Karen E. Nelson, PhD

President
Professor, Genomic Medicine Group

Karen E. Nelson, PhD is the President of the J. Craig Venter Institute (JCVI). Prior to being appointed President, she held a number of other positions at the Institute, including Director of JCVI's Rockville Campus, and Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at JCVI. Dr. Nelson received her undergraduate degree from the University of the West Indies, and her PhD from Cornell University. She has authored or co-authored over 200 peer reviewed publications, edited three books, and is currently Editor-in-Chief of the journal Microbial Ecology.

Dr. Nelson is an elected member of the National Academy of Sciences. Other honors include being named ARCS Scientist of the Year 2017; a Fellow of the American Academy of Microbiology; being inducted into the Indian National Academy of Sciences in 2018; and being appointed an Honorary Professor at the University of the West Indies as well as a Helmholtz International Fellow.

Dr. Nelson has extensive experience in microbial ecology, microbial genomics, microbial physiology and metagenomics. Dr. Nelson has led several genomic and metagenomic efforts, and led the first human metagenomics study that was published in 2006. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other -omics studies.

Research Priorities

Microbiome in health and disease

Interrogating microbiome profiles and host microbe interactions

Emergence of Antimicrobial Resistance

Understanding the intricate play between infectious species, gene transfer and the emergence of resistance

Understanding Resistance mechanisms in microbial species

Deep investigations into how microbes respond to different types of drugs

Identification of novel species

In different environments including the oral cavity, plants, and artic sediments

Publications

Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R

Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort.

GeroScience. 2020-09-24;

PMID: 32974878

Kleinstein SE, Nelson KE, Freire M

Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease.

Journal of dental research. 2020-09-01; 99.10: 1131-1139.

PMID: 32459164

Yu Y, O'Rourke A, Lin YH, Singh H, Eguez RV, Beyhan S, Nelson KE

Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes.

ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.

PMID: 32673475

Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL

Applications of weighted association networks applied to compositional data in biology.

Environmental microbiology. 2020-08-01; 22.8: 3020-3038.

PMID: 32436334

Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA

Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.

Nature communications. 2020-06-16; 11.1: 3132.

PMID: 32546784

Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Das S, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.

Nature communications. 2020-05-21; 11.1: 2537.

PMID: 32439901

Torralba MG, Kuelbs C, Moncera KJ, Roby R, Nelson KE

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.

Microbial ecology. 2020-05-21;

PMID: 32440698

Freire M, Moustafa A, Harkins DM, Torralba MG, Zhang Y, Leong P, Saffery R, Bockmann M, Kuelbs C, Hughes T, Craig JM, Nelson KE

Longitudinal Study of Oral Microbiome Variation in Twins.

Scientific reports. 2020-05-14; 10.1: 7954.

PMID: 32409670

Rajagopala SV, Singh H, Yu Y, Zabokrtsky KB, Torralba MG, Moncera KJ, Frank B, Pieper R, Sender L, Nelson KE

Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.

Microbial ecology. 2020-05-01; 79.4: 1034-1043.

PMID: 31754744

Li W, Tapiainen T, Brinkac L, Lorenzi HA, Moncera K, Tejesvi M, Salo J, Nelson KE

Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth.

The Journal of infectious diseases. 2020-04-02;

PMID: 32239170

Vuillermin PJ, O'Hely M, Collier F, Allen KJ, Tang MLK, Harrison LC, Carlin JB, Saffery R, Ranganathan S, Sly PD, Gray L, Molloy J, Pezic A, Conlon M, Topping D, Nelson K, Mackay CR, Macia L, Koplin J, Dawson SL, Moreno-Betancur M, Ponsonby AL, J. Craig Venter Institute, BIS Investigator Group

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring.

Nature communications. 2020-03-24; 11.1: 1452.

PMID: 32210229

O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.

Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:

PMID: 31907190

Shomorony I, Cirulli ET, Huang L, Napier LA, Heister RR, Hicks M, Cohen IV, Yu HC, Swisher CL, Schenker-Ahmed NM, Li W, Nelson KE, Brar P, Kahn AM, Spector TD, Caskey CT, Venter JC, Karow DS, Kirkness EF, Shah N

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.

Genome medicine. 2020-01-10; 12.1: 7.

PMID: 31924279

Menon RK, Gomez A, Brandt BW, Leung YY, Gopinath D, Watt RM, Crielaard W, Nelson KE, Botelho MG

Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study.

Scientific reports. 2019-12-10; 9.1: 18761.

PMID: 31822712

Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K

A new antibiotic selectively kills Gram-negative pathogens.

Nature. 2019-12-01; 576.7787: 459-464.

PMID: 31747680

Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE, Pieper R

Gastro-intestinal and oral microbiome signatures associated with healthy aging.

GeroScience. 2019-12-01; 41.6: 907-921.

PMID: 31620923

Pessoa L, Aleti G, Choudhury S, Nguyen D, Yaskell T, Zhang Y, Li W, Nelson KE, Neto LLS, Sant'Ana ACP, Freire M

Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.

Frontiers in immunology. 2019-11-12; 10.2602.

PMID: 31781106

Visconti A, Le Roy CI, Rosa F, Rossi N, Martin TC, Mohney RP, Li W, de Rinaldis E, Bell JT, Venter JC, Nelson KE, Spector TD, Falchi M

Interplay between the human gut microbiome and host metabolism.

Nature communications. 2019-10-03; 10.1: 4505.

PMID: 31582752

Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints.

mSphere. 2019-07-31; 4.4:

PMID: 31366708

Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM, Tejesvi MV

Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants.

Scientific reports. 2019-07-23; 9.1: 10635.

PMID: 31337807

Pafčo B, Sharma AK, Petrželková KJ, Vlčková K, Todd A, Yeoman CJ, Wilson BA, Stumpf R, White BA, Nelson KE, Leigh S, Gomez A

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors.

American journal of physical anthropology. 2019-07-01; 169.3: 575-585.

PMID: 31025322

Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Goliusinski W, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y

Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery.

Journal of proteome research. 2019-04-05; 18.4: 1907-1915.

PMID: 30848925

Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, Tovchigrechko A, Madupu R, Yooseph S, Nelson KE, Shanmugam VK, Chan AP

Co-occurrence of Anaerobes in Human Chronic Wounds.

Microbial ecology. 2019-04-01; 77.3: 808-820.

PMID: 30141127

Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.

The ISME journal. 2019-03-01; 13.3: 576-587.

PMID: 29995839

Roachford OSE, Nelson KE, Mohapatra BR

A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2019-03-01; 68.68-76.

PMID: 30529087

Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE

OMeta: an ontology-based, data-driven metadata tracking system.

BMC bioinformatics. 2019-01-07; 20.1: 8.

PMID: 30612540

Rafeek R, Carrington CVF, Gomez A, Harkins D, Torralba M, Kuelbs C, Addae J, Moustafa A, Nelson KE

Xylitol and sorbitol effects on the microbiome of saliva and plaque.

Journal of oral microbiology. 2019-01-01; 11.1: 1536181.

PMID: 30598728

Weiss H, Hertzberg VS, Dupont C, Espinoza JL, Levy S, Nelson K, Norris S, FlyHealthy Research Team

The Airplane Cabin Microbiome.

Microbial ecology. 2019-01-01; 77.1: 87-95.

PMID: 29876609

Li X, Rensing C, Taylor WL, Costelle C, Brejnrod AD, Ferry RJ, Higgins PB, Folli F, Kottapalli KR, Hubbard GB, Dick EJ, Yooseph S, Nelson KE, Schlabritz-Loutsevitch N

Papio spp. Colon microbiome and its link to obesity in pregnancy.

Journal of medical primatology. 2018-12-01; 47.6: 393-401.

PMID: 30039863

Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL

Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.

mBio. 2018-11-27; 9.6:

PMID: 30482830

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Gebretsadik T, Halpin RA, Nelson KE, Moore ML, Anderson LJ, Peebles RS, Das SR, Hartert TV

Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy.

The Journal of allergy and clinical immunology. 2018-11-01; 142.5: 1447-1456.e9.

PMID: 29330010

Vlčková K, Pafčo B, Petrželková KJ, Modrý D, Todd A, Yeoman CJ, Torralba M, Wilson BA, Stumpf RM, White BA, Nelson KE, Leigh SR, Gomez A

Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas.

Frontiers in microbiology. 2018-06-15; 9.1202.

PMID: 29963018

Brinkac L, Clarke TH, Singh H, Greco C, Gomez A, Torralba MG, Frank B, Nelson KE

Spatial and Environmental Variation of the Human Hair Microbiota.

Scientific reports. 2018-06-13; 8.1: 9017.

PMID: 29899411

Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R, Telenti A

Microbial metagenome of urinary tract infection.

Scientific reports. 2018-03-12; 8.1: 4333.

PMID: 29531289

Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, Stumpf R, White B, Nelson KE, Baden AL, Tecot SR

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality.

The Journal of animal ecology. 2018-03-01; 87.2: 388-399.

PMID: 29205327

Russo CD, Weller DW, Nelson KE, Chivers SJ, Torralba M, Grimes DJ

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques.

Microbial ecology. 2018-02-01; 75.2: 303-309.

PMID: 29080910

Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.

Clinical and translational gastroenterology. 2018-01-18; 9.1: e132.

PMID: 29345635

Vlčková K, Shutt-Phillips K, Heistermann M, Pafčo B, Petrželková KJ, Todd A, Modrý D, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Gomez A

Impact of stress on the gut microbiome of free-ranging western lowland gorillas.

Microbiology (Reading, England). 2018-01-01; 164.1: 40-44.

PMID: 29205130

Roachford OSE, Nelson KE, Mohapatra BR

Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.

International journal of medical microbiology : IJMM. 2017-12-01; 307.8: 508-520.

PMID: 28927691

Brim H, Yooseph S, Lee E, Sherif ZA, Abbas M, Laiyemo AO, Varma S, Torralba M, Dowd SE, Nelson KE, Pathmasiri W, Sumner S, de Vos W, Liang Q, Yu J, Zoetendal E, Ashktorab H

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.

Genes. 2017-11-09; 8.11:

PMID: 29120399

Brinkac L, Voorhies A, Gomez A, Nelson KE

The Threat of Antimicrobial Resistance on the Human Microbiome.

Microbial ecology. 2017-11-01; 74.4: 1001-1008.

PMID: 28492988

Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, Gillevet PM, Xu J, Kisseleva T, Ho SB, Depew J, Du X, Sørensen HT, Vilstrup H, Nelson KE, Brenner DA, Fouts DE, Schnabl B

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.

Nature communications. 2017-10-16; 8.1: 837.

PMID: 29038503

Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L

Strain Level Streptococcus Colonization Patterns during the First Year of Life.

Frontiers in microbiology. 2017-09-06; 8.1661.

PMID: 28932211

Clarke TH, Gomez A, Singh H, Nelson KE, Brinkac LM

Integrating the microbiome as a resource in the forensics toolkit.

Forensic science international. Genetics. 2017-09-01; 30.141-147.

PMID: 28728057

Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Theranostics. 2017-07-07; 7.10: 2704-2717.

PMID: 28819457

Amato KR, Van Belle S, Di Fiore A, Estrada A, Stumpf R, White B, Nelson KE, Knight R, Leigh SR

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate.

Microbial ecology. 2017-07-01; 74.1: 250-258.

PMID: 28124727

Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.

PMID: 28467925

Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.

BMC genomics. 2017-04-13; 18.1: 296.

PMID: 28407798

Jones MB, Nierman WC, Shan Y, Frank BC, Spoering A, Ling L, Peoples A, Zullo A, Lewis K, Nelson KE

Reducing the Bottleneck in Discovery of Novel Antibiotics.

Microbial ecology. 2017-04-01; 73.3: 658-667.

PMID: 27896376

Danaher RJ, Fouts DE, Chan AP, Choi Y, Depew J, McCorrison JM, Nelson KE, Wang C, Miller CS

HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.

Journal of neurovirology. 2017-04-01; 23.2: 171-185.

PMID: 27739035

Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE

The Human Microbiome and Cancer.

Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.

PMID: 28096237

Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A

The blood DNA virome in 8,000 humans.

PLoS pathogens. 2017-03-22; 13.3: e1006292.

PMID: 28328962

Gomez A, Nelson KE

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.

Microbial ecology. 2017-02-01; 73.2: 492-503.

PMID: 27628595

Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R

Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections.

PLoS pathogens. 2017-01-27; 13.1: e1006151.

PMID: 28129394

Torralba MG, Franks JS, Gomez A, Yooseph S, Nelson KE, Grimes DJ

Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.

Microbial ecology. 2017-01-01; 73.1: 91-100.

PMID: 27815589

Yu Y, Sikorski P, Smith M, Bowman-Gholston C, Cacciabeve N, Nelson KE, Pieper R

Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.

Theranostics. 2017-01-01; 7.2: 238-252.

PMID: 28042331

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Shankar J, Yooseph S, Nelson KE, Halpin RA, Moore ML, Anderson LJ, Peebles RS, Das SR, Hartert TV

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.

The Journal of infectious diseases. 2016-12-15; 214.12: 1924-1928.

PMID: 27923952

Vlčková K, Gomez A, Petrželková KJ, Whittier CA, Todd AF, Yeoman CJ, Nelson KE, Wilson BA, Stumpf RM, Modrý D, White BA, Leigh SR

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla).

Microbial ecology. 2016-11-01; 72.4: 943-954.

PMID: 26984253

Cui J, Chen CH, Lo MT, Schork N, Bettencourt R, Gonzalez MP, Bhatt A, Hooker J, Shaffer K, Nelson KE, Long MT, Brenner DA, Sirlin CB, Loomba R, For The Genetics Of Nafld In Twins Consortium

Shared genetic effects between hepatic steatosis and fibrosis: A prospective twin study.

Hepatology (Baltimore, Md.). 2016-11-01; 64.5: 1547-1558.

PMID: 27315352

Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.

Scientific reports. 2016-08-25; 6.31731.

PMID: 27558918

Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

BMC genomics. 2016-08-15; 17.1: 635.

PMID: 27527070

Bennett G, Malone M, Sauther ML, Cuozzo FP, White B, Nelson KE, Stumpf RM, Knight R, Leigh SR, Amato KR

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta).

American journal of primatology. 2016-08-01; 78.8: 883-92.

PMID: 27177345

Abeles SR, Jones MB, Santiago-Rodriguez TM, Ly M, Klitgord N, Yooseph S, Nelson KE, Pride DT

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

Microbiome. 2016-07-30; 4.1: 39.

PMID: 27473422

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Chappell JD, Larkin EK, Nelson KE, Moore ML, Anderson LJ, Das SR, Hartert TV

Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk.

American journal of respiratory and critical care medicine. 2016-05-15; 193.10: 1180-3.

PMID: 27174483

Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.

Cell reports. 2016-03-08; 14.9: 2142-2153.

PMID: 26923597

Amato KR, Martinez-Mota R, Righini N, Raguet-Schofield M, Corcione FP, Marini E, Humphrey G, Gogul G, Gaffney J, Lovelace E, Williams L, Luong A, Dominguez-Bello MG, Stumpf RM, White B, Nelson KE, Knight R, Leigh SR

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species.

Oecologia. 2016-03-01; 180.3: 717-33.

PMID: 26597549

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.

PMID: 26890609

Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JH, Pedra JHF, Nelson DR, Unger MF, Tubio JM, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Nature communications. 2016-02-09; 7.10507.

PMID: 26856261

Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vlckova K, Umaña JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, Blekhman R, White BA, Leigh SR

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

The ISME journal. 2016-02-01; 10.2: 514-26.

PMID: 26315972

Shilts MH, Rosas-Salazar C, Tovchigrechko A, Larkin EK, Torralba M, Akopov A, Halpin R, Peebles RS, Moore ML, Anderson LJ, Nelson KE, Hartert TV, Das SR

Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery.

Microbial ecology. 2016-01-01; 71.1: 233-42.

PMID: 26370110

Edlund A, Yang Y, Yooseph S, Hall AP, Nguyen DD, Dorrestein PC, Nelson KE, He X, Lux R, Shi W, McLean JS

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism.

The ISME journal. 2015-12-01; 9.12: 2605-19.

PMID: 26023872

Loomba R, Schork N, Chen CH, Bettencourt R, Bhatt A, Ang B, Nguyen P, Hernandez C, Richards L, Salotti J, Lin S, Seki E, Nelson KE, Sirlin CB, Brenner D, Genetics of NAFLD in Twins Consortium

Heritability of Hepatic Fibrosis and Steatosis Based on a Prospective Twin Study.

Gastroenterology. 2015-12-01; 149.7: 1784-93.

PMID: 26299412

Amato KR, Yeoman CJ, Cerda G, Schmitt CA, Cramer JD, Miller ME, Gomez A, Turner TR, Wilson BA, Stumpf RM, Nelson KE, White BA, Knight R, Leigh SR

Variable responses of human and non-human primate gut microbiomes to a Western diet.

Microbiome. 2015-11-16; 3.53.

PMID: 26568112

Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, Fabani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC

Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Proceedings of the National Academy of Sciences of the United States of America. 2015-11-10; 112.45: 14024-9.

PMID: 26512100

Alivisatos AP, Alivisatos AP, Blaser MJ, Balskus EP, Biteen JS, Brodie EL, Chun M, Blaser MJ, Dangl JL, Brodie EL, Donohue TJ, Browning ND, Dorrestein PC, Cardon ZG, Cavanaugh CM, Gilbert JA, Green JL, Chun M, Jansson JK, Cliffel DE, Colwell RR, Knight R, Dangl JL, Maxon ME, McFall-Ngai MJ, Donohue TJ, Miller JF, Dorrestein PC, Pollard KS, Fraser SE, Ruby EG, Friesen ML, Gilbert JA, Taha SA, Gilbert SF, Unified Microbiome Initiative Consortium, Green JL, Harwood CS, Henriksen JR, Highlander SK, Huang Y, Jansson JK, Johnson AT, Kasper DL, Knight R, Kujawinski EB, Martin CL, Maxon ME, McFall-Ngai MJ, Miller JF, Moran MA, Nelson KE, Orphan VJ, Ozcan A, Paša-Tolić L, Pollard KS, Regev A, Rubin EM, Ruby EG, Segre JA, Silver PA, Taha SA, Vivanco JM, Weinstock GM, Weiss PS, Yang P

MICROBIOME. A unified initiative to harness Earth's microbiomes.

Science (New York, N.Y.). 2015-10-30; 350.6260: 507-8.

PMID: 26511287

Yu Y, Zielinski MD, Rolfe MA, Kuntz MM, Nelson H, Nelson KE, Pieper R

Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria.

Infection and immunity. 2015-10-01; 83.10: 4142-53.

PMID: 26238715

Yooseph S, Kirkness EF, Tran TM, Harkins DM, Jones MB, Torralba MG, O'Connell E, Nutman TB, Doumbo S, Doumbo OK, Traore B, Crompton PD, Nelson KE

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.

BMC genomics. 2015-08-22; 16.631.

PMID: 26296559

Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R

Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes.

Journal of proteome research. 2015-08-07; 14.8: 3123-35.

PMID: 26143644

Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Durkin AS, Nelson KE, Epstein SS

High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.

Standards in genomic sciences. 2015-07-18; 10.37.

PMID: 26221418

Gomez A, Petrzelkova K, Yeoman CJ, Vlckova K, Mrázek J, Koppova I, Carbonero F, Ulanov A, Modry D, Todd A, Torralba M, Nelson KE, Gaskins HR, Wilson B, Stumpf RM, White BA, Leigh SR

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology.

Molecular ecology. 2015-05-01; 24.10: 2551-65.

PMID: 25846719

Yu Y, Sikorski P, Bowman-Gholston C, Cacciabeve N, Nelson KE, Pieper R

Diagnosing inflammation and infection in the urinary system via proteomics.

Journal of translational medicine. 2015-04-08; 13.111.

PMID: 25889401

Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H

Where next for microbiome research?

PLoS biology. 2015-01-20; 13.1: e1002050.

