Michael Zilliox PhD

  • Ophthalmology

Health Sciences Library Discover Research Network | ResearchGate



B.S. Biology, Philosophy - University of Minnesota, Minneapolis, MN


Ph.D. Microbiology, Immunology - John Hopkins University, Baltimore, MD


Postdoctoral Fellow - Emory University School of Medicine, Atlanta, GA

Research Focus: Corneal & Ocular Surface Diseases, Ocular Microbiome

Summary of Research Intersts

Our laboratory is interested in the ocular microbiome (OM) in healthy individuals and patients with ocular surface diseases (OSDs). We have found that about 50% of individuals have the same OM in each eye, while the other 50% have different OMs in each eye. Even though the OMs can differ in each eye, we find that measures of diversity show that the right and left eyes are equally diverse, suggesting that the environment limits the number of genera that can inhabit the niche, but the particular bacteria can vary. By comparing healthy individuals to patients with OSDs, we found that healthy individuals and patients with Graft-vs.-host disease (GVHD) have more diverse microbiomes than patients with Steven’s-Johnson Syndrome (SJS), Floppy Eyelid Syndrome (FES) and Dry Eye Disease (DED). Our hypothesis is that a diverse microbial environment promotes a healthy ocular surface. Preliminary data shows that bacteria may differ between OSDs as well. Finally, longitudinal studies have shown that patients can have stable OMs over several weeks, while other patients show variation between timepoints.



  • Herrnreiter CJ, Li X, Luck ME, Zilliox MJ, Choudhry MA. Integrated analysis of dysregulated microRNA and mRNA expression in intestinal epithelial cells following ethanol intoxication and burn injury. Scientific Reports. 2021 Oct 12;11(1):20213. doi: 10.1038/s41598-021-99281-1. PMID: 34642361; PMCID: PMC8510995.
  • Lynch, T.L., Kumar, M., McNamara, J.W., Kuster, D.W.D., Sivaguru, M., Previs, M.J., Lee, K.H., Kuffel, G., Zilliox, M.J., Lin, B.L., Ma, W., Gibson, A.M., Blaxall, B.C., Lorenz, J.N., Leichter, D.M., Leary, O.P., Janssen, P.M.L., de Tombe, P.P., Gilbert, R.J., Craig, R., Irving, T.C., Warshaw, D.M., and Sadayappan, S. Amino terminus of cardiac myosin binding protein-C regulates cardiac contractility. 2021. J. Mol. Cell. Cardiol. 156:33-44.


  • Zilliox MJ, Gange WS, Kuffel G, Mores CR, Joyce C, De Bustros P, Bouchard CS. Assessing the Ocular Surface Microbiome in Severe Ocular Surface Diseases. The Ocular Surface. 2020 July. doi: 10.1016/j.jtos.2020.07.007. PMID: 32717380.
  • Nelson, M.H., Knockelmann, H.M., Bailey, S.R., Huff, L.W., Bowers, J.S., Majchrzak-Kuligowska, K., Wyatt, M.M., Rubinstein, M.P., Mehrotra, S., Nishimura, M.I., Armeson, K.E., Giresi, P.G., Zilliox, M.J., Broxmeyer, H.E., and Paulos, C.M. 2020. Identification of human CD4+ T cell populations with distinct antitumor activity. Science Advances 6:eaba7443. PMCID: PMC7458458.


  • Zilliox, M.J., Schreckenberger, P.C., and Putonti, C. 2019. Draft genome sequence of clinical isolate Alcaligenaceae sp. Strain 429. Microbiol. Resour. Announce. 9:19. PMCID: PMC6509538.
  • Chakraborty P., Vaena S.G., Thyagarajan K., Chatterjee S., Al-Khami, A., Selvam, S.P., Nguyen H., Kang, I., Wyatt, M.W., Baliga, U., Hedley, Z., Ngang, R.N., Guo, B., Beeson, G.C., Husain, S., Paulos, C.M., Beeson, C.C., Zilliox, M.J., Hill, E.G, Mehrotra, M., Yu, X.Z., Ogretmen, B., and Mehrotra, S. 2019. Pro-survival lipid sphingosine-1-phosphate metabolically programs T cells to limit anti-tumor activity. Cell Rep. 13:1879-1893. PMCID: PMC6889821.
  • Shang, N., Wang, H., Bank, T., Perera, A., Joyce, C., Kuffel, G., Zilliox, M.J., Cotler, S.J., Ding, X., Dhanarajan, A., Breslin, P. and Qiu, W. 2019. Focal adhesion kinases and b-catenin cooperate to induce hepatocellular carcinoma. Hepatology 70:1631-1645. PMCID: PMC6819211.
  • Kuster, D.W.D., Lynch, T.L., Barefield, D.Y., Sivaguru, M., Kuffel, G, Zilliox, M.J., Lee, K.H., Craig, R., Namakkal-Soorappan, R., Sadayappan, S. 2019. Altered C10 domain in cardiac myosin binding protein-C results in hypertrophic cardiomyopathy. Cardiovasc. Res. 115:1986-1997. PMCID: PMC6872972.


  • Adam N, Iqbal O, De Alba F, Kuffel G, Zilliox MJ, Adams W, Siddiqui Z, Patel R, O'Malley P, Park P, Stefonowicz C, Bouchard CS. Genetic Polymorphisms Associated with Risk of Developing Age-Related Macular Degeneration in Patients with Chronic Aspirin Usage. Journal of Ophthalmology Eye Care. 2018 May; 1(1): 101.
  • Luther, K.M., Haar, L., McGuinness, M., Wang, Y., Song, Y., Shen, Z., Gardner, G., Kuffel, G., Ren, X., Zilliox, M.J. and Jones, W.K. 2018. Exosomal miR-21a-5p mediates cardioprotection by mesenchymal stem cells. J. of Mol. and Cellular Cardiol. 119:125-137.
  • Kramer, H., Kuffel, G., Thomas-White, K., Wolfe, A.J., Vellanki, K., Leehey, D.J., Bansal, V.K., Brubaker, L., Flanigan, R., Koval, J., Wadhwa, A. and Zilliox, M.J. 2018. Diversity of the midstream urine microbiome in adults with chronic kidney disease. Int. Uro. and Neph. 50:1123-1130. PMCID: PMC5986845.
  • Viswanathan, S.K., Puckelwartz, M.J., Mehta, A., Ramachandra, C.J.A., Jagadeesan, A., Fritsche-Danielson, R., Bhat, R.V., Wong, P., Kandoi, S., Schwanekamp, J.A., Kuffel, G., Pesce, L.L., Zilliox, M.J., Durai, U.N.B., Verma, R.S., Molokie, R.E., Suresh, D.P., Khoury, P.R., Thomas, A., Sanagala, T., Tang, H.C., Becker, R.C., Knoll, R., Shim, W., McNally, E.M. and Sadayappan, S. 2018. Association of Cardiomyopathy with MYBPC3 D389V and MYBPC3delta25bp intronic deletion in South Asian descendents. JAMA Cardiol. 3:481-488. PMCID: PMC6054452.


  • Bailey, S.R., Nelson, M.H., Majchrzak, K., Bowers, J.S., Wyatt, M.M., Smith, A.S., Neal, L.R., Shirai, K., Carpenito, C., June, C.H., Zilliox, M.J., and Paulos, C.M. 2017. Human CD26high T cells elicit tumor immunity against multiple malignancies via enhanced migration and persistence. Nat. Commun. 8:1961. PMCID: PMC5719008.
  • Plichta, J.K., Holmes, C.J., Nienhouse, V., Puszynski, M., Gao, X., Dong, Q., Lin, H., Sinacore, S., Zilliox, M., Toh, E., Nelson, DE, Gamelli, R.I., and Radek, K.A.. 2017. Cutaneous burn injury modulates urinary antimicrobial peptide responses and the urinary microbiome. Crit. Care Med. 45:e543-e551.


  • Lynch TL 4th, Ismahil MA, Jegga AG, Zilliox MJ, Troidl C, Prabhu SD, Sadayappan S. 2016. Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation. J. Mol. Cell Cardiol. 102:83-93. PMCID: PMC5316303.
  • Malki, K., Shapiro, J.W., Price, T.K., Hilt, E.E., Thomas-White, K., Sircar, T., Rosenfeld, A.B., Kuffel, G., Zilliox, M.J., Wolfe, A.J., Putonti, C. 2016. Genomes of gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS One. 11:e0166757. PMCID: PMC5115800.
  • Yang, S.F., Bier-Laning, C.M., Adams, W., Zilliox, M.J. 2016. Candidate biomarkers for HPV-negative head and neck cancer identified via gene expression barcode analysis. Otolaryngology- Head and Neck Surgery 155:416-422.


  • Thomas-White, K.J., Hilt, E.E., Fok, C., Pearce, M.M., Mueller, E.R., Kliethermes, S., Jacobs, K., Zilliox, M.J., Brincat, C., Price, T.K., Kuffel, G., Schreckenberger, P., Gai, X., Brubaker, L., Wolfe, A.J. 2015. Incontinence medication response relates to the female urinary microbiota. Int. Urogynecol. J. 27:723-733. PMCID: PMC5119460.
  • Pearce, M.M.#, Zilliox, M.J.#, Rosenfeld, A.B., Thomas-White, K.J., Richter, H.E., Nager, C.W., Visco, A.G., Nygaard, I.E., Barber, M.D., Schaffer, J., Moalli, P., Sung, V.W., Smith, A.L., Rogers, R., Nolen, T.L., Wallace, D., Meikle, S.F., Gai, X., Wolfe, A.J., Brubaker, L. Pelvic Floor Disorder Network. 2015. The female urinary microbiome in urgency urinary incontinence. Am. J. Obstet. Gynecol. 213:347.e1-347.e11.


  • Hilt, E., McKinley, K., Pearce, M., Rosenfeld, A., Zilliox, M.J., Mueller, E., Brubaker, L., Gai, X., Wolfe, A. and Schreckenberger, P. 2014. Urine is not sterile; use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J. Clinical Microbiology 52:871-876.
  • Pearce, M.M., Hilt E.E., Rosenfeld, A.B., Zilliox, M.J., Thomas-White, K., Fok C., Kliethermes, S., Schreckenberger P.C., Brubaker, L., Gai, X. and Wolfe, A.J. 2014. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio 8:e01283-e01284.
  • McCall, M.N., Jaffee, H.A., Zelisko, S.J., Sinha, N., Hooiveld, G., Irizarry, R.A. and Zilliox, M.J. 2014. The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Research 42:D938-43.


  • Iyer, S.S., Latner, D.R., Zilliox, M.J., McCausland, M., Akondy, R.S., MacMaster-Penaloza, P., Hale, J.S., Ye, L., Mohammed, A.U.R., Yamaguchi, T., Sakaguchi, S., Amara, R.R. and Ahmed, R. 2013. Identification of novel markers for mouse CD4+ T follicular helper cells. Eur. J. Immunol. 43:3219-32.
  • Wu, G., Yustein, J.T., McCall, M.N., Zilliox, M., Irizarry, R.A., Zeller, K., Dang, C.V. and Ji, H. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. 2013. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics 29:1182-1189.
  • Tan, W.G., Jin, H.T., West, E.E., Panalzoa-MacMaster, P., Wieland A., Zilliox, M.J., McElrath, M.J., Barouch, D.H. and Ahmed, R. 2013. Comparative analysis of simian immunodeficiency virus gag-specific effector and memory CD8+ T cells induced by different adenovirus vectors. Journal of Virology 87:1359-1372.