Publications

Ecological succession and viability of human-associated microbiota on restroom surfaces

Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. 2014. Appl Environ Microbiol. 2014 pii: EM.03117-14: PDF:Appl. Environ. Microbiol.-2014-Gibbons-AEM.03117-14

Probing the Microbial Mysteries of Wine

Zarraonaindia I and Gilbert JA. 2014. Microbe-Volume9. PDF: znw01114000442

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness.

Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JC. 2014. mBio. 5:e01361-14. (PDF): mBio-2014-Zaborin-

The role of macrobiota in structuring microbial communities along rocky shores

Catherine A Pfister, Jack A Gilbert, Sean M Gibbons. 2014. PeerJ. 16;2:e631. doi: 0.7717/peerj.631(PDF);peerj-631

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome

LaBelle EV, Marshall CW, Gilbert JA, May HD. 2014. PLoS One: 15;9(10):e109935 (PDF):journal.pone.0109935.

Development of the preterm infant gut microbiome: a research priority.

Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. 2014. Microbiome. 13;2:38. (PDF):2049-2618-2-38

Science is innate!

Gilbert JA, 2014 Genome Biology 15:477. (PDF):Gilbert-GenomeBiol2014

Longitudinal analysis of microbial interaction between humans and the indoor environment
Lax S, Smith DP, Hampton-Marcell J, Owens S, Handley K, et al. 2014 Science 345: 1048-1052 doi: 10.1126/Science.1254529.  Abstract, Full-text and Re-print.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, et al. 2014 MBio 15:e01371-14. doi: 10.1128/mBio.01371-14. (PDF):mBio-2014-Shade-(1).

The Earth Microbiome project: successes and aspirations

Gilbert JA, Jansson, JK, Knight R. 2014 BMC Biol. 12, 69. (PDF):s12915-014-0069-1.

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, et al. 2014 PeerJ.21, e545. doi: 10.7717/peerj.545. eCollection 2014. (PDF):peerj-545.

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.
Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, et al. 2013 Standards in Genomic Sciences 8: 1. doi:10.4056/sigs.3717348.

Metagenome Sequencing of Prokaryotic Microbiota Collected from Byron Glacier, Alaska.
Choudhari S, Smith S, Owens S, Gilbert JA, Shain DH, et al. 2013 Genome Announcements 1: e00099–13–e00099–13. doi:10.1128/genomeA.00099-13.

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

Evidence for a persistent microbial seed bank throughout the global ocean.
Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, et al. 2013 Proceedings of the National Academy of Sciences 110: 4651–4655. doi:10.1073/pnas.1217767110.

Studying the microbiology of the indoor environment.
Kelley ST, Gilbert JA 2013 Genome Biology 14: 202. doi:10.1186/gb-2013-14-2-202.

Beyond the Genome: Community-Level Analysis of the Microbial World.
Zarraonaindia I, Smith DP, Gilbert JA 2013 Biology & Philosophy 28: 261-181. doi:10.1007/s10539-012-9357-8.

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms.
Roy A-S, Gibbons SM, Schunck H, Owens S, Caporaso JG, et al. 2013 Biogeosciences 10: 555–566. doi:10.5194/bg-10-555-2013.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, et al. 2012 Proceedings of the National Academy of Sciences 109: 21390–21395. doi:10.1073/pnas.1215210110.

Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15.
Trimble WL, Phung LT, Meyer F, Gilbert JA, Silver S 2012 Journal of Bacteriology 194: 6986–6987. doi:10.1128/JB.01912-12.

A call for an international network of genomic observatories (GOs).
Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, et al. 2012 GigaScience 1: 5. doi:10.1186/2047-217X-1-5.

Draft Genome Sequence of Achromobacter piechaudii Strain HLE.
Trimble WL, Phung LT, Meyer F, Silver S, Gilbert JA 2012 Journal of Bacteriology 194: 6355–6355. doi:10.1128/JB.01660-12.

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.
Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, et al. 2012 Standards in Genomic Sciences 7: 159–165. doi:10.4056/sigs.3156511.

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels.
Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, et al. 2012 PLoS ONE 7: e46219. doi:10.1371/journal.pone.0046219.

Draft Genome Sequence of Alcaligenes faecalis subsp faecalis NCIB 8687 (CCUG 2071).
Phung LT, Trimble WL, Meyer F, Gilbert JA, Silver S 2012 Journal of Bacteriology 194: 5153–5153. doi:10.1128/JB.01185-12.

Intestinal Tissues Induce an SNP Mutation in Pseudomonas aeruginosa That Enhances Its Virulence: Possible Role in Anastomotic Leak.
Olivas AD, Shogan BD, Valuckaite V, Zaborin A, Belogortseva N, et al. 2012 PLoS ONE 7: e44326. doi:10.1371/journal.pone.0044326.

Effect of elevated CO2 on the dynamics of particle attached and free living bacterioplankton communities in an Arctic fjord.
Sperling M, Piontek J, Gerdts G, Wichels A, Schunck H, et al. 2012 Biogeosciences Discussions 9: 10725–10755. doi:10.5194/bgd-9-10725-2012.

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.
Trimble WL, Keegan KP, D’Souza M, Wilke A, Wilkening J, et al. 2012 BMC Bioinformatics 13: 183. doi:10.1186/1471-2105-13-183.

Modeling microbial community structure and functional diversity across time and space.
Larsen PE, Gibbons SM, Gilbert JA 2012 FEMS Microbiology Letters 332: 91–98. doi:10.1111/j.1574-6968.2012.02588.x.

Isolation and initial characterization of a novel type of Baeyer-Villiger monooxygenase activity from a marine microorganism.
Willetts A, Joint I, Gilbert JA, Trimble W, Mühling M 2012 Microbial Biotechnology 5: 549–559. doi:10.1111/j.1751-7915.2012.00337.x.

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life.
Foster JA, Bunge J, Gilbert JA, Moore JH 2012 Briefings in Bioinformatics 13: 420–429. doi:10.1093/bib/bbr080.

Unlocking the potential of metagenomics through replicated experimental design.
Knight R, Jansson J, Field D, Fierer N, Desai N, et al. 2012 Nature Biotechnology 30: 513–520. doi:10.1038/nbt.2235.

Report of the 13th Genomic Standards Consortium Meeting.
Gilbert JA, Bao Y, Wang H, Sansone S-A, Edmunds SC, et al. 2012 Standards in Genomic Sciences 6: 276–286. doi:10.4056/sigs.2876184.

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

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, et al. 2012 The ISME Journal. doi:10.1038/ismej.2012.8.

Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction.
Larsen P, Hamada Y, Gilbert J 2012 J Biotechnol. doi:10.1016/j.jbiotec.2012.03.009

Omics for understanding microbial functional dynamics.
Jansson JK, Neufeld JD, Moran MA, Gilbert JA 2012 Environ Microbiol 14: 1–3. doi:10.1111/j.1462-2920.2011.02518.x.

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

Defining seasonal marine microbial community dynamics.
Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, et al. 2012 ISME J 6: 298–308. doi:10.1038/ismej.2011.107.

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011.
Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, et al. 2011 SIGS 5: 243–247. doi:10.4056/sigs.2134923.

The Western English Channel contains a persistent microbial seed bank.
Caporaso JG, Paszkiewicz K, Field D, Knight R, Gilbert JA 2011 The ISME Journal. doi:10.1038/ismej.2011.162.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, et al. 2011 Nature Biotechnology 29: 415–420. doi:10.1038/nbt.1823.

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

Microbial Metagenomics: Beyond the Genome.
Gilbert JA, Dupont CL 2011 Annu Rev Mar Sci 3: 347–371. doi:10.1146/annurev-marine-120709-142811.

Survey data are still vital to science.
Gilbert J, O’Dor R, Vogel T 2011 Nature 469: 162–162. doi:10.1038/469162a.

Predicted Relative Metabolomic Turnover (PRMT) – determining metabolic turnover from a coastal marine metagenomic dataset.
Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, et al. 2011 Microbial Informatics and Experimentation 1: 4. doi:10.1186/2042-5783-1-4.

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

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel.
Gilbert JA, Meyer F, Schriml L, Joint IR, Mühling M, et al. 2010 Standards in Genomic Sciences 3: 183–193. doi:10.4056/sigs.1202536.

Metagenomics: A foundling finds its feet.
Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM 2010 Standards in Genomic Sciences 3: 212–213. doi:10.4056/sigs.1213842.

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices.
Mitra S, Gilbert JA, Field D, Huson DH 2010 The ISME Journal 4: 1236–1242. doi:10.1038/ismej.2010.51.

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, et al. 2010 SIGS 3: 249–253. doi:10.4056/aigs.1443528.

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project.
Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, et al. 2010 SIGS 3: 243–248. doi:10.4056/sigs.1433550.

Pyrosequencing of Mytilus galloprovincialis cDNAs Tissue-Specific Expression Patterns.
Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, et al. 2010 PLoS ONE 5: e8875. doi:10.1371/journal.pone.0008875.

Evidence for phosphonate usage in the coral holobiont.
Thomas S, Burdett H, Temperton B, Wick R, Snelling D, et al. 2009 The ISME Journal 4: 459–461. doi:10.1038/ismej.2009.129.

The seasonal structure of microbial communities in the Western English Channel.
Gilbert JA, Field D, Swift P, Newbold L, Oliver A, et al. 2009 Environ Microbiol 11: 3132–3139. doi:10.1111/j.1462-2920.2009.02017.x.

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.
Temperton B, Field D, Oliver A, Tiwari B, Mühling M, et al. 2009 The ISME Journal 3: 792–796. doi:10.1038/ismej.2009.32.

Nitrogen fixation in the western English Channel (NE Atlantic Ocean).
Rees A, Gilbert J, Kelly-Gerreyn B 2009 Marine Ecology Progress Series 374: 7–12. doi:10.3354/meps07771.

The First RSBI (ISA-TAB) Workshop: Can a Simple Format Work for Complex Studies OMICS: A Journal of Integrative Biology 12: 143–149. Sansone S-A, Rocca-Serra P, Brandizi M, Brazma A, Field D, et al.
2008 doi:10.1089/omi.2008.0019.

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome.
Gilbert JA, Mühling M, Joint I 2008 The ISME Journal 2: 790–793. doi:10.1038/ismej.2008.49.

The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, et al. 2008 Nature Biotechnology 26: 541–547. doi:10.1038/nbt1360.

A Ca2+-dependent bacterial antifreeze protein domain has a novel b-helical ice-binding fold.
Garnham CP, Gilbert JA, Hartman CP, Campbell RL, Laybourn-Parry J, et al. 2008 Biochemical Journal 411: 171. doi:10.1042/BJ20071372.

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

The basis for hyperactivity of antifreeze proteins.
Scotter AJ, Marshall CB, Graham LA, Gilbert JA, Garnham CP, et al.
2006 Cryobiology 53: 229–239. doi:10.1016/j.cryobiol.2006.06.006.

A hyperactive, Ca2+-dependent antifreeze protein in an Antarctic bacterium.
Gilbert JA, Davies PL, Laybourn-Parry J
2005 FEMS Microbiology Letters 245: 67–72. doi:10.1016/j.femsle.2005.02.022.

Demonstration of antifreeze protein activity in Antarctic lake bacteria.
Gilbert JA, Hill PJ, Dodd CER, Laybourn-Parry J
2004 Microbiology 150: 171–180. doi:10.1099/mic.0.26610-0.

A facile method for determining ice recrystallization inhibition by antifreeze proteins.
Tomczak MM, Marshall CB, Gilbert JA, Davies PL
2003 Biochemical and Biophysical Research Communications 311: 1041–1046. doi:10.1016/j.bbrc.2003.10.106.