PMID: 25602283

Nelson KE

An Update on the Status of Current Research on the Mammalian Microbiome.

ILAR journal. 2015-01-01; 56.2: 163-8.

PMID: 26323626

Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, Depew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B

Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice.

Gastroenterology. 2015-01-01; 148.1: 203-214.e16.

PMID: 25239591

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH

Standardized metadata for human pathogen/vector genomic sequences.

PloS one. 2014-01-01; 9.6: e99979.

PMID: 24936976

O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M

Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.

Genome announcements. 2013-02-21; 1.1:

PMID: 23469340

Madupu R, Szpakowski S, Nelson KE

Microbiome in human health and disease.

Science progress. 2013-01-01; 96.Pt 2: 153-70.

PMID: 23901633

Brim H, Yooseph S, Zoetendal EG, Lee E, Torralbo M, Laiyemo AO, Shokrani B, Nelson K, Ashktorab H

Microbiome analysis of stool samples from African Americans with colon polyps.

PloS one. 2013-01-01; 8.12: e81352.

PMID: 24376500

Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME, Larson CL, Nelson KE, Qu A, Schook LB, Yang F, White BA, Goldenfeld N

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.

Proceedings of the National Academy of Sciences of the United States of America. 2012-06-19; 109.25: 9692-8.

PMID: 22615407

Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.

Journal of hepatology. 2012-06-01; 56.6: 1283-92.

PMID: 22326468

Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

BMC bioinformatics. 2012-03-19; 13.42.

PMID: 22429538

Ling Z, Kong J, Liu F, Zhu H, Chen X, Wang Y, Li L, Nelson KE, Xia Y, Xiang C

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.

BMC genomics. 2010-09-07; 11.488.

PMID: 20819230

Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA

Bacterial diversity in the oral cavity of 10 healthy individuals.

The ISME journal. 2010-08-01; 4.8: 962-74.

PMID: 20336157

Chain PS, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC

Genomics. Genome project standards in a new era of sequencing.

Science (New York, N.Y.). 2009-10-09; 326.5950: 236-7.

PMID: 19815760

Deboy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE

Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.

Journal of bacteriology. 2008-08-01; 190.15: 5455-63.

PMID: 18556790

Bek-Thomsen M, Tettelin H, Hance I, Nelson KE, Kilian M

Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy.

Infection and immunity. 2008-05-01; 76.5: 1889-96.

PMID: 18316382

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE

Metagenomic analysis of the human distal gut microbiome.

Science (New York, N.Y.). 2006-06-02; 312.5778: 1355-9.

PMID: 16741115

Deboy RT, Mongodin EF, Emerson JB, Nelson KE

Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.

Journal of bacteriology. 2006-04-01; 188.7: 2364-74.

PMID: 16547022

Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA

Molecular analysis of the bacterial microbiota in the human stomach.

Proceedings of the National Academy of Sciences of the United States of America. 2006-01-17; 103.3: 732-7.

PMID: 16407106

Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA

Diversity of the human intestinal microbial flora.

Science (New York, N.Y.). 2005-06-10; 308.5728: 1635-8.

PMID: 15831718

Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, Deboy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.

PLoS biology. 2005-01-01; 3.1: e15.

PMID: 15660156

Nelson KE, Fouts DE, Mongodin EF, Ravel J, Deboy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM

Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.

Nucleic acids research. 2004-01-01; 32.8: 2386-95.

PMID: 15115801

Resolving the Bottleneck in Antibiotic Discovery

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This study aims to identify specific biomarkers that correlate with longevity and healthy aging using genomics and proteomics approaches.

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Leonardo da Vinci DNA Project

This project utilizes genomics approaches to confirm the identity of the remains purported to be that of Leonardo da Vinci as well as to characterize the microbial population on aging artwork.

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Vaginal Microbiome Project

A metagenomics approach to understanding the relationship between the vaginal microbiome, bacterial vaginosis, vaginal health and preterm birth.

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Mouse Microbiome

Enteric dysbiosis associated with a mouse model of alcoholic liver disease. The translocation of bacteria and bacterial products into the circulation contributes to alcoholic liver disease.

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