The Microbiome and Its Potential for Pharmacology.

[1]  Ngoc Hung Nguyen,et al.  Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data , 2019, bioRxiv.

[2]  Lajia Zha,et al.  Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome , 2019, Pathogens.

[3]  Francesco Asnicar,et al.  Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 , 2019, Nature Biotechnology.

[4]  Wei-Lin Gao,et al.  Strategies in anti-Mycobacterium tuberculosis drug discovery based on phenotypic screening , 2019, The Journal of Antibiotics.

[5]  J. Ursing,et al.  Efficacy of Routine Fecal Microbiota Transplantation for Treatment of Recurrent Clostridium difficile Infection: A Retrospective Cohort Study , 2019, International journal of microbiology.

[6]  Diogo M. Camacho,et al.  A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip , 2019, Nature Biomedical Engineering.

[7]  Kevin S. Bonham,et al.  Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases , 2019, Nature.

[8]  Young-Mo Kim,et al.  Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice , 2019, Cell.

[9]  R. Schooley,et al.  Engineered bacteriophages for treatment of a patient with a disseminated drug resistant Mycobacterium abscessus , 2019, Nature Medicine.

[10]  Alexander A. Aksenov,et al.  MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data , 2019, bioRxiv.

[11]  Jingyuan Fu,et al.  Structural variation in the gut microbiome associates with host health , 2019, Nature.

[12]  R. Knight,et al.  Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease , 2019, mSystems.

[13]  B. Kuster,et al.  Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae , 2019, Proteomes.

[14]  Rohit Loomba,et al.  Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians , 2019, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[15]  D. Plichta,et al.  A defined commensal consortium elicits CD8 T cells and anti-cancer immunity , 2019, Nature.

[16]  T. Rabesandratana Microbiome conservancy stores global fecal samples. , 2018, Science.

[17]  Austin D. Swafford,et al.  High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity , 2018, mSystems.

[18]  Karsten Zengler,et al.  GABA Modulating Bacteria of the Human Gut Microbiota , 2018, Nature Microbiology.

[19]  R. Knight,et al.  Preserving microbial diversity , 2018, Science.

[20]  Itai Sharon,et al.  Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT , 2018, Cell.

[21]  K. West,et al.  Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria , 2018, Nature Biotechnology.

[22]  Michael A Fischbach,et al.  Microbiome: Focus on Causation and Mechanism , 2018, Cell.

[23]  Timothy K Lu,et al.  An ingestible bacterial-electronic system to monitor gastrointestinal health , 2018, Science.

[24]  Patrice D Cani,et al.  The DPP-4 inhibitor vildagliptin impacts the gut microbiota and prevents disruption of intestinal homeostasis induced by a Western diet in mice , 2018, Diabetologia.

[25]  Rob Knight,et al.  Evaluating the Information Content of Shallow Shotgun Metagenomics , 2018, mSystems.

[26]  D. Raoult,et al.  Culturing the human microbiota and culturomics , 2018, Nature Reviews Microbiology.

[27]  Peer Bork,et al.  Extensive impact of non-antibiotic drugs on human gut bacteria , 2018, Nature.

[28]  Rob Knight,et al.  American Gut: an Open Platform for Citizen Science Microbiome Research , 2018, mSystems.

[29]  A. Kurilshikov,et al.  Environment dominates over host genetics in shaping human gut microbiota , 2018, Nature.

[30]  D. Gevers,et al.  Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. , 2018, Cell host & microbe.

[31]  Gabriel A. Al-Ghalith,et al.  Systematic review: human gut dysbiosis induced by non‐antibiotic prescription medications , 2018, Alimentary pharmacology & therapeutics.

[32]  Mark A Underwood,et al.  Probiotics and necrotizing enterocolitis. , 2018, Seminars in pediatric surgery.

[33]  Laurence Zitvogel,et al.  Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors , 2018, Science.

[34]  E. Le Chatelier,et al.  Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients , 2018, Science.

[35]  Riyue Bao,et al.  The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients , 2018, Science.

[36]  E. Burstein,et al.  Precision editing of the gut microbiota ameliorates colitis , 2018, Nature.

[37]  A. Mira,et al.  Inhibition of Steptococcus mutans biofilm formation by extracts of Tenacibaculum sp. 20J, a bacterium with wide-spectrum quorum quenching activity , 2018, Journal of oral microbiology.

[38]  T. Dinan,et al.  Anxiety, Depression, and the Microbiome: A Role for Gut Peptides , 2017, Neurotherapeutics.

[39]  Luc Bijnens,et al.  Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice , 2017, Nature Microbiology.

[40]  Rick L. Stevens,et al.  A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.

[41]  R. Kordek,et al.  New Peptide Inhibitor of Dipeptidyl Peptidase IV, EMDB-1 Extends the Half-Life of GLP-2 and Attenuates Colitis in Mice after Topical Administration , 2017, The Journal of Pharmacology and Experimental Therapeutics.

[42]  A. Ciobica,et al.  Proton pump inhibitors therapy and risk of Clostridium difficile infection: Systematic review and meta-analysis , 2017, World journal of gastroenterology.

[43]  Arthur Brady,et al.  Strains, functions and dynamics in the expanded Human Microbiome Project , 2017, Nature.

[44]  Stephen L. Hauser,et al.  Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models , 2017, Proceedings of the National Academy of Sciences.

[45]  S. Zeisel,et al.  Trimethylamine N-Oxide, the Microbiome, and Heart and Kidney Disease. , 2017, Annual review of nutrition.

[46]  Erica M. Hartmann,et al.  Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems , 2017, Microbiome.

[47]  R. Schooley,et al.  Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection , 2017, Antimicrobial Agents and Chemotherapy.

[48]  David Torrents,et al.  Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug , 2017, Nature Medicine.

[49]  J. Overmann,et al.  Cultured microbes represent a substantial fraction of the human and mouse gut microbiota , 2017, Gut microbes.

[50]  William E Bentley,et al.  Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models , 2017, Nature Communications.

[51]  A. Mira,et al.  Health-Associated Niche Inhabitants as Oral Probiotics: The Case of Streptococcus dentisani , 2017, Front. Microbiol..

[52]  A. Hekmatdoost,et al.  Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet. , 2017, Advances in nutrition.

[53]  P. Dorrestein,et al.  Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis , 2017, Science Translational Medicine.

[54]  Pieter C Dorrestein,et al.  Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy. , 2017, Trends in pharmacological sciences.

[55]  Justine W. Debelius,et al.  Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease , 2016, Cell.

[56]  Daniel H. Geschwind,et al.  The Central Nervous System and the Gut Microbiome , 2016, Cell.

[57]  Eric D. Kelsic,et al.  Spatiotemporal microbial evolution on antibiotic landscapes , 2016, Science.

[58]  Dan Knights,et al.  Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice , 2016, Nature Microbiology.

[59]  Kristian Fog Nielsen,et al.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.

[60]  J Licinio,et al.  Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism , 2016, Molecular Psychiatry.

[61]  M. Yassour,et al.  Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans , 2016, Cell.

[62]  J. Raes,et al.  Population-level analysis of gut microbiome variation , 2016, Science.

[63]  Peter J. Turnbaugh,et al.  The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism , 2016, Nature Reviews Microbiology.

[64]  D. Wishart Emerging applications of metabolomics in drug discovery and precision medicine , 2016, Nature Reviews Drug Discovery.

[65]  M. Jenmalm,et al.  Probiotics for treatment and primary prevention of allergic diseases and asthma: looking back and moving forward , 2016, Expert review of clinical immunology.

[66]  Ron Milo,et al.  Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans , 2016, Cell.

[67]  R. Kishony,et al.  Multidrug evolutionary strategies to reverse antibiotic resistance , 2016, Science.

[68]  Angela C. Poole,et al.  Proton pump inhibitors alter the composition of the gut microbiota , 2015, Gut.

[69]  William A. Walters,et al.  Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys , 2015, mSystems.

[70]  Jens Roat Kultima,et al.  Disentangling the effects of type 2 diabetes and metformin on the human gut microbiota , 2015, Nature.

[71]  Daniel Patrick Smith,et al.  Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis , 2015, Nature Communications.

[72]  S. Frye,et al.  Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity. , 2015, Chemistry & biology.

[73]  M. Fischbach,et al.  Small molecules from the human microbiota , 2015, Science.

[74]  Lars Konermann,et al.  Exploring the mechanism of salt-induced signal suppression in protein electrospray mass spectrometry using experiments and molecular dynamics simulations. , 2015, Analytical chemistry.

[75]  K. Lewis,et al.  A new antibiotic kills pathogens without detectable resistance , 2015, Nature.

[76]  Didier Raoult,et al.  The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota , 2015, Clinical Microbiology Reviews.

[77]  R. Knight,et al.  Meta‐analyses of human gut microbes associated with obesity and IBD , 2014, FEBS letters.

[78]  Angela C. Poole,et al.  Human Genetics Shape the Gut Microbiome , 2014, Cell.

[79]  Peter Cimermancic,et al.  A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics , 2014, Cell.

[80]  M. Blaser,et al.  Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences , 2014, Cell.

[81]  A. Kostic,et al.  The microbiome in inflammatory bowel disease: current status and the future ahead. , 2014, Gastroenterology.

[82]  Cristina Solano,et al.  Biofilm dispersion and quorum sensing. , 2014, Current opinion in microbiology.

[83]  M. Redinbo,et al.  Bacterial β-glucuronidase inhibition protects mice against enteropathy induced by indomethacin, ketoprofen or diclofenac: mode of action and pharmacokinetics , 2014, Xenobiotica; the fate of foreign compounds in biological systems.

[84]  J. Petrosino,et al.  Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders , 2013, Cell.

[85]  F. Marincola,et al.  Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment , 2013, Science.

[86]  Eric Vivier,et al.  The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide , 2013, Science.

[87]  L. Ursell,et al.  Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota , 2013, Proceedings of the National Academy of Sciences.

[88]  J. Clemente,et al.  Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice , 2013, Science.

[89]  P. Turnbaugh,et al.  Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta , 2013, Science.

[90]  M. Hattori,et al.  Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota , 2013, Nature.

[91]  F. Bäckhed,et al.  The gut microbiota — masters of host development and physiology , 2013, Nature Reviews Microbiology.

[92]  E. Zoetendal,et al.  Duodenal infusion of donor feces for recurrent Clostridium difficile. , 2013, The New England journal of medicine.

[93]  Curtis Huttenhower,et al.  Biodiversity and functional genomics in the human microbiome. , 2013, Trends in genetics : TIG.

[94]  B. Finlay,et al.  Perinatal antibiotic treatment affects murine microbiota, immune responses and allergic asthma , 2013, Gut microbes.

[95]  R. Knight,et al.  Spatial and temporal variability of the human microbiota. , 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[96]  C. Mathieu,et al.  Reversal of autoimmune diabetes by restoration of antigen-specific tolerance using genetically modified Lactococcus lactis in mice. , 2012, The Journal of clinical investigation.

[97]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[98]  Rob Knight,et al.  The mind-body-microbial continuum , 2011, Dialogues in clinical neuroscience.

[99]  S. Mazmanian,et al.  Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System? , 2010, Science.

[100]  John E. Scott,et al.  Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme , 2010, Science.

[101]  Rob Knight,et al.  Human oral, gut, and plaque microbiota in patients with atherosclerosis , 2010, Proceedings of the National Academy of Sciences.

[102]  D. Relman,et al.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation , 2010, Proceedings of the National Academy of Sciences.

[103]  L. T. Angenent,et al.  Succession of microbial consortia in the developing infant gut microbiome , 2010, Proceedings of the National Academy of Sciences.

[104]  R. Knight,et al.  Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns , 2010, Proceedings of the National Academy of Sciences.

[105]  Amy Linsky,et al.  Proton pump inhibitors and risk for recurrent Clostridium difficile infection. , 2010, Archives of internal medicine.

[106]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[107]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[108]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[109]  John C Lindon,et al.  Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism , 2009, Proceedings of the National Academy of Sciences.

[110]  F. Rohwer,et al.  Explaining microbial population genomics through phage predation , 2009, Nature Reviews Microbiology.

[111]  A. Aromaa,et al.  Antibiotic use predicts an increased risk of cancer , 2008, International journal of cancer.

[112]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

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

[114]  Jeffrey I. Gordon,et al.  Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection , 2006, Cell.

[115]  F. Chan,et al.  Drug-induced side effects affecting the gastrointestinal tract , 2006, Expert opinion on drug safety.

[116]  Philippe Marteau,et al.  Specificities of the fecal microbiota in inflammatory bowel disease , 2006, Inflammatory bowel diseases.

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

[118]  C. Woese,et al.  Phylogenetic structure of the prokaryotic domain: The primary kingdoms , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[119]  M. Peppercorn,et al.  The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. , 1972, The Journal of pharmacology and experimental therapeutics.

[120]  Audrey Lee-Gosselin,et al.  Tunable thermal bioswitches for in vivo control of microbial therapeutics. , 2017, Nature chemical biology.

[121]  M. Tvede,et al.  Rectal bacteriotherapy for recurrent Clostridium difficile-associated diarrhoea: results from a case series of 55 patients in Denmark 2000-2012. , 2015, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[122]  Waleed Younis,et al.  Repurposing Non-Antimicrobial Drugs and Clinical Molecules to Treat Bacterial Infections. , 2015, Current pharmaceutical design.

[123]  Russ B Altman,et al.  PharmGKB: the Pharmacogenomics Knowledge Base. , 2013, Methods in molecular biology.

[124]  I. Kato,et al.  Streptomycin alleviates irinotecan-induced delayed-onset diarrhea in rats by a mechanism other than inhibition of β-glucuronidase activity in intestinal lumen , 2010, Cancer Chemotherapy and Pharmacology.

[125]  T. Molinski,et al.  Drug development from marine natural products , 2009, Nature Reviews Drug Discovery.

[126]  N. Pace,et al.  Microbial ecology and evolution: a ribosomal RNA approach. , 1986, Annual review of microbiology.

[127]  J. T. Staley,et al.  Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. , 1985, Annual review of microbiology.