Dr Xochitl Morgan
| Position | Senior Lecturer |
|---|---|
| Department | Department of Microbiology and Immunology |
| Qualifications | BSc, PhD |
| Research summary | Environmental microbiology, host-microbe interactions, inflammatory bowel disease, human microbiome |
Research
My research uses sequencing and computational biology approaches to understand the composition and metabolism of microbial communities, both in the context of human health and in other environments, such as the rare biosphere.High-throughput sequencing lets us study the microbial communities of many environments in high resolution, as well as understanding how these communities change and interact with their environments over time. However, only by applying appropriate quantitative methods to microbial community analysis can we both understand basic biology and translational potential.
In the context of human health, the genetic potential of the 1-2 kg of microbiota resident in the gut is vastly greater than that of their human hosts; it is critical to understand both how these microbiota interact with their hosts over time and in response to stimuli, and the translational potential of these discoveries. From studying the rare biosphere, we will continue to learn novel microbial biochemistry, strategies for environmental adaptation, and potentially novel therapeutics.
Publications
Yasuda, K., Hsu, T., Gallini, C. A., Mclver, L. J., Schwager, E., Shi, A., … Morgan, X. C. (2017). Fluoride depletes acidogenic taxa in oral but not gut microbial communities in mice. mSystems, 2(4), e00047-17. doi: 10.1128/mSystems.00047-17
Hsu, T., Joice, R., Vallarino, J., Abu-Ali, G., Hartmann, E. M., Shafquat, A., … Morgan, X. C., … Huttenhower, C. (2016). Urban transit system microbial communities differ by surface type and interaction with humans and the environment. mSystems, 1(3), e00018-16. doi: 10.1128/mSystems.00018-16
Yassour, M., Lim, M. Y., Yun, H. S., Tickle, T. L., Sung, J., Song, Y.-M., … Morgan, X. C., … Huttenhower, C. (2016). Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Medicine, 8(1), 17. doi: 10.1186/s13073-016-0271-6
Lee, K. C., Stott, M. B., Dunfield, P. F., Huttenhower, C., McDonald, I. R., & Morgan, X. C. (2016). The Chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in New Zealand's Taupō Volcanic Zone. Applied & Environmental Microbiology, 82(12), 3572-3581. doi: 10.1128/aem.00139-16
Morgan, X. C., Kabakchiev, B., Waldron, L., Tyler, A. D., Tickle, T. L., Milgrom, R., … Huttenhower, C. (2015). Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biology, 16, 67. doi: 10.1186/s13059-015-0637-x
Journal - Research Article
Yasuda, K., Hsu, T., Gallini, C. A., Mclver, L. J., Schwager, E., Shi, A., … Morgan, X. C. (2017). Fluoride depletes acidogenic taxa in oral but not gut microbial communities in mice. mSystems, 2(4), e00047-17. doi: 10.1128/mSystems.00047-17
Hsu, T., Joice, R., Vallarino, J., Abu-Ali, G., Hartmann, E. M., Shafquat, A., … Morgan, X. C., … Huttenhower, C. (2016). Urban transit system microbial communities differ by surface type and interaction with humans and the environment. mSystems, 1(3), e00018-16. doi: 10.1128/mSystems.00018-16
Lee, K. C., Stott, M. B., Dunfield, P. F., Huttenhower, C., McDonald, I. R., & Morgan, X. C. (2016). The Chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in New Zealand's Taupō Volcanic Zone. Applied & Environmental Microbiology, 82(12), 3572-3581. doi: 10.1128/aem.00139-16
Yassour, M., Lim, M. Y., Yun, H. S., Tickle, T. L., Sung, J., Song, Y.-M., … Morgan, X. C., … Huttenhower, C. (2016). Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Medicine, 8(1), 17. doi: 10.1186/s13073-016-0271-6
Morgan, X. C., Kabakchiev, B., Waldron, L., Tyler, A. D., Tickle, T. L., Milgrom, R., … Huttenhower, C. (2015). Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biology, 16, 67. doi: 10.1186/s13059-015-0637-x
Lee, K. C.-Y., Morgan, X. C., Power, J. F., Dunfield, P. F., Huttenhower, C., & Stott, M. B. (2015). Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22T. Standards in Genomic Sciences, 10, 101. doi: 10.1186/s40793-015-0099-5
Houghton, K. M., Morgan, X. C., Lagutin, K., MacKenzie, A. D., Vyssotski, M., Mitchell, K. A., … Stott, M. B. (2015). Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus. International Journal of Systematic & Evolutionary Microbiology, 65(12), 4479-4487. doi: 10.1099/ijsem.0.000598
Börnigen, D., Moon, Y. S., Rahnavard, G., Waldren, L., McIver, L., Shafquat, A., … Morgan, X. C., … Huttenhower, C. (2015). A reproducible approach to high-throughput biological data acquisition and integration. PeerJ, 3, e791. doi: 10.7717/peerj.791
Franzosa, E. A., Hsu, T., Sirota-Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015). Sequencing and beyond: Integrating molecular 'omics' for microbial community profiling. Nature Reviews Microbiology, 13(6), 360-372. doi: 10.1038/nrmicro3451
Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., … Morgan, X. C. (2015). Biogeography of the intestinal mucosal and lumenal microbiome in the Rhesus Macaque. Cell Host & Microbe, 17(3), 385-391. doi: 10.1016/j.chom.2015.01.015
Lee, K. C.-Y., Morgan, X. C., Dunfield, P. F., Tamas, I., McDonald, I. R., & Stott, M. B. (2014). Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. ISME Journal, 8(7), 1522-1533. doi: 10.1038/ismej.2013.251
Crowe, M. A., Power, J. F., Morgan, X. C., Dunfield, P. F., Lagutin, K., Rijpstra, W. I. C., … Stott, M. B. (2014). Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils. International Journal of Systematic & Evolutionary Microbiology, 64, 220-227. doi: 10.1099/ijs.0.055079-0
Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., … Huttenhower, C. (2014). Relating the metatranscriptome and metagenome of the human gut. PNAS, 111(22), E2329-E2338. doi: 10.1073/pnas.1319284111
Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., … Morgan, X. C., … Xavier, R. J. (2014). The treatment-naive microbiome in new-onset Crohn's disease. Cell Host & Microbe, 15(3), 382-392. doi: 10.1016/j.chom.2014.02.005
Morgan, X. C., & Huttenhower, C. (2014). Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology, 146(6), 1437-1448.e1. doi: 10.1053/j.gastro.2014.01.049
Rooks, M. G., Veiga, P., Wardwell-Scott, L. H., Tickle, T., Segata, N., Michaud, M., … Morgan, X. C., … Garrett, W. S. (2014). Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME Journal, 8(7), 1403-1417. doi: 10.1038/ismej.2014.3
Börnigen, D., Morgan, X. C., Franzosa, E. A., Ren, B., Xavier, R. J., Garrett, W. S., & Huttenhower, C. (2013). Functional profiling of the gut microbiome in disease-associated inflammation. Genome Medicine, 5, 65. doi: 10.1186/gm469
Segata, N., Börnigen, D., Morgan, X. C., & Huttenhower, C. (2013). PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature Communications, 4, 2304. doi: 10.1038/ncomms3304
Lee, K. C. Y., Herbold, C. W., Dunfield, P. F., Morgan, X. C., McDonald, I. R., & Stott, M. B. (2013). Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions. Applied & Environmental Microbiology, 79(7), 2484-2487. doi: 10.1128/AEM.03333-12
Morgan, X. C., Segata, N., & Huttenhower, C. (2013). Biodiversity and functional genomics in the human microbiome. Trends in Genetics, 29(1), 51-58. doi: 10.1016/j.tig.2012.09.005
Segata, N., Boernigen, D., Tickle, T. L., Morgan, X. C., Garrett, W. S., & Huttenhower, C. (2013). Computational meta'omics for microbial community studies. Molecular Systems Biology, 9(1), 666. doi: 10.1038/msb.2013.22
Dunfield, P. F., Tamas, I., Lee, K. C., Morgan, X. C., McDonald, I. R., & Stott, M. B. (2012). Electing a candidate: A speculative history of the bacterial phylum OP10. Environmental Microbiology, 14(12), 3069-3080. doi: 10.1111/j.1462-2920.2012.02742.x
Morgan, X. C., & Huttenhower, C. (2012). Chapter 12: Human microbiome analysis. PLoS Computational Biology, 8(12), e1002808. doi: 10.1371/journal.pcbi.1002808
Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., … Huttenhower, C. (2012). Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biology, 13, R79. doi: 10.1186/gb-2012-13-9-r79
Vyssotski, M., Ryan, J., Lagutin, K., Wong, H., Morgan, X., & Stott, M. (2012). A novel fatty acid, 12,17-dimethyloctadecanoic acid, from the extremophile Thermogemmatispora sp. (strain T81). Lipids, 47(6), 601-606. doi: 10.1007/s11745-012-3668-z
Lee, K. C.-Y., Dunfield, P. F., Morgan, X. C., Crowe, M. A., Houghton, K. M., Vyssotski, M., … Stott, M. B. (2011). Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. International Journal of Systematic & Evolutionary Microbiology, 61(10), 2482-2490. doi: 10.1099/ijs.0.027235-0
Vyssotski, M., Lee, K. C.-Y., Lagutin, K., Ryan, J., Morgan, X. C., & Stott, M. B. (2011). Fatty acids of Chthonomonas calidirosea, of a novel class chthonomonadetes from a recently described phylum Armatimonadetes. Lipids, 46(12), 1155-1161. doi: 10.1007/s11745-011-3597-2
Morgan, X. C., Ni, S., Miranker, D. P., & Iyer, V. R. (2007). Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics, 8, 445. doi: 10.1186/1471-2105-8-445
Kim, J., Bhinge, A. A., Morgan, X. C., & Iyer, V. R. (2005). Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods, 2(1), 47-53. doi: 10.1038/nmeth726
Journal - Research Other
Joice, R., Yasuda, K., Shafquat, A., Morgan, X. C., & Huttenhower, C. (2014). Determining microbial products and identifying molecular targets in the human microbiome [Perspective]. Cell Metabolism, 20(5), 731-741. doi: 10.1016/j.cmet.2014.10.003
