4.7 Review

Analyzing the Human Microbiome: A How To guide for Physicians

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Diet rapidly and reproducibly alters the human gut microbiome

Lawrence A. David et al.

NATURE (2014)

Article Microbiology

Diet, the human gut microbiota, and IBD

Gary D. Wu et al.

ANAEROBE (2013)

Article Multidisciplinary Sciences

The Long-Term Stability of the Human Gut Microbiota

Jeremiah J. Faith et al.

SCIENCE (2013)

Review Genetics & Heredity

Biodiversity and functional genomics in the human microbiome

Xochitl C. Morgan et al.

TRENDS IN GENETICS (2013)

Review Biochemistry & Molecular Biology

Immunoregulation by the gut microbiota

Junko Nishio et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2012)

Review Immunology

The yin yang of bacterial polysaccharides: lessons learned from B. fragilis PSA

Neeraj K. Surana et al.

IMMUNOLOGICAL REVIEWS (2012)

Article Ecology

Host genetic and environmental effects on mouse intestinal microbiota

James H. Campbell et al.

ISME JOURNAL (2012)

Article Gastroenterology & Hepatology

Distinct Gut Microbiota in Southeastern African and Northern European Infants

Lukasz Grzeskowiak et al.

JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION (2012)

Article Multidisciplinary Sciences

A framework for human microbiome research

Barbara A. Methe et al.

NATURE (2012)

Article Multidisciplinary Sciences

Gut microbiota composition correlates with diet and health in the elderly

Marcus J. Claesson et al.

NATURE (2012)

Article Multidisciplinary Sciences

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower et al.

NATURE (2012)

Review Gastroenterology & Hepatology

The gut microbiota in IBD

Chaysavanh Manichanh et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2012)

Article Multidisciplinary Sciences

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

Ian Holmes et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing

Kathleen Sim et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

Doyle V. Ward et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

Susan M. Huse et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Succession in the Gut Microbiome following Antibiotic and Antibody Therapies for Clostridium difficile

Gregory L. Peterfreund et al.

PLOS ONE (2012)

Article Biochemical Research Methods

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

Steven W. Kembel et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Xochitl C. Morgan et al.

GENOME BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

Patrick D. Schloss et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biochemical Research Methods

UCHIME improves sensitivity and speed of chimera detection

Robert C. Edgar et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Andre Gilles et al.

BMC GENOMICS (2011)

Article Gastroenterology & Hepatology

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

Patricia Lepage et al.

GASTROENTEROLOGY (2011)

Article Biochemistry & Molecular Biology

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Brian J. Haas et al.

GENOME RESEARCH (2011)

Article Gastroenterology & Hepatology

Disease Phenotype and Genotype Are Associated with Shifts in Intestinal-associated Microbiota in Inflammatory Bowel Diseases

Daniel N. Frank et al.

INFLAMMATORY BOWEL DISEASES (2011)

Article Biochemical Research Methods

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Minseok Kim et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2011)

Article Multidisciplinary Sciences

Enterotypes of the human gut microbiome

Manimozhiyan Arumugam et al.

NATURE (2011)

Article Multidisciplinary Sciences

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

Patrick D. Schloss et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

Les Dethlefsen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

Philipp Rausch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

Koji Atarashi et al.

SCIENCE (2011)

Article Multidisciplinary Sciences

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

Gary D. Wu et al.

SCIENCE (2011)

Article Multidisciplinary Sciences

Bacterial biogeography of the human digestive tract

Jennifer C. Stearns et al.

SCIENTIFIC REPORTS (2011)

Article Biotechnology & Applied Microbiology

Moving pictures of the human microbiome

J. Gregory Caporaso et al.

GENOME BIOLOGY (2011)

Article Multidisciplinary Sciences

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin et al.

NATURE (2010)

Letter Biochemical Research Methods

QIIME allows analysis of high-throughput community sequencing data

J. Gregory Caporaso et al.

NATURE METHODS (2010)

Article Multidisciplinary Sciences

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

Nadja Larsen et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Carlotta De Filippo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Maria G. Dominguez-Bello et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biotechnology & Applied Microbiology

Optimized Method for Preparation of DNA from Pathogenic and Environmental Mycobacteria

Michael Kaeser et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Pyrosequencing of the Chaperonin-60 Universal Target as a Tool for Determining Microbial Community Composition

John Schellenberg et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Gastroenterology & Hepatology

Twin Studies Reveal Specific Imbalances in the Mucosa-associated Microbiota of Patients with Ileal Crohn's Disease

Ben Willing et al.

INFLAMMATORY BOWEL DISEASES (2009)

Article Neurosciences

The core gut microbiome, energy balance and obesity

Peter J. Turnbaugh et al.

JOURNAL OF PHYSIOLOGY-LONDON (2009)

Article Multidisciplinary Sciences

A core gut microbiome in obese and lean twins

Peter J. Turnbaugh et al.

NATURE (2009)

Article Multidisciplinary Sciences

Bacterial Community Variation in Human Body Habitats Across Space and Time

Elizabeth K. Costello et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Functional metagenomic profiling of nine biomes

Elizabeth A. Dinsdale et al.

NATURE (2008)

Article Biochemistry & Molecular Biology

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Zongzhi Liu et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Multidisciplinary Sciences

Evolution of mammals and their gut microbes

Ruth E. Ley et al.

SCIENCE (2008)

Article Biotechnology & Applied Microbiology

DNA extraction method affects microbial community profiles from soils and sediment

Cora Carrigg et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2007)

Article Multidisciplinary Sciences

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Daniel N. Frank et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Evolution of symbiotic bacteria in the distal human intestine

Jian Xu et al.

PLOS BIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

Catherine A. Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity

DE Hunt et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Article Biotechnology & Applied Microbiology

At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies

KE Ashelford et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)

Article Multidisciplinary Sciences

Diversity of the human intestinal microbial flora

PB Eckburg et al.

SCIENCE (2005)

Article Biochemical Research Methods

A comparison of five methods for extraction of bacterial DNA from human faecal samples

AL McOrist et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2002)

Article Zoology

Themes from variation: Probing the commonalities of symbiotic associations

MB Saffo

INTEGRATIVE AND COMPARATIVE BIOLOGY (2002)

Article Biochemical Research Methods

DNA sequence quality trimming and vector removal

HH Chou et al.

BIOINFORMATICS (2001)