Ramaley C351C
Department of Integrative Physiology
University of Colorado
Boulder, CO 80309-0354

Research Interests

The human microbiome is an entire ecosystem of microscopic organisms that live on our skin and inside our body. These microbes are integrated into our immune, digestive, and nervous systems, and are critical to our overall wellbeing. At the Integrative Microbiome Research Laboratory, we aim to increase our understanding of the human microbiome and its connections to our physiology, and to apply our findings to improve human health.

Our research laboratory uses cutting edge computer-based analysis and experimental techniques to study the microbiome. We specialize in “omics” methods, including metagenomics and metabolomics, which use state-of-the-art instruments to study entire microbial communities simultaneously.

Current research topics include:

  • From where do we get our microbiome? How do our microbes spread from person to person?
  • How does our intestinal immune system control our gut microbiome? How do failures in this control lead to diseases like inflammatory bowel disease?
  • Can we use wastewater or other aggregate sources to understand population-level microbiome variation and/or to provide early detection of the next pandemic?

The Integrative Microbiome Research Laboratory will open within the CU Boulder Department of Integrative Physiology in Fall 2024.

Microbes within the colon (top left corner) are separated from mammalian cells (blue; bottom right corner) by a layer of mucus (diagonal green across the image)

Microbes within the colon (top left corner) are separated from mammalian cells (blue; bottom right corner) by a layer of mucus (diagonal green across the image) (Earle et. al., Cell Host & Microbe, 2015).


Opportunities for Graduate Students

The Integrative Microbiome Research Laboratory is currently accepting applications for graduate students to start in Fall 2024. Further details about applying to the Graduate Program can be found here (Application Deadline: December 1, 2023 for Fall 2024). The lab would be a particularly strong fit for students interested in conducting research at the cutting edge of computational biology. No prior computational experience required. To learn more about opportunities in the lab, reach out to Dr. Olm prior to applying.

Opportunities for Undergraduates

We are looking for enthusiastic, motivated undergraduate students to start in Fall 2024. Candidates must commit to at least 8 hours of research per week. Both computational and laboratory-based opportunities are available. Please contact Dr. Olm for more information.

Opportunities for Postdoctoral Fellows

Postdoctoral fellow positions are available contingent upon research funding. For more information, please contact Dr. Olm.

Select Publications

For a complete list of publications click here.

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