Recommended Readings: David A. Relman, M.D., February 19

Friday Lecture Series
Friday, February 19
3:45 p.m., Caspary Auditorium

David A. Relman, M.D.
Thomas C. and Joan M. Merigan Professor,
Department of Medicine,
Department of Microbiology and Immunology,
Stanford University

The Human Microbiome Across Space and Time

Recommended Readings

Empirical Article

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., … & Stevenson, D. K. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences, 112(35), 11060-11065. doi: 10.1073/pnas.1502875112.

Hoy, Y. E., Bik, E. M., Lawley, T. D., Holmes, S. P., Monack, D. M., Theriot, J. A., & Relman, D. A. (2015). Variation in taxonomic composition of the fecal microbiota in an inbred mouse strain across individuals and time. PLOS ONE, 10(11), e0142825. doi: 10.1371/journal.pone.0142825.

Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLOS ONE, 8(1), e53838. doi: 10.1371/journal.pone.0053838.

Review Paper

Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J., & Relman, D. A. (2012). The application of ecological theory toward an understanding of the human microbiome. Science, 336(6086), 1255-1262. doi: 10.1126/science.1224203.

Recommended Readings: Julie Segre, Ph.D., February 12

Friday Lecture Series
Friday, February 12, 2016
3:45 p.m., Caspary Auditorium

Julie Segre, Ph.D.,
Senior Investigator, Microbial Genomics Section,
Chief, Translational and Functional Genomics Branch,
National Human Genome Research Institute,
National Institutes of Health

Human Skin Microbiome in Health and Disease

Recommended Reading

Empirical Papers

Conlan, S., Thomas, P. J., Deming, C., Park, M., Lau, A. F., Dekker, J. P., … & Segre, J. A. (2014). Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Science Translational Medicine, 6(254), 254ra126-254ra126. doi: 10.1126/scitranslmed.3009845.

Naik, S., Bouladoux, N., Linehan, J. L., Han, S. J., Harrison, O. J., Wilhelm, C., … & Belkaid, Y. (2015). Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 520(7545), 104-108. doi: 10.1038/nature14052.

Oh, J., Byrd, A. L., Deming, C., Conlan, S., Kong, H. H., Segre, J. A., & NISC Comparative Sequencing Program. (2014). Biogeography and individuality shape function in the human skin metagenome. Nature, 514(7520), 59-64. doi: 10.1038/nature13786.

Review Article

Belkaid, Y., & Segre, J. A. (2014). Dialogue between skin microbiota and immunity. Science, 346(6212), 954-959. doi: 10.1126/science.1260144.

Recommended Readings: Howard Hang, Ph.D. November 17

Monday Lecture Series
Monday, November 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Howard Hang, Ph.D.
Professor and Head,
Laboratory of Chemical Biology and Microbial Pathogenesis,
The Rockefeller University

A C. elegans Model for Commensal Bacteria Function Reveals a Secreted Peptidoglycan Hydrolase Activator of Host Immunity

Recommended Readings

Empirical Articles

Charron, G., Zhang, M. M., Yount, J. S., Wilson, J., Raghavan, A. S., Shamir, E., & Hang, H. C. (2009). Robust fluorescent detection of protein fatty-acylation with chemical reporters. Journal of the American Chemical Society, 131(13), 4967–4975. doi:10.1021/ja810122f

Hang, H. C., Geutjes, E.-J., Grotenbreg, G., Pollington, A. M., Bijlmakers, M. J., & Ploegh, H. L. (2007). Chemical probes for the rapid detection of Fatty-acylated proteins in Mammalian cells. Journal of the American Chemical Society, 129(10), 2744–2745. doi:10.1021/ja0685001

Yount, J. S., Moltedo, B., Yang, Y.-Y., Charron, G., Moran, T. M., López, C. B., & Hang, H. C. (2010). Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nature Chemical Biology, 6(8), 610–614. doi:10.1038/nchembio.405

Review Paper

Grammel, M., & Hang, H. C. (2013). Chemical reporters for biological discovery. Nature Chemical Biology, 9(8), 475–484. doi:10.1038/nchembio.1296

Recommended Readings: Rob Knight, Ph.D. Wednesday, Oct. 30, 2013

SPECIAL SEMINAR
Wednesday, October 30, 2013
4:00 p.m., Carson Family Auditorium

Rob Knight, Ph.D.
HHMI Early Career Scientist and Professor
Department of Chemistry & Biochemistry, Department of Computer Science, and BioFrontiers Institute
University of Colorado at Boulder

Gut Microbes and their Role in Malnutrition and Obesity

Recommended Readings:

Review Papers

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), 1258–1270. doi:10.1016/j.cell.2012.01.035

Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., … Huttenhower, C. (2012). The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biology, 10(8), e1001377. doi:10.1371/journal.pbio.1001377

Hamady, M., & Knight, R. (2009). Microbial community profiling for human microbiome projects : Tools , techniques , and challenges, Genome Research, 19(7), 1141–1152. doi:10.1101/gr.085464.108.19

Ley, R. E., Lozupone, C. a, Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiotaNature Reviews Microbiology6(10), 776–788. doi:10.1038/nrmicro1978

Empirical Articles

Costello, E., Lauber, C., & Hamady, M. (2009). Bacterial community variation in human body habitats across space and time. Science, 326, 8–11.

The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–14. doi:10.1038/nature11234

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A, Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11070–5. doi:10.1073/pnas.0504978102

Lozupone, C. A., Stombaugh, J., Gonzalez, A., Ackermann, G., Jansson, J. K., Gordon, J. I., … Knight, R. (2013). Meta-analyses of studies of the human microbiota, Genome Research, 23,1704–1714. doi:10.1101/gr.151803.112

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. doi:10.1038/nature07540

Turnbaugh, P. J., Ley, R. E., Mahowald, M. a, Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–31. doi:10.1038/nature05414

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–7. doi:10.1038/nature11053