Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota.

The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing), we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2), in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.

[1]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[2]  W. Garrett,et al.  The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis , 2013, Science.

[3]  J. Kopečný,et al.  Detection of possible AI-2-mediated quorum sensing system in commensal intestinal bacteria , 2008, Folia Microbiologica.

[4]  B. Bassler,et al.  Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli , 2005, Journal of bacteriology.

[5]  Harry J Flint,et al.  Interactions and competition within the microbial community of the human colon: links between diet and health. , 2007, Environmental microbiology.

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

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

[8]  Ned S Wingreen,et al.  Quantifying the Integration of Quorum-Sensing Signals with Single-Cell Resolution , 2009, PLoS biology.

[9]  Paul S. Cohen,et al.  Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine , 2008, Infection and Immunity.

[10]  D. Hartl,et al.  An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations , 2006, Science.

[11]  B. Weimer,et al.  Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens , 2013, Nature.

[12]  J. Salojärvi,et al.  Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men , 2014, The ISME Journal.

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

[14]  A. Macpherson,et al.  Interactions Between the Microbiota and the Immune System , 2012, Science.

[15]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[16]  Bonnie L. Bassler,et al.  Interference with AI-2-mediated bacterial cell–cell communication , 2005, Nature.

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

[18]  Chris Sander,et al.  Precision microbiome restoration of bile acid-mediated resistance to Clostridium difficile , 2014, Nature.

[19]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[20]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[21]  Shawn R Campagna,et al.  Salmonella typhimurium recognizes a chemically distinct form of the bacterial quorum-sensing signal AI-2. , 2004, Molecular cell.

[22]  M. Taga,et al.  Sinorhizobium meliloti, a bacterium lacking the autoinducer‐2 (AI‐2) synthase, responds to AI‐2 supplied by other bacteria , 2008, Molecular microbiology.

[23]  Harry J. Flint,et al.  The gut microbiota, bacterial metabolites and colorectal cancer , 2014, Nature Reviews Microbiology.

[24]  Richard A. Juneau,et al.  Indirect Pathogenicity of Haemophilus influenzae and Moraxella catarrhalis in Polymicrobial Otitis Media Occurs via Interspecies Quorum Signaling , 2010, mBio.

[25]  G. Núñez,et al.  Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota , 2012, Science.

[26]  Sang-Uk Seo,et al.  Role of the gut microbiota in immunity and inflammatory disease , 2013, Nature Reviews Immunology.

[27]  Eunseog Youn,et al.  Pyrosequencing study of fecal microflora of autistic and control children. , 2010, Anaerobe.

[28]  R. Domingues,et al.  Bacteroides species produce Vibrio harveyi autoinducer 2-related molecules. , 2005, Anaerobe.

[29]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[30]  Paul S. Cohen,et al.  Precolonized Human Commensal Escherichia coli Strains Serve as a Barrier to E. coli O157:H7 Growth in the Streptomycin-Treated Mouse Intestine , 2009, Infection and Immunity.

[31]  James A. Foster,et al.  Phylogenetics Clearcut : a fast implementation of relaxed neighbor joining , 2006 .

[32]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[33]  K. Krogfelt,et al.  The Life of Commensal Escherichia coli in the Mammalian Intestine. , 2004, EcoSal Plus.

[34]  C. von Mering,et al.  Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria , 2010, PLoS pathogens.

[35]  M. Hogardt,et al.  Pretreatment of Mice with Streptomycin Provides a Salmonella enterica Serovar Typhimurium Colitis Model That Allows Analysis of Both Pathogen and Host , 2003, Infection and Immunity.

[36]  M. Taga,et al.  Methods for Analysis of Bacterial Autoinducer‐2 Production , 2011, Current protocols in microbiology.

[37]  M. Reis,et al.  Microbial characterization of mercury-reducing mixed cultures enriched with different carbon sources. , 2011, Microbes and environments.

[38]  M. Taga.  Methods for Analysis of Bacterial Autoinducer‐2 Production , 2006, Current protocols in microbiology.

[39]  Nora C. Toussaint,et al.  Intestinal Microbiota Containing Barnesiella Species Cures Vancomycin-Resistant Enterococcus faecium Colonization , 2013, Infection and Immunity.

[40]  N. Socci,et al.  Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. , 2010, The Journal of clinical investigation.

[41]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[42]  William E Bentley,et al.  Cross species quorum quenching using a native AI-2 processing enzyme. , 2010, ACS chemical biology.

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

[44]  Paulo B. Correia,et al.  Phosphoenolpyruvate phosphotransferase system regulates detection and processing of the quorum sensing signal autoinducer‐2 , 2012, Molecular microbiology.

[45]  A. Viale,et al.  Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis , 2011, Infection and Immunity.

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

[47]  D. Savage.  Microbial ecology of the gastrointestinal tract. , 1977, Annual review of microbiology.

[48]  B. Haas,et al.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. , 2011, Genome research.

[49]  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.

[50]  Vincent B. Young,et al.  Suppression of Clostridium difficile in the Gastrointestinal Tracts of Germfree Mice Inoculated with a Murine Isolate from the Family Lachnospiraceae , 2012, Infection and Immunity.

[51]  Liping Zhao,et al.  Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers , 2011, The ISME Journal.

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

[53]  M. Bohnhoff,et al.  Enhanced susceptibility to Salmonella infection in streptomycin-treated mice. , 1962, The Journal of infectious diseases.

[54]  Susan M. Huse,et al.  Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing , 2008, PLoS genetics.

[55]  N. Mcneil.  The contribution of the large intestine to energy supplies in man. , 1984, The American journal of clinical nutrition.

[56]  Bernard Henrissat,et al.  Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins , 2010, Proceedings of the National Academy of Sciences.

[57]  B. Bassler,et al.  Multiple signalling systems controlling expression of luminescence in Vibrio harveyi: sequence and function of genes encoding a second sensory pathway , 1994, Molecular microbiology.

[58]  M. Surette,et al.  The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum‐sensing signal molecule , 2001, Molecular microbiology.

[59]  A. Walker,et al.  Intestinal colonization resistance , 2013, Immunology.

[60]  R. Xavier,et al.  Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43 , 2009, Nature.

[61]  A. Rudensky,et al.  Metabolites produced by commensal bacteria promote peripheral regulatory T cell generation , 2013, Nature.

[62]  João C Marques,et al.  An efficient synthesis of the precursor of AI-2, the signalling molecule for inter-species quorum sensing. , 2011, Bioorganic & medicinal chemistry.

[63]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[64]  Rashidul Haque,et al.  Members of the human gut microbiota involved in recovery from Vibrio cholerae infection , 2014, Nature.

[65]  R. Berg,et al.  The indigenous gastrointestinal microflora. , 1996, Trends in microbiology.

[66]  R. Medzhitov,et al.  The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition , 2014, Proceedings of the National Academy of Sciences.

[67]  S. Winter,et al.  Streptomycin-Induced Inflammation Enhances Escherichia coli Gut Colonization Through Nitrate Respiration , 2013, mBio.

[68]  E. Ruby.  Symbiotic conversations are revealed under genetic interrogation , 2008, Nature Reviews Microbiology.

[69]  S. Dowd,et al.  Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota , 2014, BMC Microbiology.

[70]  Bonnie L Bassler,et al.  Bacterial quorum sensing: its role in virulence and possibilities for its control. , 2012, Cold Spring Harbor perspectives in medicine.

[71]  B. Bassler,et al.  Structural identification of a bacterial quorum-sensing signal containing boron , 2002, Nature.

[72]  M. Tomita,et al.  Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells , 2013, Nature.

[73]  E. Greenberg,et al.  Induction of luciferase synthesis in Beneckea harveyi by other marine bacteria , 1979, Archives of Microbiology.

[74]  K. Xavier,et al.  AI-2-mediated signalling in bacteria. , 2013, FEMS microbiology reviews.

[75]  A. Rickard,et al.  Autoinducer-2 influences interactions amongst pioneer colonizing streptococci in oral biofilms. , 2012, Microbiology.