A predictive index for health status using species-level gut microbiome profiling

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample

(2020) Sarah L. Hagerty et al.   PLoS One

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level

(2020) Douglas J. Kenny et al.   Cell Host & Microbe

Toward unrestricted use of public genomic data

(2019) Rudolf I. Amann et al.   SCIENCE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Health, ecology and the microbiome

(2019) S Andrew Inkpen   eLife

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

(2019) Courtney R. Armour et al.   mSystems

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions

(2019) Michael I McBurney et al.   JOURNAL OF NUTRITION

The internationalization of human microbiome research

(2019) Ana Maria Porras et al.   CURRENT OPINION IN MICROBIOLOGY

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction

(2018) Youlian Zhou et al.   mSystems

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

On the Road to Strain-Resolved Comparative Metagenomics

(2018) Nicola Segata   mSystems

From hype to reality: data science enabling personalized medicine

(2018) Holger Fröhlich et al.   BMC Medicine

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

(2018) Celeste Allaband et al.   Clinical Gastroenterology and Hepatology

Clinician Guide to Microbiome Testing

(2018) Christopher Staley et al.   DIGESTIVE DISEASES AND SCIENCES

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Emerging evidence linking the gut microbiome to neurologic disorders

(2018) Jessica A. Griffiths et al.   Genome Medicine

The gut microbiota and psychiatric illness

(2017) Glenda MacQueen et al.   JOURNAL OF PSYCHIATRY & NEUROSCIENCE

Microbiome at the Frontier of Personalized Medicine

(2017) Purna C. Kashyap et al.   MAYO CLINIC PROCEEDINGS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

A wellness study of 108 individuals using personal, dense, dynamic data clouds

(2017) Nathan D Price et al.   NATURE BIOTECHNOLOGY

Human genetic variation and the gut microbiome in disease

(2017) Andrew Brantley Hall et al.   NATURE REVIEWS GENETICS

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(2017) Michael Tessler et al.   Scientific Reports

Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine

(2017) Nicole M. Vega et al.   PLOS BIOLOGY

Power analysis for random-effects meta-analysis

(2017) Dan Jackson et al.   Research Synthesis Methods

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

(2017) Adrian Tett et al.   npj Biofilms and Microbiomes

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

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

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

Alterations of the human gut microbiome in multiple sclerosis

(2016) Sushrut Jangi et al.   Nature Communications

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses

(2015) Vegard Nygaard et al.   BIOSTATISTICS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

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

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Identifying strains that contribute to complex diseases through the study of microbial inheritance

(2015) Jeremiah J. Faith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

(2015) Steven N. Steinway et al.   PLoS Computational Biology

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

(2014) Mariel M. Finucane et al.   PLoS One

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Measuring the Effect of Inter-Study Variability on Estimating Prediction Error

(2014) Shuyi Ma et al.   PLoS One

Diabetes, obesity and gut microbiota

(2013) Amandine Everard et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

From deep sequencing to viral tagging: Recent advances in viral metagenomics

(2013) Dana Willner et al.   BIOESSAYS

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

(2013) Kelvin Li et al.   PLoS One

Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

(2013) Jaeyun Sung et al.   PLoS Computational Biology

Molecular signatures from omics data: From chaos to consensus

(2012) Jaeyun Sung et al.   Biotechnology Journal

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

A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory

(2012) Leroy Hood et al.   New Biotechnology

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

The microbiome and rheumatoid arthritis

(2011) Jose U. Scher et al.   Nature Reviews Rheumatology

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

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology