Potential and active functions in the gut microbiota of a healthy human cohort

Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse

(2017) Alessandro Tanca et al.   Frontiers in Microbiology

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

Microbiota-Produced Succinate Improves Glucose Homeostasis via Intestinal Gluconeogenesis

(2016) Filipe De Vadder et al.   Cell Metabolism

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

(2016) Kenichiro Takahashi et al.   DIGESTION

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

(2016) Thilo Muth et al.   Expert Review of Proteomics

Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease

(2016) Darrell W. Cockburn et al.   JOURNAL OF MOLECULAR BIOLOGY

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Bifidobacteria and Their Role as Members of the Human Gut Microbiota

(2016) Amy O'Callaghan et al.   Frontiers in Microbiology

The Neuro-endocrinological Role of Microbial Glutamate and GABA Signaling

(2016) Roberto Mazzoli et al.   Frontiers in Microbiology

The impact of sequence database choice on metaproteomic results in gut microbiota studies

(2016) Alessandro Tanca et al.   Microbiome

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults

(2016) Carolin A. Kolmeder et al.   PLoS One

Aguamiel concentrate from Agave salmiana and its extracted saponins attenuated obesity and hepatic steatosis and increased Akkermansia muciniphila in C57BL6 mice

(2016) Ana María Leal-Díaz et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella

(2015) Petia Kovatcheva-Datchary et al.   Cell Metabolism

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Dietary Polyphenols Promote Growth of the Gut BacteriumAkkermansia muciniphilaand Attenuate High-Fat Diet–Induced Metabolic Syndrome

(2015) Diana E. Roopchand et al.   DIABETES

Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

(2015) Maria Carlota Dao et al.   GUT

Fitness Trade-Offs Determine the Role of the Molecular Chaperonin GroEL in Buffering Mutations

(2015) Beatriz Sabater-Muñoz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

(2015) Carlo Sidore et al.   NATURE GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

(2015) Alessandro Tanca et al.   PROTEOMICS

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities

(2015) Andrew Dopheide et al.   PLoS One

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

BoxPlotR: a web tool for generation of box plots

(2014) Michaela Spitzer et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis

(2014) Rafael Tojo   WORLD JOURNAL OF GASTROENTEROLOGY

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Is butyrate the link between diet, intestinal microbiota and obesity-related metabolic diseases?

(2013) L. K. Brahe et al.   Obesity Reviews

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of theEscherichia coliproteome

(2013) Alessandro Tanca et al.   PROTEOMICS

Butyrate

(2012) Alda J. Leonel et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

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

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

(2012) A. R. Fernie et al.   PLANT PHYSIOLOGY

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Extracellular Superoxide Dismutase Protects Histoplasma Yeast Cells from Host-Derived Oxidative Stress

(2012) Brian H. Youseff et al.   PLoS Pathogens

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Assessing Significance in High-Throughput Experiments by Sequential Goodness of Fit and q-Value Estimation

(2011) Antonio Carvajal-Rodriguez et al.   PLoS One

Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments

(2011) Brandi L. Cantarel et al.   PLoS One

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Functional analysis of natural microbial consortia using community proteomics

(2009) Nathan C. VerBerkmoes et al.   NATURE REVIEWS MICROBIOLOGY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal