Sarah Highlander, Ph.D.
Department of Molecular Virology & Microbiology
Microbial Genomics and Metagenomics
The total number of prokaryotic cells inhabiting our planet is estimated to be in the nonillions (1030). Those within and on the human body number mere trillions (1014), yet their identity, distribution and function are still obscure. Significantly, the contribution and effect of the human “microbiome” on human health and disease is still largely unknown.
Progress has been made to catalog and characterize these organisms and their genomes, but most studies have focused on a single body site, a single disease (often on a single pathogenic organism), and most of these have been restricted to culture-dependent methods. Recent advances in DNA sequencing technologies have enabled more comprehensive analyses of the human microbiota; thus, a concerted effort was launched to leverage these advances to expand our insight into the microbial communities that inhabit distinct niches within the human body. It is now possible to sequence the DNA of the collective genome (or metagenome) of entire communities of microbes from all body sites, effectively enabling the characterization of the “Human Microbiome”.
Since 2007, our laboratory has played a leadership role in the NIH Human Microbiome Project (HMP) (commonfund.nih.gov/hmp/). The overarching goal of the HMP is to develop tools and resources for characterization of the human microbiota and to relate these microbiota to human health and disease. A primary focus of the laboratory has been the sequencing and annotation of hundreds of bacterial “reference genomes” to contribute to a catalog of strains (www.hmpdacc.org) that serves as a database against which metagenomic data from human samples are compared. We also played an active role in the processing and characterization of thousands of samples collected from a healthy cohort of subjects and we developed “mock” metagenomic communities to aid in benchmarking activities for HMP sample preparation and sequencing (www.beiresources.org).
Current and ongoing activities are focused on comparative microbial genomics, 16S ribosomal RNA gene surveys and metagenomics of clinical and environmental samples.
Department of Molecular Virology & Microbiology
Baylor College of Medicine
One Baylor Plaza, MS BCM280
Houston, TX, 77030, U.S.A.
B.S. University of Michigan, Ann Arbor
M.S., Ph.D., New York University Sackler School of Graduate Biomedical Sciences
Postdoctoral Training, University of Texas Health Science Center, Houston
Highlander, Sarah K. (2013) Encyclopedia of Metagenomics, Volume III. Humans (Karen E. Nelson, Editor-in-Chief; Bryan A. White, Sarah K. Highlander, Karen E. Nelson, and Francisco Rodriguez-Valera, Volume Editors), Springer-Verlag, Heidelberg.
Highlander, Sarah K. (2012) High throughput sequencing methods for microbiome profiling: application to food animal systems. Animal Health Research Reviews 13:40-53.
Methé, Barbara, et al. (2012) A framework for human microbiome research. Nature 486: 215-224. www-ncbi-nlm-nih-gov.ezproxyfallback.library.tmc.edu/pmc/articles/PMC3377744/
Huttenhower, Curtis, et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
Ward, Doyle V., Dirk Gevers, Georgia Giannoukos, Ashlee M. Earl, Barbara A. Methé, Erica Sodergren, Michael Feldgarden, Dawn M. Ciulla, Diana Tabbaa, Cesar Arze, Elizabeth Appelbaum, Leigh Aird, Scott Anderson, Tulin Ayvaz, Edward Belter, Monika Bihan, Toby Bloom, Jonathan Crabtree, Laura Courtney, Lynn Carmichael, David Dooling, Rachel L. Erlich, Candace Farmer, Lucinda Fulton, Robert Fulton, Hongyu Gao, John A. Gill, Brian J. Haas, Lisa Hemphill, Otis Hall, Susanna G. Hamilton, Theresa A. Hepburn, Niall J. Lennon, Vandita Joshi, Cristyn Kells, Christie L. Kovar, Divya Kalra, Kelvin Li, Lora Lewis, Shawn Leonard, Donna M. Muzny, Elaine Mardis, Kathie Mihindukulasuriya, Vincent Magrini, Michelle O’Laughlin, Craig Pohl, Xiang Qin, Keenan Ross, Matthew C. Ross, Yu-Hui A. Rogers, Navjeet Singh, Yue Shang, Katarzyna Wilczek-Boney, Jennifer R. Wortman, Kim C. Worley, Bonnie P. Youmans, Shibu Yooseph, Yanjiao Zhou, Patrick D. Schloss, Richard Wilson, Richard A. Gibbs, Karen E. Nelson, George Weinstock, Todd Z. DeSantis, Joseph F. Petrosino,, Sarah K. Highlander,, Bruce W. Birren (2012) Evaluation of 16S rDNA-based community profiling for human microbiome research PLoS ONE 7: e39315.
Haas, Brian J., Dirk Gevers, Ashlee Earl, Michael Feldgarden, Doyle Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah Highlander, Erica Sodergren, Barbara Methe, Todd DeSantis, The Human Microbiome Consortium, Joseph Petrosino, Rob Knight, and Bruce Birren (2011) Chimeric 16S rDNA formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 21:494-504.
Highlander, Sarah K., James Versalovic and Joseph F. Petrosino (2011) Chapter 13. The Human Microbiome. In, Manual of Clinical Microbiology, 10th Edition, Volume I, Section I. (James Versalovic, editor) ASM Press, Washington DC.
Klaassens, Eline S., Mark Morrison and Sarah K. Highlander (2010) Selection and sequencing of strains as references for human microbiome studies. In, “Metagenomics of the Human Body” (Karen Nelson, ed.), pages 79-90. Springer Press, New York.
Yeoman, Carl J., Suleyman Yildrim, Susan M. Thomas, Anthony S. Durkin, Ramana Madupu, Manolito Torralba, Granger Sutton, Christian J. Buhay, Yan Ding, Shannon P. Dugan-Rocha, Donna M. Muzny, Xiang Qin, Richard A. Gibbs, Steven R. Leigh, Rebecca Stumpf, Bryan White, Sarah K. Highlander, Karen E. Nelson and Brenda A. Wilson (2010) Comparative genomics of two Gardnerella vaginalis strains reveals genomic differences that may be important to the etiology of bacterial vaginosis. PLoS ONE 5: e12411.
Lawrence, Paulraj K., Sudarvili Shanthalingam, Rohana P. Dassanayake, Renuka Subramaniam, Caroline N. Herndon, Donald P. Knowles, William J. Foreyt, Gary Wayman, Sarah K. Highlander, Ann Marie Marciel and Subramaniam Srikumaran. (2010) Transmission of Mannheimia haemolytica from domestic sheep (Ovis aries) to bighorn sheep (Ovis canadensis): unequivocal demonstration with green fluorescent protein-tagged organisms. Journal of Wildlife Disease 46: 706-717.
Human Microbiome Jumpstart Reference Strains Consortium, Karen E. Nelson, George M. Weinstock, Sarah K. Highlander, Kim C. Worley, Heather H. Creasy, Jennifer R. Wortman, D.B. Rusch, Makedona Mitreva, Erica Sodergren, Asif T. Chinwalla, Michael Feldgarden, Dirk Gevers, Brian J. Haas, Ramana Madupu, Doyle V. Ward, Bruce W. Birren, Richard A. Gibbs, Barbara Methe, Joseph F. Petrosino, Robert L. Strausberg, Granger G. Sutton, Owen R. White, R. K. Wilson, S. Durkin, Michelle. G. Giglio, S. Gujja, C. Howarth, C. D. Kodira, Nikos Kyrpides, Teena Mehta, Donna M. Muzny, M. Pearson, K. Pepin, A. Pati, Xiang Qin, C. Yandava, Q. Zeng, Lan Zhang, A. M. Berlin, L. Chen, T. A. Hepburn, J. Johnson, J. McCorrison, J. Miller, P. Minx, Chad Nusbaum, C. Russ, S. M. Sykes, C. M. Tomlinson, S. Young, W. C. Warren, Jonathon Badger, Jonathon Crabtree, Victor M. Markowitz, J. Orvis, Andrew Cree, S. Ferriera, Lucinda L. Fulton, Robert S. Fulton, M. Gillis, Lisa D. Hemphill, Vandita Joshi, Christie Kovar, Manolito Torralba, Kris A. Wetterstrand, A. Abouelleil, A. M. Wollam, Christian J. Buhay, Yan Ding, Shannon Dugan, Michael G. FitzGerald, Michael Holder, Jennifer Hostetler, Sandra W. Clifton, E. Allen-Vercoe, Ashlee M. Earl, C. N. Farmer, K. Liolios, M. G. Surett, Q. Xu, C. Pohl, Katarzyna Wilczek-Boney, D. Zhu (2010) A catalog of reference genomes from the Human Microbiome. Science, 328: 994-999.
Chain, Patrick S. G., D. V. Grafahm, Robert S. Fulton, Michael G. FitzGerald, Jennifer Hostetler, Donna Muzny, J.C. Detter, J. Ali, Bruce Birren, T. S. Brettin, D. C. Bruce, Christina Buhay, James R. Cole, Yan Ding, D. Field, G. M. Garrity, Richard A. Gibbs, T. Graves, C. S. Han, S. H. Harrison, Sarah Highlander, Michael Holder, Philip Hugenholtz, H.M. Khouri, Nykos C. Kyrpides, D. Lang, A. Lapidus, S. A. Malfatt, Karen E. Nelson, Julian Parkhill, Joseph Petrosino, S. Pitluck, Xiang Qin, T. D. Read, J. Schmutz, S. Sozhamannan, Robert Strausberg, Granger Sutton, N. R. Thomson, J. M. Tiedje, George Weinstock, A. Wollam and the entire GSC and HMP Jumpstart consortia (2009) Genome project standards in a new era of sequencing. Science. 326: 236-237.
Highlander, Sarah K., Kristina G. Hultén, Xiang Qin, Huaiyang Jiang, Shailaja Yerrapragada, Edward O. Mason, Jr., Yue Shang, Tiffany M. Williams, Régine M. Fortunov, Yamei Liu, Okezie Igboeli, Joseph Petrosino, Madhan Tirumalai, Akif Uzman, George E, Fox, Ana Maria Cardenas, Donna M. Muzny, Lisa Hemphill, Yan Ding, Shannon Dugan, Peter R. Blyth, Christian J. Buhay, Huyen H. Dinh, Alicia C. Hawes, Michael Holder, Christie L. Kovar, Sandra L. Lee, Wen Liu, Lynne V. Nazareth, Qiaoyan Wang, Jianling Zhou, Sheldon L. Kaplan, and George M. Weinstock (2007) Subtle genetic changes enhance virulence of methicillin resistant and sensitive strains of Staphylococcus aureus. BMC Microbiology 6: 99-113.
Bonnie Youmans, B.S.