Dionysios Antonopoulos Lab

About the Lab

My laboratory specializes in microbial ecology and using metagenomic-enabled approaches to study communities of microorganisms in a variety of environments. We apply next -generation DNA sequencing technologies towards describing both the structure and function of microbial communities in these systems, taking advantage of the computational resources available at Argonne for handling the scale of data afforded by these technologies. I started my 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.  My interest in understanding mammalian gastrointestinal function has expanded to research in environmental systems (subsurface and topsoil systems) using metagenomics. Although the scales are vastly different between the two, similar approaches based in classical ecological theory can be used for both gastrointestinal and field research to circumnavigate the complex microbial communities underlying system function.

In collaboration with colleagues at the University of Chicago these approaches were used to understand the role that diet plays in promoting complex immune disorders such as inflammatory bowel disease (IBD). This study, which appeared in the journal Nature, provides new insights into why some people are more likely than others to develop IBD (Devkota et al, 2012). Working with a mouse model, we traced both the shift in the microbial community structure and the corresponding host immune response to a diet high in saturated (milk-derived) fats. To dissolve such fats, the liver produces a form of bile rich in sulfur. When the bile reaches the intestines, a microbe called Bilophila wadsworthia – the name means “bile loving” – blooms. Such blooms can trigger the immune system in people with a genetic predisposition. Moreover, the byproducts of this microbe’s interaction with bile can amplify the effect, making the bowel more permeable and unleashing an unregulated immune response in individuals at high risk for diseases such as IBD.

Presently, as part of the Human Microbiome Project, my laboratory is focused on understanding how microbial communities re-establish themselves in the GI tract following resectioning of the lower GI tract (creation of an ileal pouch-anal anastomosis [IPAA]) used to treat ulcerative colitis, a form of inflammatory bowel disease (IBD). As the microbial community restablishes itself following this surgical procedure we want to understand what aspects of the community lead to a healthy state versus reversion to the disease state (pouchitis). In collaboration with the University of Michigan, Michigan State University, and the Marine Biological Laboratory we are using a multi-pronged approach to studying this phenomenon by way of both cultivation and non-cultivation based approaches (Young et al, 2013)(Vital et al, 2013).

Selected publications

Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grimm SL, Vineis JH, Dalal SM, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, ML Sogin. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anastomosis.  BMC Microbiome. 2013 1:9. doi:10.1186/2049-2618-1-9.

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin M, 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. BMC Microbiome. 2013 1:8. doi:10.1186/2049-2618-1-8.

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 5;487(7405):104-8. doi: 10.1038/nature11225.

Desai N, Antonopoulos D, Gilbert JA, Glass EM, Meyer F. From genomics to metagenomics. Curr Opin Biotechnol. 2012 Feb;23(1):72-6. doi: 10.1016/j.copbio.2011.12.017.

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. doi: 10.1371/journal.pone.0032545.