2018 Microbiome Award Judges

David Coil Elisabeth Bik Emily Hollister Daryl Gohl Christopher Stewart

 


 

David Coil

Project Scientist at University of California, Davis

BIO:

David Coil is a Project Scientist responsible for supervising undergraduate research projects in microbiology, microbial ecology, and genomics in the lab of Jonathan Eisen. Also managing research projects/collaborations in the lab including microbial sampling, metagenomics, and bacterial genome assembly. And finally, performing public outreach in microbiology through the microBEnet project, which is focused on communication in the context of studies of microbiology of the built environment (including sending bacteria into space). David is the creator of Gut Check: The Microbiome GameĀ.

David received his PhD in 2005 from the Fred Hutchinson Cancer Research Center/University of Washington, working on retroviruses. Since then he has lectured at the UW, done a post-doc in Belgium working on Legionella, and helps direct a non-profit in Alaska called Ground Truth Trekking.

Twitter: @davidacoil

PUBLICATIONS:

To see a complete list of publications. visit Google Scholar


 

Elisabeth Bik

Science Editor at uBiome, Inc, San Francisco, CA

BIO:

After receiving her PhD at Utrecht University in The Netherlands with work on epidemic Vibrio cholerae strains, she worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein, where she set up a molecular microbiology unit for the detection and typing of clinical and nosocomical strains. In 2001, she joined the School of Medicine at Stanford, where she worked on the characterization of the human microbiome in oral, gastric, and intestinal samples. In addition, she studied the microbiome of marine mammals, including dolphins and sea lions. In November 2016, Elisabeth joined uBiome as a Science Editor. When she is not in the lab or writing, she can be found working on her blog Microbiome Digest, an almost daily compilation of scientific papers in the rapidly growing microbiome field, or on Twitter at @MicrobiomDigest. She also searches the biomedical literature for inappropriatedly duplicated or manipulated photographic images and plagiarized text.

Twitter: @microbiomdigest

Website: http://www.microbiomedigest.com

PUBLICATIONS:

  • Bik EM. The Hoops, Hopes, and Hypes of Human Microbiome Research. Yale J Biol Med. 2016 Sep 30;89(3):363-373. eCollection 2016 Sep 30. Review. PubMed PMID: 27698620; PubMed Central PMCID: PMC5045145. 
  • Bik EM, Casadevall A, Fang FC. The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications. MBio. 2016 Jun 7;7(3). pii: e00809-16. doi: 10.1128/mBio.00809-16. PubMed PMID: 27273827; PubMed Central PMCID: PMC4941872. 
  • Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun. 2016 Feb 3;7:10516. doi: 10.1038/ncomms10516. PubMed PMID: 26839246; PubMed Central PMCID: PMC4742810. 
  • Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA. Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time. PLoS One. 2015 Nov 13;10(11):e0142825. doi: 10.1371/journal.pone.0142825. eCollection 2015 Nov 13. PubMed PMID: 26565698; PubMed Central PMCID: PMC4643986. 
  • Bik EM. You Lose Some, You Win Some: Weight Loss Induces Microbiota and Metabolite Shifts. EBioMedicine. 2015 Jul 30;2(8):806-7. doi: 10.1016/j.ebiom.2015.07.037. eCollection 2015 Jul 30. Review. PubMed PMID: 26425686; PubMed Central PMCID: PMC4563139. 
  • Bik EM, Relman DA. Unrest at home: diarrheal disease and microbiota disturbance. Genome Biol. 2014 Jun 27;15(6):120. doi: 10.1186/gb4182. PubMed PMID: 25002208; PubMed Central PMCID: PMC4072979. 
  • Costello EK, Carlisle EM, Bik EM, Morowitz MJ, Relman DA. Microbiome assembly across multiple body sites in low-birthweight infants. MBio. 2013 Oct 29;4(6):e00782-13. doi: 10.1128/mBio.00782-13. PubMed PMID: 24169577; PubMed Central PMCID: PMC3809564. 
  • Diaz MA, Bik EM, Carlin KP, Venn-Watson SK, Jensen ED, Jones SE, Gaston EP, Relman DA, Versalovic J. Identification of Lactobacillus strains with probiotic features from the bottlenose dolphin (Tursiops truncatus). J Appl Microbiol. 2013 Oct;115(4):1037-51. doi: 10.1111/jam.12305. Epub 2013 Aug 1. PubMed PMID: 23855505; PubMed Central PMCID: PMC4063339. 
  • Staubach F, Baines JF, Künzel S, Bik EM, Petrov DA. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One. 2013 Aug 13;8(8):e70749. doi: 10.1371/journal.pone.0070749. eCollection 2013 Aug 13. PubMed PMID: 23967097; PubMed Central PMCID: PMC3742674. 
  • Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One. 2013;8(1):e53838. doi: 10.1371/journal.pone.0053838. Epub 2013 Jan 22. PubMed PMID: 23349750; PubMed Central PMCID: PMC3551965. 
  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21. PubMed PMID: 22824070. 
  • 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. ISME J. 2010 Aug;4(8):962-74. doi: 10.1038/ismej.2010.30. Epub 2010 Mar 25. PubMed PMID: 20336157; PubMed Central PMCID: PMC2941673. 
  • DiGiulio DB, Romero R, Kusanovic JP, Gómez R, Kim CJ, Seok KS, Gotsch F, Mazaki-Tovi S, Vaisbuch E, Sanders K, Bik EM, Chaiworapongsa T, Oyarzún E, Relman DA. Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes. Am J Reprod Immunol. 2010 Jul 1;64(1):38-57. doi: 10.1111/j.1600-0897.2010.00830.x. Epub 2010 Mar 21. PubMed PMID: 20331587; PubMed Central PMCID: PMC2907911. 
  • Bik EM. Composition and function of the human-associated microbiota. Nutr Rev. 2009 Nov;67 Suppl 2:S164-71. doi: 10.1111/j.1753-4887.2009.00237.x. Review. Erratum in: Nutr Rev. 2010 Mar;68(3):189. PubMed PMID: 19906220. 
  • DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, Kim CJ, Erez O, Edwin S, Relman DA. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One. 2008 Aug 26;3(8):e3056. doi: 10.1371/journal.pone.0003056. PubMed PMID: 18725970; PubMed Central PMCID: PMC2516597. 
  • Bik EM. [The microbiotics of the human body]. Ned Tijdschr Geneeskd. 2008 Mar 22;152(12):668-73. Review. Dutch. PubMed PMID: 18438061. 
  • Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11889-94. Epub 2007 Jul 9. PubMed PMID: 17620602; PubMed Central PMCID: PMC1924555. 
  • Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007 Jul;5(7):e177. Epub 2007 Jun 26. PubMed PMID: 17594176; PubMed Central PMCID: PMC1896187. 
  • Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006 Sep;21(9):517-23. Epub 2006 Jul 3. Review. PubMed PMID: 16820245. 
  • 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. Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):732-7. Epub 2006 Jan 4. PubMed PMID: 16407106; PubMed Central PMCID: PMC1334644. 
  • Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 2006 Jan 10;34(1):e5. PubMed PMID: 16407321; PubMed Central PMCID: PMC1326253. 
  • 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. 2005 Jun 10;308(5728):1635-8. Epub 2005 Apr 14. PubMed PMID: 15831718; PubMed Central PMCID: PMC1395357. 
  • v Dijk Y, Bik EM, Hochstenbach-Vernooij S, v d Vlist GJ, Savelkoul PH, Kaan JA, Diepersloot RJ. Management of an outbreak of Enterobacter cloacae in a neonatal unit using simple preventive measures. J Hosp Infect. 2002 May;51(1):21-6. PubMed PMID: 12009816. 
  • Visser IJ, Vellema P, Weitenberg AM, Bik EM. [Severe watery diarrhea caused by Vibrio cholerae in lambs]. Tijdschr Diergeneeskd. 1997 Nov 1;122(21):600-3. Dutch. PubMed PMID: 9534795. 
  • Mooi FR, Bik EM. The evolution of epidemic Vibrio cholerae strains. Trends Microbiol. 1997 Apr;5(4):161-5. Review. PubMed PMID: 9141191. 
  • Bik EM, Gouw RD, Mooi FR. DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains. J Clin Microbiol. 1996 Jun;34(6):1453-61. PubMed PMID: 8735097; PubMed Central PMCID: PMC229041. 
  • Bik EM, Bunschoten AE, Willems RJ, Chang AC, Mooi FR. Genetic organization and functional analysis of the otn DNA essential for cell-wall polysaccharide synthesis in Vibrio cholerae O139. Mol Microbiol. 1996 May;20(4):799-811. PubMed PMID: 8793876. 
  • Bik EM, Bunschoten AE, Gouw RD, Mooi FR. Genesis of the novel epidemic Vibrio cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis. EMBO J. 1995 Jan 16;14(2):209-16. PubMed PMID: 7835331; PubMed Central PMCID: PMC398072. 
  • Rijpkema SG, Bik EM, Jansen WH, Gielen H, Versluis LF, Stouthamer AH, Guinée PA, Mooi FR. Construction and analysis of a Vibrio cholerae delta-aminolevulinic acid auxotroph which confers protective immunity in a rabbit model. Infect Immun. 1992 Jun;60(6):2188-93. PubMed PMID: 1587587; PubMed Central PMCID: PMC257142. 
  • Hermans PW, van Soolingen D, Bik EM, de Haas PE, Dale JW, van Embden JD. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun. 1991 Aug;59(8):2695-705. PubMed PMID: 1649798; PubMed Central PMCID: PMC258075. 
  • Hermans PW, Schuitema AR, Van Soolingen D, Verstynen CP, Bik EM, Thole JE, Kolk AH, van Embden JD. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J Clin Microbiol. 1990 Jun;28(6):1204-13. PubMed PMID: 2116445; PubMed Central PMCID: PMC267906.

 

Emily Hollister

Vice President, Information Technology and Analytics at Diversigen, Houston, TX

BIO:

Dr. Emily Hollister is a microbial ecologist with training in bioinformatics and statistics. Dr. Hollister holds a Bachelor’s degree in Biological and Chemical Sciences from Wells College and a Ph.D. in Molecular and Environmental Plant Sciences from Texas A&M University. She also completed her postdoctoral training in Molecular Microbial Ecology in the Department of Soil & Crop Sciences at Texas A&M University.

Prior to joining Diversigen, Dr. Hollister served as an Assistant Professor in the Department of Pathology & Immunology at Baylor College of Medicine and as the Director of Microbial Ecology and Bioinformatics at the Texas Children’s Microbiome Center at Texas Children’s Hospital. Her microbiome experience ranges from soils and biofuel production systems to the human microbiome, built environment, and pre-clinical models of disease.

SELECTED PUBLICATIONS:

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartman M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, and Weber CF. 2009. Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541. 
  • Hollister EB, Engledow AS, Hammett AM, Provin TL, Wilkinson HH, and Gentry TJ. 2010. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. The ISME Journal 4: 829-838. 
  • Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, and Gentry TJ. 2010. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Applied Microbiology and Biotechnology 88: 389-399. 
  • Hollister EB, Gao C, Versalovic J. 2014. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology doi:10.1053/j.gastro.2014.01.052 
  • Hollister EB, Riehle K, Luna RA, Wiedler EM, Rubio-Gonzalez M, Mistretta TA, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino J, Shulman RJ, Versalovic J. 2015. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome doi: 10.1186/s40168-015-0101-x 
  • Durgan DJ, Ganesh BP, Cope JL, Adjami NJ, Phillips SC, Petrosino JF, Hollister EB, Bryan RM. 2016. Role of the gut microbiome in obstructive sleep apnea-induced hypertension. Hypertension 67: 469-474. 
  • Kao CC, Cope JL, Hsu JW, Dwarkanath P, Karmes JM, Luna RA, Hollister EB, Thame MM, Kurpad AV, Jahoor F. 2016. The gut microbiome and its relationship to gut function, arginine, and citrulline metabolism in American, Indian, and Jamaican women. The Journal of Nutrition. doi:10.3945/jn.115.227579 
  • Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. 2016. Transfer of viral communities between human individuals during fecal microbiota transplantation. mBio doi:10.1128/mbio.00322-16. 
  • Shulman RJ, Hollister EB, Cain K, Czyzewski D, Self M, Weidler EM, Devaraj S, Luna RA, Versalovic J, Heitkemper MM. 2016. Randomized, double blind trial of psyllium fiber in children with irritable bowel syndrome. Clinical Gastroenterology and Hepatology doi: 10.1016/j.cgh.2016.03.045. 
  • Pammi M, Cope JL, Tarr P, Warner B, Morrow AL, Gregory KE, Kroll JS, Ferris MJ, Engstrand L, Lilja HE, Hollister EB, Versalovic J, Neu J. 2017. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: A systematic review and meta-analysis. Microbiome 5:31. doi: 10.1186/s40168-017-0248-8. 
  • Shah M, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal J, Hollister EB. 2017. Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer from the fecal microbiome. Gut (manuscript accepted)

 

Daryl Gohl

R&D Lead at University of Minnesota Genomics Center Innovation Lab, Minneapolis, MN

Co-founder and Chief Scientific Officer of CoreBiome, St. Paul, MN

BIO:

Daryl Gohl leads the University of Minnesota Genomics Center Innovation Lab and is a co-founder and Chief Scientific Officer of CoreBiome. His academic work has focused on the development of novel tools and technologies for answering biological questions and for improving genomics-based measurements of the microbiome. Dr. Gohl received his Ph.D. in Molecular Biology from Princeton University, followed by postdoctoral training at Stanford University.

