Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

Despite widespread use of antibiotics, few studies have measured their effects on the burden or diversity of bacteria in the mammalian intestine. We developed an oral antibiotic treatment protocol and characterized its effects on murine intestinal bacterial communities and immune cell homeostasis. Antibiotic administration resulted in a 10-fold reduction in the amount of intestinal bacteria present and sequencing of 16S rDNA segments revealed significant temporal and spatial effects on luminal and mucosal-associated communities including reductions in luminal Firmicutes and mucosal-associated Lactobacillus species, and persistence of bacteria belonging to the Bacteroidetes and Proteobacteria phyla. Concurrently, antibiotic administration resulted in reduced RELMβ production, and reduced production of interferon-γ and interleukin-17A by mucosal CD4+ T lymphocytes. This comprehensive temporal and spatial metagenomic analyses will provide a resource and framework to test the influence of bacterial communities in murine models of human disease.

[1]  D. Relman,et al.  Archaea and Their Potential Role in Human Disease , 2003, Infection and Immunity.

[2]  L. Lynd,et al.  Antibiotic Use in Children Is Associated With Increased Risk of Asthma , 2009, Pediatrics.

[3]  G. Thompson,et al.  Progress report Gastrointestinal structure and function in germ-free or gnotobiotic animals , 2006 .

[4]  S. Hanauer,et al.  Treatment of inflammatory bowel disease: a review of medical therapy. , 2008, World journal of gastroenterology.

[5]  Masahiro Yamamoto,et al.  ATP drives lamina propria TH17 cell differentiation , 2008, Nature.

[6]  R. Knight,et al.  Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities , 2007, Applied and Environmental Microbiology.

[7]  N. Jones,et al.  The use of probiotics in the prevention and treatment of antibiotic-associated diarrhea with special interest in Clostridium difficile-associated diarrhea. , 2009, Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition.

[8]  N. Pace,et al.  Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases , 2007, Proceedings of the National Academy of Sciences.

[9]  F. Bushman,et al.  The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis , 2008, PLoS pathogens.

[10]  Rob Knight,et al.  UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context , 2006, BMC Bioinformatics.

[11]  D. Hoban.  Antibiotics and collateral damage. , 2004, Clinical cornerstone.

[12]  J. Cebra,et al.  Influences of microbiota on intestinal immune system development. , 1999, The American journal of clinical nutrition.

[13]  Herman Goossens,et al.  Early intestinal Bacteroides fragilis colonisation and development of asthma , 2008, BMC pulmonary medicine.

[14]  R. Flavell,et al.  An Antibiotic-Responsive Mouse Model of Fulminant Ulcerative Colitis , 2008, PLoS medicine.

[15]  A. Saxon.  Faculty Opinions recommendation of Toll-like receptor 4 signaling by intestinal microbes influences susceptibility to food allergy. , 2004 .

[16]  Hilary G. Morrison,et al.  Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation , 2009, Infection and Immunity.

[17]  D. Antonopoulos,et al.  Perturbation of the Small Intestine Microbial Ecology by Streptomycin Alters Pathology in a Salmonella enterica Serovar Typhimurium Murine Model of Infection , 2009, Infection and Immunity.

[18]  R. Ley,et al.  Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine , 2006, Cell.

[19]  P. Hugenholtz.  Exploring prokaryotic diversity in the genomic era , 2002, Genome Biology.

[20]  S. Mazmanian,et al.  A microbial symbiosis factor prevents intestinal inflammatory disease , 2008, Nature.

[21]  G. Dougan,et al.  Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota , 2007, PLoS biology.

[22]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[23]  N. Salzman,et al.  Prolonged Impact of Antibiotics on Intestinal Microbial Ecology and Susceptibility to Enteric Salmonella Infection , 2009, Infection and Immunity.

[24]  Les Dethlefsen,et al.  The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing , 2008, PLoS biology.

[25]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[26]  P. François,et al.  Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray. , 2008, FEMS immunology and medical microbiology.

[27]  J. Berzofsky,et al.  Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. , 2008, Immunity.

[28]  D. Littman,et al.  The orphan nuclear receptor RORgammat directs the differentiation program of proinflammatory IL-17+ T helper cells. , 2006, Cell.

[29]  B. Finlay,et al.  Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection , 2008, Infection and Immunity.

[30]  Gary J. Olsen,et al.  Ribosomal RNA phylogeny and the primary lines of evolutionary descent , 1986, Cell.

[31]  R. Kastelein,et al.  Commensal-dependent expression of IL-25 regulates the IL-23–IL-17 axis in the intestine , 2008, The Journal of experimental medicine.

[32]  L. Beaugerie,et al.  Effect of Antibiotic Therapy on Human Fecal Microbiota and the Relation to the Development of Clostridium difficile , 2008, Microbial Ecology.

[33]  Jeffrey I. Gordon,et al.  Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Daniel B. DiGiulio,et al.  Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.

[35]  R. Blumberg,et al.  The immunology of mucosal models of inflammation. , 2002, Annual review of immunology.

[36]  M. Lazar,et al.  RELMbeta/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[38]  A. Martner,et al.  Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics. , 2007, The Journal of antimicrobial chemotherapy.

[39]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[40]  T. S. Guseinov,et al.  Effect of dehydration on morphogenesis of the lymphatic network and immune structures in the small intestine , 2008, Bulletin of Experimental Biology and Medicine.

[41]  E. Zoetendal,et al.  Mucosa-Associated Bacteria in the Human Gastrointestinal Tract Are Uniformly Distributed along the Colon and Differ from the Community Recovered from Feces , 2002, Applied and Environmental Microbiology.

[42]  M. Falagas,et al.  Probiotics for the Treatment or Prevention of Atopic Dermatitis , 2008, American journal of clinical dermatology.

[43]  M. Bohnhoff,et al.  CHANGES IN THE MOUSE'S ENTERIC MICROFLORA ASSOCIATED WITH ENHANCED SUSCEPTIBILITY TO SALMONELLA INFECTION FOLLOWING STREPTOMYCIN TREATMENT. , 1963, The Journal of infectious diseases.

[44]  G. Wu,et al.  Regulation of RELM/FIZZ isoform expression by Cdx2 in response to innate and adaptive immune stimulation in the intestine. , 2005, American journal of physiology. Gastrointestinal and liver physiology.

[45]  K. Julge,et al.  Allergy development and the intestinal microflora during the first year of life. , 2001, The Journal of allergy and clinical immunology.

[46]  J. Gordon,et al.  How host-microbial interactions shape the nutrient environment of the mammalian intestine. , 2002, Annual review of nutrition.

[47]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[48]  R Balfour Sartor,et al.  Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. , 2008, Cell host & microbe.

[49]  P. Hellström,et al.  Intestinal microflora stimulates myoelectric activity of rat small intestine by promoting cyclic initiation and aboral propagation of migrating myoelectric complex , 1994, Digestive Diseases and Sciences.

[50]  G. Adler,et al.  Commensal Gut Flora Drives the Expansion of Proinflammatory CD4 T Cells in the Colonic Lamina Propria under Normal and Inflammatory Conditions1 , 2008, The Journal of Immunology.

[51]  D. Artis.  Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut , 2008, Nature Reviews Immunology.

[52]  Ruslan Medzhitov,et al.  Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis , 2004, Cell.

[53]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[54]  G. Toews,et al.  Role of Antibiotics and Fungal Microbiota in Driving Pulmonary Allergic Responses , 2004, Infection and Immunity.

[55]  Ting Wang,et al.  The gut microbiota as an environmental factor that regulates fat storage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.