PUBLICATIONS

Links to all Jack Gilbert’s Publications:
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POPULAR LITERATURE

2017

Jack A Gilbert, Rob Knight, Sandra Blakeslee. 2017. Dirt is Good. St Martins Press.

PATENTS

2021

  • United States Patent 10,934,596. Gilbert, JA, Catlett C, Beckman P. Automated microbial detection and quantification

2020

  • United States Patent Application Gilbert, JA, Van Der Lelie D, Taghavi S. Immune response modulation using live biotherapeutics, for conditions such as allergy desensitization.

2018

  • United States Patent Application 20180305772. Automated Microbial detection and quantification.

SCHOLARSHIP

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

2022

  1. Yan Z, Chen B, Yang Y, Yi X, Wei M, Ecklu-Mensah G, Buschmann MM, Liu H, Gao J, Liang W, Liu X, Yang J, Ma W, Liang Z, Wang F, Chen D, Wang L, Shi W, Stampfli MR, Li P, Gong S, Chen X, Shu W, El-Omar EM, Gilbert JA, Blaser MJ, Zhou H, Chen R, Wang Z. (2022). Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions. Nature Microbiology, 7:1361–1375. 22 Aug 2022. DOI: 10.1038/s41564-022-01196-8
  2. Björk JR, Dasari MR, Roche K, Grieneisen L, Gould TJ, Grenier J, Yotova V, Gottel N, Jansen D, Gesquiere LR, Gordon JB, Learn NH, Wango TL, Mututua RS, Warutere JK, Siodi L, Mukherjee S, Barreiro LB, Alberts SC, Gilbert JA, Tung J, Blekhman R, Archie EA. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nature Ecology & Evolution, 6:955–964. 02 June 2022. DOI: 10.1038/s41559-022-01773-4
  3. Reese TO, Bovet P, Choo-Kang C, Bedu-Addo K, Forrester T, Gilbert JA, Goedecke JH, Lambert EV, Layden BT, Micklesfield LK, Plange-Rhule J, Rae D, Viswanathan B, Luke A, Dugas LR. (2022). Utility of silhouette showcards to assess adiposity in three countries across the epidemiological transition. PLOS Global Public Health, 2(5):e000127. 19 May 2022. DOI: 10.1371/journal.pgph.0000127
  4. Kunselman E, Minich JJ, Horwith M, Gilbert JA, Allen EE. (2022). Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiology Spectrum, e01982-21. 10 May 2022. DOI: 10.1128/spectrum.01982-21
  5. Hu B, Das P, Lv X, Shi M, Aa J, Wang K, Duan L, Gilbert JA, Nie Y, Wu X-L. (2022). Effects of ‘Healthy’Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats. mSystems, e00218-22. 28 April 2022. DOI: 10.1128/msystems.00218-22
  6. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim H-C, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems, 7(2):e00167-22. 04 April 2022. DOI: 10.1128/msystems.00167-22
  7. Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song SJ, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, Leibel SL. The impact of maternal asthma on the preterm infants’ gut metabolome and microbiome (MAP study). Sci Rep 12, 6437 (2022). DOI: 10.1038/s41598-022-10276-y
  8. Kodera SM, Das P, Gilbert JA, Lutz HL. (2022) Conceptual strategies for characterizing interactions in microbial communities. iScience, 25(2), 103775. 18 Feb 2022. DOI: 10.1016/j.isci.2022.103775
  9. Priyadarshini M, Navarro G, Reiman DJ, Sharma A, Xu K, Lednovich K, Manzella CR, Khan W, Salas-Garcia M, Allard S, Wicksteed B, Chlipala GE, Szynal B, Bernabe BP, Maki PM, Gill RK, Perdew GH, Gilbert JA, Dai Y, Layden BT. (2022). Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2, 3-dioxygenase axis. Gastroenterology, online. 12 Jan 2022. DOI: 10.1053/j.gastro.2022.01.008
  10. Schulkers Escalante K, Bai-Tong SS, Thoemmes M, Weldon K, Hansen S, Motazavi D, Kitsen J, Song SJ, Gilbert JA, Dorrestein P, Knight R, Leibel S, Leibel SL. (2022). Evaluating the Effects of Breastfeeding Versus Bottle Feeding on the Preterm Infants’ Microbiome and Metabolome. J of Investigative Med, 70(1): 211-212.
  11. Ecklu-Mensah G, Gilbert JA, Devkota S. (2022). Dietary Selection Pressures and Their Impact on the Gut Cellular and Molecular Gastroenterology and Hepatology, 13(1):7-18. DOI: 10.1016/j.jcmgh.2021.07.009

2021

  1. Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah E, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. (2021) SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome,9(1): 1-15. 08 June 2021. DOI: 10.1186/s40168-021-01083-0
  2. Minch JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD.(2021). Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome, 9(1): 1- 13. 22 Jan 2021, DOI: 10.1186/s40168-020-00960-4
  3. Ni Y, Yang T, Ma Y, Zhang K, Soltis PS, Soltis DE, Gilbert JA, Zhao Y, Fu C, Chu H. (2021) Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China. Global Ecology and Biogeography, 30(11): 2164-2177. 16 August 2021. DOI: 10.1111/geb.13373
  4. Li HY, Wang H, Tao X, Wang X, Jin W, Gilbert JA, Zhu Y, Zhang Z. (2021). Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction. mSystems, 6(5): e01368. 21 Sept 2021. DOI: 10.1128/mSystems.01368-20
  5. Geynisman-Tan J, Kenton K, Tavathia M, Yee Al, Gilbert JA, Collins SA, Lewicky-Gaupp C, Mueller M. (2021) Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? Female Pelvic Medicine & Reconstructive Surgery, 27(9): 532-537. 01 Sept 2021. DOI: 10.1097/SPV.0000000000000968
  6. Kahn R, Lee AL, Gilbert JA, Haider A, Jamal SB, Muhammad F. (2021). Triclosan-containing sutures: safety and resistance issues need to be addressed prior to generalized use. Applied Nanoscience, 1 – 10. 9 Aug 2021. DOI: 10.1007/s13204-021-01979-1
  7. Geynisman-Tan J, Kenton K, Tavathia M, Yee A, Gilbert JA, Collins S, Lewicky-Gaupp C, Mueller M. (2021) Bare Versus Hair: Do Pubic Hair Grooming Pheritabilityreferences Dictate the Urogenital Microbiome? Female Pelvic Medicine & Reconstructive Surgery,27(9): 532-537. 1 Sept 2021. DOI: 10.1097/SPV.0000000000000968
  8. Ecklu-Mensah, Gilbert JA, Devkota, S. (2021). Dietary Selection Pressures and Their Impact on the Gut Microbiome. Cellular and Molecular Gastroenterology and Hepatology.9 Aug 2021. DOI: 10.1016/j.jcmgh.2021.07.009
  9. Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. 2021. Gut microbiome heritability is nearly universal but environmentally contingent. Science, 373(6551): 181-186. 09 July 2021. DOI: 10.1126/science.aba5483
  10. Lutz HL, Gilbert JA, Dick CW. 2021. Associations between Afrotropical bats, eukaryotic parasites, and microbial symbionts. Molecular Ecology, cover. 28 June 2021. DOI: 10.1111/mec.16044
  11. Martin A, Ecklu-Mensah G, Ha CWY, Hendrick G, Layman DK, Gilbert JA, Devkota S. 2021. Gut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice. Nature Communications, 12:3838. 22 June 2021. DOI: 10.1038/s41467-021-24074-z
  12. Swain TD, Lax S, Gilbert JA, Backman V, Marcelino LA. 2021. A Phylogeny-Informed Analysis of the Global Coral-Symbiodiniaceae Interaction Network Reveals that Traits Correlated with Thermal Bleaching Are Specific to Symbiont Transmission Mode. mSystems,6(3):e00266-21. 04 May 2021. DOI: 10.1128/mSystems.00266-21
  13. David MM, Tataru C, Daniels J, Schwartz J, Keating J, Hampton-Marcell J, Gottel N, Gilbert JA, Wall DP. 2021. Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes. mSystems, 6(2):e00193-20. 27 April 2021. DOI: 10.1128/mSystems.00193-20
  14. Yang K, Hou Y, Zhang Y, Liang H, Sharma A, Zheng W, Wang L, Torres R, Tatebe K, Chmura SJ, Pitroda SP, Gilbert JA, Fu Y, Weichselbaum RR. (2021). Suppression of local type I interferon by gut microbiota–derived butyrate impairs antitumor effects of ionizing radiation. J Exp Med, 218(3): e20201915. 26 Jan 2021. DOI: 10.1084/jem.20201915
  15. Xu Y, Tandon R, Ancheta C, Arroyo P, Gilbert JA, Stephens B, Kelly ST. (2021). Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions. Indoor Air, 31(1):188-205. Jan 2021. DOI: 10.1111/ina.12727

2020

  1. Salido RA, Morgan SC, Rojas MI, Magallanes CG, Marotz C, DeHoff P, Belda-Ferre P, Aigner S, Kado DM, Yeo GW, Gilbert JA, Laurent L, Rohwer F, Knight R. Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. mSystems, 5(6). 2020. DOI: 10.1128/mSystems.01074-20
  2. Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, Faust K, Knight R, Jansson JK, Cordona C, Rottjers L, Xu J. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome, 8:82-94. 2020. DOI: 10.1186/s40168-020-00857-2
  3. Qin N, Liang P, Wu C, Wang G, Xu Q, Xiong X, Wang T, Zolfo M, Segata N, Qin H, Knight R, Gilbert JA, Zhu TF. 2020. Longitudinal survey of microbiome associated with particulate matter in a megacity. Genome Biology; 21(1), 1-11. DOI: 10.1186/s13059-020-01964-x
  4. Zarraonaindia I, Martínez-Goñi XS, Liñero O, Muñoz-Colmenero M, Aguirre M, Abad D, Baroja-Careaga I, de Diego A, Gilbert JA, Estonba A. Response of Horticultural Soil Microbiota to Different Fertilization Practices. Plants, 9(11):1501. 2020. DOI: 10.3390/plants9111501
  5. Allard SM, Costa MT, Bulseco AN, Helfer V, Wilkins LGE, Hassenrück C, Zengler K, Zimmer M, Erazo N, Rodrigues JLM, Duke N, Melo VMM, Vanwonterghem I, Junca H, Makonde HM, Jiménez DJ, Tavares TCL, Fusi M, Daffonchio D, Duarte CM, Peixoto RS, Rosado AS, Gilbert JA, Bowman J. Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. mSystems, 5(5): e00658-20. 2020. DOI: 10.1128/mSystems.00658-20
  6. Hopper CP, De La Cruz LK, Lyles KV, Wareham LK, Gilbert JA, EichenbaumZ, Magierowski M, K Poole R, Wollborn J, Wang B. Role of Carbon Monoxide in Host–Gut Microbiome Communication. Chemical Reviews, Oct 22, 2020. DOI: 10.1021/acs.chemrev.0c00586
  7. Zhao D, Cardona C, Gottel N, Winton VJ, Thomas PM, Raba DA, Kelley ST, Henry C. Gilbert JA, Stephens B. 2020. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials. Scientific Reports, 10:14500. DOI:10.1038/s41598-020-71560-3
  8. 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 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987. Microbiology resource announcements, 9(34). Aug 2020. DOI: 10.1128/MRA.00748-20
  9. Alverdy JC, Gilbert JA, Hyman N. Surgical Site Infections Following Elective Surgery – Authors’ Reply. The Lancet Infectious Diseases, 20(8):899. DOI: 10.1016/S1473-3099(20)30564-8
  10. Skondra D, Rodriguez SH, Sharma A, Gilbert JA, Andrews B, Claud EC. The early gut microbiome could protect against severe retinopathy of prematurity. J of Am Assoc for Pediatric Opthamology and Stabismus, July 2020. DOI: 10.1016/j.jaapos.2020.03.010h
  11. Zaborin A, Bernabe BP, Keskey R, Sangwan N, Hyoju S, Gottel N, Gilbert JA, Zaborina O, Alverdy JC. Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics. mSystems, 5(3):e00377-20. May/June 2020. DOI: 10.1128/mSystems.00377-20
  12. Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ, 8:e9235. June 9, 2020.
  13. Hampton-Marcell JT, Larsen P, Anton T, Cralle L, Sangwan N, Lax S, Gottel N, Salas-Garcia M, Young C, Duncan G, Lopez JV, Gilbert JA. (2020). Detecting personal microbiota signatures at artificial crime scenes. Forensic Science International, 33:110351. Aug 2020. DOI: 10.1016/j.forsciint.2020.110351
  14. Polster SP, Sharma A, Tanes C, Tang AT, Mericko P, Cao Y, Carrion-Penagos J, Girard R, Koskimaki J, Zhang D, Stadnik A, Romanos SG, Lyne SB, Shenkar R, Yan K, Lee C, Akers A, Morrison L, Robinson M, Zafar A, Bittinger K, Kim H, Gilbert JA, Kahn ML, Shen L, Awad IA. (2020). Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma. Nature Communications, 11(1): 2659. May 27, 2020. DOI: 10.1038/s41467-020-16436-w
  15. Kim SM, DeFazio JR, Hyoju SK, Sangani K, Keskey R, Krezalek MA, Kodarev NN, Sangwan N, Christley S, Harris KG, Malik A, Zaborin A, Bouziat R, Ranoa DR, Wiegerink M, Ernest JD, Shakhsheer BA, Fleming ID, Weichsekbaum RR, Antonopoulos DA, Gilbert JA, Barreiro LB, Zaborina O, Jabri B, Alverdy JC. (2020). Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity. Nat Commun, 11:2354. May 11 2020. DOI: 10.1038/s41467-020-15545-w
  16. Christley S, Shogan B, Levine Z, Koo H, Guyton K, Owens S, Gilbert JA, Zaboina O, Alverdy JC. (2020). Comparative genetics of Enterococcus faecalisintestinal tissue isolates before and after surgery in a rat model of colon anastomosis. PLoS ONE, 15(4): e0232165. DOI: 10.1371/journal.pone.0232165
  17. Groer MW, Miller EM, D’Agata A, Ho TTB, Dutra SV, Yoo JY, Yee AL, Gilbert JA, Dishaw LJ. (2020). Contributors to Dysbiosis in Very-Low-Birth-Weight Infants. Journal of Obstetric, Gynecologic & Neonatal Nursing. Online 2 April 2020. DOI: 10.1016/j.jogn.2020.02.003
  18. Zurita MF, Cárdenas PA, Sandoval ME, Peña MC, Fornasini M, Flores N, Monaco MH, Berding K, Donovan SM, Kuntz T, Gilbert JA, Baldeón ME. (2019). Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador. Gut microbes, 11(3): 453-464. 2020. DOI: 10.1080/19490976.2019.1662260h
  19. Swanson KS, de Vos WM, Martens EC, Gilbert JA, Menon RS, Soto-Vaca A, Hautvast J, Meyer PD, Borewicz K, Vaughn EE, Slavin JL. (2020). Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review. Beneficial Microbes, 11(2):101-129. DOI: 10.3920/BM2019.0082h
  20. Chen EB, Shapiro LE, Wun K, Kuntz T, Theriault BR, Nooromid MJ, Leone VA, Harris KG, Jian Q, Spedale M, Xiong L, Gilbert JA, Chang EB, Ho KJ. (2020). Microbial Colonization of Germ‐Free Mice Restores Neointimal Hyperplasia Development After Arterial Injury. Journal of the American Heart Association, 9(5):e013496. DOI: 10.1161/JAHA.119.013496
  21. Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R. 2020. Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. mBio, 11(1):e02901-19. DOI: 10.1128/mBio.02901-19
  22. Peñalver-Bernabé B, Maki PM, Dowty SM, Salas-Garcia M, Cralle L, Shah Z, Gilbert JA. (2020). Precision medicine in perinatal depression in light of the human microbiome. Psychopharmacology, online 17 Feb 2020. DOI: 10.1007/s00213-019-05436-4
  23. Cason CA, Kuntz TM, Chen EB, Wun K, Nooromid MJ, Xiong L, Gottel NR, Harris KG, Morton TC, Avram MJ, Chang EB, Gilbert JA, Ho KJ. (2020). Microbiota composition modulates inflammation and neointimal hyperplasia after arterial angioplasty. Journal of Vascular Surgery, online 5 Feb 2020. DOI: 10.1016/j.jvs.2019.06.208
  24. Lutz HL, Gilbert JA. (2020). Bat Biome. Natural History, 128(2): 12 – 13.
  25. Alverdy JC, Hyman N, Gilbert JA. (2020). Re-examining causes of surgical site infections following elective surgery in the era of asepsis. The Lancet Infectious Diseases, online 29 January 2020. DOI: 10.1016/S1473-3099(19)30756-X
  26. Hampton-Marcell JT, Eshoo TW, Cook MD, Gilbert JA, Horswill CA, Porestsky R. 2020. Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers. International Journal of Sports Medicine, e1. DOI: 10.1055/a-1079-5450
  27. Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert JA, Hofmockel KS, Holtz ML, Knight R, Welch DBM, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. 2020. The emergence of microbiome centres. Nature Microbiology, 5(1):2-3. DOI:10.1038/s41564-019-0644-x
  28. Sharma A, Das P, Buschmann M, Gilbert JA. (2019). The future of microbiome‐based therapeutics in clinical applications. Clinical Pharmacology & Therapeutics, 107(1):123-128, Jan 2020 (Online 16 Oct 2019). DOI: 10.1002/cpt.1677

2019

  1. Hyoju SK, Adriaansens C, Wienholts K, Sharma A, Keskey A, Arnold W, van Dalen D, Gottel N, Hyman N, Zaborin A, Gilbert JA, van Goor H, Zaborina O, Alverdy JC. 2019. Low‐fat/high‐fibre diet prehabilitation improves anastomotic healing via the microbiome: an experimental model. British Journal of Surgery, Online 12 Dec 2019. DOI: 10.1002/bjs.11388
  2. Lutz HL, Jackson EW, Webala PW, Babyesiza WS, Kerbis Peterhans JC, Demos TC, Patterson BD, Gilbert JA. 2019. Ecology and host identity outweigh evolutionary history in shaping the bat microbiome. mSystems, 4(6):e00511-19. DOI: 10.1128/mSystems.00511-19h
  3. Luu I, Sharma A, Guaderrama M, Peru M, Nation J, Page N, Carvalho D, Magit A, Jiang W, Leuin S, Bliss M, Bothwell M, Brigger M, Kearns D, Newbury R, Pransky S, Gilbert JA, Broderick L. 2019. Immune Dysregulation in the Tonsillar Microenvironment of Periodic Fever, Aphthous Stomatitis, Pharyngitis, Adenitis (PFAPA) Syndrome. Journal of Clinical Immunology, Online 05 Dec 2019. DOI: 10.1007/s10875-019-00724-2
  4. Zhu T, Xing X, Kong F, Duan YY, Yee AL, Kim M, Galzote C, Gilbert JA, Quan ZX. (2019). Age and Mothers: Potent Influences of Children’s Skin Microbiota. Journal of Investigative Dermatology, 139(12):2497-2505. DOI: 10.1016/j.jid.2019.05.018.
  5. Richardson M, Gottel N, Gilbert JA, Gordon J, Gandhi P, Reboulet R, & Hampton-Marcell JT. (2019). Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area. Microbiome, 2019, 7(1):82. DOI: 10.1186/s40168-019-0695-5
  6. 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. (2019). Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets. Microbiome, 2019, 7(1):70. DOI: 10.1186/s40168-019-0686-6
  7. Sharma A, Laxman B, Naureckas ET, Hogwarth DK, Sperling AI, Solway J, Ober C, Gilbert JA, White SR. (2019). Associations between fungal and bacterial microbiota of airways and asthma endotypes. Journal of Allergy and Clinical Immunology, Nov 2019, 144(5):1214-1227.e7. DOI: 10.1016/j.jaci.2019.06.025h
  8. Jackrel SL, Gilbert JA, Wootton J. (2019). The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition. mBio, September 2019, 10(5): e01703-19. DOI: 10.1128/mBio.01703-19
  9. Gaines S, van Praagh, JB, Williamson AJ, Jacobson RA, Hyoju S, Zaborin A, Mao J, Koo HY, Alpert L, Bissonnette M, Weichselbaum R, Gilbert JA, Chang E, Hyman N, Zaborina O, Shogan BD, Alverdy JC. (2019). Western Diet Promotes Intestinal Colonization by Collagenolytic Microbes and Promotes Tumor Formation Following Colorectal Surgery. Gastroenterology, 23 October 2019. DOI: 10.1053/j.gastro.2019.10.020
  10. Hyoju SK, Zaborin A, Keskey R, Sharma A, Arnold W, van den Berg F, Kim SM, Gottel N, Bethel C, Charnot-Katsikas A, Jianxin P, Adriaansens C, Papazian E, Gilbert JA, Zaborina O, Alverdy JC. (2019). Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts. mBio, July 2019, 10(4): e00903-19. DOI: 10.1128/mBio.00903-19
  11. Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. 2019. Quantifying and understanding well-to-well contamination in microbiome research. mSystems 4(4):e00186-19. DOI: 10.1128/mSystems.00186-19.
  12. Lutz HL, Ramírez-Puebla ST, Abbo L, Durand A, Schlundt C, Gottel NR, Sjaarda AK, Hanlon RT, Gilbert JA & Welch JLM. (2019). A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems. 4(4):e00177-19. DOI: 10.1128/mSystems.00177-19.
  13. Sharma A, Buschmann MM, & Gilbert JA. (2019) Pharmacomicrobiomics: The holy grail to variability in drug response? Clinical Pharmacology & Therapeutics,106(2):317-328. DOI: 10.1002/cpt.1437
  14. Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R. (2019). Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. BioTechniques, 67(1): 29-32. DOI: 10.2144/btn-2018-0192
  15. Dodiya HB, Kuntz T, Shaik SM, Baufeld C, Leibowitz J, Zhang X, Gottel N, Zhang X, Butovsky O, Gilbert JA, Sisodia SS. (2019). Sex-specific effects of microbiome perturbations on cerebral Aβ amyloidosis and microglia phenotypes. J Exp Med, 216(7):1542-1560. DOI: 10.1084/jem.20182386
  16. Hu J, Maamar SB, Glawe AJ, Gottel N, Gilbert JA, & Hartmann EM. (2019). Impacts of Indoor Surface Finishes on Bacterial Viability. Indoor Air. DOI: 10.1111/ina.12558.
  17. Gupta N, Skinner KA, Summers ZM, Edirisinghe JN, Faria JP, Marshall CW, Sharma A, Gottel NR, Gilbert JA, Henry CS, O’Loughlin EJ. (2019). Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium. Microbiology resource announcements, 8(25):e00403-19. American Society for Microbiology.
  18. Gilbert, JA & Lynch, SV. (2019). Community ecology as a framework for human microbiome research. Nature Medicine, 25:884–889. DOI: 10.1038/s41591-019-0464-9h
  19. Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, De Lorenzo V, Pruzzo C, Timmis J, Martín JLR, Verstraete W, Jetten M, Danchin A, Huang W, Gilbert JA, Lal R, Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E, Karahan ZC, van der Meer JR, Artunkal S, Jahn D, & Harper L. (2019). The urgent need for microbiology literacy in society. Environmental microbiology, 21(5):1513-1528.  DOI: 10.1111/1462-2920.14611
  20. Urbaniak C, van Dam P, Zaborin A, Zaborina O,  Gilbert JA,  Torok T, Clay C, Wang C, & Venkateswaran K. (2019). Genomic Characterization and Virulence Potential of Two Fusarium oxysporumIsolates Cultured from the International Space Station. mSystems, 4(2): e00345- 8, 2019.  DOI:1128/mSystems.00345-18
  21. 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. (2019). Microbial and metabolic succession on common building materials under high humidity conditions. Nature Communications, 10(1):1767. DOI: 10.1038/s41467-019-09764-z
  22. 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. 2019. GABA-modulating bacteria of the human gut microbiota. Nature Microbiology, 4(3):396. DOI: 10.1038/s41564-018-0307-3
  23. Yang T, Tedersoo L, Soltis PS, Soltis DE, Gilbert JA, Sun M, Shi Y, Wang H, Li Y, Zhang J, Chen Z, Lin H, Zhao Y, Fu C & Chu H. (2019). Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. ISME Journal, 13(3):686-697. DOI:10.1038/s41396-018-0303-x
  24. Yee AL,  Miller E, Dishaw LJ, Gordon JM, Ji M, Dutra S, Ho TTB, Gilbert JA& Groer MW. (2019 Feb). Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants. mSystems, 4(1) e00229-18. DOI:1128/mSystems.00229-18
  25. Han M, Dsouza M, Zhou C, Li H, Zhang J, Chen C, Yao Q, Zhong C, Zhou H, Gilbert JA, WangZ, & Ning K. (2019). Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake. Genomics, Proteomics & Bioinformatics, 17(1):76-90. DOI: 10.1016/j.gpb.2018.04.008
  26. Ho TB, Groer MW, Kane B, Yee AL, Torres BA, Gilbert JA, Maheshwari A. 2019. Enteric dysbiosis and fecal calprotectin expression in premature infants. Pediatric Research, February 2019, 85(3):361-368. DOI: 10.1038/s41390-018-0254-y
  27. Richardson M, Gottel, N, Gilbert, JA, Lax, S. (2019). Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures. mBio, July 2019, 10(4):e01054-19. DOI: 10.1128/mBio.01054-19
  28. 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 A, 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. (2019) Toward unrestricted use of public genomic data. Science, 363(6425):350-352. DOI: 10.1126/science.aaw1280
  29. Fei N, Bernabe BP, Lie L, Baghdan D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet O, Gottel NR, Riesen W, Korte W, Luke A, Kliethermes SA, Layden BT, Gilbert JA, Dugas LR. (2019). The Human Microbiota is Associated with Cardiometabolic Risk Acroess the Epidemiological Transition. PLoS One, 14(7):e0215262. DOI: 10.1371/journal.pone.0215262

2018

  1. Guadalupe Navarro, Anukriti Sharma, Lara R Dugas, Terrence Forrester, Jack A Gilbert, Brian T Layden. 2018. Gut microbial features can predict host phenotype response to protein deficiency. Physiological Reports. 6(23); e13932.
  2. Sharma A, Schmidt M, Kiesel B, Cralle LE, Mahato NK, Singh Y, Richnow HH, Gilbert JA, Arnold W, Lal R. 2018. Bacterial and Archaeal viruses of Himalayan hot springs at Manikaran modulate host genomes. Frontiers in Microbiology. doi:10.3389/fmicb.2018.03095
  3. Lara R Dugas, Beatriz Peñalver Bernabé, Medha Priyadarshini, Na Fei, Seo Jin Park, Laquita Brown, Jacob Plange-Rhule, David Nelson, Evelyn C Toh, Xiang Gao, Qunfeng Dong, Jun Sun, Stephanie Kliethermes, Neil Gottel, Amy Luke, Jack A Gilbert, Brian T Layden. 2018. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Scientific Reports. 8: 1713.
  4. Ladau J, Yu Shi, Xin Jing, Jin-Sheng He, Litong Chen, Xiangui Lin, Noah Fierer, Jack A Gilbert, Katherine S Pollard, Haiyan Chu. 2018. Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. mSystems, 3(5). e00167-18
  5. Hong-Yi Li, Hang Wang, Hai-Tiao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A Gilbert, Zhi-Jian Zhang. 2018. The chemodiversity of paddy soil dissolved organic matter correlates with microbial cNK, ommunity at continental scales. Microbiome. 6(1): 187
  6. Dominguez Bello MG, Knight R, Gilbert JA, Blaser MJ. 2018. Preserving Microbial Diversity. Science; 362:6410, 33-34
  7. Thao TB Ho, Maureen W Groer, Bradley Kane, Alyson L Yee, Benjamin A Torres, Jack A Gilbert, Akhil Maheshwari. 2018. Dichotomous development of the gut microbiome in preterm infants. Microbiome. 6: 157. https://doi.org/10.1186/s40168-018-0547-8
  8. Sharma A, Gilbert JA. 2018. Microbial Exposure and Human Health. Current Opinion in Microbiology. 44; 79-87.
  9. Berni Canani R, Dr Filippis F, Nocerino R, Paparo L, Dr Scala C, Cosenza L, Della Gatta G, Galignano A, De Caro C, Laiola M, Gilbert JA, Ercolini D. 2018. Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow’s milk allergy. Scientific Reports, 8, 12500
  10. Gilbert JA and Stephens B. 2018. Microbiology of the Built Environment. Nature Reviews Microbiology. DOI: 1038/s41579-018-0065-5
  11. Dugas LR, Lie L, Plange-Rhule J, Bedu-Addo K, Bovet P, Lambert EV, Forrester TE, Luke A, Gilbert JA, Layden BT. 2018. Gut microbiota, short chain fatty acids, and obesity across the epidemiological transition: the METS-Microbiome study protocol. BMC Public Health, 18:978. org/10.1186/s12889-018-5879-6
  12. Fan K, Weisenhorn P, Gilbert JA, Chu H. 2018. Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. Soil Biology and Biochemistry. 125; 251- doi.org/10.1016/j.soilbio.2018.07.022
  13. Ma B, Zhao K, Lv X, Su W, Dai Z, Gilbert JA, Brookes PC, Faust K, Xu J. 2018. Genetic correlation network prediction of forest soil microbial functional organization. ISME J. org/10.1038/s41396-018-0232-8
  14. Salas Garcia MC, Yee AL, Gilbert JA, Dsouza M. 2018. Dysbiosis in Children Born by Caesarean Section. Annals of Nutrition and Metabolism. 73(3): 24-32. org/10.1159/000492168
  15. Cardona C, Lax S, Larsen P, Stephens B, Hampton-Marcel J, Edwardson CF, Henry C, Van Bonn B, Gilbert JA. Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics. mSystems. DOI:10.1128/mSystems.00052-18
  16. Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight, American Gut Consortium. 2018. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 3,3. DOI:1128/mSystems.00031-18
  17. Wang H, Cheng M, Dsouza M, Weisenhorn P, Zheng T, Gilbert JA. 2018. Soil bacterial diversity is associated with human population density in urban greenspaces. Environmental Science and Technology. DOI: 1021/acs.est.7b06417
  18. Chen EB, Cason C, Gilbert JA, Ho KJ. 2018. Current state of knowledge on implications of gut microbiome for surgical conditions. Journal of Gastrointestinal Surgery. https://doi.org/10.1007/s11605-018-3755-4
  19. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. 2018. Current understanding of the human microbiome. Nature Medicine. 24, 4, 392-400.
  20. Wang H, JA Gilbert, Y Zhu, X Yang. 2018. Salinity is a key factor driving the nitrogen cycling in the mangrove sediment. Science of The Total Environment 631, 1342-1349
  21. K Fan, P Weisenhorn, JA Gilbert, Y Shi, Y Bai, H Chu. 2018. Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biology and Biochemistry 121, 185-192.
  22. BP Bernabé, L Cralle, JA Gilbert. 2018. Systems Biology of the Human Microbiome. Current Opinion in Biotechnology 51, 146-153.
  23. Seyler LM, McGuiness LR, Gilbert JA, Biddle JF, Gong D, Kerhof LJ. 2018. Discerning autotrophy, mixotrophy, and heterotrophy in marine TACK archaea from the North Atlantic. FEMS Microbiology Ecology. fiy014; https://doi.org/10.1093/femsec/fiy014
  24. Lang JM, Coil DA, Neches RY, Brown WE, Cavalier D, Severance M, Hampton-Marcell JT, Gilbert JA, Eisen JA.(2018) A microbial survey of the International Space Station (ISS) PeerJ 5:e4029

2017

  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/femsec/fix120
  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. *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,Jeremy A Dodsworth, Shibu Yooseph, Granger Sutton, 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,Ilene Karsch-Mizrachi, Gene W Tyson, Christian Rinke, The Genome Standards Consortium, Alla Lapidus, Folker Meyer, Pelin Yilmaz, Donovan H Parks, A M Eren, Lynn Schriml, Jillian F Banfield, Philip Hugenholtz &Tanja Woyke. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35,725–731
  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. 11, 2569–2583
  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, 275–284
  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. DOI:1128/mSystems.00195-16
  10. Linwei 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. 1038/ismej.2017.7
  11. Roshan 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 mSystems. 2 (3); e00020-17
  12. Simon 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. Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine. Vol. 9, Issue 391, eaah6500. DOI: 10.1126/scitranslmed.aah6500
  13. John 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.jamcollsurg.2017.05.005
  14. Joshua 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. Sci. Technol. DOI: 10.1021/acs.est.7b00882
  15. Alfredo Franco-Obregón, Jack A. Gilbert. 2017. The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals. mSystems. DOI:1128/mSystems.00018-17
  16. JN 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.
  17. Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter. 2017. Celebrating Parasites. Nature Genetics. 49 (4). 483-484.
  18. Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA. 2017. Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. https://doi.org/10.1128/mSystems.00178-16
  19. Highfield 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
  20. Hampton-Marcell JT, Lopez JV, Gilbert JA. 2017. The human microbiome: an emerging tool in forensics. Microbial Biotechnology. 10 (2) 228-230.
  21. Bin 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. DOI:10.1128/mSystems.00174-16
  22. Thomas M Kuntz, Jack A Gilbert. 2017. Introducing the Microbiome into Precision Medicine. Trends in Pharmacological Sciences. http://dx.doi.org/10.1016/j.tips.2016.10.001
  23. Alverdy JC, Hyoju SK, Weigerinck M, JA Gilbert. 2017. The gut microbiome and the mechanism of surgical infection. British Journal of Surgery. DOI: 1002/bjs.10405.
  24. Hang Wang, Naseer Sangwan, Hong-Yi Li, Jian-Qiang Su, Wei-Yin Oyang, Zhi-Jian Zhang, Jack A Gilbert, Yong-Guan Zhu, Fan Ping, Han-Luo Zhang. 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

2016

  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: 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. 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: 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: 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: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.buildenv.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: 1111/1462-2920.13512.
  10. Embriette R Hyde, Jose A Navas-Molina, Se Jin Song, Jordan G Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R Mendelson, Valerie J McKenzie, Jack A Gilbert, Rob Knight. 2016. The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems. 1; 4 e00046-16
  11. Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, dos Santos MM, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI. 2016. Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. N Engl J Med 2016; 375:411-421
  12. Yee A & Gilbert JA. 2016. Is Triclosan Harming Your Microbiome? Science, 353, (6297), 348-349.
  13. Vipin Gupta, Shazia Haider, Utkarsh Sood, Gilbert JA, Meenakshi Ramjee, Ken Forbes, Yogendra Singh, Bruno S Lopes, Rup Lal. 2016. Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach. Scientific Reports. 6, 29043. doi:10.1038/srep29043
  14. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature, 535, 94–103 doi:10.1038/nature18850
  15. Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FS-M, Medeiros JD, Assis Geraldo J, Gilbert JA, Volpini AC, Rocha Fernandes (2016) ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms. PLoS Negl Trop Dis 10(6): e0004817. doi:10.1371/journal.pntd.0004817
  16. Torsten Thomas, Lucas Moitinho-Silva, Miguel Lurgi, Johannes R. Björk, Cole Easson, Carmen Astudillo-García, Julie B. Olson, Patrick M. Erwin, Susanna López-Legentil, Heidi Luter, Andia Chaves-Fonnegra, Rodrigo Costa, Peter J. Schupp, Laura Steindler, Dirk Erpenbeck, Jack A. Gilbert, Rob Knight, Gail Ackermann, Jose Victor Lopez, Michael W. Taylor, Robert W. Thacker, Jose M. Montoya, Ute Hentschel & Nicole S. Webster. 2016. Diversity, structure and convergent evolution of the global sponge microbiome. Nature Communications. 7, 11870 doi:10.1038/ncomms11870.
  17. Hu Li, Xiaoru Yang, Bosen Weng, Jianqiang Su, San’an Nie, Jack A Gilbert, Yong-Guan Zhu. 2016. The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil. Soil Biology and Biochemistry. 100; 59-65.
  18. Kuntz T, Gilbert JA. 2016. Does the Brain Listen to the Gut? eLife. 5: e17052.
  19. Sangwan N, Zarraonaindia I, Hampton-Marcel JT, Ssegane H, Eshoo TW, Rijal G, Negri MC, Gilbert JA. 2016. Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter mSystems. DOI: 10.1128/mSystems.00003-16
  20. Sharma A, Gilbert JA, Lal R. 2016. (Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans. Scientific Reports. 6; 25527.
  21. Cardona C, Weisenhorn P, Henry C, Gilbert JA. 2016. Network-based metabolic analysis and microbial community modeling. Current Opinions in Microbiology. 31, 124-131.
  22. Sangwan N, Xia FF, Gilbert JA. 2016. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 4:8 DOI: 1186/s40168-016-0154-5
  23. De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D. 2016. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Scientific reports. 6:21871.
  24. O’Brien SL, Gibbons SM, Owens SM, Hampton‐Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. 2016. Spatial scale drives patterns in soil bacterial diversity. Environmental Microbiology. DOI: 1111/1462-2920.13231
  25. Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, Brookes PC, Xu J, Gilbert JA. 2016. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. doi:10.1038/ismej.2015.261
  26. Burstein D, Amaro F, Zusman T, Lifshitz Z, Cohem O, Gilbert JA, Pupko T, Shuman HA, Segal G. 2016. Genomic analysis of 38 Legionella species identified large and diverse effector repertoires. Nature Genetics. doi:10.1038/ng.3481
  27. Dugas LR, Fuller M, Gilbert JA, Layden BT. 2016. The obese gut microbiome across the epidemiologic transition. Emerging Themes in Epidemiology. 13 (1) 1.
  28. Gilbert JA, Alverdy JA. 2016. Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? Gut 65 (1), 1-2. doi:10.1136/gutjnl-2015-310043.
  29. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song, SJ, Amir A, Larsen P, Sangwan N, Harman D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Busheli SR, Carter DO, Knight R. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 351 (6269) 158-162 DOI:10.1126/science.aad2646

2015

  1. Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J and Gilbert JA. 2015. A simple novel device for air sampling by electrokinetic capture. Microbiome. 3:79; DOI: 1186/s40168-015-0141-2
  2. Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight B. 2015. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1(1):e00009-15. doi:10.1128/ mSystems.00009-15.
  3. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Frazer SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. 2015. Tools for the Microbiome: Nano and Beyond. ACS Nano. DOI: 1021/acsnano.5b07826
  4. Maya Britstein, Giulia Devescovi, Kim M Handley, Assaf Malik, Markus Haber, Kumar Saurav, Roberta Teta, Valeria Costantino, Ilia Burgsdorf, Jack A Gilbert, Noa Sher, Vittorio Venturi, Laura Steindler. 2015. A new N-acyl homoserine lactone synthase in an uncultured symbiont of the red sea sponge Theonella swinhoei. Applied and Environmental Microbiology. 03111-15
  5. Teng Yang, Pamela Weisenhorn, Jack A Gilbert, Yingying Ni, Ruibo Sun, Yu Shi, Haiyan Chu. 2015. Carbon constrains fungal endophyte assemblages along the timberline. Environmental Microbiology. 2015/12/1
  6. Gibbons SM and Gilbert JA. 2015. Microbial Diversity – exploration of natural ecosystems and microbiomes. Current Opinion in Genetics and Development. 35, 66-72
  7. Ying S, Zeng D-N, Chi L, Tan Y, Galzote C, Cardona C, Lax S. Gilbert JA, Quan Z-X. 2015. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations. PLoS ONE 10(10): e0141842. doi:10.1371/journal.pone.0141842
  8. Alivisatos AP, MJ Blaser, EL Brodie, M Chun, JL Dangl, TJ Donohue, PC Dorrestein, JA Gilbert, JL Green, JK Jansson, R Knight, ME Maxon, MJ McFall-Ngai, JF Miller, KS Pollard, EG Ruby, SA Taha, Unified Microbiome Initiative Consortium. 2015. A unified initiative to harness Earth’s microbiomes. Science. 350 (6260): 507-508.
  9. Denner DR, N Sangwan, JB Becker, DK Hogarth, J Oldham, J Castillo, AI Sperling, J Solway, ET Naureckas, C Ober, JA Gilbert, and SR White. 2015. Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways. Journal of Allergy and Clinical Immunology. S0091-6749(15)01563-8. doi: 10.1016/j.jaci.2015.10.017..
  10. Miles Fuller, Medha Priyadarshini, Sean M Gibbons, Anthony R Angueira, Michael Brodsky, M. Geoffrey Hayes, Petia Kovatcheva-Datchary, Fredrik Backhed, Jack A Gilbert, William L. Lowe, Brian T. Layden. 2015. The Short Chain Fatty Acid Receptor, FFA2, contributes to gestational glucose homeostasis. American Journal of Physiology – Endocrinology and Metabolism DOI:1152/ajpendo.00171.2015
  11. Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA and Nagler CR. 2015. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J. doi:10.1038/ismej.2015.151
  12. Perisin M, Vetter M, Gilbert JA, and Bergelson J. 2015. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME J. doi:10.1038/ismej.2015.161
  13. Wang H, Li H, Gilbert JA, Li H, Wu L, Liu M, Wang L, Zhou Q, Yuan J, Zhang Z. 2015. Housefly Larvae Vermicomposting efficiently attenuates Antibiotic Resistant Genes in Swine Manure Coupled with distinct bacterial population change. Applied and Environmental Microbiology, 01367-15
  14. Karim H Lüchmann, Melody S Clark, Afonso CD Bainy, Jack A Gilbert, John A Craft, J Kevin Chipman, Michael AS Thorne, Jacó J Mattos, Marília N Siebert, Declan C Schroeder. 2015. Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana. Aquatic Toxicology. doi:10.1016/j.aquatox.2015.06.012
  15. Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT. 2015. Athletic equipment microbiota are shaped by interactions with human skin. Microbiome. 3:25  doi:10.1186/s40168-015-0088-3
  16. Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L. 2015. Lifestyle evolution in cyanobacterial symbionts of sponges. mBio 6(3):e00391-15. doi:10.1128/mBio.00391-15.
  17. Van Bonn W, LaPointe A, Gibbons SM, Frazier A, Hampton-Marcel J, Gilbert JA. 2015. Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management. Zoo Biology. DOI: 10.1002/zoo.21220
  18. Lin X, Handley KM, Gilbert JA, Kostka JE. 2015. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J. doi:10.1038/ismej.2015.77
  19. Gilbert JA. 2015. Our Unique Microbial Identity. Genome Biology. 16:97 doi:10.1186/s13059-015-0664-7
  20. Lax S, Hampton-Marcell TJ, Gibbons S, Colares G, Smith D, Eisen AJ, Gilbert JA. 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome. 3:21  doi:10.1186/s40168-015-0082-9
  21. Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. 2015. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12297
  22. Shogun BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers, R, Hancock LE, Gilbert JA, Zborina O, Alverdy JC. 2015. Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak, Science Translational Medicine. 7, Issue 286, p. 286ra68. DOI: 10.1126/scitranslmed.3010658
  23. Lax S and Gilbert JA. 2015. Hospital-associated microbiota and implications for nosocomial infections. Trends in Molecular Medicine. DOI: http://dx.doi.org/10.1016/j.molmed.2015.03.005
  24. Leone V, Gibbons SM, Martinez K, Hutchinson AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpali A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB. 2015. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host & Microbe. http://dx.doi.org/10.1016/j.chom.2015.03.006
  25. Dedesko S, Stephens B, Gilbert JA, Siegel JA. 2015. Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms. Building and Environment. doi:10.1016/j.buildenv.2015.03.029
  26. Canani RB, Gilbert JA, Nagler CR. 2015. The role of the commensal microbiota in the regulation of tolerance to dietary allergens. Curr Opin Allergy Clin Immunol. 15. Online.
  27. Gilbert JA. Metagenomics: Social behavior and the microbiome. eLife 2015;4:e07322
  28. Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA. 2015. The soil microbiome influences grapevine-associated microbiota. mBio 6(2):e02527-14. doi:10.1128/mBio.02527-14.
  29. Daniel McDonald, Mady Hornig, Catherine Lozupone, Justine Debelius, Jack A Gilbert, Rob Knight. 2015. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microbial Ecology in Health & Disease 2015, 26: 26555 – http://dx.doi.org/10.3402/mehd.v26.26555
  30. Huang EY, Inoue T, Leone V, Dalal S, Touw K, Wang Y, Musch M, Theriault B, Higuchi K, Donovan S, Gilbert JA, Chang E. 2015. Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases. Inflammatory Bowel Diseases. 21(5):963-721097/MIB.0000000000000332
  31. Lax S, Nagler CR. Gilbert JA. 2015. Our interface with the built environment: immunity and the indoor microbiota. Trends in Immunology. http://dx.doi.org/10.1016/j.it.2015.01.001
  32. Gilbert JA and Henry C. 2015. Predicting ecosystem emergent properties at multiple scales. Environmental Microbiology. DOI: 10.1111/1758-2229.12258
  33. Ramos T, Dedesko S, Siegel JA, Gilbert JA, Stephens B (2015) Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building. PLoS ONE 10(3): e0118207. doi:10.1371/journal.pone.0118207
  34. Stephen A Wood, Mark A Bradford, Gilbert JA, Krista L McGuire, Cheryl A Palm, Katherine L Tully, Jizhong Zhou, Shahid Naeem. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. Journal of Applied Ecology. DOI: 10.1111/1365-2664.12416
  35. Haowei Yue, Mengmeng Wang, Shiping Wang, Gilbert JA, Xin Sun, Linwei Wu, Qiaoyan Lin, Yigang Hu, Xiangzhen Li, Zhili He, Jizhong Zhou, Yunfeng Yang. 2015. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME Journal. 17 February 2015; doi:10.1038/ismej.2015.19
  36. Shade A, Gilbert JA. 2015. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends in Microbiology. doi:10.1016/j.tim.2015.01.007
  37. Amaro F, Wang W, Gilbert JA, Anderson OR, Shuman HA. 2015. Diverse protist grazers select for virulence-related traits in Legionella. ISME Journal. 2015/1/9.
  38. Vitaglione P, Mennella I, Ferracane R, Rivellese AA, Giacco R, Ercolini D, Gibbons SM, La Storia A, Gilbert JA, Jonnalagadda A, Thielecke F, Gallo MA, Scalfi L, Fogliano V. 2015. Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber. The American Journal of Clinical Nutrition. ajcn. 088120
  39. Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. 2015. Ecological succession and viability of human-associated microbiota on restroom surfaces. Applied and Environmental Microbiology. 81(2), 765-773.
  40. Xiao-Ru Yang, Hu Li, San-An Nie, Jian-Qiang Su, Bo-Sen Weng, Gui-Bing Zhu, Huai-Ying Yao, Gilbert JA and Yong-Guan Zhu. 2015. The potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Applied and Environmental Microbiology. 81 (3), 938-947.

2014

  1. Gilbert JA, Neufeld JD (2014) Life in a World without Microbes. PLoS Biol 12(12): e1002020. doi:10.1371/journal.pbio.1002020
  2. Helianthous Verma, Roshan Kumar, Phoebe Oldach, Naseer Sangwan, Jitendra P Khurana, Jack A Gilbert, Rup Lal. 2014. Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics, 15:1014  doi:10.1186/1471-2164-15-1014
  3. Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. 2014. Development of the preterm infant gut microbiome: a research priority. Microbiome 2014, 2:38  doi:10.1186/2049-2618-2-38
  4. Pfister CA, Gilbert JA, Gibbons SM. (2014) The role of macrobiota in structuring microbial communities along rocky shores. PeerJ 2:e631 http://dx.doi.org/10.7717/peerj.631
  5. LaBelle EV, Marshall CW, Gilbert JA, May HD (2014) Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome. PLoS ONE 9(10): e109935. doi:10.1371/journal.pone.0109935
  6. Gilbert JA. 2014. Science is innate! Genome Biology. 15:477.
  7. Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JC. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. mBio 5(5):e01361-14. doi:10.1128/mBio.01361-14.
  8. Rubin BER, Sanders JG, Hampton-Marcell J, Owens SM, Gilbert JA, and Moreau CS. 2014. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. Microbiology Open. Article first published online: 26 SEP 2014. DOI: 10.1002/mbo3.216
  9. Shogan BD, Smith DP, Christley S, Gilbert JA, Zaborina O, and Alverdy JC. 2014. Intestinal anastomotic injury alters spatially defined microbiome composition and function. Microbiome 2014, 2:35  doi:10.1186/2049-2618-2-35
  10. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 345 no. 6200 pp. 1048-1052. DOI: 10.1126/science.1254529
  11. Gilbert JA, Jansson JK, and Knight R. 2014. The Earth Microbiome project: successes and aspirations. BMC Biology, 12:69  doi:10.1186/s12915-014-0069-1
  12. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong X-Z, Ehrlich DS, Fraser C, Gibbs R, Gilbert JA, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee J-S, Li W-J, Juncai M, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K-i, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou Y-G, Field D, Whitman WB, Garrity GM, Klenk H-P. 2014. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biology. 12:8, e1001920. DOI: 10.1371/journal.pbio.1001920.
  13. Larsen PE, Scott N, Post, AF, Field D, Knight R, Hamada Y, Gilbert JA. 2014. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME Journal. Advanced Online Publication July 29th doi: 10.1038/ismej.2014.107
  14. ShadeA, 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
  15. Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA, Hartsel J, Kennedy S, Gibbons S. (2014) Understanding Cultivar-Specificity and Soil Determinants of the Cannabis PLoS ONE 9(6): e99641. doi:10.1371/journal.pone.0099641
  16. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou H, Knight R, Caporaso JG. (2014) Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2:e545 http://dx.doi.org/10.7717/peerj.545
  17. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA. (2014) Human and Environmental Impacts on River Sediment Microbial Communities. PLoS ONE 9(5): e97435. doi:10.1371/journal.pone.0097435
  18. Nielsen S, Minchin T, Kimber S, van Zwieten L, Gilbert JA, Munroe P, Joseph S, Thomas T. 2014. Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilizers. Agriculture, Ecosystems and the Environment. DOI:10.1016/j.agee.2014.04.006
  19. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA and Knight R (2014) Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Microbiol. 5:298. doi: 10.3389/fmicb.2014.00298
  20. Kumar A, Dames JF, Gupta A, Sharma S, Gilbert JA, and Ahmad P. 2014. Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation: a biotechnological perspective. Crit Rev Biotechnol, Early Online: 1–14. DOI: 10.3109/07388551.2014.899964
  21. Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B, Mellilo D, Meuller MG, Natale L, Zucchetti I, De Santis R, Pinto MR, Litman GW, Gilbert JA. (2014) The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota. PLoS ONE 9(4): e93386. doi:10.1371/journal.pone.0093386
  22. O’Malley MA, Brigandt I, Love AC, Crawford JA, Gilbert JA, Knight R. Mitchell SD, Rohwer F. 2014. Multilevel research strategies and biological systems. Philosophy of Science. 81(5) 811-828.
  23. Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA. 2014. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Frontiers in Microbiolology, 5:108. doi: 10.3389/fmicb.2014.00108
  24. Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE and Banfield JF. 2014. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental Microbiology. DOI: 10.1111/1462-2920.12467
  25. Hamada Y, Gilbert JA, Larsen PE, Norgaard MJ. 2014. Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing. Photogrammetric Engineering & Remote Sensing 80 (4), 311-321
  26. Handley KM, Bartels D, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonoploulos D, Kemner KM, Meyer F. 2014. The complete genome sequence for putative H2-and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environmental Microbiology, DOI: 10.1111/1462-2920.12453.
  27. Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, Gilbert JA, Chu H. 2014. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbial Ecology. 1111/1574-6941.12289
  28. Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D. 2014. Saliva from Obese individuals suppresses the released of aroma compounds from wine. PLoS ONE 9(1): e85611. doi:10.1371/journal.pone.0085611.
  29. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicus D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. 2014. Metagenomics reveals sediment microbial community response to the Deepwater Horizon oil spill. ISME Journal. 8, 1464–1475; doi:10.1038/ismej.2013.254
  30. Peer X, Gilbert JA, An GC. 2014. Examining the Microbial Ecological Dynamics of Clostridium difficile Infections and the Efficacy of Fecal Microbiome Transplant (FMT) using an Agent-based Model. Journal of Surgical Research 186 (2), 689.
  31. Gilbert JA, van der Lelie D, Zarraonaindia I. 2014. Microbial terroir for wine grapes. 111 (1), 5-6.

2013

  1. Gilbert JA, Krajmalnik-Brown R, Porazinska DL, Weiss SJ, Knight R. 2013. Toward Effective Probiotics for Autism and Other Neurodevelopmental Disorders. Cell. 155(7) 1446-1448.
  2. Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert JA, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Čapek P, Šantrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C and Urich T. 2013. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J. Advanced online publication. doi:10.1038/ismej.2013.219
  3. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. 2013. Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science. 342, 621-624.
  4. Gilbert JA. 2013. Biological Oceanography: Some Phytoplankton Like it Hot. Nature Climate Change. 3, 954-955.
  5. Laverock B, Tait K, Gilbert JA, Osborn AM, Widdicombe S. 2013. Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12115.
  6. 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.
  7. 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
  8. 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.
  9. 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.
  10. 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
  11. Bourlat SJ, Borja A, Gilbert JA, Taylor MI, Davies N, Weisberg SB, Griffith JF, Lettieri T, Field D, Benzie J, Glockner FO, Rodriguez-Ezpeleta N, Faith DP, Bean TP, Obst M. 2013. Genomics in marine monitoring: New opportunities for assessing marine health status. Marine Pollution Bulletin. Volume 74, Issue 1, 15 September 2013, Pages 19–31
  12. Kelley ST, Gilbert JA. 2013. Studying the microbiology of the indoor environment. Genome Biology. 14(2), 1-9.
  13. 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
  14. Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA. Evidence for a persistent microbial seed bank throughout the global ocean. PNAS. 110 (12); 4651-4655
  15. 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.
  16. Zarraonaindia I, Smith D, Gilbert JA. 2013. Beyond the genome: community-level analysis of the microbial world. Biology & Philosophy. 10.1007/s10539-012-9357-8

2012

  1. 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.
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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.
  7. Larsen, P, Gibbons S, Gilbert JA. Bacterial diversity and function across time and space: modeling microbial community structure. FEMS Microbiology Letters. Volume 332, Issue 2, pages 91–98,
  8. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman J, Hugenholtz P, Meyer F, Stevens R, Bailey M, Gordon JI, Kowalchuk G, Gilbert JA. 2012. Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology. 30 (6), 513–520
  9. Larsen PE, Field D, Gilbert JA. Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods. 9 621-625 doi:10.1038/nmeth.1975
  10. 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.
  11. Larsen PE, Hamada Y, Gilbert JA. Modeling Microbial Communities. Journal of Biotechnology. 160 (1–2) 17–24.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Gilbert JA, Meyer F. 2012. Modeling the Earth’s Microbiome: A real world deliverable for microbial ecology. ASM Microbe Magazine. 7 (2), 64
  17. Desai N, Antonopoulos D, Gilbert JA, Glass E, and Meyer F. 2012. From genomics to metagenomics. Current Opinions in Biotechnology. 23(1): 72-6.
  18. Sansone S-A, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman L, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert JA, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I & Hide W. 2012. Toward interoperable bioscience data. Nature Genetics 44, 121–126 (2012) doi:10.1038/ng.1054.
  19. 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.
  20. 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
  21. Davies N, Field D, Meyer C, Gilbert JA et al Sequencing data: A genomic network to monitor Earth. Nature. 481, 145.
  22. Caporaso JG, Field D, Paszkiewicz K, Knight R, Gilbert JA. 2012. Evidence for a persistent microbial community in the Western English Channel. ISME J. 6, 1089–1093.
  23. Jansson J, Neufeld J, Moran MA, Gilbert JA. 2012. Omics for Understanding Microbial Functional Dynamics. Environmental Microbiology: Special Issue: OMICS Driven Microbial Ecology. 14(1), 1-3.

2011

  1. 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
  2. Gilbert JA. 2011. The Smallest Champions in the World. Marine Scientist. 34:16-19
  3. 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.
  4. Gilbert JA, O’Dor R, King N, Vogel T. 2011. The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial Informatics and Experimentation,1:5
  5. Larsen PE, Collart F, 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. Microbial Informatics and Experimentation. 1:4
  6. 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.
  7. 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.
  8. 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
  9. 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.
  10. 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.
  11. 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.
  12. 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
  13. 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
  14. 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
  15. Gilbert JA and Dupont C. 2011. Marine Metagenomics. Annual Review of Marine Science. Volume 3: 347-371.
  16. Gilbert JA, O’Dor R, Vogel T. 2011. Survey studies are still vital to science. Nature. 469, 162.

2010

  1. 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.
  2. 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+.
  3. Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM. 2010. Metagenomics: A foundling finds its feet. Standards in Genomic Science. Vol 3 (2).
  4. Heidelberg KB, Gilbert JA and Joint I. 2010. Mini Review: Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microbial Biotechnology. 3(5), 531–543
  5. Laverock B., Widdicombe S, Tait K, Smith C, Osborn M, Gilbert JA. 2010. The impact of burrowing shrimp on bacterial diversity in temperate coastal sediments. ISME J. 4, 1531–1544.
  6. Gilbert JA. Beyond the Infinite – tracking bacterial gene expression. Microbiology Today. 37:2; 82-85.
  7. 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
  8. 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.
  9. Thomas S, Burdett H, Temperton B, Wick R, Snelling D, Woodward M, McGrath J, Quinn J, Munn C and Gilbert JA. 2010. The diversity of phnA gene homologues in temperature-stressed Cnidarian-associated Bacteria. ISME J. 4, 459-461 doi:10.1038/ismej.2009.129

2009

  1. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield P, Huse S, Joint I. 2009. Seasonal succession of microbial communities in the Western English Channel using 16S rDNA-tag pyrosequencing. Environmental Microbiology. 11(12), 3132–3139
  2. 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.
  3. 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.
  4. Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I. 2009. Potential for Phosphonate utilisation by marine bacteria in temperate coastal waters. Environmental microbiology. 11(1):111-25

2008

  1. Rees AP, Gilbert JA, Kelly-Gerreyn BA. 2008. Evidence of Nitrogen fixation in a temperate coastal sea (western English Channel). Marine Ecology Progress Series 374: 7–12
  2. 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
  3. 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
  4. 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?”. 12(2):143-9.
  5. 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.
  6. Garnham C.P., Gilbert JA*, Hartman C, Campbell RL, Laybourn-Parry J. and Davies PL. 2008. Ca2+-dependent bacterial antifreeze protein domain has a novel beta-helical ice-binding fold. Biochemistry Journal. 411, 171-180

2007

  1. 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. 42(3):300-02

2006

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

2005

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

2004

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

2003

  1. 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:

2022

  1. Liu Q, Gilbert JA, Zhu H, Huang SM, Kunkoski E, Das P, Bergman K, Buschmann M, ElZarrad MK. (2022). Chapter 36 – Emerging clinical pharmacology topics in drug development and precision medicine. Atkinson’s Principles of Clinical Pharmacology (Fourth Edition), 691-708. DOI: 10.1016/B978-0-12-819869-8.00028-8

2019

  1. Yee A.L., Buschmann M.M., Ciaccio C.E., Gilbert J.A. (2020) The Microbiome in Food Allergy and Eosinophilic Esophagitis. In: Gupta R. (eds) Pediatric Food Allergy. Springer, Cham
  2. McDonald JE, Harris RN, Doonan J, Carryl S, Sze M, McKenzie V, Gilbert JA. (2020). Host Microbiomes and disease. In: Microbiomes of Soils, Plants and Animals: An Integrated Approach. Antwis RE, et al. (eds). Cambridge University Press.
  3. Salas Garcia M.C., Schorr A.R., Arnold W., Fei N., Gilbert J.A. (2020) Pets as a Novel Microbiome-Based Therapy. In: Pastorinho M., Sousa A. (eds) Pets as Sentinels, Forecasters and Promoters of Human Health. Springer, Cham. DOI: 10.1007/978-3-030-30734-9_11

2019

  1. Kuntz T, Kim M, Jill ES, Salas Garcia MC, Gilbert JA. 2019. Chapter 9, Probiotics in the World, “Bugs-as-Drugs.” In: James O’Donnell III et al, (eds.) Drug Discovery and Development, Third Edition. CRC Press.
  2. Arnold WM, Hill ES, Fei N, Yee AL, Salas Garcia M, Cralle LE, Gilbert JA. 2019. The human microbiome in health and disease. In: Netto G., Kaul K. (eds) Genomic Applications in Pathology. Springer, Cham. doi.org/10.1007/978-3-319-96830-8_39

2017

  1. Lax S, Gilbert JA. 2017. Forensic Microbiology in Built Environments. In:

Forensic Microbiology. ED. David O. Carter, Jeffery K. Tomberlin, M. Eric Benbow, Jessica L. Metcalf. John Wiley and Sons.

2014

  1. 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. InJ.McGenity et al., (eds.) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocol Handbooks. DOI: 10.1007/8623_2014_5
  2. Gilbert, J.A. and Scott, N.M. (2014) Introduction to Genetic, Genomic, and System Analyses for Communities. Humana Press, Totowa, NJ. InJ.McGenity et al., (eds.) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocol Handbooks. DOI: 10.1007/8623_2014_5
  3. Owens S, Wilkening J, Fessler J, Gilbert JA. 2014. Metagenomics: Biofouling Methods. Wiley and Sons.

2013

  1. 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
  2. Lopez, J., Cuvelier, M., Gilbert, J. A., Larsen, P., Willoughby, D., Wu, Y., … & Thurber, V. R. (2013, April). Synergistic Effects of Crude Oil and Corexit Dispersant on a Sponge Holobiont System. In INTEGRATIVE AND COMPARATIVE BIOLOGY (Vol. 53, pp. E130-E130). JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA: OXFORD UNIV PRESS INC.

2012

  1. Gilbert JA, Li L-L, Taghavi S, McCorkle SM, Tringe S, van der Lelie N. 2012. Bioprospecting metagenomics for new glycoside hydrolases. In: Methods in Molecular Biology Vol. 908 – Biomass Conversion. Ed. Himmel, Michael E. Humana Press. ISBN 978-1-61779-955-6

2011

  1. Gilbert J.A. and Hughes M. 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.
  2. 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.) ISBN: 978-1-61779-088-1.

2010

  1. 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.
  2. Gilbert JA, Zhang K & Neufeld J. 2010. Multiple Displacement Amplification. In: HANDBOOK OF HYDROCARBON AND LIPID MICROBIOLOGY. Ed. Timmis, K. Springer-Verlag Berlin Heidelberg. 1007/978-3-540-77587-4_333. 4255-4263
  3. Gilbert JA. 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:

2015

  1. Anna Kopf, Mesude Bicak, Renzo Kottmann, Julia Schnetzer, Ivaylo Kostadinov, Katja Lehmann, Antonio Fernandez-Guerra, Christian Jeanthon, Eyal Rahav, Matthias Ullrich, Antje Wichels, Gunnar Gerdts, Paraskevi Polymenakou, Giorgos Kotoulas, Rania Siam, Rehab Z Abdallah, Eva C Sonnenschein, Thierry Cariou, Fergal O’Gara, Stephen Jackson, Sandi Orlic, Michael Steinke, Julia Busch, Bernardo Duarte, Isabel Caçador, João Canning-Clode, Oleksandra Bobrova, Viggo Marteinsson, Eyjolfur Reynisson, Clara Magalhães Loureiro, Gian Marco Luna, Grazia Marina Quero, Carolin R Löscher, Anke Kremp, Marie E DeLorenzo, Lise Øvreås, Jennifer Tolman, Julie LaRoche, Antonella Penna, Marc Frischer, Timothy Davis, Barker Katherine, Christopher P Meyer, Sandra Ramos, Catarina Magalhães, Florence Jude-Lemeilleur, Ma Leopoldina Aguirre-Macedo, Shiao Wang, Nicole Poulton, Scott Jones, Rachel Collin, Jed A Fuhrman, Pascal Conan, Cecilia Alonso, Noga Stambler, Kelly Goodwin, Michael M Yakimov, Federico Baltar, Levente Bodrossy, Jodie Van De Kamp, Dion MF Frampton, Martin Ostrowski, Paul Van Ruth, Paul Malthouse, Simon Claus, Klaas Deneudt, Jonas Mortelmans, Sophie Pitois, David Wallom, Ian Salter, Rodrigo Costa, Declan C Schroeder, Mahrous M Kandil, Valentina Amaral, Florencia Biancalana, Rafael Santana, Maria Luiza Pedrotti, Takashi Yoshida, Hiroyuki Ogata, Tim Ingleton, Kate Munnik, Naiara Rodriguez-Ezpeleta, Veronique Berteaux-Lecellier, Patricia Wecker, Ibon Cancio, Daniel Vaulot, Christina Bienhold, Hassan Ghazal, Bouchra Chaouni, Soumya Essayeh, Sara Ettamimi, El Houcine Zaid, Noureddine Boukhatem, Abderrahim Bouali, Rajaa Chahboune, Said Barrijal, Mohammed Timinouni, Fatima El Otmani, Mohamed Bennani, Marianna Mea, Nadezhda Todorova, Ventzislav Karamfilov, Petra ten Hoopen, Guy Cochrane, Stephane L’Haridon, Kemal Can Bizsel, Alessandro Vezzi, Federico M Lauro, Patrick Martin, Rachelle M Jensen, Jamie Hinks, Susan Gebbels, Riccardo Rosselli, Fabio De Pascale, Riccardo Schiavon, Antonina dos Santos, Emilie Villar, Stéphane Pesant, Bruno Cataletto, Francesca Malfatti, Ranjith Edirisinghe, Jorge A Herrera Silveira, Michele Barbier, Valentina Turk, Tinkara Tinta, Wayne J Fuller, Ilkay Salihoglu, Nedime Serakinci, Mahmut Cerkez Ergoren, Eileen Bresnan, Juan Iriberri, Paul Anders Fronth Nyhus, Edvardsen Bente, Hans Erik Karlsen, Peter N Golyshin, Josep M Gasol, Snejana Moncheva, Nina Dzhembekova, Zackary Johnson, Christopher David Sinigalliano, Maribeth Louise Gidley, Adriana Zingone, Roberto Danovaro, George Tsiamis, Melody S Clark, Ana Cristina Costa, Monia El Bour, Ana M Martins, R Eric Collins, Anne-Lise Ducluzeau, Jonathan Martinez, Mark J Costello, Linda A Amaral-Zettler, Jack A Gilbert, Neil Davies, Dawn Field, Frank Oliver Glöckner. 2015. The ocean sampling day consortium. Giga Science. 4, 1, 1-5.

2014

  1. Jack Westwood, Matthew Burnett, David Spratt, Michael Ball, Daniel J Wilson, Sally Wellsteed, David Cleary, Andy Green, Emma Hutley, Anna Cichowska, Susan Hopkins, Mark Wilcox, Anthony Kessel, Ghada Zoubiane, Lara Bethke, Derrick W Crook, Jimmy Walker, Mark Sutton, Philip Marsh, Ginny Moore, Peter Wilson, Alison Holmes, Peter Hoffman, Chris Smith, Beryl Oppenheim, Julian Parkhill, Neil Woodford, Julie Robotham, Claire Kidgell, Martin Anyim, Gabriella Gilkes, Dawn Field, Josh Quick, Tony Pickering, Benjamin C Kirkup, Jack A. Gilbert. 2014. The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013. Standards in genomic Science. 9(1), 12; http://www.standardsingenomics.com/content/9/1/12
  2. Jack A Gilbert, Madeleine Ball, Paul Blainey, Martin J Blaser, Brendan JM Bohannan, Ashley Bateman, John Bunge, Maria G Dominguez-Bello, Slava Epstein, Noah Fierer, Dirk Gevers, Tracy Grikscheit, Leila J Hamdan, James Harvey, Curtis Huttenhower, Benjamin Kirkup, Heidi H Kong, Christian Lauber, Katherine P Lemon, Susan V Lynch, Lance Martin, Charlene Mello, Joseph Palma, Roy Parker, Joseph Petrosino, Julia A Segre, Leslie Vosshall, Rui Yi, Rob Knight. 2014. Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012. Standards in Genomic Science. 9(1); 13. http://www.standardsingenomics.com/content/9/1/13
  3. Shogan Benjamin D., An Gary C., Schardey Hans M., Matthews Jeffrey B., Umanskiy Konstantin, Fleshman James W. Jr., Hoeppner Jens, Fry Donald E., Garcia-Granereo Eduardo, Jeekel Hans, van Goor Harry, Dellinger E. Patchen, Konda Vani, Gilbert Jack A., Auner Gregory W., and Alverdy John C. 2014. Proceedings of the First International Summit on Intestinal Anastomotic Leak, Chicago, Illinois, October 4–5, 2012. Surgical Infections. doi:10.1089/sur.2013.114.
  4. 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
  5. 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
  6. 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).
  7. 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. The founding charter of the Genomic Observatories Network. GigaScience 2014, 3:2 doi:10.1186/2047-217X-3-2
  8. 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. Genomic Sci. 2014 9:3
  9. John Alverdy, Jack A. Gilbert, Jennifer R DeFazio, Michael J Sadowsky, Eugene B Chang, Michael J Morowitz, Daniel H Teitelbaum. 2014. Proceedings of the ASPEN-Sponsored Workshop The Interface Between Nutrition and the Gut Microbiome: Implications and Applications for Human Health. Journal of Parenteral and Enteral Nutrition. Published online before print December 30, 2013, doi: 10.1177/0148607113517904.

2013

  1. 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.
  2. 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.
  3. Smith D, Alverdy J, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley S, Kirkup B, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert JA. 2013. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Standards in Genomic Science. 8:1.

2012

  1. 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)
  2. 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 Standards in Genomic Science. 6(2): 276–286.
  3. Amaro F, Gilbert JA, Owens S, Trimble W, Shuman HA. 2012. Whole-genome sequence of the human pathogen Legionella pneumophila Serotype 12 strain 570-CO-H. Journal of Bacteriology. 194 (6), 1613-1614

2011

  1. 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).
  2. 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)
  3. Amanda Birmingham, Jose C Clemente, Narayan Desai, Jack A. Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B Leontis, Craig Zirbel, Rob Knight, Alain Laederach. 2011. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Science, 4:2.

2010

  1. 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
  2. Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity G, Cochrane G, Wooley J, and Gilbert J.A. Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Special Interest Group at ISMB 2009. Standards in Genomic Science. Vol 1, No 3.
  3. 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 Standards in Genomic Science. 3:3
  4. 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.
  5. 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 Standards in Genomic Science. 3:3.
  6. 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.
  7. DavidsenT, 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:

2018

  1. Shawn M Doyle, Naseer Sangwan, Guanqun Wang, Jack A Gilbert, Brent C Christner, Ting F Zhu. 2018. Metagenomic analysis of basal ice from an Alaskan Glacier. Microbiome, 6(1), 123.

2014

  1. 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.
  2. Erik R Hawley, Hailan Piao, Nicole M Scott, Stephanie Malfatti, Ioanna Pagani, Marcel Huntemann, Amy Chen, Tijana Glavina del Rio, Brian Foster, Alex Copeland, Janet Jansson, Amrita Pati, Jack A Gilbert, Susannah Tringe, Thomas D Lorenson, Matthias Hess. 2014. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Standards in Genomic Science, 9;3.

2013

  1. Choudhari S, Smith S, Owens S, Gilbert JA, Shain DH, Dial RJ, Grigoriev A. 2013. Metagenome Sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska. Genome Announcements, 1 (2).

2012

  1. 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.
  2. 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.
  3. 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
  4. Phung L, Silver S, Trimble W, Gilbert JA. 2012. Draft genome of Halomonas strain GFAJ-1 (ATCC BAA-2256). Journal of Bacteriology. 194 (7), 1835-1836.

2011

  1. Temperton B, Thomas S, Tait K, Parry H, Emery M, Allen M, Quinn J, McGrath J, Gilbert JA. 2011. Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Standards in Genomic Science. 4:2

2010

  1. Gilbert JA, Meyer F, Joint I, Mühling M, Field D. 2010. Short Metagenome Report: Metagenomes and metatranscriptomes from the L4 long term coastal monitoring station in the Western English Channel. Standards in Genomic Science. Vol 3 (2).

Editorial:

2020

  1. Schloss PD, Junior M, Alvania R, Arias CA, Baumler A, Casadevall A, Detweiler C, Drake H, Gilbert JA, Imperiale MJ, Lovett S, Maloy S, McAdam AJ, Newton ILG, Sadowsky MJ, Sandri-Goldin RM, Silhavy TJ, Tontonoz P, Young JH, Cameron CE, Cann I, Fuller AO, Kozik AJ. 2020. The ASM Journals Committee Values the Contributions of Black Microbiologists. mBio, 11(4):e01998-20. DOI: 10.1128/mBio.01998-20

2019

  1. Ileana M. Cristea, Pieter C. Dorrestein, Jonathan A. Eisen, Jack A. Gilbert, Julie A. Huber, Janet K.Jansson, Rob Knight, Katherine S. Pollard, Jeroen Raes, Pamela A. Silver, Nicole S. Webster, Jian Xu. 2019. Early-Career Scientists Shaping the World. mSystems  4 (3) e00196-19; DOI:1128/mSystems.00196-19
  2. Gilbert JA. (2019). Acknowledgment of Ad Hoc Reviewers. mSystems, 4(6):e00797-19.

2018

  1. Gilbert JA. 2018. Ecological Medicine. Environmental Microbiology. doi: 10.1111/1462-2920.1411
  2. Gilbert JA, Jannson J, Knight R. 2018. Earth Microbiome Project and Global Systems Biology. mSystems mSystems 3 (3), e00217-17
  3. Gilbert JA., 2018. Early-Career Systems Microbiology Scientists. mSystems 3(2) e00002-18

2016

  1. 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:1128/mSystems.00088-16
  2. Gilbert JA, Klyczek KK, Elliott SL. 2016. Introducing the JMBE Themed Issue on Scientific Citizenship. Journal of Microbiology and Biology Education. 17(1). DOI: http://dx.doi.org/10.1128/jmbe.v17i1.1114.

2015

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

Abstracts:

2021

  1. Ozen S, Lutz HL, Rivera VM, Reiff A, Batu ED, Anderson E, Salas Garcia M, Aldrovandi G, Akbaba TH, Pazarbasi I, Bilginer Y, Balat A, Balci-Peynicioglu B, Gilbert JA, Dedeoglu F, Hausmann JS.. Microbiome is not linked to clinical disease severity of familial Mediterranean fever in an international cohort of children. Clinical and Experimental Rheumatology. 2021 Jul. PMID: 34251310.
  2. Yang K, Hou Y, Zhang Y, Liang H, Sharma A, Zheng W, Wang L, Torres R, Tatebe K, Chmura SJ, Pitroda SP, Gilbert JA, Fu Y, Weichselbaum RR. (2021). Suppression of local type I interferon by gut microbiota–derived butyrate impairs antitumor effects of ionizing radiation. J Exp Med, 218(3): e20201915. DOI: 10.1084/jem.20201915

2020

  1. Bernabe BP, Dowty S, Pezley L, Goel N, Hill E, Gibbons R, Tussing-Humphreys L, Maki P, Gilbert JA. Depression During Pregnancy is Associated With an Altered Gut Microbiome in an Urban Diverse Population. Biological Psychiatry, 87(9):S36. 2020. DOI: 10.1016/j.biopsych.2020.02.114
  2. Bernabe BP, Rackers H, Dowty S, Tussing-Humphreys L, Pezley L, Meltzer-Brody S, Knickmeyer R, Carroll I, Maki P, Gilbert JA, Kimmel M. Host Immunity, the Microbiome, and Perinatal Anxiety. Biological Psychiatry, 87(9):S36-37. 2020. DOI: 10.1016/j.biopsych.2020.02.115
  3. Barr GM, Hrusch CL, Leone V, Fei N, Mills KAM, Hollinger MK, Chang EB, Gilbert JA, Sperling AI. (2020). Microbiome-Dependent Effects Influence Susceptibility to Lung Injury and Fibrosis. Am J Respir Crit Care Med, 201:A5413. DOI: 10.1164/ajrccm-conference.2020.201.1_MeetingAbstracts.A5413
  4. Dodiya HB, Lutz H, Weigle I, Roman-Santiago C, Patel P, Olszewski M, Zhang C, Zhang X, Schipma MJ, Tanzi RE, Gilbert JA, Sisodia SS. Gut microbiome perturbations influence brain amyloidosis only in the presence of microglia in APPPS1-21 mice. 2020 Alzheimer’s Association International Conference, July 2020. https://alz.confex.com/alz/20amsterdam/meetingapp.cgi/Paper/40609
  5. Grieneisen L, Dasari M, Gould TJ, Bjork JR, Grenier J, Yotova V, Jansen D, Gottel N, Gilbert JA, Barreiro L, Alberts SA, Tung J, Archie E, Blekhman R. (2020) Heritability of the Gut Microbiome in Wild Baboons (Papio Cynocephalus). American Journal of Primatology, Volume 82.
  6. Urlacher SS, Sharma A, Gilbert JA, Pontzer H, Snodgrass JJ, Gildner TE, Madimenos FC, Leibert MA, Sugiyama LS, Dugas LR. (2020). Childhood gut microbiome composition among the Amazonian Shuar: Testing links to changing diet, lifestyle, energy expenditure, and health. American Journal of Physical Anthropology, 171:290-291.
  7. Chen LW, Xu J, Soh SE, Aris IM, Tint MT, Gluckman PD, Tan KH, Shek LPC, Chong YS, Yap F, Godfrey KM, Gilbert JA, Karnani N, Lee YS. (2020). Implication of gut microbiota in the association between infant antibiotic exposure and childhood obesity and adiposity accumulation. International Journal of Obesity, online 22 April 2020. DOI: 10.1038/s41366-020-0572-0

2019

  1. Gilbert, JA. (Dec 2019). The Human Microbiome in Precision Medicine. Menopause – The Journal of the North American Menopause Society, 26(12):1447. Lippincott Williams & Wilkins.
  2. Geynisman-Tan J, Kenton K, Tavathia M, Yee Al, Gilbert JA, Collins SA, Lewicky-Gaupp C, Mueller M. Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? International Urogynecology Journal, 30:S265-S266. Springer London LTD.
  3. Dasari M, Jansen D, Gould T, Grieneisen LE, Bjorl JR, Grenier J, Yotova V, Gottel NR, Gilbert JA, Barreiro L, Blekham R, Altmann J, Alberts SC, Tung J, Archie EA. (Aug 2019). Does the host-associated microbiome undergo successional changes with age? 2019 ESA Annual Meeting (August 11–16).
  4. Gilbert JA. (Aug 2019). Earth Microbiome Project: Human and environmental microbial health concepts. 2019 ESA Annual Meeting (August 11–16).
  5. Chew J, Sharma A, Rodriguez SH, Andrew B, Schechet S, Gilbert JA, Claud E, Skondra D. (July 2019). Early gut microbiome profile in high-risk preterm infants with and without retinopathy of prematurity. Investigative Ophthalmology & Visual Science, 60(9):1661. 
  6. Dodiya HB, Kuntz T, Shaik SM, Baufield C, Leibowitz J, Zhang Xioqiong, Butovsky O, Gilbert JA, Sisodia SS. (July 2019). Sex-Specific Perturbations in Cerebral Amyloidosis and Microglia Phenotypes in Antibiotic-Treated APPSWE/PS1L166P Transgenic Mice. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, 15(7)L P319. Elsevier.
  7. Gilbert JA, Knight R, Dominquez-Bello MG, Blaser M. (June 2019). Microbiome Archiving Done Right. SCIENTIST, 33(6):22-23. LABX Media Group.
  8. Swoboda AT, Sharma A, Olopade OI, Nanda R, Gilbert JA. Characterizing the Gut Microbiome of Patients with Triple-Negative Breast Cancer. Journal of Clinical Oncology, 37(15 Supp):e14186. American Society of Clinical Oncology.
  9. Bernabe BP, Dowty S, Pezley L, Shah Z, Goel N, Hill E, Gibbons R, Tussing-Humphreys L, Maki P, Gilbert JA. (May 2019). S87 Depression During Pregnancy is Associated With an Altered Gut Microbiome. Biological Psychiatry, 85(10):S330. Elsevier.
  10. Gaines S, Williamson A, Pena R, Jacobson R, Mozdzen J, Alverdy JC, Zaborina O, Hyman N, Gilbert JA, Shogan BD. (May 2019). 234 – Preoperative Bowel Preparation Decreases Colonization with Collagenase Producing Bacteria in Non-Obese Patients. Gastroenterology, 156(6):S1393-1394. Elsevier.
  11. Sperling AI, Fei N, Leone V, Barron GM, Mills KAM, Gilbert JA, Hrusch CL. (May 2019). Microbial Regulation of Lung Injury in Mice. D92 The Microbiome and Lung Disease, A7029. American Thoracic Society. DOI: 10.1164/ajrccm-conference.2019.199.1_MeetingAbstracts.A7029
  12. Honeker LK, Sharma A, Gozdz J, Theriault B, Patil K, Gimenes JA, Hotner A, Piviniouk V, Igartua C, Stein MM, Holbreich M, von Mitius E, Ober C, Gilbert JA, Vercelli D. (May 2019). Gut Microbiota from Amish but Not Hutterite Children Protect Germ-Free Mice from Experimental Asthma. D92 The Microbiome and Lung Disease, A7022. American Thoracic Society.
  13. Sharma A, Laxman B, Naureckas ET, Hogarth DK, Sperling AI, Solway J, Ober C, Gilbert JA, White SR. (May 2019). Reciprocal Fungal and Bacterial Microbiota in Airways of Patients with T2-High Associated Asthma. A21 Advances in Asthma Pathogenesis, A1047. American Thoracic Society. DOI: 10.1164/ajrccm-conference.2019.199.1_MeetingAbstracts.A1047
  14. Shojaee S, Sharma A, Gottel N, Sanchez T, Gilbert JA, Rahman N. (May 2019). Microbiome Profile Associations in Malignant Pleural Effusion. A30 What’s New in International Pulmonary and Pleural Disease, A1249. American Thoracic Society. DOI: 10.1164/ajrccm-conference.2019.199.1_MeetingAbstracts.A1249
  15. Groer M, Dutra SV, Miller E, Yee AL, Gilbert JA. (April 2019). The Preterm Infant Gut Microbiome, Human Milk Volume and Immunobiology, and Growth. The FASEB Journal, 33(1 Supp):722.1. The Federation of American Societies for Experimental Biology.
  16. Bernabe BP, Gilbert JA. (Mar 2019). Dynamic Core Taxonomical and Metabolic Signatures in the Perinatal Period. Reproductive Sciences, 26:346A. Sage Publications Inc.
  17. El Andaloussi A, Gilbert JA, Sharma A, Al-Hendy A, Nahed I. (Mar 2019). Impact of Uterine Microbiota on the Prevalence of Uterine Fibroids in Women of Color. Reproductive Sciences, 26:202A. Sage Publications Inc.
  18. Mueller MG, Geynisman J, Arnold W, Kenton K, Tavathia M, Gilbert JA. (Mar 2019). 82: Bladder arithmetic: can subtraction help determine the true urinary microbiome? American Journal of Obstetrics & Gynocology, 220(3 Supp):S757-S758. Elsevier. DOI: 10.1016/j.ajog.2019.01.112
  19. Polster SP, Shen L, Sharma A, Stadnik A, Carrion-Penagos J, Girard R, Koskimaki J, Romanos S, Lyne S, Shenkar R, Cao Y, Yan K, Lee C, Akers A, Morrison L, Robinson M, Zafar A, Tang A, Mericko-Ishizuke P, Gilbert JA, Kim H, Kahm M, Awad IA. (Feb 2019). Stroke, 50(Supp 1):ATMP107. Lippincott Williams & Wilkins. DOI: 10.1161/str.50.suppl_1.TMP107