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Research Interests

• Human microbiome
• Mucosal immunology
• Inflammatory bowel disease (IBD)
• Computational biology and software development
• Integrative Microbiome Research Laboratory

Education                  

• 2014-2019, Ph.D., The University of California, Berkeley
• 2010-2014, B.S., The University of Pittsburgh

Professional Experience

• Starting Fall 2024, Assistant Professor, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
• 2020-2024, Postdoctoral Fellow, Stanford University
• 2019-2020, Interim Postdoctoral Scholar, The University of California, Berkeley

Honors and Awards

• 2021-2024, Ruth S. Kirschstein F32 National Research Service Award
• 2020-2021, T32 NIH Postdoctoral Training Fellowship
• 2021, Research article highlighted as one of “5 Top Cited Papers” of mSystems
• 2019, Keystone National Institute of Allergy and Infectious Diseases Travel Scholarship
• 2017, Research article selected as Cover Image of Genome Research
• 2017, Research article selected as “Editor’s Pick” of mBio
• 2014-2019, National Science Foundation Graduate Research Fellowship

Select Publications

For a complete list of publications .

Carter, M.M.*, Olm, M.R.*, Merrill, B.D.*, Dahan, D., Tripathi, S., Spencer, S.P., Yu, F.B., Jain, S., Neff, N., Jha, A.R., Sonnenburg, E.D., Sonnenburg, J.L., (2023). Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 186, 3111-3124.e13. https://doi.org/10.1016/j.cell.2023.05.046

Olm M. R.*, Dahan, D.*, Carter M. M., Merrill B. D., Yu F. B., Jain S., Meng X., Tripathi S., Wastyk H., Neff N., Holmes S., Sonnenburg E. D., Jha A. R., Sonnenburg J. L. (2022). Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science, 376, 1220–1223. https://doi.org/10.1126/science.abj2972

Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021). inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nature Biotechnology, 39(6), 727–736. https://doi.org/10.1038/s41587-020-00797-0

Crits-Christoph, A., Kantor, R. S., Olm, M. R., Whitney, O. N., Al-Shayeb, B., Lou, Y. C., Flamholz, A., Kennedy, L. C., Greenwald, H., Hinkle, A., Hetzel, J., Spitzer, S., Koble, J., Tan, A., Hyde, F., Schroth, G., Kuersten, S., Banfield, J. F., & Nelson, K. L. (2021). Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. MBio, 12(1), e02703-20. https://doi.org/10.1128/mBio.02703-20

Olm, M. R., Bhattacharya, N., Crits-Christoph, A., Firek, B. A., Baker, R., Song, Y. S., Morowitz, M. J., & Banfield, J. F. (2019). Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Science Advances, 5(12), eaax5727. https://doi.org/10.1126/sciadv.aax5727

Olm, M. R.*, West, P. T.*, Brooks, B., Firek, B. A., Baker, R., Morowitz, M. J., & Banfield, J. F. (2019). Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. Microbiome, 7(1), 26. https://doi.org/10.1186/s40168-019-0638-1

Rahman, S. F., Olm, M. R., Morowitz, M. J., & Banfield, J. F. (2018). Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. mSystems, 3(1), e00123-17. https://doi.org/10.1128/mSystems.00123-17

Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017). Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nature Communications, 8(1), 1814. https://doi.org/10.1038/s41467-017-02018-w

Olm, M. R., Brown, C. T., Brooks, B., Firek, B., Baker, R., Burstein, D., Soenjoyo, K., Thomas, B. C., Morowitz, M., & Banfield, J. F. (2017). Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Research, 27(4), 601–612. https://doi.org/10.1101/gr.213256.116

     * Denotes authors contributed equally to this work