Shotgun metagenomics, from sampling to analysis

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

(2017) Daniel H. Huson et al.   Microbiome

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Microbiology: the road to strain-level identification

(2016) Vivien Marx   NATURE METHODS

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing

(2016) Claudio Donati et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

The Theory and Practice of Genome Sequence Assembly

(2015) Jared T. Simpson et al.   Annual Review of Genomics and Human Genetics

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Jason M. Norman et al.   CELL

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification

(2015) Alexander J. Probst et al.   PLoS One

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents

(2014) S Motley et al.   BMC GENOMICS

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

(2014) J. D. O'Brien et al.   GENETICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections

(2014) L. Cuthbertson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh 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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Olfactory exposure to males, including men, causes stress and related analgesia in rodents

(2014) Robert E Sorge et al.   NATURE METHODS

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

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome

(2014) Hannah Lees et al.   PLoS One

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Phylogeny, culturing, and metagenomics of the human gut microbiota

(2014) Alan W. Walker et al.   TRENDS IN MICROBIOLOGY

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

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

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Meta-analyses of studies of the human microbiota

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

Two-stage microbial community experimental design

(2013) Timothy L Tickle et al.   ISME Journal

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

(2013) Jonathan McCafferty et al.   ISME Journal

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier 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

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA

(2013) Helena M B Seth-Smith et al.   Nature Protocols

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust 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

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture

(2011) Bethany N. Kent et al.   Genome Biology and Evolution

Integrative analysis of environmental sequences using MEGAN4

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

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations

(2010) Suzan Yilmaz et al.   ISME Journal

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME BIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

ARDB--Antibiotic Resistance Genes Database

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