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Dionysios A. Antonopoulos

Division Director

Dionysios Antonopoulos is a microbiologist studying how communities of microorganisms live and thrive together in a variety of environments.


Dion began his career as a microbiologist studying the cellulose-degrading capabilities of bacteria from production livestock, making extensive use of anaerobic cultivation buoyed by the then emerging area of comparative microbial genomics.  His initial interest in understanding mammalian gastrointestinal function has expanded since then by his ongoing research in environmental systems using metagenomics. Currently, he is particularly interested in understanding how microbial communities maintain their stability in different environments. As a result, his research team is actively involved in creating new approaches for minimizing the complexity of natural microbial communities so that they can be studied in the laboratory.

Dion’s group has created sub-community levels of organization (“minimal communities”) in the laboratory from a variety of environments, in order to understand the building blocks of stability in these systems. Unlike synthetic communities, which are created from predetermined associations of microorganisms, the minimal stable communities his group works with are sourced directly from natural environments; they serve as an intermediate between complex natural communities and atomized collections of isolates in the laboratory.

In addition to his duties at Argonne, Dion is also an Assistant Professor in the Section of Gastroenterology, Department of Medicine at the University of Chicago and is Director of the Enteric Microbiology Component of the Digestive Diseases Research Core Center there. The focus of his research at both institutions is on understanding how natural microbial communities boot up” in the first place.


  • American Society for Microbiology (ASM)
  • American Association for the Advancement of Science (AAAS)
  • International Society for Microbial Ecology (ISME)
  • Chair, Microbial Ecology Section, ASM, 2015-2016



  • Flynn, T.M., J.C. Koval, S.M. Greenwald, S.M. Owens, K.M. Kemner, and D.A. Antonopoulos. (2017) Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities. Frontiers in Microbiology. 8:2321. doi:10.3389/fmicb.2017.02321. PMID:29234312.
  • Bunker, J.J., S.A. Erickson, T.M. Flynn, C.J. Henry Dunand,J.C. Koval, M. Meisel, B. Jabri, D.A. Antonopoulos, P.C. Wilson,and A. Bendelac. (2017) Natural polyreactive IgA antibodies coat the intestinal microbiota. Science. 358(6361):eaan6619. doi:10.1126/science.aan6619. PMID:28971969.
  • Antonopoulos, D.A., R. Assaf, R.K. Aziz, T. Brettin, C. Bun, N. Conrad, J.J. Davis, E.M. Dietrich, T. Disz, S. Gerdes, R.W. Kenyon, D. Machi, C. Mao, D.E. Murphy-Olson, E.K. Nordberg, G.J. Olsen, R. Olson, R. Overbeek, B. Parrello, G.D. Pusch, J. Santerre, M. Shukla, R.L. Stevens, M. VanOeffelen, V. Vonstein, A.S. Warren, A.R. Wattam, F. Xia, and H. Yoo. (2017) PATRIC as a unique resource for studying antimicrobial resistance. Briefings in Bioinformatics. 2017:1–9. doi:10.1093/bib/bbx083. PMID:28968762.
  • Meisel, M., T. Mayassi, H. Fehlner-Peach, J.C. Koval, S.L. O’Brien, R. Hinterleitner, K. Lesko, S. Kim, R. Bouziat, L. Chen, C.R. Weber, S.K. Mazmanian, B. Jabri, and D.A. Antonopoulos. (2017) Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis. ISME Journal. 11(1):15-30. doi:10.1038/ismej.2016.114. PMID:27648810.
  • O’Brien, S.L., S.M. Gibbons, S.M. Owens, J. Hampton-Marcell, E. Johnston, J.D. Jastrow, J.A. Gilbert, F. Meyer, and D.A. Antonopoulos. (2016) Spatial scale drives patterns in soil microbial diversity. Environmental Microbiology. 18(6):2039-51. doi:10.1111/1462-2920.13231. PMID:26914164.
  • Kwon, M.J., E.J. O’Loughlin, M.I. Boyanov, J.M. Brulc, E.R. Johnston, K.M. Kemner, and D.A. Antonopoulos. (2016) Impact of organic carbon electron donors on microbial community development under iron- and sulfate-reducing conditions. PLOS ONE. 11(1):e0146689. doi:10.1371/journal.pone. 0146689. PMID:26800443.