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

Effect of Cell Concentration on the Persistence in the Human Intestine of Four Probiotic Strains Administered through a Multispecies Formulation

(2019) Valentina Taverniti et al.   Nutrients

Beneficial effects of Bifidobacterium longum subsp. longum BB536 on human health: Modulation of gut microbiome as the principal action

(2019) Chyn Boon Wong et al.   Journal of Functional Foods

Efficacy and safety of statin therapy in older people: a meta-analysis of individual participant data from 28 randomised controlled trials

(2019) Jane Armitage et al.   LANCET

Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial

(2019) Yi Wan et al.   GUT

The ancestral and industrialized gut microbiota and implications for human health

(2019) Erica D. Sonnenburg et al.   NATURE REVIEWS MICROBIOLOGY

Disbiome database: linking the microbiome to disease

(2018) Yorick Janssens et al.   BMC MICROBIOLOGY

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

(2018) Bjoern O. Schroeder et al.   Cell Host & Microbe

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes

(2018) Jens Walter et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial

(2018) Valerie J. Flaherman et al.   JOURNAL OF PEDIATRICS

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Evaluation of randomized controlled trials of foods with functional claims request: The learning outcomes from studies in Japan

(2018) Nanae Tanemura et al.   Journal of Functional Foods

Preterm Delivery and Future Risk of Maternal Cardiovascular Disease: A Systematic Review and Meta‐Analysis

(2018) Pensée Wu et al.   Journal of the American Heart Association

Association of Exposure to Formula in the Hospital and Subsequent Infant Feeding Practices With Gut Microbiota and Risk of Overweight in the First Year of Life

(2018) Jessica D. Forbes et al.   JAMA Pediatrics

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community

(2018) Efrem S. Lim et al.   Microbiome

Probiotic Bifidobacterium strains and galactooligosaccharides improve intestinal barrier function in obese adults but show no synergism when used together as synbiotics

(2018) Janina A. Krumbeck et al.   Microbiome

Microbiome: Focus on Causation and Mechanism

(2018) Michael A. Fischbach   CELL

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography

(2018) Mélanie Deschasaux et al.   NATURE MEDICINE

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

(2018) Yan He et al.   NATURE MEDICINE

Prospects for primary prevention of type 1 diabetes by restoring a disappearing microbe

(2018) Richard Insel et al.   PEDIATRIC DIABETES

Causality in dietary interventions—building a case for gut microbiota

(2018) Yan Y. Lam et al.   Genome Medicine

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

(2018) Inés Martínez et al.   eLife

US Immigration Westernizes the Human Gut Microbiome

(2018) Pajau Vangay et al.   CELL

Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations

(2018) Nhan T. Ho et al.   Nature Communications

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

(2018) Jacob S. Leiby et al.   Microbiome

Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants

(2018) Katri Korpela et al.   Microbiome

Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants

(2018) Eirin Esaiassen et al.   Frontiers in Pediatrics

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

(2018) Tommi Vatanen et al.   Nature Microbiology

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

European consensus conference on faecal microbiota transplantation in clinical practice

(2017) Giovanni Cammarota et al.   GUT

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Moving beyond microbiome-wide associations to causal microbe identification

(2017) Neeraj K. Surana et al.   NATURE

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

(2017) Glenn R. Gibson et al.   Nature Reviews Gastroenterology & Hepatology

Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide

(2017) Justin Carlson et al.   Nutrients

Recent Development of Prebiotic Research—Statement from an Expert Workshop

(2017) Giorgio La Fata et al.   Nutrients

Oligofructose Provides Laxation for Irregularity Associated with Low Fiber Intake

(2017) Randal Buddington et al.   Nutrients

Cohort profile: the Healthy Life in an Urban Setting (HELIUS) study in Amsterdam, The Netherlands

(2017) Marieke B Snijder et al.   BMJ Open

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

(2017) Vinod K. Gupta et al.   Frontiers in Microbiology

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

(2017) Maria Elisa Perez-Muñoz et al.   Microbiome

Resistant starch can improve insulin sensitivity independently of the gut microbiota

(2017) Laure B. Bindels et al.   Microbiome

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Stool frequency is associated with gut microbiota composition

(2016) Fatemeh Hadizadeh et al.   GUT

Biomarkers and Surrogate Endpoints

(2016) Melissa A. Robb et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

(2016) Jun Wang et al.   NATURE GENETICS

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults

(2016) Gregory E. Miller et al.   PLoS One

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Alterations of the human gut microbiome in multiple sclerosis

(2016) Sushrut Jangi et al.   Nature Communications

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

(2016) Amy Langdon et al.   Genome Medicine

The healthy human microbiome

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

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials

(2016) Nadja B. Kristensen et al.   Genome Medicine

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants

(2016) Katherine E. Gregory et al.   Microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch

(2016) A. Venkataraman et al.   Microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

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

(2016) Se Jin Song et al.   mSystems

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

(2016) Rocio Martin et al.   PLoS One

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

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

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Gut Microbiota in Multiple Sclerosis

(2015) Brandi L. Cantarel et al.   JOURNAL OF INVESTIGATIVE MEDICINE

Towards a more comprehensive concept for prebiotics

(2015) Laure B. Bindels et al.   Nature Reviews Gastroenterology & Hepatology

The infant microbiome development: mom matters

(2015) Noel T. Mueller et al.   TRENDS IN MOLECULAR MEDICINE

Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption

(2015) Emiley A. Eloe-Fadrosh et al.   mBio

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice

(2015) Marc Schneeberger et al.   Scientific Reports

Wheat bran extract alters colonic fermentation and microbial composition, but does not affect faecal water toxicity: a randomised controlled trial in healthy subjects

(2014) Karen Windey et al.   BRITISH JOURNAL OF NUTRITION

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

Development of the HELIUS food frequency questionnaires: ethnic-specific questionnaires to assess the diet of a multiethnic population in The Netherlands

(2014) M H Beukers et al.   EUROPEAN JOURNAL OF CLINICAL NUTRITION

High dose of prebiotics reduces fecal water cytotoxicity in healthy subjects

(2014) Karen Windey et al.   MOLECULAR NUTRITION & FOOD RESEARCH

CODEX-aligned dietary fiber definitions help to bridge the ‘fiber gap’

(2014) Julie Miller Jones   Nutrition Journal

Prebiotics in healthy infants and children for prevention of acute infectious diseases: a systematic review and meta-analysis

(2014) Szimonetta Lohner et al.   NUTRITION REVIEWS

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Quantitative evaluation of synbiotic strategies to improve persistence and metabolic activity of Lactobacillus reuteri DSM 17938 in the human gastrointestinal tract

(2014) Monchaya Rattanaprasert et al.   Journal of Functional Foods

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months

(2013) M. B. Azad et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section

(2013) Hedvig E Jakobsson et al.   GUT

Effects of Wheat Bran Extract Containing Arabinoxylan Oligosaccharides on Gastrointestinal Parameters in Healthy Preadolescent Children

(2013) Isabelle E.J.A. François et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

Development of intestinal microbiota in infants and its impact on health

(2013) Sebastien Matamoros et al.   TRENDS IN MICROBIOLOGY

Associations between the human intestinal microbiota,Lactobacillus rhamnosusGG and serum lipids indicated by integrated analysis of high-throughput profiling data

(2013) Leo Lahti et al.   PeerJ

Effects of a wheat bran extract containing arabinoxylan oligosaccharides on gastrointestinal health parameters in healthy adult human volunteers: a double-blind, randomised, placebo-controlled, cross-over trial

(2012) Isabelle E. J. A. François et al.   BRITISH JOURNAL OF NUTRITION

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

Gut Microbiota Composition and Activity in Relation to Host Metabolic Phenotype and Disease Risk

(2012) Elaine Holmes et al.   Cell Metabolism

Human milk oligosaccharide consumption by intestinal microbiota

(2012) A. Marcobal et al.   CLINICAL MICROBIOLOGY AND INFECTION

Intestinal colonization resistance

(2012) Trevor D. Lawley et al.   IMMUNOLOGY

An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice

(2012) Na Fei et al.   ISME Journal

Selective carbohydrate utilization by lactobacilli and bifidobacteria

(2012) D. Watson et al.   JOURNAL OF APPLIED MICROBIOLOGY

Consumption of Breads Containing In Situ–Produced Arabinoxylan Oligosaccharides Alters Gastrointestinal Effects in Healthy Volunteers

(2012) Bram Damen et al.   JOURNAL OF NUTRITION

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

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

Modulation of Protein Fermentation Does Not Affect Fecal Water Toxicity: A Randomized Cross-Over Study in Healthy Subjects

(2012) Karen Windey et al.   PLoS One

High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health

(2011) Wendy R Russell et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials

(2011) Michael V Holmes et al.   LANCET

Barcoded Pyrosequencing Reveals That Consumption of Galactooligosaccharides Results in a Highly Specific Bifidogenic Response in Humans

(2011) Lauren M. G. Davis et al.   PLoS One

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Persistence of probiotic strains in the gastrointestinal tract when administered as capsules, yoghurt, or cheese

(2010) Maija Saxelin et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Resistant Starches Types 2 and 4 Have Differential Effects on the Composition of the Fecal Microbiota in Human Subjects

(2010) Inés Martínez et al.   PLoS One

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY

Early-life exposures associated with antibiotic use and risk of subsequent Crohn's disease

(2008) Hans Hildebrand et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY