Microbial strain-level population structure and genetic diversity from metagenomes

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

(2016) Peter Spanogiannopoulos et al.   NATURE REVIEWS MICROBIOLOGY

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

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

Exploring Vertical Transmission of Bifidobacteria from Mother to Child

(2015) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

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

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

(2015) Tali Raveh-Sadka et al.   eLife

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

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

(2014) Michael Imelfort et al.   PeerJ

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

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

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

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Modulating the innate immune response by combinatorial engineering of endotoxin

(2013) Brittany D. Needham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

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

Pathogenesis of Helicobacter pylori Infection

(2012) Robin M. Delahay et al.   HELICOBACTER

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

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori

(2011) Rumiko Suzuki et al.   INFECTION GENETICS AND EVOLUTION

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

(2011) Martina Bielaszewska et al.   LANCET INFECTIOUS DISEASES

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

(2011) Peter A. Bron et al.   NATURE REVIEWS MICROBIOLOGY

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

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

Persistence, Replacement, and Rapid Clonal Expansion of Meningococcal Carriage Isolates in a 2008 University Student Cohort

(2010) F. A. Bidmos et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) M. Hamady et al.   GENOME RESEARCH

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives

(2008) Mogens Kilian et al.   PLoS One

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA