PUBLICATIONS

2020

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes
Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, Faust K, Knight R, Jansson JK, Cordona C, Rottjers L, Xu J. 
GenomMicrobiome
, 8:82-94 (June 2020) DOI: 10.1186/s40168-020-00857-2

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
Zaborin A, Bernabe BP, Keskey R, Sangwan N, Hyoju S, Gottel N, Gilbert JA, Zaborina O, Alverdy JC.  
mSystems, 5(3):e00377-20. May/June 2020. DOI: 10.1128/mSystems.00377-20

Longitudinal survey of microbiome associated with particulate matter in a megacity
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. 
Genome Biology; 21(1), 1-11 (March 2020) DOI: 10.1186/s13059-020-01964-x

2019

82: Bladder arithmetic: can subtraction help determine the true urinary microbiome?
MG Mueller, J Geynisman, W Arnold, K Kenton, M Tavathia, J Gilbert
American Journal of Obstetrics & Gynecology 220 (3), S757-S758, 2019 link

Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants
AL Yee, E Miller, LJ Dishaw, JM Gordon, M Ji, S Dutra, TTB Ho, JA Gilbert, …
mSystems 4 (1), e00229-18, 2019 link

Bacterial communities associated with cell phones and shoes
DA Coil, RY Neches, JM Lang, G Jospin, WE Brown, D Cavalier, …
PeerJ Preprints, 2019 link

 

 

Toward unrestricted use of public genomic data
RI Amann, S Baichoo, BJ Blencowe, P Bork, M Borodovsky, …
Science 363 (6425), 350-352, 2019 link

The Human Microbiome in Health and Disease
WM Arnold, ES Hill, N Fei, AL Yee, MS Garcia, LE Cralle, JA Gilbert
Genomic Applications in Pathology, 783-798, 2019 link

2018

GABA-modulating bacteria of the human gut microbiota
P Strandwitz, KH Kim, D Terekhova, JK Liu, A Sharma, J Levering, …
Nature microbiology, 1, 2018 link

Enteric dysbiosis and fecal calprotectin expression in premature infants
TTB Ho, MW Groer, B Kane, AL Yee, BA Torres, JA Gilbert, A Maheshwari
Pediatric research, 1, 2018 link

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales
HY Li, H Wang, HT Wang, PY Xin, XH Xu, Y Ma, WP Liu, CY Teng, …
Microbiome 6 (1), 187, 2018 link

Dichotomous development of the gut microbiome in preterm infants
TTB Ho, MW Groer, B Kane, AL Yee, BA Torres, JA Gilbert, A Maheshwari
Microbiome 6 (1), 157, 2018 link

Gut microbial features can predict host phenotype response to protein deficiency
G Navarro, A Sharma, LR Dugas, T Forrester, JA Gilbert, BT Layden
Physiological reports 6 (23), e13932, 2018 link

Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol
LR Dugas, L Lie, J Plange-Rhule, K Bedu-Addo, P Bovet, EV Lambert, …
BMC public health, 2018 link

Metagenomic analysis of basal ice from an Alaskan glacier
SM Doyle, N Sangwan, G Wang, JA Gilbert, BC Christner, TF Zhu
Microbiome, 2018 link

Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil
K Fan, P Weisenhorn, JA Gilbert, H Chu
Soil Biology and Biochemistry, 2018 link

Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow’s milk allergy
RB Canani, F De Filippis, R Nocerino, L Paparo, C Di Scala, L Cosenza, …
Scientific reports, 2018 link

Microbiology of the built environment
JA Gilbert, B Stephens
Nature Reviews Microbiology, 2018 link

Microbial exposure and human health
JA Sharma, JA Gilbert
Current opinion in microbiology 44, 79-87, 2018 link

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment
H Wang, JA Gilbert, Y Zhu, X Yang
Science of The Total Environment 631, 1342-1349, 2018 link

Genetic correlation network prediction of forest soil microbial functional organization
B Ma, K Zhao, X Lv, W Su, Z Dai, JA Gilbert, PC Brookes, K Faust, J Xu
The ISME journal, 2018 link

Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields
K Fan, P Weisenhorn, JA Gilbert, Y Shi, Y Bai, H Chu
Soil Biology and Biochemistry 121, 185-192, 2018 link

Systems biology of the human microbiome
BP Bernabé, L Cralle, JA Gilbert
Current opinion in biotechnology 51, 146-153 2018 link

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics
C Cardona, S Lax, P Larsen, B Stephens, J Hampton-Marcell, …
MSystems 3 (3), e00052-18 2018 link

Earth Microbiome Project and Global Systems Biology
JA Gilbert, JK Jansson, R Knight
MSystems 3 (3), e00217-17 2018 link

American Gut: an Open Platform for Citizen Science Microbiome Research
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, …
MmSystems 3 (3), e00031-18 2018 link

Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions
EB Chen, C Cason, JA Gilbert, KJ Ho
Journal of Gastrointestinal Surgery, 1-12 link

Early-Career Systems Microbiology Scientists
JA Gilbert
MSystems 3 (2), e00002-18 2018 link

Soil bacterial diversity is associated with human population density in urban greenspaces
H Wang, M Cheng, M Dsouza, P Weisenhorn, T Zheng, JA Gilbert
Environmental science & technology 52 (9), 5115-5124 link

Ecological medicine
JA Gilbert
Environmental microbiology 2018 link

Current understanding of the human microbiome
JA Gilbert, MJ Blaser, JG Caporaso, JK Jansson, SV Lynch, R Knight
Nature medicine 24 (4), 392 2018 link

Correction: A microbial survey of the International Space Station (ISS)
JM Lang, DA Coil, RY Neches, WE Brown, D Cavalier, M Severance, …
PeerJ 5, e4029/correction-1 2018 link

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017)
RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, … 2018 link

Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic
LM Seyler, LR McGuinness, JA Gilbert, JF Biddle, D Gong, LJ Kerkhof
FEMS microbiology ecology 94 (3), fiy014 2018 link

Gut microbial features can predict host phenotype response to protein deficiency
JM Lang, DA Coil, RY Neches, WE Brown, D Cavalier, M Severance, …G Navarro, A Sharma, LR Dugas, T Forrester, JA Gilbert, BT Layden bioRxiv, 398248 2018 link

Dysbiosis in Children Born by Caesarean Section
MCS Garcia, AL Yee, JA Gilbert, M Dsouza
Annals of Nutrition and Metabolism 73 (3), 24-32 2018 link

Associations between Afrotropical bats, parasites, and microbial symbionts
HL Lutz, EW Jackson, C Dick, PW Webala, WS Babyesiza, JCK Peterhans, …
bioRxiv, 340109 2018 link

Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes …
MM David, C Tataru, J Daniels, J Schwartz, J Keating, J Hampton-Marcell, …
bioRxiv, 319236 2018 link

Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake
M Han, M Dsouza, C Zhou, H Li, J Zhang, C Chen, Q Yao, C Zhong, …
bioRxiv, 244657 2018 link

2017

Taxonomic and functional patterns across soil microbial communities of global biomes

MF Noronha, GVL Júnior, JA Gilbert, VM de Oliveira
Science of The Total Environment 609, 1064-1074 2017 link

A microbial survey of the International Space Station (ISS)

JM Lang, DA Coil, RY Neches, WE Brown, D Cavalier, M Severance, …
PeerJ 5, e4029 5 2017 link

A communal catalogue reveals Earth’s multiscale microbial diversity

LR Thompson, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, …
Nature 551 (7681) 2017 link

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill

KM Handley, YM Piceno, P Hu, LM Tom, OU Mason, GL Andersen, …
The ISME journal 11 (11), 2569 2017 link

Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields

K Fan, C Cardona, Y Li, Y Shi, X Xiang, C Shen, H Wang, JA Gilbert, …
Soil Biology and Biochemistry 113, 275-284 2017 link

Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure

SA Wood, JA Gilbert, JW Leff, N Fierer, H D’Angelo, C Bateman, …
Soil Biology and Biochemistry 112, 258-268 2017 link

Microbial diversity in an intensively managed landscape is structured by landscape connectivity

JS Griffin, N Lu, N Sangwan, A Li, M Dsouza, AJ Stumpf, T Sevilla, …
FEMS microbiology ecology 93 (10), fix120 2017 link

Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings

LL Dent, SN Mandape, S Pratap, J Dong, J Davis, JA Gaddy, K Amoah, …
BMC Proceedings 11 (9), 2017 link

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling

L Wu, Y Yang, S Wang, H Yue, Q Lin, Y Hu, Z He, JD Van Nostrand, …
The ISME journal 11 (9), 2102 2017 link

Identifying the plant‐associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery

SL Jackrel, SM Owens, JA Gilbert, CA Pfister
Molecular Ecology Resources 17 (5), 931-942 2017 link

Metabolic reconstruction and modeling microbial electrosynthesis

CW Marshall, DE Ross, KM Handley, PB Weisenhorn, JN Edirisinghe, …
Scientific Reports 7 (1), 8391 2017 link

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, …
Nature biotechnology 35 (8), 725 2017 link

Preparing the Bowel for Surgery: Learning from the Past and Planning for the Future

JC Alverdy, N Hyman, J Gilbert, JN Luo, M Krezalek
Journal of the American College of Surgeons 225 (2), 324-332 2017 link

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74

RB Canani, F De Filippis, R Nocerino, M Laiola, L Paparo, A Calignano, …
Applied and environmental microbiology, AEM. 01206-17 2017 link

Erratum for Linz et al.,“Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes”

AM Linz, BC Crary, A Shade, S Owens, JA Gilbert, R Knight, KD McMahon
mSphere 2 (4) 2017 link

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

AM Linz, BC Crary, A Shade, S Owens, JA Gilbert, R Knight, KD McMahon
mSphere 2 (3), e00169-17 2017 link

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

JW Neilson, K Califf, C Cardona, A Copeland, W van Treuren, …
MSystems 2 (3), e00195-16 2017 link

Comparative genomic analysis reveals habitat-specific genes and regulatory hubs within the genus Novosphingobium

R Kumar, H Verma, S Haider, A Bajaj, U Sood, K Ponnusamy, S Nagar, …
MSystems 2 (3), e00020-17 2017 link

The microbiome-mitochondrion connection: common ancestries, common mechanisms, common goals

A Franco-Obregón, JA Gilbert
MSystems 2 (3), e00018-17 2017 link

Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System

J Gilbert, R Knight
St. Martin’s Press 2017 link

Size, composition, and source profiles of inhalable bioaerosols from Colorado dairies

JW Schaeffer, S Reynolds, S Magzamen, A VanDyke, NR Gottel, …
Environmental science & technology 51 (11), 6430-6440 2017 link

Bacterial colonization and succession in a newly opened hospital
S Lax, N Sangwan, D Smith, P Larsen, KM Handley, M Richardson, …
Science translational medicine 9 (391), eaah6500 2017 link

Modulation of Neointimal Hyperplasia Severity in Rats by Commensal Microbial Transfer
CA Cason, TM Kuntz, N Gottel, L Xiong, Q Jiang, EB Chang, JA Gilbert, …
Arteriosclerosis, Thrombosis, and Vascular Biology 37 (suppl_1), A318-A318 2017 link

Fecal microbiota transplantation provokes systemic host immune changes that drive the clearance of lethal disseminated pathogens
SM Kim, J DeFazio, S Hyoju, M Krezalek, N Khodarev, N Sangwan, …
The Journal of Immunology 198 (1 Supplement), 199.19-199.19 2017 link

Optimum Operating Room Environment for the Prevention of Surgical Site Infections
S Gaines, JN Luo, J Gilbert, O Zaborina, JC Alverdy
Surgical infections 18 (4), 503-507 2017 link

Correction for Gonzalez et al.,“Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort”
A Gonzalez, E Hyde, N Sangwan, JA Gilbert, E Viirre, R Knight
MSystems 2 (2), e00023-17 2017 link

Invasive plants rapidly reshape soil properties in a grassland ecosystem
SM Gibbons, Y Lekberg, DL Mummey, N Sangwan, PW Ramsey, …
MSystems 2 (2), e00178-16 2017 link

Celebrating parasites
CS Greene, LX Garmire, JA Gilbert, MD Ritchie, LE Hunter
Nature genetics 49 (4), 483 2017 link

Forensic microbiology in built environments
S Lax, JA Gilbert
Forensic Microbiology, 328 2017 link

Change in Emiliania huxleyi virus assemblage diversity but not in host genetic composition during an ocean acidification mesocosm experiment
A Highfield, I Joint, JA Gilbert, KJ Crawfurd, DC Schroeder
Viruses 9 (3), 41 2017 link

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

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in Eastern China B Ma, Z Dai, H Wang, M Dsouza, X Liu, Y He, J Wu, JLM Rodrigues, … msystems 2 (1), e00174-16 8 2017

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’ TE Brewer, KM Handley, P Carini, JA Gilbert, N Fierer Nature microbiology 2 (2), 16198 27 2017

The Chicago River Microbiome Project: Update from Argonne National Laboratory MC Negri, J Cacho, H Ssegane, M Dsouza, JA Gilbert, G Rijal Proceedings of the Water Environment Federation 2017 (4), 5754-5765 2017

A New Era for the Chicago Area Waterway System: Update from the Metropolitan Water Reclamation District of Greater Chicago G Rijal, A Fore, DS Pierre, MC Negri, JA Gilbert Proceedings of the Water Environment Federation 2017 (4), 5738-5753 2017

Three Year-Long Amplicon Study of the Chicago Area Waterway System (Caws) Microbiome M Dsouza, N Sangwan, JH Marcell, JA Gilbert, C Negri, G Rijal Proceedings of the Water Environment Federation 2017 (4), 5766-5782 1 2017

Climate change will lead to pronounced shifts in the diversity of soil microbial communities J Ladau, Y Shi, X Jing, JS He, L Chen, X Lin, N Fierer, JA Gilbert, … bioRxiv, 180174 2017

The gut microbiome and the mechanism of surgical infection JC Alverdy, SK Hyoju, M Weigerinck, JA Gilbert British Journal of Surgery 104 (2), e14-e23 8 2017

The microbiome as a source of new enterprises and job creation: considering clinical faecal and synthetic microbiome transplants and therapeutic regulation D van der Lelie, S Taghavi, C Henry, JA Gilbert Microbial biotechnology 10 (1), 4-5 5 2017

Introducing the microbiome into precision medicine TM Kuntz, JA Gilbert Trends in pharmacological sciences 38 (1), 81-91 23 2017

How do we make indoor environments and healthcare settings healthier? JA Gilbert Microbial biotechnology 10 (1), 11-13, 2017

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome H Wang, N Sangwan, HY Li, JQ Su, WY Oyang, ZJ Zhang, JA Gilbert, … The ISME journal 11 (1), 100, 2017

2016

The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals
Alfredo Franco-Obregón, Jack A. Gilbert.
mSystems, 2016 PDF

Optimum Operating Room Environment for the Prevention of Surgical Site Infections
JN Luo, JA Gilbert, O Zaborina, JC Alverdy
Surgical Infections, 2016 link

Celebrating Parasites
Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter
Nature Genetics, 2016 link

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem
Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA
mSystems, 2016 PDF

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment
Highfield A, Joint I, Gilbert JA, Crawfurd KJ, Schroeder DC
Viruses, 2016 PDF

The human microbiome: an emerging tool in forensics
Hampton-Marcell JT, Lopez JV, Gilbert JA
Microbial Biotechnology, 2016 PDF

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China
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
mSystems, 2016 PDF

Introducing the Microbiome into Precision Medicine
Thomas M Kuntz, Jack A Gilbert
Trends in Pharmacological Sciences, 2016 PDF

The gut microbiome and the mechanism of surgical infection
Alverdy JC, Hyoju SK, Weigerinck M, JA Gilbert
British Journal of Surgery, 2016 link

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome
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
ISME J, 2016 PDF

Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery
Jackrel SL, Owens SM, Gilbert JA, Pfister CA
Molecular Ecology Resources, 2016 PDF

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System
Gibbons SM, Scholtz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML
mBio, 2016 PDF

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’
Brewer T, Handley KM, Carini P, Gilbert JA, Fierer N
Nature Microbiology 2, 2016 PDF

How do we make indoor environments and healthcare settings healthier?
Jack A Gilbert
Microbial Biotechnology, 2016 PDF

Printing-Assisted Surface Modifications of Patterned Ultrafiltration Membranes
Nathaniel Charles Wardrip, Melissa Dsouza, Meltem Urgun-Demirtas, Seth W Snyder, Jack A. Gilbert, and Christopher J. Arnusch
ACS Appl. Mater. Interfaces, 2016 PDF

Migraines are correlated with higher levels of nitrate-, nitrite-, and nitric oxide-reducing oral microbes in the American Gut Project Cohort
Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R
mSystems, 2016 PDF

Responses of microbial communities to hydrocarbon exposures
Samantha B Joye, Sara Kleindienst, Jack A Gilbert, Kim M Handley, Pam Weisenhorn, Will A Overholt, Joel E Kostka
Oceanography, 2016 PDF

Ten questions concerning the microbiomes of buildings
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
Building and Environment, 2016 PDF

Fungal community composition in soils subjected to long‐term chemical fertilization is most influenced by the type of organic matter
Ruibo Sun, Melissa Dsouza, Jack A Gilbert, Xisheng Guo, Daozhong Wang, Zhibin Guo, Yingying Ni, Haiyan Chu
Environmental Microbiology, 2016 link

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat
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
mSystems Journal, 2016 PDF

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children
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
N Engl J Med, 2016 PDF

Is Triclosan Harming Your Microbiome?
Yee A and Gilbert JA
Science, 2016 link

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

Microbiome-wide association studies link dynamic microbial consortia to disease
Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R.
Nature, 2016 PDF

ZIKV-CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms
Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FS-M, Medeiros JD, Assis Geraldo J, Gilbert JA, Volpini AC, Rocha Fernandes G.
PLoS Negl Trop Dis, 2016 link

Diversity, structure and convergent evolution of the global sponge microbiome
Torsten Thomas, Lucas Moitinho-Silva, Miguel Lurgi, et al
Nature Communications, 2016 PDF

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

Does the Brain Listen to the Gut?
Kuntz T, Gilbert JA
eLife, 2016 link

Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter populations
Sangwan N, Zarraonaindia I, Hampton-Marcel JT, Ssegane H, Eshoo TW, Rijal G, Negri MC, Gilbert JA
mSystems, 2016 PDF

(Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans
Sharma A, Gilbert JA, Lal R
Scientific Reports, 2016 link

Network-based metabolic analysis and microbial community modeling
Cardona C, Weisenhorn P, Henry C, Gilbert JA
Current Opinions in Microbiology, 2016 PDF

Recovering complete and draft population genomes from metagenome datasets
Sangwan N, Xia FF, Gilbert JA
Microbiome, 2016 link

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

Spatial scale drives patterns in soil bacterial diversity
O’Brien SL, Gibbons SM, Owens SM, Hampton‐Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA
Environmental Microbiology, 2016 PDF

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

Genomic analysis of 38 Legionella species identified large and diverse effector repertoires
Burstein D, Amaro F, Zusman T, Lifshitz Z, Cohem O, Gilbert JA, Pupko T, Shuman HA, Segal G
Nature Genetics, 2016 PDF

The obese gut microbiome across the epidemiologic transition
Dugas LR, Fuller M, Gilbert JA, Layden BT
Emerging Themes in Epidemiology, 2016 link

Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?
Gilbert JA, Alverdy JC
Gut, 2016 link

Microbial community assembly and metabolic function during mammalian corpse decomposition
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.
Science, 2016 link

2015

A simple novel device for air sampling by electrokinetic capture
Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J and Gilbert JA
Microbiome, 2015 link

Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys
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
mSystems, 2015 PDF

Tools for the Microbiome: Nano and Beyond
Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Frazer SE, Gilbert JA, et al
ACS Nano, 2015 PDF

A new N-acyl homoserine lactone synthase in an uncultured symbiont of the red sea sponge Theonella swinhoei
Maya Britstein, Giulia Devescovi, Kim M Handley, et al
Applied and Environmental Microbiology, 2015 PDF

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

Microbial Diversity – exploration of natural ecosystems and microbiomes

Gibbons SM and Gilbert JA
Current Opinion in Genetics and Development, 2015 PDF

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations

Ying S, Zeng D-N, Chi L, Tan Y, Galzote C, Cardona C, Lax S. Gilbert JA, Quan Z-X
PLoS ONE, 2015 link

A unified initiative to harness Earth’s microbiomes

Alivisatos AP, MJ Blaser, EL Brodie, M Chun, et al
Science, 2015 link

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways

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
Journal of Allergy and Clinical Immunology, 2015 PDF

The Short Chain Fatty Acid Receptor, FFA2, contributes to gestational glucose homeostasis

Miles Fuller, Medha Priyadarshini, Sean M Gibbons, et al
American Journal of Physiology – Endocrinology and Metabolism, 2015 link

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA and Nagler CR
ISME J, 2015 PDF

16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies

Perisin M, Vetter M, Gilbert JA, and Bergelson J
ISME J, 2015 PDF

Housefly Larvae Vermicomposting efficiently attenuates Antibiotic Resistant Genes in Swine Manure Coupled with distinct bacterial population change

Wang H, Li H, Gilbert JA, Li H, Wu L, Liu M, Wang L, Zhou Q, Yuan J, Zhang Z
Applied and Environmental Microbiology, 2015 PDF

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

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
Aquatic Toxicology, 2015 link

Athletic equipment microbiota are shaped by interactions with human skin

Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT
Microbiome, 2015 PDF

Lifestyle evolution in cyanobacterial symbionts of sponges

Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L
mBio, 2015 PDF

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management

Van Bonn W, LaPointe A, Gibbons SM, Frazier A, Hampton-Marcel J, Gilbert JA
Zoo Biology, 2015 PDF

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

Lin X, Handley KM, Gilbert JA, Kostka JE
ISME J, 2015 PDF

Our Unique Microbial Identity

Gilbert JA
Genome Biology, 2015 PDF

Forensic analysis of the microbiome of phones and shoes

Lax S, Hampton-Marcell TJ, Gibbons S, Colares G, Smith D, Eisen AJ, Gilbert JA
Microbiome. 3:21, 2015 PDF

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes

Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R
Environmental Microbiology Reports, 2015 PDF

Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak

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
Science Translational Medicine, 2015 PDF

Hospital-associated microbiota and implications for nosocomial infections

Lax S and Gilbert JA
Trends in Molecular Medicine, 2015. PDF

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.

Leone V, Gibbons SM, Martinez K, Hutchinson AL, Huang EY, et al
Cell Host & Microbe, 2015 PDF

Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms

Dedesko S, Stephens B, Gilbert JA, Siegel JA
Building and Environment, 2015
DOI: 10.1016/j.buildenv.2015.03.029 PDF

The role of the commensal microbiota in the regulation of tolerance to dietary allergens

Canani RB, Gilbert JA, Nagler CR
Curr Opin Allergy Clin Immunol, 2015 PDF

Metagenomics: Social behavior and the microbiome

Gilbert JA
eLife, 2015 PDF

The soil microbiome influences grapevine-associated microbiota

Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, vanderLelie D, Gilbert JA
mBio, 2015 PDF

Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients

Daniel McDonald, Mady Hornig, Catherine Lozupone, Justine Debelius, Jack A Gilbert, Rob Knight
Microbial Ecology in Health & Disease, 2015 PDF

Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases

Huang EY, Inoue T, Leone V, Dalal S, Touw K, Wang Y, Musch M, Theriault B, Higuchi K, Donovan S, Gilbert JA, Chang E
Inflammatory Bowel Diseases. 21(5):963-72, 2015 PDF

Our interface with the built environment: immunity and the indoor microbiota

Lax S, Nagler CR. Gilbert JA
Trends in Immunology, 2015 PDF

Predicting ecosystem emergent properties at multiple scales

Gilbert JA and Henry C
Environmental Microbiology, 2015 PDF

Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building

Ramos T, Dedesko S, Siegel JA, Gilbert JA, Stephens B
PLoS ONE 10(3): e0118207, 2015 link

Agricultural intensification and the functional capacity of soil microbes on smallholder African farms

Stephen A Wood, Mark A Bradford, Gilbert JA, Krista L McGuire, Cheryl A Palm, Katherine L Tully, Jizhong Zhou, Shahid Naee
Journal of Applied Ecology, 2016 PDF

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

Haowei Yue, Mengmeng Wang, Shiping Wang, Gilbert JA, et al
ISME Journal. 17 February, 2015 PDF

Temporal patterns of rarity provide a more complete view of microbial diversity

Shade A, Gilbert JA
Trends in Microbiology, 2015 link

Diverse protist grazers select for virulence-related traits in Legionella

Amaro F, Wang W, Gilbert JA, Anderson OR, Shuman HA.
ISME Journal, 2015 PDF

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

Vitaglione P, Mennella I, Ferracane R, Rivellese AA, et al
The American Journal of Clinical Nutrition,, 2015 PDF

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
Applied and Environmental Microbiology. 81(2), 765-773, 2015 PDF

The potential contribution of anammox to nitrogen loss from paddy soils in Southern China

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
Applied and Environmental Microbiology, 81 (3), 938-947, 2015. PDF

The ocean sampling day consortium

Ann Kopf, Meduse Biwak, Renzo Kottmann, Julia Schnetzer, et al
Giga Science. 4, 1, 1-5, 2015 link

2014

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
Applied and Environmental Microbioogy, 2014 PDF

Probing the Microbial Mysteries of Wine
Zarraonaindia I and Gilbert JA
Microbe, 2014 PDF

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 mBio, 2014 PDF

The role of macrobiota in structuring microbial communities along rocky shores
Pfister CA, Gilbert JA, Gibbons SM
PeerJ, 2014 PDF

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome
LaBelle EV, Marshall CW, Gilbert JA, May HD
PLoS One, 2014 PDF

Development of the preterm infant gut microbiome: a research priority
Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA
Microbiome, 2014 PDF

Science is innate!
Gilbert JA
Genome Biology, 2014 PDF

Longitudinal analysis of microbial interaction between humans and the indoor environment
Lax S, Smith DP, Hampton-Marcell J, Owens S, Handley K, et al.
Science, 2014 PDF

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, et al.
mBio, 2014 PDF

The Earth Microbiome project: successes and aspirations
Gilbert JA, Jansson, JK, Knight R
BMC Biology, 2014 PDF

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.
PeerJ, 2014 PDF

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.
Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, et al.
Standards in Genomic Sciences, 2013 PDF

Metagenome Sequencing of Prokaryotic Microbiota Collected from Byron Glacier, Alaska
Choudhari S, Smith S, Owens S, Gilbert JA, Shain DH, et al.
Genome Announcements, 2013 PDF

Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology
Larsen P, Gilbert J
PLoS One, 2013 PDF

Evidence for a persistent microbial seed bank throughout the global ocean
Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, et al.
PNAS, 2014 PDF

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

Beyond the Genome: Community-Level Analysis of the Microbial World
Zarraonaindia I, Smith DP, Gilbert JA
Biology and Philosophy, 2013 PDF
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.
Biogeosciences, 2013 PDF
doi:10.5194/bg-10-555-2013.

2012

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, et al.
PNAS, 2012 PDF
doi:10.1073/pnas.1215210110.

Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15
Trimble WL, Phung LT, Meyer F, Gilbert JA, Silver S
Journal of Bacteriology, 2012 PDF
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.
GigaScience, 2012 PDF
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
Journal of Bacteriology, 2012 PDF
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.
Standards in Genomic Sciences, 2012 PDF
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.
PLoS One, 2012 PDF
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
Journal of Bacteriology, 2012 PDF
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.
PLoS One, 2012 PDF
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.
Biogeosciences Discussions, 2012 PDF
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.
BMC Bioinformatics, 2012 PDF
doi:10.1186/1471-2105-13-183.

Modeling microbial community structure and functional diversity across time and space
Larsen PE, Gibbons SM, Gilbert JA
FEMS Microbiology Letters, 2012 PDF
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
Microbial Biotechnology, 2012 PDF
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
Briefings in Bioinformatics, 2012 PDF
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.
Nature Biotechnology, 2012 PDF
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.
Standards in Genomic Sciences, 2012 PDF
doi:10.4056/sigs.2876184.

Predicting bacterial community assemblages using an artificial neural network approach
Larsen PE, Field D, Gilbert JA
Nature Methods, 2012 PDF
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.
The ISME Journal, 2012 PDF
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
Journal of Biotechnology, 2012 PDF
doi:10.1016/j.jbiotec.2012.03.009

Omics for understanding microbial functional dynamics
Jansson JK, Neufeld JD, Moran MA, Gilbert JA
Environmental Microbiology, 2012 PDF
doi:10.1111/j.1462-2920.2011.02518.x.

Metagenomics – a guide from sampling to data analysis
Thomas T, Gilbert J, Meyer F
Microbial Informatics and Experimentation, 2012 PDF
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.
The ISME Journal, 2012 PDF
doi:10.1038/ismej.2011.107.

2011

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.
Standards in Genomic Sciences, 2011 PDF
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
The ISME Journal, 2011 PDF
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.
Nature Biotechnology, 2011 PDF
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
PLoS One, 2011 PDF
doi:10.1371/journal.pone.0016499.

Microbial Metagenomics: Beyond the Genome
Gilbert JA, Dupont CL
Annual Reviews Marine Science, 2011 PDF
doi:10.1146/annurev-marine-120709-142811.

Survey data are still vital to science
Gilbert J, O’Dor R, Vogel T
Nature, 2011 PDF
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.
Microbial Informatics and Experimentation, 2011 PDF
doi:10.1186/2042-5783-1-4.

2010

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.
PLoS One, 2010 PDF
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.
Standards in Genomic Sciences, 2010 PDF
doi:10.4056/sigs.1202536.

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

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
Mitra S, Gilbert JA, Field D, Huson DH
The ISME Journal, 2010 PDF
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.
Standards in Genomic Sciences, 2010 PDF
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.
Standards in Genomic Sciences, 2010 PDF
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.
PLoS One, 2010 PDF
doi:10.1371/journal.pone.0008875.

2009

Evidence for phosphonate usage in the coral holobiont
Thomas S, Burdett H, Temperton B, Wick R, Snelling D, et al.
The ISME Journal, 2009 PDF
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.
Environmental Microbiology, 2009 PDF
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.
The ISME Journal, 2009 PDF
doi:10.1038/ismej.2009.32.

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

2008

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome
Gilbert JA, Mühling M, Joint I
The ISME Journal, 2008 PDF
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.
Nature Biotechnology, 2008 PDF
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.
Biochemical Journal, 2008 PDF
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.
PLoS One, 2008 PDF
doi:10.1371/journal.pone.0003042.

2006

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

2005

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

2004

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

2003

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