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DIONYSIOS ANTONOPOULOS

TitleASSISTANT PROFESSOR, PART-TIME
InstitutionUniversity of Chicago
DepartmentMEDICINE
AddressChicago IL 60637

 Overview 
 overview
Dr. Antonopoulos joined the IGSB and Biosciences Division at Argonne National Laboratory in June 2008 and holds a joint appointment in the Department of Medicine, Section of Gastroenterology, at the University of Chicago. Dr. Antonopoulos is a microbiologist interested in studying the formation and development of microbial communities. His interest in understanding mammalian gastrointestinal function has been complemented by ongoing research in environmental systems (subsurface and topsoil systems). Although the scales are vastly different between the two, many of the approaches used in both GI and field research are steeped in classical ecological theory and serve to circumnavigate the complex nature of the microbial communities underlying system function. His group is actively involved in applying second-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 National Laboratory to handle the scale of data afforded by these technologies. His joint appointment between the University of Chicago (Dept of Medicine) and Argonne enables interactions between the clinical and next generation laboratory approaches (including shotgun metagenomics) to understanding the microbial world.


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Antonopoulos D, Balatsos NAA, Gourgoulianis KI. Cancer's smart bombs: tumor-derived exosomes target lung epithelial cells triggering pre-metastatic niche formation. J Thorac Dis. 2017 Apr; 9(4):969-972.
    View in: PubMed
  2. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 Mar; 23(3):366-378.
    View in: PubMed
  3. Touw K, Ringus DL, Hubert N, Wang Y, Leone VA, Nadimpalli A, Theriault BR, Huang YE, Tune JD, Herring PB, Farrugia G, Kashyap PC, Antonopoulos DA, Chang EB. Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models. Physiol Rep. 2017 Mar; 5(6).
    View in: PubMed
  4. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 Feb 13.
    View in: PubMed
  5. Rodriguez-Palacios A, Corridoni D, Di Stefano G, Di Martino L, Antonopoulos DA, Chang E, Pizarro TT, Cominelli F. O-014 Bacterial Sensor NOD2 Deletion Causes Th2-Inflammatory Bowel Disease Improvement Without Inducing Acute Metatranscriptomic Dysbiosis in Mice. Inflamm Bowel Dis. 2017 Feb; 23 Suppl 1:S5.
    View in: PubMed
  6. Corridoni D, Rodriguez-Palacios A, Di Stefano G, Di Martino L, Antonopoulos DA, Chang EB, Arseneau KO, Pizarro TT, Cominelli F. Genetic deletion of the bacterial sensor NOD2 improves murine Crohn's disease-like ileitis independent of functional dysbiosis. Mucosal Immunol. 2017 Jul; 10(4):971-982.
    View in: PubMed
  7. Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML. Patient-Specific Bacteroides Genome Variants in Pouchitis. MBio. 2016 Nov 15; 7(6).
    View in: PubMed
  8. Arvans D, Jung YC, Antonopoulos D, Koval J, Granja I, Bashir M, Karrar E, Roy-Chowdhury J, Musch M, Asplin J, Chang E, Hassan H. Oxalobacter formigenes-Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells. J Am Soc Nephrol. 2017 Mar; 28(3):876-887.
    View in: PubMed
  9. Meisel M, Mayassi T, Fehlner-Peach H, Koval JC, O'Brien SL, Hinterleitner R, Lesko K, Kim S, Bouziat R, Chen L, Weber CR, Mazmanian SK, Jabri B, Antonopoulos DA. Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis. ISME J. 2017 Jan; 11(1):15-30.
    View in: PubMed
  10. Antonopoulos DA, Chang EB. Transplanting a Microbial Organ: the Good, the Bad, and the Unknown. MBio. 2016 May 03; 7(3).
