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Dionysios Antonopoulos

TitleAssistant Professor, Part-Time
InstitutionUniversity of Chicago
DepartmentMedicine
AddressChicago IL 60637
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    Dr. Antonopoulos started as a microbiologist studying the cellulose-degrading capabilities of bacteria from the rumen, making extensive use of anaerobic cultivation buoyed by the then emerging area of comparative microbial genomics. Since that time his interest in understanding mammalian gastrointestinal function has been complemented by ongoing research in environmental systems. Currently, he is interested in understanding how microbial communities maintain their stability in a variety of environments. Stability is likely the result of “functional redundancy” via ultra-high levels of microbial community diversity. In this model, an increase in the redundancy of specific functions exhibited by the community contributes to its ability to resist perturbation. His group has created sub-community levels of organization (“minimal communities”) in the laboratory from a variety of natural environments, in order to understand the building blocks of stability in these systems. They also serve as an intermediate between complex natural communities and atomized collections of isolates in the laboratory. Dr. Antonopoulos' joint appointment between the University of Chicago (Dept of Medicine) and Argonne National Laboratory (Biosciences Division) enables interactions between the clinical and next generation DNA sequencing enabled laboratory approaches to understanding the microbial world. This has also been facilitated by his appointment as the Co-Director for the Host-Microbe Core of the Digestive Diseases Research Core Center (DDRCC) at the University.


    Collapse Biography 
    Collapse education and training
    The University of Michigan, Ann Arbor, MIResearch fellow05/2008Infectious Diseases
    Michigan State University, East Lansing, MIPostdoctoral fellow08/2006Microbiology
    University of Illinois at Urbana-Champaign, Champaign, ILPhD05/2004Animal Sciences (Microbiology)
    University of Illinois at Urbana-Champaign, Champaign, ILMS01/2001Animal Sciences (Microbiology)
    University of Illinois at Urbana-Champaign, Champaign, ILBS01/1996Biology

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    Collapse Bibliographic 
    Collapse 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. Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, de Pooter R, Antonopoulos DA, Golovkina T, Chervonsky A. Polymorphic Immune Mechanisms Regulate Commensal Repertoire. Cell Rep. 2019 Oct 15; 29(3):541-550.e4. PMID: 31618625.
      View in: PubMed
    2. Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H. PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2019 07 19; 20(4):1094-1102. PMID: 28968762.
      View in: PubMed
    3. Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R, Nagler CR. Healthy infants harbor intestinal bacteria that protect against food allergy. Nat Med. 2019 03; 25(3):448-453. PMID: 30643289.
      View in: PubMed
    4. Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA. Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities. Front Microbiol. 2017; 8:2321. PMID: 29234312.
      View in: PubMed
    5. Bunker JJ, Erickson SA, Flynn TM, Henry C, Koval JC, Meisel M, Jabri B, Antonopoulos DA, Wilson PC, Bendelac A. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science. 2017 10 20; 358(6361). PMID: 28971969.
      View in: PubMed
    6. Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM. Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics. Microbiome. 2017 05 04; 5(1):50. PMID: 28473000.
      View in: PubMed
    7. 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). PMID: 28320888.
      View in: PubMed
    8. 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 03; 23(3):366-378. PMID: 28221248.
      View in: PubMed
    9. 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. PMID: 28248733.
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    10. 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. PMID: 28125562.
      View in: PubMed
    11. 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 07; 10(4):971-982. PMID: 27848951.
      View in: PubMed
    12. 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 11 15; 7(6). PMID: 27935837.
      View in: PubMed
    13. 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. PMID: 27738124.
      View in: PubMed
    14. 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 01; 11(1):15-30. PMID: 27648810.
      View in: PubMed
    15. Antonopoulos DA, Chang EB. Transplanting a Microbial Organ: the Good, the Bad, and the Unknown. MBio. 2016 05 03; 7(3). PMID: 27143392.
      View in: PubMed
    16. 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 06 01; 310(11):G973-88. PMID: 27079612.
      View in: PubMed
    17. 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 06; 18(6):2039-51. PMID: 26914164.
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    18. 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. PMID: 26800443.
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    19. 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. PMID: 26764594.
      View in: PubMed
    20. 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. PMID: 26320660.
      View in: PubMed
    21. 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. PMID: 25157157.
      View in: PubMed
    22. 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. PMID: 24628880.
      View in: PubMed
    23. 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. PMID: 24670791.
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    24. 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. PMID: 24529162.
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    25. 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. PMID: 23973225.
      View in: PubMed
    26. 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. PMID: 24450928.
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    27. 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. PMID: 24451334.
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    28. 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. PMID: 24451366.
      View in: PubMed
    29. 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. PMID: 22722865.
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    30. 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. PMID: 22389708.
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    31. Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F. From genomics to metagenomics. Curr Opin Biotechnol. 2012 Feb; 23(1):72-6. PMID: 22227326.
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    32. 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. PMID: 22529620.
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    33. 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. PMID: 22180822.
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    34. 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. PMID: 21571682.
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    35. 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. PMID: 21664641.
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    36. 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. PMID: 21627820.
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    37. 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. PMID: 21304727.
      View in: PubMed
    38. 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. PMID: 21042588.
      View in: PubMed
    39. 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. PMID: 20931185.
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    40. 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. PMID: 20864653.
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    41. 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. PMID: 20814577.
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    42. 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. PMID: 20463896.
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    43. 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. PMID: 20430746.
      View in: PubMed
    44. 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. PMID: 20150127.
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    45. 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. PMID: 20011103.
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    46. 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. PMID: 19680555.
      View in: PubMed
    47. 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. PMID: 19433544.
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    48. 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. PMID: 19369970.
      View in: PubMed
    49. 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. PMID: 19307217.
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    50. 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. PMID: 19181843.
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    51. 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. PMID: 18199029.
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    52. 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. PMID: 18642606.
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    53. 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. PMID: 16997963.
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    54. 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. PMID: 15305918.
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    55. 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. PMID: 15008812.
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    56. 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. PMID: 14568141.
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    57. 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. PMID: 12610723.
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    58. 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. PMID: 9704114.
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