Application of metagenomics in the human gut microbiome

Geographical variation of human gut microbial composition

(2014) T. A. Suzuki et al.   Biology Letters

Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease

(2014) Ernst Holler et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Non-invasive fecal metabonomic detection of colorectal cancer

(2014) Lee Cheng Phua et al.   CANCER BIOLOGY & THERAPY

Obesity and Cancer: A Gut Microbial Connection

(2014) N. Ohtani et al.   CANCER RESEARCH

Aberrant gut microbiota composition at the onset of type 1 diabetes in young children

(2014) Marcus C. de Goffau et al.   DIABETOLOGIA

The Gut Microbiome in Health and Disease

(2014) Chung Owyang et al.   GASTROENTEROLOGY

Microbiota and diabetes: an evolving relationship

(2014) Herbert Tilg et al.   GUT

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

Gut Microbiome, Obesity-Related Comorbidities, and Low-Grade Chronic Inflammation

(2014) Giovanni Tarantino   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Minireview: Gut Microbiota: The Neglected Endocrine Organ

(2014) Gerard Clarke et al.   MOLECULAR ENDOCRINOLOGY

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Understanding gut microbiota in new-onset Crohn's disease

(2014) Katrina Ray   Nature Reviews Gastroenterology & Hepatology

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combination of Metagenomics and Culture-Based Methods to Study the Interaction Between Ochratoxin A and Gut Microbiota

(2014) Mingzhang Guo et al.   TOXICOLOGICAL SCIENCES

Overgrowth of the indigenous gut microbiome and irritable bowel syndrome

(2014) William Bye   WORLD JOURNAL OF GASTROENTEROLOGY

Inflammation and colorectal cancer, when microbiota-host mutualism breaks

(2014) Marco Candela   WORLD JOURNAL OF GASTROENTEROLOGY

Role of gut microbiota and Toll-like receptors in nonalcoholic fatty liver disease

(2014) Kouichi Miura   WORLD JOURNAL OF GASTROENTEROLOGY

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome

(2014) Eamonn P. Culligan et al.   Frontiers in Microbiology

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

(2014) Mihai Pop et al.   GENOME BIOLOGY

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans

(2013) Junhai Ou et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach

(2013) Xiao Wei et al.   BMC GASTROENTEROLOGY

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing

(2013) Suparna Mitra et al.   BMC GENOMICS

Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

(2013) Tao Wu et al.   BMC GENOMICS

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Low gut microbiota diversity in early infancy precedes asthma at school age

(2013) T. R. Abrahamsson et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Human intestinal metagenomics: state of the art and future

(2013) Hervé M Blottière et al.   CURRENT OPINION IN MICROBIOLOGY

Rifaximin Alters Intestinal Bacteria and Prevents Stress-Induced Gut Inflammation and Visceral Hyperalgesia in Rats

(2013) Dabo Xu et al.   GASTROENTEROLOGY

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

(2013) Sunghee Lee et al.   ISME Journal

Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity

(2013) Anne Vrieze et al.   JOURNAL OF HEPATOLOGY

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches

(2013) Aya Brown Kav et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The Gut Microbiome, Kidney Disease, and Targeted Interventions

(2013) A. Ramezani et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Human Gut Microbiome and Risk for Colorectal Cancer

(2013) Jiyoung Ahn et al.   JNCI-Journal of the National Cancer Institute

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The gut microbiota manages host metabolism

(2013) Patrice D. Cani   Nature Reviews Endocrinology

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

The microbiome explored: recent insights and future challenges

(2013) Martin Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Your gut microbiota are what you eat

(2013) Claire Chewapreecha   NATURE REVIEWS MICROBIOLOGY

The gut–microbiome–brain connection

(2013) Monica Hoyos Flight   NATURE REVIEWS NEUROSCIENCE

High-Throughput System for the Presentation of Secreted and Surface-Exposed Proteins from Gram-Positive Bacteria in Functional Metagenomics Studies

(2013) Dragana Dobrijevic et al.   PLoS One

Microbiome Analysis of Stool Samples from African Americans with Colon Polyps

(2013) Hassan Brim et al.   PLoS One

Liver Ischemic Preconditioning (IPC) Improves Intestinal Microbiota Following Liver Transplantation in Rats through 16s rDNA-Based Analysis of Microbial Structure Shift

(2013) Zhigang Ren et al.   PLoS One

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

(2013) Aimée M. Moore et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Microbiota impact on the epigenetic regulation of colorectal cancer

(2013) Tao Yang et al.   TRENDS IN MOLECULAR MEDICINE

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion

(2012) Gong Cheng et al.   FEMS MICROBIOLOGY LETTERS

A metagenomic insight into our gut's microbiome

(2012) Patricia Lepage et al.   GUT

Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH

(2012) Lixin Zhu et al.   HEPATOLOGY

A framework for human microbiome research

(2012)   NATURE

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Reciprocal interactions of the intestinal microbiota and immune system

(2012) Craig L. Maynard et al.   NATURE

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome

(2012) I. M. Carroll et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Ageing and gut microbes: Perspectives for health maintenance and longevity

(2012) Elena Biagi et al.   PHARMACOLOGICAL RESEARCH

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

(2012) Dirk Gevers et al.   PLOS BIOLOGY

Characterization of fecal microbial communities in patients with liver cirrhosis

(2011) Yanfei Chen et al.   HEPATOLOGY

Low diversity of the gut microbiota in infants with atopic eczema

(2011) Thomas R. Abrahamsson et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Identification of NF-κB Modulation Capabilities within Human Intestinal Commensal Bacteria

(2011) Omar Lakhdari et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Metabolomics of Fecal Extracts Detects Altered Metabolic Activity of Gut Microbiota in Ulcerative Colitis and Irritable Bowel Syndrome

(2011) Gwénaëlle Le Gall et al.   JOURNAL OF PROTEOME RESEARCH

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes

(2010) Peter J. Turnbaugh et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The intestinal microbiota in inflammatory bowel diseases: time to connect with the host

(2010) Harry Sokol et al.   CURRENT OPINION IN GASTROENTEROLOGY

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

(2010) L. Tasse et al.   GENOME RESEARCH

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Functional Metagenomics: A High Throughput Screening Method to Decipher Microbiota-Driven NF-κB Modulation in the Human Gut

(2010) Omar Lakhdari et al.   PLoS One

A metagenomic  -glucuronidase uncovers a core adaptive function of the human intestinal microbiome

(2010) K. Gloux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea

(2010) Kathrin Endt et al.   PLoS Pathogens

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

(2009) Luen-Luen Li et al.   Biotechnology for Biofuels

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

Distribution of Tetracycline and Erythromycin Resistance Genes Among Human Oral and Fecal Metagenomic DNA

(2009) Lorna A. Seville et al.   Microbial Drug Resistance

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

(2008) B. V. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA