Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential

[1]  Jared C Malke,et al.  Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response , 2021, Science.

[2]  Manu Sebastian,et al.  Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis , 2021, Cell reports.

[3]  R. Waller,et al.  The convoluted history of haem biosynthesis , 2021, Biological reviews of the Cambridge Philosophical Society.

[4]  A. Bäumler,et al.  The longitudinal and cross-sectional heterogeneity of the intestinal microbiota. , 2021, Current opinion in microbiology.

[5]  W. Eisenreich,et al.  High CO2 levels drive the TCA cycle backwards towards autotrophy , 2021, Nature.

[6]  Jonathan M Stokes,et al.  Clinically relevant mutations in core metabolic genes confer antibiotic resistance , 2021, Science.

[7]  J. Imlay,et al.  How Microbes Evolved to Tolerate Oxygen. , 2020, Trends in microbiology.

[8]  O. Pedersen,et al.  Gut microbiota in human metabolic health and disease , 2020, Nature Reviews Microbiology.

[9]  Sang-Woon Choi,et al.  High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease. , 2020, Cell host & microbe.

[10]  M. Obrenovich,et al.  The Microbiota–Gut–Brain Axis Heart Shunt Part I: The French Paradox, Heart Disease and the Microbiota , 2020, Microorganisms.

[11]  Qi Yang,et al.  Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review , 2020, Nutrients.

[12]  Dominik G Grimm,et al.  Current challenges and best-practice protocols for microbiome analysis , 2019, Briefings Bioinform..

[13]  N. Neff,et al.  Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs. , 2019, Cell host & microbe.

[14]  Hu Li,et al.  Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. , 2019, Cell metabolism.

[15]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[16]  William A. Walters,et al.  Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 , 2019, Nature Biotechnology.

[17]  Feng Li,et al.  MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies , 2019, PeerJ.

[18]  O. Husson,et al.  A method to measure redox potential (Eh) and pH in agar media and plants shows that fungal growth is affected by and affects pH and Eh. , 2019, Fungal biology.

[19]  Bas E. Dutilh,et al.  Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT , 2019, Genome Biology.

[20]  D. Raoult,et al.  Linking gut redox to human microbiome , 2018, Human Microbiome Journal.

[21]  A. Bäumler,et al.  Colonocyte metabolism shapes the gut microbiota , 2018, Science.

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

[23]  H. M. Kim,et al.  Microbial metabolites, short‐chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice , 2018, European journal of immunology.

[24]  K. Whelan,et al.  Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. , 2018, The American journal of clinical nutrition.

[25]  J. DiRuggiero,et al.  MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis , 2018, Microbiome.

[26]  Benjamin D. Kaehler,et al.  Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin , 2018, Microbiome.

[27]  J. Slavin,et al.  Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide , 2017, Nutrients.

[28]  Michelle L. Treiber,et al.  SAMSA2: a standalone metatranscriptome analysis pipeline , 2017, BMC Bioinformatics.

[29]  E. Le Chatelier,et al.  Protection of the Human Gut Microbiome From Antibiotics , 2017, bioRxiv.

[30]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[31]  Jonathan M Stokes,et al.  Bacterial Metabolism and Antibiotic Efficacy , 2019, Cell metabolism.

[32]  A. Neish,et al.  Redox signaling mediated by the gut microbiota. , 2017, Free radical biology & medicine.

[33]  Fabian Rivera-Chávez,et al.  Oxygen as a driver of gut dysbiosis. , 2017, Free radical biology & medicine.

[34]  P. Wilmes,et al.  A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility , 2016, Cell.

[35]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[36]  Blake A. Simmons,et al.  MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets , 2016, Bioinform..

[37]  O. Husson,et al.  Practical improvements in soil redox potential (Eh) measurement for characterisation of soil properties. Application for comparison of conventional and conservation agriculture cropping systems. , 2016, Analytica chimica acta.

[38]  Justin L Sonnenburg,et al.  Quantitative Imaging of Gut Microbiota Spatial Organization. , 2015, Cell host & microbe.

[39]  Saloni R. Jain,et al.  Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage. , 2015, Cell reports.

[40]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[41]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[42]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[43]  Ahmad S Khalil,et al.  Antibiotics induce redox-related physiological alterations as part of their lethality. , 2014, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[45]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[46]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[47]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[48]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

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

[50]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[51]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[52]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[53]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[54]  Se Jin Song,et al.  LSU LSU A communal catalogue reveals Earth's multiscale microbial A communal catalogue reveals Earth's multiscale microbial diversity diversity , 2021 .

[55]  O. Husson Redox potential (Eh) and pH as drivers of soil/plant/microorganism systems: a transdisciplinary overview pointing to integrative opportunities for agronomy , 2012, Plant and Soil.