Systems biology perspective for studying the gut microbiota in human physiology and liver diseases

[1]  J. Nielsen,et al.  Defining the human adipose tissue proteome to reveal metabolic alterations in obesity. , 2014, Journal of proteome research.

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

[3]  Luke R. Thompson,et al.  Best practices for analysing microbiomes , 2018, Nature Reviews Microbiology.

[4]  Lanjuan Li,et al.  Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma , 2018, Gut.

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

[6]  Lanjuan Li,et al.  Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study , 2018, Front. Microbiol..

[7]  Marju Orho-Melander,et al.  The gut microbiome as a target for prevention and treatment of hyperglycaemia in type 2 diabetes: from current human evidence to future possibilities , 2017, Diabetologia.

[8]  Lawrence A. David,et al.  The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota , 2016, Hepatology.

[9]  P. Gérard,et al.  The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD) , 2019, Cellular and Molecular Life Sciences.

[10]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[11]  Wei Jia,et al.  Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis , 2018, Nature Reviews Gastroenterology & Hepatology.

[12]  Jens Nielsen,et al.  Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD , 2017, Molecular systems biology.

[13]  Jens Nielsen,et al.  An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans. , 2018, Cell metabolism.

[14]  R. Schwabe,et al.  The gut microbiome and liver cancer: mechanisms and clinical translation , 2017, Nature Reviews Gastroenterology &Hepatology.

[15]  Eddy J. Bautista,et al.  Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. , 2018, Cell systems.

[16]  J. Nielsen,et al.  Systems biology in hepatology: approaches and applications , 2018, Nature Reviews Gastroenterology & Hepatology.

[17]  P. Paci,et al.  Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta‐omics‐based approach , 2017, Hepatology.

[18]  Andmorgan R. Fisher,et al.  Altered profile of human gut microbiome is associated with cirrhosis and its complications. , 2014, Journal of hepatology.

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

[20]  Ines Thiele,et al.  Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico , 2015, Applied and Environmental Microbiology.

[21]  J. Bajaj Alcohol, liver disease and the gut microbiota , 2019, Nature Reviews Gastroenterology & Hepatology.

[22]  Justine W. Debelius,et al.  The gut–liver axis and the intersection with the microbiome , 2018, Nature Reviews Gastroenterology & Hepatology.

[23]  E. Ferrannini,et al.  The diabetes pandemic and associated infections: suggestions for clinical microbiology , 2018, Reviews in medical microbiology : a journal of the Pathological Society of Great Britain and Ireland.

[24]  S. Rabot,et al.  Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice , 2012, Gut.

[25]  Nicholas Chia,et al.  MMinte: an application for predicting metabolic interactions among the microbial species in a community , 2016, BMC Bioinformatics.

[26]  Caroline H. Johnson,et al.  Metabolomics: beyond biomarkers and towards mechanisms , 2016, Nature Reviews Molecular Cell Biology.

[27]  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.

[28]  M. Doebeli,et al.  Calibration and analysis of genome-based models for microbial ecology , 2015, eLife.

[29]  J. Raes,et al.  Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults , 2016, PloS one.

[30]  Ali R. Zomorrodi,et al.  d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. , 2014, ACS synthetic biology.

[31]  M. Uhlén,et al.  Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling , 2018, Front. Physiol..

[32]  S. Sarin,et al.  Microbiome as a therapeutic target in alcohol-related liver disease. , 2019, Journal of hepatology.

[33]  M. Simon,et al.  Microbial Regulation of Glucose Metabolism and Insulin Resistance , 2017, Genes.

[34]  E. Balskus,et al.  Exploring and Understanding the Biochemical Diversity of the Human Microbiota. , 2016, Cell chemical biology.

[35]  Xuan-xian Peng,et al.  Functional metabolomics: from biomarker discovery to metabolome reprogramming , 2015, Protein & Cell.

[36]  Beatriz García Jiménez,et al.  FLYCOP: metabolic modeling-based analysis and engineering microbial communities , 2018, Bioinform..

[37]  Eran Elinav,et al.  Use of Metatranscriptomics in Microbiome Research , 2016, Bioinformatics and biology insights.

[38]  J. Nielsen,et al.  Predicting growth of the healthy infant using a genome scale metabolic model , 2017, npj Systems Biology and Applications.

[39]  A. Gasbarrini,et al.  Hepatocellular Carcinoma Is Associated With Gut Microbiota Profile and Inflammation in Nonalcoholic Fatty Liver Disease , 2018, Hepatology.

[40]  K. Rioux,et al.  Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol , 2015, BMC Gastroenterology.

[41]  J. Bajaj,et al.  Microbiota, cirrhosis, and the emerging oral-gut-liver axis. , 2017, JCI insight.

[42]  Cheng Zhang,et al.  Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine , 2016, Front. Physiol..

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

[44]  Nicholas Chia,et al.  Microbiome at the Frontier of Personalized Medicine , 2017, Mayo Clinic proceedings.

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

[46]  Nichole Reisdorph,et al.  Microbiome and metabolome data integration provides insight into health and disease. , 2017, Translational research : the journal of laboratory and clinical medicine.

[47]  R. Gan,et al.  Gut Microbiota’s Relationship with Liver Disease and Role in Hepatoprotection by Dietary Natural Products and Probiotics , 2018, Nutrients.

[48]  W. Liao,et al.  Influence of diet on the gut microbiome and implications for human health , 2017, Journal of Translational Medicine.

[49]  D. Ciocan,et al.  Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis , 2018, Scientific Reports.

[50]  Wataru Iwasaki,et al.  Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond , 2016, Microbes and environments.

[51]  M. Heikenwalder,et al.  The Liver at the Nexus of Host-Microbial Interactions. , 2016, Cell host & microbe.

[52]  John C. Earls,et al.  A wellness study of 108 individuals using personal, dense, dynamic data clouds , 2017, Nature Biotechnology.

[53]  Stephen T. C. Wong,et al.  Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction , 2019, Bioinform..

[54]  J. Nicholson,et al.  Impact of the gut microbiota on inflammation, obesity, and metabolic disease , 2016, Genome Medicine.

[55]  Jos Boekhorst,et al.  A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets , 2013, BMC Genomics.

[56]  L. Hood,et al.  A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory. , 2012, New biotechnology.

[57]  F. Bäckhed,et al.  Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks , 2018, Proceedings of the National Academy of Sciences.

[58]  W. Si,et al.  Histopathological Features and Composition of Gut Microbiota in Rhesus Monkey of Alcoholic Liver Disease , 2019, Front. Microbiol..

[59]  M. Marco,et al.  Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. , 2016, The Journal of nutrition.

[60]  Daniel Segrè,et al.  Synthetic Ecology of Microbes: Mathematical Models and Applications. , 2016, Journal of molecular biology.

[61]  Partho Sen,et al.  Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. , 2015, Cell metabolism.

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

[63]  Jens Nielsen,et al.  The gut microbiota modulates host amino acid and glutathione metabolism in mice , 2015 .

[64]  Timothy J. Hanly,et al.  Dynamic flux balance modeling of microbial co‐cultures for efficient batch fermentation of glucose and xylose mixtures , 2011, Biotechnology and bioengineering.

[65]  H. Tilg,et al.  Liver-Microbiome Axis in Health and Disease. , 2018, Trends in immunology.

[66]  Shibu Yooseph,et al.  Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. , 2017, Cell metabolism.

[67]  Junhua Li,et al.  Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children , 2019, Microbiome.

[68]  K. Venema,et al.  Gut microbial metabolites in obesity, NAFLD and T2DM , 2019, Nature Reviews Endocrinology.

[69]  Alex H. Lang,et al.  Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. , 2014, Cell reports.

[70]  Oskar Hallatschek,et al.  Evolutionary dynamics of bacteria in the gut microbiome within and across hosts , 2018, bioRxiv.

[71]  F. Bäckhed,et al.  Diet–microbiota interactions as moderators of human metabolism , 2016, Nature.

[72]  J. Schattenberg,et al.  Insulin resistance alters hepatic ethanol metabolism: studies in mice and children with non-alcoholic fatty liver disease , 2015, Gut.

[73]  F. Bruggeman,et al.  Community Flux Balance Analysis for Microbial Consortia at Balanced Growth , 2013, PloS one.

[74]  Barbara M. Bakker,et al.  The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism , 2013, Journal of Lipid Research.

[75]  Intawat Nookaew,et al.  Understanding the interactions between bacteria in the human gut through metabolic modeling , 2013, Scientific Reports.

[76]  A. Goodman,et al.  Mapping human microbiome drug metabolism by gut bacteria and their genes , 2019, Nature.

[77]  K. Zengler,et al.  Elucidation of complexity and prediction of interactions in microbial communities , 2017, Microbial biotechnology.

[78]  J. Mohammadnejad,et al.  A Systems Biology Approach to Understanding Alcoholic Liver Disease Molecular Mechanism: The Development of Static and Dynamic Models , 2017, Bulletin of Mathematical Biology.

[79]  N. Lundbom,et al.  Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome , 2018, Scientific Reports.

[80]  Intawat Nookaew,et al.  Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction , 2014, BMC Systems Biology.

[81]  Dmitry S. Ischenko,et al.  Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease , 2017, Microbiome.

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

[83]  Radhakrishnan Mahadevan,et al.  Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments , 2011, The ISME Journal.

[84]  T. Dinan,et al.  Friends with social benefits: host-microbe interactions as a driver of brain evolution and development? , 2014, Front. Cell. Infect. Microbiol..

[85]  Costas D. Maranas,et al.  OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities , 2012, PLoS Comput. Biol..

[86]  Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish , 2019, Scientific Reports.

[87]  W. Liu,et al.  Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach , 2013, BMC Gastroenterology.

[88]  Miguel Pignatelli,et al.  Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota , 2011, PloS one.

[89]  L. Henry,et al.  Global epidemiology of nonalcoholic fatty liver disease—Meta‐analytic assessment of prevalence, incidence, and outcomes , 2016, Hepatology.

[90]  H. Flint,et al.  Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis. , 2015, FEMS microbiology letters.

[91]  Yongzhong Zhao,et al.  Gut microbiota derived metabolites in cardiovascular health and disease , 2018, Protein & Cell.

[92]  C. Lynch,et al.  Branched-chain amino acids in metabolic signalling and insulin resistance , 2014, Nature Reviews Endocrinology.

[93]  Eran Segal,et al.  Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples , 2015, Science.

[94]  Chongle Pan,et al.  Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota , 2015, Proteomics.

[95]  A. Heintz‐Buschart,et al.  Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes , 2016, Nature Microbiology.