A Guide to Diet-Microbiome Study Design

Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production

(2020) Edward C. Deehan et al.   Cell Host & Microbe

Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles

(2020) Chieh-Chang Chen et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles

(2020) Yali Liang et al.   mSphere

Impact of storage conditions on the human stool metabolome and lipidome: Preserving the most accurate fingerprint

(2020) Margot De Spiegeleer et al.   ANALYTICA CHIMICA ACTA

Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in 4 days: a pilot study

(2020) Chenghao Zhu et al.   NUTRITION RESEARCH

Assessing the Usability of the Automated Self-Administered Dietary Assessment Tool (ASA24) among Low-Income Adults

(2019) Julia Kupis et al.   Nutrients

Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles

(2019) Yun Kit Yeoh et al.   PeerJ

Colonization of the human gut by bovine bacteria present in Parmesan cheese

(2019) Christian Milani et al.   Nature Communications

Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease

(2019) Koichi Kikuchi et al.   Nature Communications

Precision Nutrition and the Microbiome, Part I: Current State of the Science

(2019) Mills et al.   Nutrients

Whole egg consumption compared with yolk-free egg increases the cholesterol efflux capacity of high-density lipoproteins in overweight, postmenopausal women

(2019) Lisa Sawrey-Kubicek et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain: An Inpatient Randomized Controlled Trial of Ad Libitum Food Intake

(2019) Kevin D. Hall et al.   Cell Metabolism

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

(2019) Vayu Maini Rekdal et al.   SCIENCE

An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples?

(2019) Birgit Wassermann et al.   Frontiers in Microbiology

Association of dietary patterns with the gut microbiota in older, community-dwelling men

(2019) James M Shikany et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results

(2019) Riley L Hughes et al.   Advances in Nutrition

Cooking shapes the structure and function of the gut microbiome

(2019) Rachel N. Carmody et al.   Nature Microbiology

Gut microbiota: from the forgotten organ to a potential key player in the pathology of Alzheimer disease

(2019) Dong-oh Seo et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects

(2019) Baltasar Mayo et al.   Nutrients

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

(2019) Emily R Leeming et al.   Nutrients

The Influence of Diet Interventions Using Whole, Plant Food on the Gut Microbiome: A Narrative Review

(2019) Holly J. Willis et al.   Journal of the Academy of Nutrition and Dietetics

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept

(2019) Aspen T. Reese et al.   mSystems

The role of the gut microbiome in the association between habitual anthocyanin intake and visceral abdominal fat in population-level analysis

(2019) Amy Jennings et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Intersection of the Gut Microbiome and Circadian Rhythms in Metabolism

(2019) Katya Frazier et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Validity of Dietary Assessment Methods When Compared to the Method of Doubly Labeled Water: A Systematic Review in Adults

(2019) Tracy L. Burrows et al.   Frontiers in Endocrinology

Evaluation of sampling and storage procedures on preserving the community structure of stool microbiota: A simple at-home toilet-paper collection method

(2018) Kait F. Al et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Walnut Consumption Alters the Gastrointestinal Microbiota, Microbially Derived Secondary Bile Acids, and Health Markers in Healthy Adults: A Randomized Controlled Trial

(2018) Hannah D Holscher et al.   JOURNAL OF NUTRITION

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench

(2018) Wei-Kai Wu et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Almond Consumption and Processing Affects the Composition of the Gastrointestinal Microbiota of Healthy Adult Men and Women: A Randomized Controlled Trial

(2018) Hannah Holscher et al.   Nutrients

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

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

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

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics

(2018) Jonna Sandberg et al.   EUROPEAN JOURNAL OF NUTRITION

Broccoli consumption affects the human gastrointestinal microbiota

(2018) Jennifer L. Kaczmarek et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

You are what you eat: diet, health and the gut microbiota

(2018) Niv Zmora et al.   Nature Reviews Gastroenterology & Hepatology

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

(2018) Thomas Gurry et al.   Scientific Reports

Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies

(2018) Zheng Wang et al.   Frontiers in Cellular and Infection Microbiology

US Immigration Westernizes the Human Gut Microbiome

(2018) Pajau Vangay et al.   CELL

Yogurt and other fermented foods as sources of health-promoting bacteria

(2018) Car Reen Kok et al.   NUTRITION REVIEWS

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults

(2018) Lea B. S. Hansen et al.   Nature Communications

Evaluation of New Technology-Based Tools for Dietary Intake Assessment—An ILSI Europe Dietary Intake and Exposure Task Force Evaluation

(2018) Alison Eldridge et al.   Nutrients

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Guiding longitudinal sampling in IBD cohorts

(2017) Yoshiki Vázquez-Baeza et al.   GUT

Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation

(2017) Benoit Chassaing et al.   GUT

Food additives, contaminants and other minor components: effects on human gut microbiota—a review

(2017) Paula Roca-Saavedra et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Interindividual variability in gut microbiota and host response to dietary interventions

(2017) Genelle R Healey et al.   NUTRITION REVIEWS

The challenges of control groups, placebos and blinding in clinical trials of dietary interventions

(2017) Heidi M. Staudacher et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Image-Based Dietary Assessment Ability of Dietetics Students and Interns

(2017) Erica Howes et al.   Nutrients

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

(2017) Julia Fukuyama et al.   PLoS Computational Biology

Preservation of three-dimensional spatial structure in the gut microbiome

(2017) Yuko Hasegawa et al.   PLoS One

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination

(2016) Scott A. Handley et al.   Cell Host & Microbe

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

(2016) Annika Wahlström et al.   Cell Metabolism

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate

(2016) Amrita Srivathsan et al.   Frontiers in Zoology

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New mobile methods for dietary assessment: review of image-assisted and image-based dietary assessment methods

(2016) C. J. Boushey et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

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

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

(2016) Cian J. Hill et al.   Microbiome

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction

(2015) Conny Mathay et al.   BIOPRESERVATION AND BIOBANKING

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies

(2015) R. Sinha et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis

(2015) Zeneng Wang et al.   CELL

Antibiotics, Pediatric Dysbiosis, and Disease

(2015) Pajau Vangay et al.   Cell Host & Microbe

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

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

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction

(2015) Conny Mathay et al.   Biopreservation and Biobanking

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

(2015) Monika A. Gorzelak et al.   PLoS One

Performance of the Automated Self-Administered 24-hour Recall relative to a measure of true intakes and to an interviewer-administered 24-h recall

(2014) Sharon I Kirkpatrick et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Effects of almond and pistachio consumption on gut microbiota composition in a randomised cross-over human feeding study

(2014) Maria Ukhanova et al.   BRITISH JOURNAL OF NUTRITION

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

(2014) Anne Salonen et al.   ISME Journal

FXR is a molecular target for the effects of vertical sleeve gastrectomy

(2014) Karen K. Ryan et al.   NATURE

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

(2014) Jotham Suez et al.   NATURE

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

(2014) Jenna M. Lang et al.   PeerJ

Measuring food intake with digital photography

(2013) C. K. Martin et al.   JOURNAL OF HUMAN NUTRITION AND DIETETICS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

(2013) Robert A Koeth et al.   NATURE MEDICINE

Validity of self-reported lunch recalls in Swedish school children aged 6–8 years

(2013) Monica Hunsberger et al.   Nutrition Journal

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

Nutritional biomarkers for objective dietary assessment

(2012) Gunter GC Kuhnle   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10 −/− mice

(2012) Suzanne Devkota et al.   NATURE

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

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

The Automated Self-Administered 24-Hour Dietary Recall (ASA24): A Resource for Researchers, Clinicians, and Educators from the National Cancer Institute

(2012) Amy F. Subar et al.   Journal of the Academy of Nutrition and Dietetics

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet

(2009) Fei Li et al.   JOURNAL OF NUTRITION

A Wearable Electronic System for Objective Dietary Assessment

(2009) Mingui Sun et al.   JOURNAL OF THE AMERICAN DIETETIC ASSOCIATION

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

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

(2008) Alan W. Walker et al.   ENVIRONMENTAL MICROBIOLOGY