Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization
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Patrick D. Schloss | Matthew L. Jenior | Vincent B. Young | P. Schloss | V. Young | M. Jenior | Jhansi L. Leslie | J. Leslie
[1] Christoph H Borchers,et al. Effect of Antibiotic Treatment on the Intestinal Metabolome , 2011, Antimicrobial Agents and Chemotherapy.
[2] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[3] Bo Li,et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection , 2014, Nature Communications.
[4] Patrick D. Schloss,et al. Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes , 2017, mSystems.
[5] Susumu Goto,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..
[6] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[7] Chao Xie,et al. Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.
[8] C. Huttenhower,et al. Relating the metatranscriptome and metagenome of the human gut , 2014, Proceedings of the National Academy of Sciences.
[9] Curtis J. Donskey,et al. Metabolomics Analysis Identifies Intestinal Microbiota-Derived Biomarkers of Colonization Resistance in Clindamycin-Treated Mice , 2014, PloS one.
[10] 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.
[11] S. Sørensen,et al. Antagonism correlates with metabolic similarity in diverse bacteria , 2017, Proceedings of the National Academy of Sciences.
[12] Lisa G Winston,et al. Burden of Clostridium difficile Infection in the United States , 2015 .
[13] K. Wilson,et al. Role of competition for nutrients in suppression of Clostridium difficile by the colonic microflora , 1988, Infection and immunity.
[14] Taane G. Clark,et al. Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice , 2012, PLoS pathogens.
[15] A. Moya,et al. Structural and functional changes in the gut microbiota associated to Clostridium difficile infection , 2014, Front. Microbiol..
[16] E. Fikrig,et al. Pathogen-mediated manipulation of arthropod microbiota to promote infection , 2017, Proceedings of the National Academy of Sciences.
[17] K. Turner,et al. Metatranscriptomics of the Human Oral Microbiome during Health and Disease , 2014, mBio.
[18] Jo Handelsman,et al. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity , 2014, mBio.
[19] Anne-Laure Boulesteix,et al. AUC-RF: A New Strategy for Genomic Profiling with Random Forest , 2011, Human Heredity.
[20] G. Pier,et al. RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract , 2011, Journal of visualized experiments : JoVE.
[21] P. Schloss,et al. Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile , 2015, mBio.
[22] R. Freter. The fatal enteric cholera infection in the guinea pig, achieved by inhibition of normal enteric flora. , 1955, The Journal of infectious diseases.
[23] Hilary G. Morrison,et al. Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation , 2009, Infection and Immunity.
[24] K. Wilson,et al. Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile , 1982, Journal of clinical microbiology.
[25] G. Gloor,et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut , 2013, Microbiome.
[26] Leo Breiman,et al. Random Forests , 2001, Machine Learning.
[27] E. Vollaard,et al. Colonization resistance , 1994, Antimicrobial Agents and Chemotherapy.
[28] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[29] J. Silva,et al. Antibiotic-associated colitis: effects of antibiotics on Clostridium difficile and the disease in hamsters. , 1979, Reviews of infectious diseases.
[30] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[31] G. Dick,et al. Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. , 2014, Environmental Microbiology.
[32] Bernard Henrissat,et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla , 2009, Proceedings of the National Academy of Sciences.
[33] Philipp Berens,et al. CircStat: AMATLABToolbox for Circular Statistics , 2009, Journal of Statistical Software.
[34] Xiaowei Zhang,et al. Where less may be more: how the rare biosphere pulls ecosystems strings , 2017, The ISME Journal.
[35] G E Bignardi,et al. Risk factors for Clostridium difficile infection. , 1998, The Journal of hospital infection.
[36] Casey M. Theriot,et al. Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract , 2014, Infection and Immunity.
[37] David N. Fisman,et al. Meta-Analysis of Antibiotics and the Risk of Community-Associated Clostridium difficile Infection , 2013, Antimicrobial Agents and Chemotherapy.
[38] Guoyao Wu,et al. Amino acid metabolism in intestinal bacteria and its potential implications for mammalian reproduction. , 2015, Molecular human reproduction.
[39] David A. Spratt,et al. Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces , 2015, mBio.
[40] Toni Giorgino,et al. Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package , 2009 .
[41] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[42] Chris Sander,et al. Precision microbiome restoration of bile acid-mediated resistance to Clostridium difficile , 2014, Nature.
[43] 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.
[44] D. Gerding,et al. Colonization for the Prevention of Clostridium difficile Disease in Hamsters , 2002 .
[45] R. Britton,et al. Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. , 2012, Trends in microbiology.
[46] C. Theriot,et al. Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model , 2018, mSphere.
[47] A. Sonenshein,et al. Integration of metabolism and virulence in Clostridium difficile. , 2015, Research in Microbiology.
[48] M. Ferrer,et al. Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses , 2015, The ISME Journal.
[49] M. Stevenson,et al. Antibiotics and hospital-acquired Clostridium difficile-associated diarrhoea: a systematic review. , 2003, The Journal of antimicrobial chemotherapy.