INFECTION AND IMMUNITY, June 2009, p. 2367–2375 Vol. 77, No. 60019-9567/09/$08.00!0 doi:10.1128/IAI.01520-08Copyright © 2009, American Society for Microbiology. All Rights Reserved.Reproducible Community Dynamics of the Gastrointestinal Microbiotafollowing Antibiotic Perturbation!†Dionysios A. Antonopoulos,1Susan M. Huse,3Hilary G. Morrison,3Thomas M. Schmidt,4Mitchell L. Sogin,3and Vincent B. Young1,2*Department of Internal Medicine, Division of Infectious Diseases,1and Department of Microbiology and Immunology,2University ofMichigan, Ann Arbor, Michigan 48109; Marine Biological Laboratory, Woods Hole, Massachusetts, 025433; and Department ofMicrobiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 488244Received 15 December 2008/Returned for modification 2 February 2009/Accepted 12 March 2009Shifts in microbial communities are implicated in the pathogenesis of a number of gastrointestinal diseases,but we have limited understanding of the mechanisms that lead to altered community structures. One difficultywith studying these mechanisms in human subjects is the inherent baseline variability of the microbiota indifferent individuals. In an effort to overcome this baseline variability, we employed a mouse model to controlthe host genotype, diet, and other possible influences on the microbiota. This allowed us to determine whetherthe indigenous microbiota in such mice had a stable baseline community structure and whether this commu-nity exhibited a consistent response following antibiotic administration. We employed a tag-sequencing strat-egy targeting the V6 hypervariable region of the bacterial small-subunit (16S) rRNA combined with massivelyparallel sequencing to determine the community structure of the gut microbiota. Inbred mice in a controlledenvironment harbored a reproducible baseline community that was significantly impacted by antibiotic ad-ministration. The ability of the gut microbial community to recover to baseline following the cessation ofantibiotic administration differed according to the antibiotic regimen administered. Severe antibiotic pressureresulted in reproducible, long-lasting alterations in the gut microbial community, including a decrease inoverall diversity. The finding of stereotypic responses of the indigenous microbiota to ecologic stress suggeststhat a better understanding of the factors that govern community structure could lead to strategies for theintentional manipulation of this ecosystem so as to preserve or restore a healthy microbiota.A highly diverse, complex community of microorganismsinhabits the gastrointestinal tracts of mammals. This commu-nity, referred to as the indigenous microbiota, exists in a del-icate symbiosis with the host (3, 15). A significant body ofresearch has demonstrated that disturbances in this balancecan disrupt intestinal homeostasis. Multiple disease states mayarise, at least in part, in response to altered indigenous micro-bial communities in the gut (10, 47, 53, 55). Conversely, re-search on probiotics indicates that the normal balance betweenthe indigenous microbiota and the host can be protected orrestored through the administration of beneficial microbes (6,45, 59).The relationship between the indigenous microbiota and ahost involves multiple interactions. The indigenous microbiotaplays a central role in the digestion and nutrition of the host(30, 55). These microbes also affect the regulation and ho-meostasis of the host immune system (27, 46). As part of theinnate defenses of the gastrointestinal tract, the community ofindigenous microbes forms an ecological barrier that preventsthe ingress of pathogenic microorganisms. For example, thedevelopment of Clostridium difficile-associated colitis followingantibiotic administration arises from a loss of intrinsic “colo-nization resistance” against pathogenic organisms (60). Anti-biotic disturbance of the normal community structure of themicrobiota may allow the germination of environmentally ac-quired spores, with subsequent overgrowth of the pathogenand toxin production. Alternatively, C. difficile colitis may de-velop subsequent to the expansion of low-abundance C. difficilepopulations that normally produce insignificant levels of toxin. Ineither case, the disruption of the indigenous microbiota by anti-biotic administration is a key component of pathogenesis (7).Murine models have provided important insights into theinteractions between the microbiota and the host. One consis-tent feature of microbiota studies with human subjects is thatthere is significant interindividual variation in the indigenousmicrobiota (12, 13). This variation likely arises from the accu-mulated effects of genetic and environmental influences on thegut microbial community (11). The significant baseline varia-tion makes it difficult to conduct studies that follow the dy-namics of the gut microbiota in humans, especially if the goalis to discern stereotypic responses to a given manipulation.Therefore, as with other areas of biomedical research, murinemodels offer unique advantages for microbiota experimenta-tion.Several recent studies have described murine models of dis-ease in which altered indigenous gut microbial communitiesare generated through the administration of antibiotics. Thesealtered communities can be either permissive or required forthe development of the model disease state, although in othercases they appear to be protective (5, 9, 24, 26, 52). Althoughthese studies have provided insight into many of the host re-* Corresponding author. Mailing address: The University of Mich-igan, 4618D Med. Sci. II SPC 5623, 1150 W. Medical Center Dr., AnnArbor, MI 48109-5623. Phone: (734) 764-2237. Fax: (734) 763-4168.E-mail: [email protected].† Supplemental material for this article may be found at http://iai.asm.org/.!Published ahead of print on 23 March 2009.2367 at UNIV OF MARYLAND on October 15, 2009 iai.asm.orgDownloaded fromsponses to the indigenous microbiota, we have remarkablylittle information as to the exact nature of the effect of antibi-otic administration on the microbial communities themselves.For example, these studies assume that genetically identicalmice would harbor a consistent baseline microbiota. Further-more, it is also assumed that the microbiota responds in areproducible manner to the antibiotic administration, resultingin consistent changes in the structure and function of themicrobiota that are responsible for the observed
View Full Document
Unlocking...