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Health Sciences profile

Dr Xochitl Morgan

PositionSenior Lecturer
DepartmentDepartment of Microbiology and Immunology
QualificationsBSc, PhD
Research summaryEnvironmental 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

Murphy, R., Morgan, X. C., Wang, X. Y., Wickens, K., Purdie, G., Fitzharris, P., Otal, A., Lawley, B., Stanley, T., Barthow, C., Crane, J., … Tannock, G. W. (2019). Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: Sub-sample analysis from a RCT. Beneficial Microbes, 10(1), 5-17. doi: 10.3920/bm2017.0191

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., … Morgan, X. C., … Segata, N. (2019). Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. Advance online publication. doi: 10.1016/j.cell.2019.01.001

Gardner, P. P., Watson, R. J., Morgan, X. C., Draper, J. L., Finn, R. D., Morales, S. E., & Stott, M. B. (2019). Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ, 7, e6160 . doi: 10.7717/peerj.6160

Power, J. F., Carere, C. R., Lee, C. K., Wakerley, G. L. J., Evans, D. W., Button, M., … Morgan, X. C., … Stott, M. B. (2018). Microbial biogeography of 925 geothermal springs in New Zealand. Nature Communications, 9, 2876. doi: 10.1038/s41467-018-05020-y

McIver, L. J., Abu-Ali, G., Franzosa, E. A., Schwager, R., Morgan, X. C., Waldron, L., … Huttenhower, C. (2018). bioBakery: A meta'omic analysis environment. Bioinformatics, 34(7), btx754, 1235-1237. doi: 10.1093/bioinformatics/btx754

Journal - Research Article

Murphy, R., Morgan, X. C., Wang, X. Y., Wickens, K., Purdie, G., Fitzharris, P., Otal, A., Lawley, B., Stanley, T., Barthow, C., Crane, J., … Tannock, G. W. (2019). Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: Sub-sample analysis from a RCT. Beneficial Microbes, 10(1), 5-17. doi: 10.3920/bm2017.0191

Gardner, P. P., Watson, R. J., Morgan, X. C., Draper, J. L., Finn, R. D., Morales, S. E., & Stott, M. B. (2019). Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ, 7, e6160 . doi: 10.7717/peerj.6160

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., … Morgan, X. C., … Segata, N. (2019). Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. Advance online publication. doi: 10.1016/j.cell.2019.01.001

Power, J. F., Carere, C. R., Lee, C. K., Wakerley, G. L. J., Evans, D. W., Button, M., … Morgan, X. C., … Stott, M. B. (2018). Microbial biogeography of 925 geothermal springs in New Zealand. Nature Communications, 9, 2876. doi: 10.1038/s41467-018-05020-y

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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., 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

Morgan, X. C., & Huttenhower, C. (2012). Chapter 12: Human microbiome analysis. PLoS Computational Biology, 8(12), e1002808. doi: 10.1371/journal.pcbi.1002808

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

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

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

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

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Journal - Research Other

McIver, L. J., Abu-Ali, G., Franzosa, E. A., Schwager, R., Morgan, X. C., Waldron, L., … Huttenhower, C. (2018). bioBakery: A meta'omic analysis environment. Bioinformatics, 34(7), btx754, 1235-1237. doi: 10.1093/bioinformatics/btx754

Mallick, H., Ma, S., Franzosa, E. A., Vatanen, T., Morgan, X. C., & Huttenhower, C. (2017). Experimental design and quantitative analysis of microbial community multiomics. Genome Biology, 18, 228. doi: 10.1186/s13059-017-1359-z

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

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