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

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

(2014) Annika C Mosier et al.   ISME Journal

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

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Intestinal microbiota: A source of novel biomarkers in inflammatory bowel diseases?

(2013) David Berry et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

(2013) Kishori M Konwar et al.   BMC BIOINFORMATICS

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Sewage reflects the distribution of human faecalLachnospiraceae

(2013) Sandra L. McLellan et al.   ENVIRONMENTAL MICROBIOLOGY

Two-stage microbial community experimental design

(2013) Timothy L Tickle et al.   ISME Journal

Computational meta'omics for microbial community studies

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

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

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

(2013) Mads Albertsen 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

Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis

(2013) Robert A Koeth et al.   NATURE MEDICINE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults

(2013) Tiffany L. Weir et al.   PLoS One

Metabolic Proximity in the Order of Colonization of a Microbial Community

(2013) Varun Mazumdar et al.   PLoS One

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

Metabolites Associated with Adaptation of Microorganisms to an Acidophilic, Metal-Rich Environment Identified by Stable-Isotope-Enabled Metabolomics

(2013) A. C. Mosier et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

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

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

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

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

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

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

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

(2012) Harold Tjalsma et al.   NATURE REVIEWS MICROBIOLOGY

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Human-Associated Microbial Signatures: Examining Their Predictive Value

(2011) Dan Knights et al.   Cell Host & Microbe

Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection

(2011) Ethan Gough et al.   CLINICAL INFECTIOUS DISEASES

Microbial Metabolomics

(2011) Jane Tang   CURRENT GENOMICS

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

(2011) A. D. Kostic et al.   GENOME RESEARCH

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Arthur Brady et al.   NATURE METHODS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Towards the Human Colorectal Cancer Microbiome

(2011) Julian R. Marchesi et al.   PLoS One

Exploring the Diversity of Gardnerella vaginalis in the Genitourinary Tract Microbiota of Monogamous Couples Through Subtle Nucleotide Variation

(2011) A. Murat Eren et al.   PLoS One

Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment

(2011) Rima Kaddurah-Daouk et al.   PLoS One

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Association Between Composition of the Human Gastrointestinal Microbiome and Development of Fatty Liver With Choline Deficiency

(2010) Melanie D. Spencer et al.   GASTROENTEROLOGY

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

(2010) R. J. Roberts et al.   NUCLEIC ACIDS RESEARCH

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

(2010) Christopher Y. Park et al.   PLoS Computational Biology

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Obesity and the human microbiome

(2009) Ruth E Ley   CURRENT OPINION IN GASTROENTEROLOGY

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

(2009) M. Hamady et al.   GENOME RESEARCH

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

(2008) Sarah M Sowell et al.   ISME Journal

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

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA