Dionysios Antonopoulos

Biologist
- Biosciences

Dion Antonopoulos is a microbiologist specializing in microbial ecology and using metagenomic-enabled approaches to study communities of microorganisms 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 interest in understanding mammalian gastrointestinal function has expanded since then by his ongoing research in environmental systems (subsurface and topsoil systems) using metagenomics. Although the scales are vastly different between the two, many of the approaches Dion uses in both gastrointestinal and field research are steeped in classical ecological theory and serve to circumnavigate the complex microbial communities underlying system function.

Currently, his research team is actively involved in applying next (“now”)-generation DNA sequencing technologies to describing both the structure and function of microbial communities in these systems and has taken advantage of the computational resources available at Argonne for handling the scale of data afforded by these technologies. 

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. His joint appointment between the two institutions enables interactions between the clinical and next generation DNA sequencing-enabled approaches to understand the microbial world.

Awards, Honors & Memberships

  • American Society for Microbiology
  • American Association for the Advancement of Science

Selected Publications

  • Devkota, S., Y. Wang, M. Musch, V. Leone, D. Antonopoulos, B. Jabri, and E.B. Chang.  (2012)  Dietary fat-induced taurocholic acid production promotes pathobiont and colitis in IL-10-/- mice. Nature. 487(7405):104-108. doi:10.1038/nature11225. PMID: 22722865
  • Desai, N., D. Antonopoulos, J.A. Gilbert, E.M. Glass, F. Meyer.  (2012)  From genomics to metagenomics.  Current Opinion in Biotechnology.  23(1):72-76.  PMID: 22227326
  • O’Loughlin, E.J., M.I. Boyanov, D.A. Antonopoulos, and K. Kemner. (2011) “Redox processes affecting the speciation of technetium, uranium, neptunium, and plutonium in aquatic and terrestrial environments.” In:  Aquatic Redox Chemistry.  (Ed. P. Tratnyek).  ACS Books.
  • Antonopoulos, D.A., E.M. Glass, and F. Meyer.  (2011)  “Analyzing metagenomic data:  inferring microbial community function with MG-RAST.”  In:  Metagenomics and its applications in agriculture, biomedicine, and environmental studies.  (Ed. R.W. Li).  Nova Science Publishers.  Hauppauge, NY.
  • Kwon, M.J., E.J. O’Loughlin, D.A. Antonopoulos, and K.T. Finneran.  (2011)  Geochemical and microbiological processes contributing to the transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated aquifer material.  Chemosphere. 84(9):1223-1230. doi:10.1016/j.chemosphere.2011.05.027. PMID: 21664641
  • Wang, Y., D.A. Antonopoulos, X. Zhu, L. Harrell, I. Hanan, J.C. Alverdy, F. Meyer, M. Musch, V.B. Young, E.B. Chang.  (2010)  Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.  Applied Microbiology and Biotechnology88(6):1333-42.  doi:10.1007/s00253-010-2921-8.  PMID: 20931185
  • Pfister, C.A, F. Meyer, and D.A. Antonopoulos.  (2010)  Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling.  PLoS One5(5):e10518. doi:10.1371/journal.pone.0010518.  PMID: 20463896
  • Glass, E.M., J. Wilkening, A. Wilke, D. Antonopoulos, and F. Meyer.  (2010)  Using the Metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.  Cold Spring Harbor Protocols2010(1):pdb.pro5368.  doi:10.1101/pdb.prot5368.  PMID: 20150127
  • Wang, Y., J.D. Hoenig, K.J. Malin, S. Qamar, E.O. Petrof, J. Sun, D.A. Antonopoulos, E.B. Chang, and E.C. Claud.  (2009)  16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis.  The ISME Journal3:944-54. doi:10.1038/ismej.2009.37.   PMID: 1936997022
  • Antonopoulos, D.A., S.M. Huse, H.G. Morrison, T.M. Schmidt, M.L. Sogin, and V.B. Young.  (2009)  Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.  Infection and Immunity.  77:2356-2366.  doi:10.1128/IAI.01520-08.  PMID: 19307217
  • Brulc, J.M., D.A. Antonopoulos, M.E. Berg Miller, M.K. Wilson, A.C. Yannarell, E.A. Dinsdale, R.E. Edwards, E.D. Frank, J.B. Emerson, P. Wacklin, P.M. Coutinho, B. Henrissat, K.E. Nelson, and B.A. White.  (2009)  Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.  Proceedings of the National Academy of Sciences of the United States of America106:1948-1953.  doi:10.1073/pnas.0806191105.   PMID: 19181843