219. PMID: 23029440.
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    129. Robbins RJ, 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 EÓ, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J. RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. Stand Genomic Sci. 2012 Oct 10; 7(1):159-65. PMID: 23451294.
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    130. Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, Bicak M, Rocca-Serra P, Assunta-Sansone S, Willis K, Field D. A call for an international network of genomic observatories (GOs). Gigascience. 2012 Jul 12; 1(1):5. PMID: 23587188.
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    131. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012 Jun 07; 30(6):513-20. PMID: 22678395.
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    132. Larsen PE, Gibbons SM, Gilbert JA. Modeling microbial community structure and functional diversity across time and space. FEMS Microbiol Lett. 2012 Jul; 332(2):91-8. PMID: 22553907.
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    133. Gilbert JA, Bao Y, Wang H, Sansone SA, Edmunds SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith DP, Mizrachi I, Moreau C. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Stand Genomic Sci. 2012 May 25; 6(2):276-86. PMID: 22768370.
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    134. Larsen PE, Field D, Gilbert JA. Predicting bacterial community assemblages using an artificial neural network approach. Nat Methods. 2012 Apr 15; 9(6):621-5. PMID: 22504588.
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    135. 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. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012 Aug; 6(8):1621-4. PMID: 22402401.
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    136. Gilbert JA, Catlett C, Desai N, Knight R, White O, Robbins R, Sankaran R, Sansone SA, Field D, Meyer F. Conceptualizing a Genomics Software Institute (GSI). Stand Genomic Sci. 2012 Mar 19; 6(1):136-44. PMID: 22675605.
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    137. Amaro F, Gilbert JA, Owens S, Trimble W, Shuman HA. Whole-genome sequence of the human pathogen Legionella pneumophila serogroup 12 strain 570-CO-H. J Bacteriol. 2012 Mar; 194(6):1613-4. PMID: 22374950.
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    138. O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F. Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010. Stand Genomic Sci. 2011 Nov 30; 5(2):198-202. PMID: 22180822.
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    139. Caporaso JG, Paszkiewicz K, Field D, Knight R, Gilbert JA. The Western English Channel contains a persistent microbial seed bank. ISME J. 2012 Jun; 6(6):1089-93. PMID: 22071345.
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    140. Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D. Defining seasonal marine microbial community dynamics. ISME J. 2012 Feb; 6(2):298-308. PMID: 21850055.
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    141. Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp. 2011 Jun 14; 1(1):4. PMID: 22587810.
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    142. Jansson JK, Neufeld JD, Moran MA, Gilbert JA. Omics for understanding microbial functional dynamics. Environ Microbiol. 2012 Jan; 14(1):1-3. PMID: 21651688.
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    143. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D. The genomic standards consortium: bringing standards to life for microbial ecology. ISME J. 2011 Oct; 5(10):1565-7. PMID: 21472015.
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    144. Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottmann R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O, Wooley J. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Stand Genomic Sci. 2010 Dec 25; 3(3):225-31. PMID: 21304723; PMCID: PMC3035307.
    145. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010 Dec 25; 3(3):249-53. PMID: 21304728; PMCID: PMC3035312.
    146. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010 Dec 25; 3(3):243-8. PMID: 21304727; PMCID: PMC3035311.
    147. Gilbert JA, Meyer F, Knight R, Field D, Kyrpides N, Yilmaz P, Wooley J. Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010. Stand Genomic Sci. 2010 Dec 15; 3(3):235-9. PMID: 21304725; PMCID: PMC3035306.
    148. Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, Somerfield PJ, Mühling M. The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS One. 2010 Nov 29; 5(11):e15545. PMID: 21124740.
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    149. Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM. Metagenomics: A foundling finds its feet. Stand Genomic Sci. 2010 Oct 27; 3(2):212-3. PMID: 21304751.
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    150. Gilbert JA, Meyer F, Schriml L, Joint IR, Mühling M, Field D. Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Stand Genomic Sci. 2010 Oct 27; 3(2):183-93. PMID: 21304748.
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    151. Heidelberg KB, Gilbert JA, Joint I. Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol. 2010 Sep; 3(5):531-43. PMID: 20953417.
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    152. Laverock B, Smith CJ, Tait K, Osborn AM, Widdicombe S, Gilbert JA. Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. ISME J. 2010 Dec; 4(12):1531-44. PMID: 20596074.
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    153. Mitra S, Gilbert JA, Field D, Huson DH. Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME J. 2010 Oct; 4(10):1236-42. PMID: 20428222.
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    154. Thomas S, Burdett H, Temperton B, Wick R, Snelling D, McGrath JW, Quinn JP, Munn C, Gilbert JA. Evidence for phosphonate usage in the coral holobiont. ISME J. 2010 Mar; 4(3):459-61. PMID: 19956272.
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    155. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield PJ, Huse S, Joint I. The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol. 2009 Dec; 11(12):3132-9. PMID: 19659500.
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    156. Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA. Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J. 2009 Jul; 3(7):792-6. PMID: 19340085.
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