    View in: PubMed
  11. Ward MA, Pierre JF, Leal RF, Huang Y, Shogan B, Dalal SR, Weber CR, Leone VA, Musch MW, An GC, Rao MC, Rubin DT, Raffals LE, Antonopoulos DA, Sogin ML, Hyman NH, Alverdy JC, Chang EB. Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility. Am J Physiol Gastrointest Liver Physiol. 2016 Jun 01; 310(11):G973-88.
    View in: PubMed
  12. O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol. 2016 Jun; 18(6):2039-51.
    View in: PubMed
  13. Kwon MJ, O'Loughlin EJ, Boyanov MI, Brulc JM, Johnston ER, Kemner KM, Antonopoulos DA. Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions. PLoS One. 2016; 11(1):e0146689.
    View in: PubMed
  14. Kamdar K, Khakpour S, Chen J, Leone V, Brulc J, Mangatu T, Antonopoulos DA, Chang EB, Kahn SA, Kirschner BS, Young G, DePaolo RW. Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease. Cell Host Microbe. 2016 Jan 13; 19(1):21-31.
    View in: PubMed
  15. Bunker JJ, Flynn TM, Koval JC, Shaw DG, Meisel M, McDonald BD, Ishizuka IE, Dent AL, Wilson PC, Jabri B, Antonopoulos DA, Bendelac A. Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A. Immunity. 2015 Sep 15; 43(3):541-53.
    View in: PubMed
  16. Stefka AT, Feehley T, Tripathi P, Qiu J, McCoy K, Mazmanian SK, Tjota MY, Seo GY, Cao S, Theriault BR, Antonopoulos DA, Zhou L, Chang EB, Fu YX, Nagler CR. Commensal bacteria protect against food allergen sensitization. Proc Natl Acad Sci U S A. 2014 Sep 09; 111(36):13145-50.
    View in: PubMed
  17. Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Antonopoulos D, Kemner KM, Meyer F. The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014 Nov; 16(11):3443-62.
    View in: PubMed
  18. Evans CC, LePard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ. Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PLoS One. 2014; 9(3):e92193.
    View in: PubMed
  19. Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE. Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Microbiome. 2014 Feb 14; 2(1):5.
    View in: PubMed
  20. Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. Gender bias in autoimmunity is influenced by microbiota. Immunity. 2013 Aug 22; 39(2):400-12.
    View in: PubMed
  21. Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome. 2013 Jul 10; 1(1):20.
    View in: PubMed
  22. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 2013 Mar 04; 1(1):9.
    View in: PubMed
  23. Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome. 2013 Mar 04; 1(1):8.
    View in: PubMed
  24. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature. 2012 Jul 05; 487(7405):104-8.
    View in: PubMed
  25. Harrell L, Wang Y, Antonopoulos D, Young V, Lichtenstein L, Huang Y, Hanauer S, Chang E. Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. PLoS One. 2012; 7(2):e32545.
    View in: PubMed
  26. Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F. From genomics to metagenomics. Curr Opin Biotechnol. 2012 Feb; 23(1):72-6.
    View in: PubMed
  27. Schneider JA, Vadivelu S, Liao C, Kandukuri SR, Trikamji BV, Chang E, Antonopoulos D, Prasad S, Lakshmi V. Increased Likelihood of Bacterial Pathogens in the Coronal Sulcus and Urethra of Uncircumcised Men in a Diverse Group of HIV Infected and Uninfected Patients in India. J Glob Infect Dis. 2012 Jan; 4(1):6-9.
    View in: PubMed
  28. O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F. Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010. Stand Genomic Sci. 2011 Nov 30; 5(2):198-202.
    View in: PubMed
  29. Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna KV, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI. Diversity of bacteria at healthy human conjunctiva. Invest Ophthalmol Vis Sci. 2011 Jul 20; 52(8):5408-13.
    View in: PubMed
  30. Kwon MJ, O'Loughlin EJ, Antonopoulos DA, Finneran KT. Geochemical and microbiological processes contributing to the transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated aquifer material. Chemosphere. 2011 Aug; 84(9):1223-30.
    View in: PubMed
  31. Lemke S, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae). BMC Genomics. 2011 May 31; 12:278.
    View in: PubMed
  32. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010 Dec 25; 3(3):243-8.
    View in: PubMed
  33. Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB. Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. PLoS One. 2010 Oct 22; 5(10):e13607.
    View in: PubMed
  34. Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, Alverdy JC, Meyer F, Musch MW, Young VB, Chang EB. Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol. 2010 Dec; 88(6):1333-42.
    View in: PubMed
  35. Hu S, Wang Y, Lichtenstein L, Tao Y, Musch MW, Jabri B, Antonopoulos D, Claud EC, Chang EB. Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. Am J Physiol Gastrointest Liver Physiol. 2010 Dec; 299(6):G1266-75.
    View in: PubMed
  36. Rincon MT, Dassa B, Flint HJ, Travis AJ, Jindou S, Borovok I, Lamed R, Bayer EA, Henrissat B, Coutinho PM, Antonopoulos DA, Berg Miller ME, White BA. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. PLoS One. 2010 Aug 30; 5(8):e12476.
    View in: PubMed
  37. Pfister CA, Meyer F, Antonopoulos DA. Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One. 2010 May 06; 5(5):e10518.
    View in: PubMed
  38. Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. Maternal activation of gap genes in the hover fly Episyrphus. Development. 2010 May; 137(10):1709-19.
    View in: PubMed
  39. Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010 Jan; 2010(1):pdb.prot5368.
    View in: PubMed
  40. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009 Dec; 5(12):e1000593.
    View in: PubMed
  41. Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One. 2009 Aug 14; 4(8):e6650.
    View in: PubMed
  42. Garner CD, Antonopoulos DA, Wagner B, Duhamel GE, Keresztes I, Ross DA, Young VB, Altier C. Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection. Infect Immun. 2009 Jul; 77(7):2691-702.
    View in: PubMed
  43. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J. 2009 Aug; 3(8):944-54.
    View in: PubMed
  44. Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun. 2009 Jun; 77(6):2367-75.
    View in: PubMed
  45. Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A. 2009 Feb 10; 106(6):1948-53.
    View in: PubMed
  46. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, Young VB. Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis. 2008 Feb 01; 197(3):435-8.
    View in: PubMed
  47. Galbraith EA, Antonopoulos DA, White BA. Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples. Methods Mol Biol. 2008; 410:295-333.
    View in: PubMed
  48. Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, Berg ME, White BA, Bayer EA, Lamed R. Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens. J Bacteriol. 2006 Nov; 188(22):7971-6.
    View in: PubMed
  49. Galbraith EA, Antonopoulos DA, White BA. Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ Microbiol. 2004 Sep; 6(9):928-37.
    View in: PubMed
  50. Antonopoulos DA, Nelson KE, Morrison M, White BA. Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization. Environ Microbiol. 2004 Apr; 6(4):335-46.
    View in: PubMed
  51. Antonopoulos DA, Russell WM, White BA. Phylogenetic reconstruction of Gram-positive organisms based on comparative sequence analysis of molecular chaperones from the ruminal microorganism Ruminococcus flavefaciens FD-1. FEMS Microbiol Lett. 2003 Oct 10; 227(1):1-7.
    View in: PubMed
  52. Antonopoulos DA, Aminov RI, Duncan PA, White BA, Mackie RI. Characterization of the gene encoding glutamate dehydrogenase ( gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1. Arch Microbiol. 2003 Mar; 179(3):184-90.
    View in: PubMed
  53. Sghir A, Antonopoulos D, Mackie RI. Design and evaluation of a Lactobacillus group-specific ribosomal RNA-targeted hybridization probe and its application to the study of intestinal microecology in pigs. Syst Appl Microbiol. 1998 Jun; 21(2):291-6.
    View in: PubMed
  54. Antonopoulos D. [A special method of urethral implantation in large defects of the bladder wall and in the torn urethra]. Arch Gynakol. 1975 Nov 18; 219(1-4):252-4.
    View in: PubMed
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