Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

[1]  Anne Richelle,et al.  Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 , 2019, Nature Protocols.

[2]  L. Dohnalová,et al.  The Dimension of Time in Host-Microbiome Interactions , 2019, mSystems.

[3]  William H. Bisson,et al.  Gut microbiota and intestinal FXR mediate the clinical benefits of metformin , 2018, Nature Medicine.

[4]  Jens Nielsen,et al.  Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling. , 2018, Metabolic engineering.

[5]  Ronan M. T. Fleming,et al.  Reply to "Challenges in modeling the human gut microbiome" , 2018, Nature Biotechnology.

[6]  Rick L. Stevens,et al.  KBase: The United States Department of Energy Systems Biology Knowledgebase , 2018, Nature Biotechnology.

[7]  Michael B. Mundy,et al.  Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers , 2018, Genome Medicine.

[8]  Ines Thiele,et al.  Modeling metabolism of the human gut microbiome. , 2018, Current opinion in biotechnology.

[9]  Eugen Bauer,et al.  From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease , 2018, npj Systems Biology and Applications.

[10]  Piotr Gawron,et al.  The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease , 2018, bioRxiv.

[11]  Federico Baldini,et al.  The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities , 2018, bioRxiv.

[12]  S. Devendran,et al.  Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12α-Hydroxysteroid Dehydrogenases from Bile Acid 7α-Dehydroxylating Human Gut Bacteria , 2018, Applied and Environmental Microbiology.

[13]  J. Alves,et al.  Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704. , 2018, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[14]  Ronan M. T. Fleming,et al.  When metabolism meets physiology: Harvey and Harvetta , 2018, bioRxiv.

[15]  Avlant Nilsson,et al.  Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism , 2018, Nature Biotechnology.

[16]  Daniel C. Zielinski,et al.  Recon3D enables a three-dimensional view of gene variation in human metabolism , 2018 .

[17]  Kyle Bittinger,et al.  A role for bacterial urease in gut dysbiosis and Crohn’s disease , 2017, Science Translational Medicine.

[18]  Ines Thiele,et al.  Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides , 2017, Front. Genet..

[19]  D. Iliopoulos,et al.  The IBD interactome: an integrated view of aetiology, pathogenesis and therapy , 2017, Nature Reviews Gastroenterology & Hepatology.

[20]  Ronan M. T. Fleming,et al.  Quantitative systems pharmacology and the personalized drug–microbiota–diet axis , 2017, Current opinion in systems biology.

[21]  Ruben G. A. van Heck,et al.  More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes , 2017, Microbiome.

[22]  Costas D. Maranas,et al.  SteadyCom: Predicting microbial abundances while ensuring community stability , 2017, PLoS Comput. Biol..

[23]  Johannes Zimmermann,et al.  BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities , 2017, PLoS Comput. Biol..

[24]  Anne Richelle,et al.  A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. , 2017, Cell systems.

[25]  Jens Nielsen,et al.  Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine. , 2017, Cell metabolism.

[26]  Ronan M. T. Fleming,et al.  DistributedFBA.jl: high‐level, high‐performance flux balance analysis in Julia , 2017, Bioinform..

[27]  H. Flint,et al.  Formation of propionate and butyrate by the human colonic microbiota. , 2017, Environmental microbiology.

[28]  Ronan M. T. Fleming,et al.  Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota , 2016, Nature Biotechnology.

[29]  Hanns-Ulrich Marschall,et al.  Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism. , 2016, Cell metabolism.

[30]  Paul M. Ruegger,et al.  A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients , 2016, Cellular and molecular gastroenterology and hepatology.

[31]  Ronan M. T. Fleming,et al.  MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models , 2016, Front. Physiol..

[32]  A. Braune,et al.  Bacterial species involved in the conversion of dietary flavonoids in the human gut , 2016, Gut microbes.

[33]  P. Hylemon,et al.  Consequences of bile salt biotransformations by intestinal bacteria , 2016, Gut microbes.

[34]  Christopher Staley,et al.  Interaction of gut microbiota with bile acid metabolism and its influence on disease states , 2016, Applied Microbiology and Biotechnology.

[35]  Eric Z. Chen,et al.  Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. , 2015, Cell host & microbe.

[36]  F. Turroni,et al.  Glycan cross-feeding activities between bifidobacteria under in vitro conditions , 2015, Front. Microbiol..

[37]  Michael A. Fischbach,et al.  A biosynthetic pathway for a prominent class of microbiota-derived bile acids , 2015, Nature chemical biology.

[38]  I. Thiele,et al.  Systems biology of host–microbe metabolomics , 2015, Wiley interdisciplinary reviews. Systems biology and medicine.

[39]  V. de Crécy-Lagard,et al.  Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes , 2015, Front. Genet..

[40]  Ines Thiele,et al.  Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework , 2015, Gut microbes.

[41]  S. Prakash,et al.  Bacterial Bile Metabolising Gene Abundance in Crohn's, Ulcerative Colitis and Type 2 Diabetes Metagenomes , 2014, PloS one.

[42]  Ines Thiele,et al.  Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota , 2014, Front. Microbiol..

[43]  Eran Segal,et al.  Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis , 2014, Cell.

[44]  C. Hill,et al.  Bacterial bile salt hydrolase in host metabolism: Potential for influencing gastrointestinal microbe-host crosstalk , 2014, Gut microbes.

[45]  Timothy J. Hanly,et al.  Dynamic flux balance analysis for synthetic microbial communities. , 2014, IET systems biology.

[46]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[47]  Ronan M. T. Fleming,et al.  A systems biology approach to studying the role of microbes in human health. , 2013, Current opinion in biotechnology.

[48]  Ronan M. T. Fleming,et al.  Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut , 2013, Gut microbes.

[49]  H. Sokol,et al.  Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases , 2012, Gut.

[50]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[51]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[52]  Sergio Riva,et al.  In search of sustainable chemical processes: cloning, recombinant expression, and functional characterization of the 7α- and 7β-hydroxysteroid dehydrogenases from Clostridium absonum , 2011, Applied Microbiology and Biotechnology.

[53]  F. Bushman,et al.  Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes , 2011, Science.

[54]  Ines Thiele,et al.  rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks , 2011, Bioinform..

[55]  Rick L. Stevens,et al.  High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.

[56]  Robert Olson,et al.  Accessing the SEED Genome Databases via Web Services API: Tools for Programmers , 2010, BMC Bioinformatics.

[57]  M. Liong,et al.  Removal of cholesterol by lactobacilli via incorporation and conversion to coprostanol. , 2010, Journal of dairy science.

[58]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[59]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[60]  Inna Dubchak,et al.  MicrobesOnline: an integrated portal for comparative and functional genomics , 2009, Nucleic Acids Res..

[61]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[62]  Adam Godzik,et al.  Shotgun metaproteomics of the human distal gut microbiota , 2008, The ISME Journal.

[63]  J. Doré,et al.  Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients , 2008, Proceedings of the National Academy of Sciences.

[64]  Nan Xiao,et al.  Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli , 2008, Bioinform..

[65]  Colin Hill,et al.  Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome , 2008, Proceedings of the National Academy of Sciences.

[66]  Haifeng Lu,et al.  Symbiotic gut microbes modulate human metabolic phenotypes , 2008, Proceedings of the National Academy of Sciences.

[67]  Daniel H. Huson,et al.  Dendroscope: An interactive viewer for large phylogenetic trees , 2007, BMC Bioinformatics.

[68]  Dae-Joong Kang,et al.  Bile salt biotransformations by human intestinal bacteria Published, JLR Papers in Press, November 18, 2005. , 2006, Journal of Lipid Research.

[69]  B. Palsson.  Systems Biology: Properties of Reconstructed Networks , 2006 .

[70]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[71]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[72]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[73]  S. McKnight,et al.  Cloning and Characterization of the NAD-Dependent 7α-Hydroxysteroid Dehydrogenase from Bacteroides fragilis , 2003, Current Microbiology.

[74]  R. Overbeek,et al.  Missing genes in metabolic pathways: a comparative genomics approach. , 2003, Current opinion in chemical biology.

[75]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[76]  P. Melone,et al.  Mechanism of intestinal 7 alpha-dehydroxylation of cholic acid: evidence that allo-deoxycholic acid is an inducible side-product. , 1991, Journal of lipid research.

[77]  P. Hylemon,et al.  Partial purification and characterization of NADP-dependent 12alpha-hydroxysteroid dehydrogenase from Clostridium leptum. , 1978, Biochimica et biophysica acta.