Twitter: @DarylGohl

SELECTED PUBLICATIONS:

  • Gohl, D.M. 2017. The ecological landscape of microbiome science. Nature Biotechnology. 34(9):942-949. doi:10.1038/nbt.3983
  • Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T.J., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D., Beckman, K.B. 2016. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology. 34(9):942-949. doi:10.1038/nbt.3601
  • Belda, E., Coulibaly, B., Fofana, A., Beavogui, A.H., Traore, S.F., Gohl, D.M., Vernick, K.D, Riehle, M.M. 2017. Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome. Scientific Reports. 7:3421. doi:10.1038/s41598-017-03487-1
  • Baldwin, E.A., Walther-Antonio, M., MacLean, A.M., Gohl, D.M., Beckman, K.B., Chen, J., White, B., Creedon, D.J., Chia, N. 2015. Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery. PeerJ 3:e1398. doi: 10.7717/peerj.1398
  • Fisher Y.E., Yang, H.H, Isaacman-Beck, J., Xie, M., Gohl, D.M., Clandinin, T.R. 2017. FlpStop, a tool for conditional gene control in Drosophila. eLife. 6:e22279. doi: 10.7554/eLife.22279
  • Gohl, D.M., Freifeld, L., Silies, M., Horowitz, M., Clandinin, T.R. Large-scale mapping of transposable element insertion sites using digital encoding of DNA sample identity. Genetics. 196(3):615-623. doi: 10.1534/genetics.113.159483            
  • Gohl, D.M., Silies, M.A., Gao, X.J., Bhalerao, S., Luongo,F.J., Lin, C-C., Potter, C.J., Clandinin, T.R. 2011. A versatile in vivo system for directed dissection of gene expression patterns. Nature Methods. 8 231-237. doi:10.1038/nmeth.1561

For a complete list of publications, visit Google Scholar

 


 

Christopher Stewart

RESEARCH FELLOW AT NEWCASTLE UNIVERSITY, NEWCASTLE UPON TYNE, UNITED KINGDOM

 BIO:

Dr Christopher Stewart is an independent Research Fellow at Newcastle University, UK. His lab is primarily focused on the development of the gut and respiratory microbiome in early life. He utilizes state of the art omic technologies and novel computational approaches to characterise clinical samples and determine associations with health and disease. Additionally, moving beyond associations into mechanistic understanding, he is also working on utilizing a powerful ex vivo co-culture system comprising patient derived epithelium cells to monitor bacterial-host interaction. Christopher obtained his Ph.D. and gained postdoc experience at Northumbria University, before joining the Alkek Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine as a post-doctoral associate.

Twitter: @cjstewart7

SELECTED PUBLICATIONS:

  • Stewart CJ, Auchtung T, Ajami N, Velasquez K, Smith D, De La Garza R, Salas R, Petrosino J. (2018) Effects oftobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: A pilot study. PeerJ; Accepted: In press
  • Stewart CJ, Hasegawa K, Wong MC, Ajami NJ, Petrosino JF, Piedra PA, Espinola JA, Tierney CN, Camargo Jr. CA, Mansbach JM. (2018) Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways. Journal of Infectious Disease. 217(7):1160-1169
  • Stewart CJ, Mansbach JM, Wong MC, Ajami NJ, Petrosino JF, Camargo Jr. CA, Hasegawa K. (2017) Associations of nasopharyngeal metabolome and microbiome with severity among infants with bronchiolitis: A multi-omic analysis. Am J Respir Crit Care Med. 196(7):882-891
  • Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. (2016) Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. Microbiome. 29;4(1):67
  • Abdulkadir B, Nelson A, Skeath T, Marrs ECL, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJ. (2016) Stool bacterial load in preterm infants with necrotising enterocolitis. Early Human Development. 95:1-2
  • Abdulkadir B, Nelson A, Skeath T, Marrs ECL, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJ. (2016) Routine use of probiotics in preterm infants: longitudinal impact on the microbiome and metabolome. Neonatology. 109(4):239-247
  • Stewart CJ, Skeath T, Nelson A, Fernstad SJ, Marrs ECL, Perry JD, Cummings SP, Berrington JE, Embleton ND. (2015) Preterm gut microbiota and metabolome following discharge from intensive care. Scientific Reports. 5:17141
  • Stewart CJ, Nelson A, Treumann A, SkeathT, CummingsSP, Embleton ND, Berrington JE (2015) Metabolomic and proteomic analysis of serum from preterm infants with necrotising enterocolitis and late onset sepsis. Paediatric Research. 79(3):425-3
  • Stewart CJ, Nelson A, Marrs ECL, Lanyon C, Perry JD, Embleton ND, Cummings SP, Berrington JE. (2013) Development of the Preterm Gut Microbiome in Twins at Risk of Necrotising Enterocolitis and Sepsis. PLoS One. 8(8): e73465
  • Stewart CJ, Marrs ECL, Magorrian S, Nelson A, Lanyon C, Perry JD, Embleton ND, Cummings SP, Berrington JE. (2012) The preterm gut microbiota: changes associated with necrotising enterocolitis and infection. Acta paediatrica. 101(11):1121-7 
  • Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. (2017) Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 5(1):75

 For a complete list of publications, visit Google Scholar