Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism

(2015) Sang Sun Yoon et al.   CURRENT OPINION IN MICROBIOLOGY

The gut microbiome and diet in psychiatry

(2015) Sarah Dash et al.   CURRENT OPINION IN PSYCHIATRY

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy

(2015) Jasmohan S. Bajaj et al.   HEPATOLOGY

Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria

(2015) Weiwei Wang et al.   INFLAMMATORY BOWEL DISEASES

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities

(2015) Sandi Yen et al.   JOURNAL OF PROTEOME RESEARCH

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

(2015) Samuel C. Forster et al.   NUCLEIC ACIDS RESEARCH

Role of the Gut Microbiome in Obesity and Diabetes Mellitus

(2015) Gillian M. Barlow et al.   NUTRITION IN CLINICAL PRACTICE

Where Next for Microbiome Research?

(2015) Matthew K. Waldor et al.   PLOS BIOLOGY

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Commentary on: “A common origin for immunity and digestion”

(2015) Gustav van Niekerk et al.   Frontiers in Microbiology

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Advancing the Microbiome Research Community

(2014) Curtis Huttenhower et al.   CELL

Determining Microbial Products and Identifying Molecular Targets in the Human Microbiome

(2014) Regina Joice et al.   Cell Metabolism

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes

(2014) Annick V. Hartstra et al.   DIABETES CARE

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

(2014) Jason M. Norman et al.   GASTROENTEROLOGY

Meta'omic Analytic Techniques for Studying the Intestinal Microbiome

(2014) Xochitl C. Morgan et al.   GASTROENTEROLOGY

Inflammatory Bowel Disease as a Model for Translating the Microbiome

(2014) Curtis Huttenhower et al.   IMMUNITY

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Genomics of schizophrenia: time to consider the gut microbiome?

(2014) T G Dinan et al.   MOLECULAR PSYCHIATRY

Strain/species identification in metagenomes using genome-specific markers

(2014) Qichao Tu et al.   NUCLEIC ACIDS RESEARCH

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence 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

Obesity, fatty liver disease and intestinal microbiota

(2014) Nur Arslan   WORLD JOURNAL OF GASTROENTEROLOGY

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

(2014) M. Vital et al.   mBio

The role of metagenomics in understanding the human microbiome in health and disease

(2014) Rebeca Martín et al.   Virulence

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Kefir: A Multifaceted Fermented Dairy Product

(2014) Barbara Nielsen et al.   Probiotics and Antimicrobial Proteins

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

(2013) Jianjun Wang et al.   ISME Journal

Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea

(2013) V. C. Antharam et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Translating the human microbiome

(2013) James Brown et al.   NATURE BIOTECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Commensal bacteria at the interface of host metabolism and the immune system

(2013) Jonathan R Brestoff et al.   NATURE IMMUNOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Alzheimer's disease and the microbiome

(2013) Surjyadipta Bhattacharjee et al.   Frontiers in Cellular Neuroscience

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

How much metagenomic sequencing is enough to achieve a given goal?

(2013) Jiajia Ni et al.   Scientific Reports

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection

(2013) Caroline Vincent et al.   Microbiome

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

(2012) Fabien Leprieur et al.   PLoS One

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Bioinformatics for the Human Microbiome Project

(2012) Dirk Gevers et al.   PLoS Computational Biology

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

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

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

Regulation of Homeostasis and Inflammation in the Intestine

(2011) Thomas T. MacDonald et al.   GASTROENTEROLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

The evolution of Pyrosequencing® for microbiology: From genes to genomes

(2011) R.C. Novais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity

(2010) Hanna Tuomisto   ECOGRAPHY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Diet-Induced Metabolic Improvements in a Hamster Model of Hypercholesterolemia Are Strongly Linked to Alterations of the Gut Microbiota

(2009) I. Martinez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

The core gut microbiome, energy balance and obesity

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

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

(2008) Patrick D Schloss et al.   BMC BIOINFORMATICS

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

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

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY