Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences

[1]  Elhanan Borenstein,et al.  MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline , 2020, BMC Bioinformatics.

[2]  W. D. de Vos,et al.  Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study , 2020, Cell.

[3]  Samuel I. Miller,et al.  CFTR dysregulation drives active selection of the gut microbiome , 2020, PLoS pathogens.

[4]  Samuel I. Miller,et al.  Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure , 2019, Nature Medicine.

[5]  K. Switkowski,et al.  Timing of Complementary Feeding Introduction and Adiposity Throughout Childhood , 2019, Pediatrics.

[6]  Bota Cui,et al.  Rescue fecal microbiota transplantation for antibiotic-associated diarrhea in critically ill patients , 2019, Critical Care.

[7]  H. Knutsen,et al.  Appropriate age range for introduction of complementary feeding into an infant's diet , 2019, EFSA journal. European Food Safety Authority.

[8]  H. Verkade,et al.  Impaired Intestinal Farnesoid X Receptor Signaling in Cystic Fibrosis Mice , 2019, Cellular and molecular gastroenterology and hepatology.

[9]  G. Dantas,et al.  Metagenomic signatures of early life hospitalization and antibiotic treatment in the infant gut microbiota and resistome persist long after discharge , 2019, Nature Microbiology.

[10]  D. Raftery,et al.  Metabolomic Characterization of Human Model of Liver Rejection Identifies Aberrancies Linked to Cyclooxygenase (COX) and Nitric Oxide Synthase (NOS) , 2019, Annals of transplantation.

[11]  H. Verkade,et al.  Bile acid homeostasis in gastrointestinal and metabolic complications of cystic fibrosis. , 2019, Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society.

[12]  F. De Filippis,et al.  Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype , 2018, PloS one.

[13]  G. Bergström,et al.  Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1 , 2018, Cell.

[14]  R. Gibbs,et al.  Temporal development of the gut microbiome in early childhood from the TEDDY study , 2018, Nature.

[15]  E. Robilotti,et al.  Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant , 2018, Science Translational Medicine.

[16]  E. Borenstein,et al.  Taxa-function robustness in microbial communities , 2018, Microbiome.

[17]  C. Y. Ooi,et al.  Probiotics for people with cystic fibrosis. , 2018, The Cochrane database of systematic reviews.

[18]  F. Turroni,et al.  Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. , 2017, Trends in microbiology.

[19]  J. Casadesús,et al.  Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts , 2017, Front. Med..

[20]  Aaron M. Walsh,et al.  A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis , 2017, Scientific Reports.

[21]  B. Ramsey,et al.  Effects of Diagnosis by Newborn Screening for Cystic Fibrosis on Weight and Length in the First Year of Life , 2017, JAMA pediatrics.

[22]  K. Tomizawa,et al.  Synthesis of l‐cysteine derivatives containing stable sulfur isotopes and application of this synthesis to reactive sulfur metabolome , 2017, Free radical biology & medicine.

[23]  R. Weinstein,et al.  Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles , 2017, BMC Microbiology.

[24]  N. Simmonds,et al.  Clostridium difficile and cystic fibrosis: management strategies and the role of faecal transplantation. , 2017, Paediatric respiratory reviews.

[25]  Elhanan Borenstein,et al.  Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. , 2017, Cell host & microbe.

[26]  E. Borenstein,et al.  Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome , 2017, Microbiome.

[27]  P. Palange,et al.  Cystic fibrosis , 2016, The Lancet.

[28]  W. Garrett,et al.  Gut microbiota induce IGF-1 and promote bone formation and growth , 2016, Proceedings of the National Academy of Sciences.

[29]  S. Turroni,et al.  Gut Bifidobacteria Populations in Human Health and Aging , 2016, Front. Microbiol..

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

[31]  T. Thomas,et al.  Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis , 2016, Scientific Reports.

[32]  M. Ferrer,et al.  Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. , 2016, Trends in microbiology.

[33]  M. Xian,et al.  The metabolism and biotechnological application of betaine in microorganism , 2016, Applied Microbiology and Biotechnology.

[34]  Samuel I. Miller,et al.  Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis , 2016, Scientific Reports.

[35]  Casey M. Theriot,et al.  Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation , 2016, mSystems.

[36]  J. Choo,et al.  Sample storage conditions significantly influence faecal microbiome profiles , 2015, Scientific Reports.

[37]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[38]  P. Savelkoul,et al.  The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects , 2015, PloS one.

[39]  V. Tremaroli,et al.  Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. , 2015, Cell host & microbe.

[40]  W. Bernhard,et al.  Plasma Phosphatidylcholine Alterations in Cystic Fibrosis Patients: Impaired Metabolism and Correlation with Lung Function and Inflammation , 2015, Cellular Physiology and Biochemistry.

[41]  Elhanan Borenstein,et al.  Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species , 2015, Cell.

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

[43]  Elhanan Borenstein,et al.  MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome , 2014, bioRxiv.

[44]  Daniel Raftery,et al.  Colorectal cancer detection using targeted serum metabolic profiling. , 2014, Journal of proteome research.

[45]  Qunyuan Zhang,et al.  Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children , 2014, Nature.

[46]  P. Hylemon,et al.  Bile acids and the gut microbiome , 2014, Current opinion in gastroenterology.

[47]  Samuel I. Miller,et al.  Gastrointestinal pathology in juvenile and adult CFTR-knockout ferrets. , 2014, The American journal of pathology.

[48]  Samuel I. Miller,et al.  Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis. , 2014, Clinical Infectious Diseases.

[49]  D. Borowitz,et al.  Intestinal complications of cystic fibrosis , 2013, Current opinion in pulmonary medicine.

[50]  C. Buffie,et al.  Microbiota-mediated colonization resistance against intestinal pathogens , 2013, Nature Reviews Immunology.

[51]  R. D. De Lisle,et al.  The cystic fibrosis intestine. , 2013, Cold Spring Harbor perspectives in medicine.

[52]  P. Edwards,et al.  Pleiotropic roles of bile acids in metabolism. , 2013, Cell metabolism.

[53]  Maarten Bekaert,et al.  Dysbiosis of bifidobacteria and Clostridium cluster XIVa in the cystic fibrosis fecal microbiota. , 2013, Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society.

[54]  M. Lucarelli,et al.  Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Allelic Variants Relate to Shifts in Faecal Microbiota of Cystic Fibrosis Patients , 2013, PloS one.

[55]  George C. Runger,et al.  Gene selection with guided regularized random forest , 2012, Pattern Recognit..

[56]  R. Curi,et al.  Regulation of Inflammation by Short Chain Fatty Acids , 2011, Nutrients.

[57]  M. Rosenfeld,et al.  Cystic Fibrosis Foundation evidence-based guidelines for management of infants with cystic fibrosis. , 2009, The Journal of pediatrics.

[58]  S. Zeisel,et al.  Choline: an essential nutrient for public health. , 2009, Nutrition reviews.

[59]  J. Gustafson,et al.  Cystic Fibrosis , 2009, Journal of the Iowa Medical Society.

[60]  Ting Wang,et al.  The gut microbiota as an environmental factor that regulates fat storage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Zhongtang Yu,et al.  Improved extraction of PCR-quality community DNA from digesta and fecal samples. , 2004, BioTechniques.

[62]  F. Guarner,et al.  Gut flora in health and disease , 2003, The Lancet.

[63]  L. Breiman.  Random Forests , 2001, Machine Learning.

[64]  J. Skinner,et al.  Transitions in infant feeding during the first year of life. , 1997, Journal of the American College of Nutrition.

[65]  H. Fenlon,et al.  Intestinal bile acid malabsorption in cystic fibrosis. , 1993, Gut.

[66]  G. Davidson,et al.  In Vivo Bile Acid Uptake from Terminal Ileum in Cystic Fibrosis , 1988, Pediatric Research.

[67]  H. Sakata,et al.  The effect of antimicrobial agents on fecal flora of children , 1986, Antimicrobial Agents and Chemotherapy.

[68]  H. Iwahashi,et al.  Enzymatic proof for the identity of the S-sulfocysteine synthase and cysteine synthase B of Salmonella typhimurium , 1984, Journal of bacteriology.