A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing

(2020) Farnaz Fouladi et al.   ENVIRONMENT INTERNATIONAL

Exposure to air pollutants and the gut microbiota: a potential link between exposure, obesity, and type 2 diabetes

(2020) Maximillian J. Bailey et al.   Gut Microbes

When possible, report a Fisher-exactPvalue and display its underlying null randomization distribution

(2020) M.-A. C. Bind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

(2020) David A. Hughes et al.   Nature Microbiology

Evaluating the impact of long-term exposure to fine particulate matter on mortality among the elderly

(2020) X. Wu et al.   Science Advances

A Guide to Diet-Microbiome Study Design

(2020) Abigail J. Johnson et al.   Frontiers in Nutrition

Moving to a World Beyond “p 

(2019) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data

(2019) Chan Wang et al.   BIOINFORMATICS

Smoking and microbiome in oral, airway, gut and some systemic diseases

(2019) Chunrong Huang et al.   Journal of Translational Medicine

Interplay between the human gut microbiome and host metabolism

(2019) Alessia Visconti et al.   Nature Communications

Relationship between gut microbiota and circulating metabolites in population-based cohorts

(2019) Dina Vojinovic et al.   Nature Communications

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome

(2018) Ece A. Mutlu et al.   ENVIRONMENTAL POLLUTION

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents

(2018) Tanya L. Alderete et al.   ENVIRONMENTAL RESEARCH

Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model

(2018) Wanjun Wang et al.   Particle and Fibre Toxicology

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

(2018) Yan He et al.   Microbiome

Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study

(2018) Su Hwan Lee et al.   Journal of Clinical Medicine

The Rotterdam Study: 2018 update on objectives, design and main results

(2017) M. Arfan Ikram et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Influence of diet on the gut microbiome and implications for human health

(2017) Rasnik K. Singh et al.   Journal of Translational Medicine

Bridging observational studies and randomized experiments by embedding the former in the latter

(2017) Marie-Abele C Bind et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

The ASA's Statement onp-Values: Context, Process, and Purpose

(2016) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

(2016) Amy Langdon et al.   Genome Medicine

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test

(2015) Ni Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Estimating diversity via frequency ratios

(2015) Amy Willis et al.   BIOMETRICS

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood LipidsNovelty and Significance

(2015) Jingyuan Fu et al.   CIRCULATION RESEARCH

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Cohort Profile: LifeLines, a three-generation cohort study and biobank

(2014) Salome Scholtens et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Smoking Cessation Induces Profound Changes in the Composition of the Intestinal Microbiota in Humans

(2013) Luc Biedermann et al.   PLoS One

Environmental Particulate Matter Induces Murine Intestinal Inflammatory Responses and Alters the Gut Microbiome

(2013) Lisa Kish et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Air pollution and mortality from diabetes mellitus

(2012) Annette Peters   Nature Reviews Endocrinology

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Active Smoking and Risk of Metabolic Syndrome: A Meta-Analysis of Prospective Studies

(2012) Kan Sun et al.   PLoS One

Non-Specific Abdominal Pain and Air Pollution: A Novel Association

(2012) Gilaad G. Kaplan et al.   PLoS One

Smokers with active Crohnʼs disease have a clinically relevant dysbiosis of the gastrointestinal microbiota*

(2011) Jane L. Benjamin et al.   INFLAMMATORY BOWEL DISEASES

Health effects of particulate air pollution: A review of epidemiological evidence

(2011) Regina Rückerl et al.   INHALATION TOXICOLOGY

Air pollution: An environmental factor contributing to intestinal disease

(2011) Leigh A. Beamish et al.   Journal of Crohns & Colitis

Particulate matter air pollution causes oxidant-mediated increase in gut permeability in mice

(2011) Ece A Mutlu et al.   Particle and Fibre Toxicology

Ambient air pollution correlates with hospitalizations for inflammatory bowel disease

(2010) Ashwin N. Ananthakrishnan et al.   INFLAMMATORY BOWEL DISEASES

Effect of ambient air pollution on the incidence of appendicitis

(2009) G. G. Kaplan et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

For objective causal inference, design trumps analysis

(2008) Donald B. Rubin   Annals of Applied Statistics