Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration

Revisit gut microbiota and its impact on human health and disease

(2019) Rui-xue Ding et al.   JOURNAL OF FOOD AND DRUG ANALYSIS

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals

(2019) Riccardo Vasapolli et al.   GASTROENTEROLOGY

Exploring the impact of Helicobacter pylori on gut microbiome composition

(2019) Nihar Ranjan Dash et al.   PLoS One

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

Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors

(2019) Melinda A. Engevik et al.   Frontiers in Microbiology

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

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

(2018) Inés Martínez et al.   eLife

Gut microbiome and type 2 diabetes: where we are and where to go?

(2018) Sapna Sharma et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Signatures within the esophageal microbiome are associated with host genetics, age, and disease

(2018) Nandan P. Deshpande et al.   Microbiome

Microbial Ecology along the Gastrointestinal Tract

(2017) Ethan T. Hillman et al.   MICROBES AND ENVIRONMENTS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Gut microbiota and IBD: causation or correlation?

(2017) Josephine Ni et al.   Nature Reviews Gastroenterology & Hepatology

Human genetic variation and the gut microbiome in disease

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

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants

(2017) Priscila T. Dobbler et al.   Frontiers in Microbiology

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine

(2016) K. Pokusaeva et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Emerging Technologies for Gut Microbiome Research

(2016) Jason W. Arnold et al.   TRENDS IN MICROBIOLOGY

The healthy human microbiome

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

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

FolC2-mediated folate metabolism contributes to suppression of inflammation by probioticLactobacillus reuteri

(2016) Carissa M. Thomas et al.   MicrobiologyOpen

Causality of small and large intestinal microbiota in weight regulation and insulin resistance

(2016) Torsten P.M. Scheithauer et al.   Molecular Metabolism

Biogenic Amine Production by Oenococcus oeni Isolates from Malolactic Fermentation of Tempranillo Wine

(2016) P. M. IZQUIERDO CAÑAS et al.   JOURNAL OF FOOD PROTECTION

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome

(2015) B. P. Chumpitazi et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

The intestinal microbiome and health

(2015) Susan Tuddenham et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

(2015) Jessica Ann Thompson et al.   Cell Reports

Outer membrane vesicles – offensive weapons or good Samaritans?

(2015) Ingar Olsen et al.   Journal of Oral Microbiology

Structure and function of the healthy pre-adolescent pediatric gut microbiome

(2015) Emily B. Hollister et al.   Microbiome

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

The cross talk between microbiota and the immune system: metabolites take center stage

(2014) Hagit Shapiro et al.   CURRENT OPINION IN IMMUNOLOGY

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

From Prediction to Function Using Evolutionary Genomics: Human-Specific Ecotypes of Lactobacillus reuteri Have Diverse Probiotic Functions

(2014) Jennifer K. Spinler et al.   Genome Biology and Evolution

Activation of Gpr109a, Receptor for Niacin and the Commensal Metabolite Butyrate, Suppresses Colonic Inflammation and Carcinogenesis

(2014) Nagendra Singh et al.   IMMUNITY

Receptors for short-chain fatty acids in brush cells at the “gastric groove”

(2014) Julia Anna-Maria Eberle et al.   Frontiers in Physiology

Recent advances in transport of water-soluble vitamins in organs of the digestive system: a focus on the colon and the pancreas

(2013) Hamid M. Said   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

GPR41/FFAR3 and GPR43/FFAR2 as Cosensors for Short-Chain Fatty Acids in Enteroendocrine Cells vs FFAR3 in Enteric Neurons and FFAR2 in Enteric Leukocytes

(2013) Mark K. Nøhr et al.   ENDOCRINOLOGY

Lactobacillus reuteri-Specific Immunoregulatory Gene rsiR Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri

(2013) P. Hemarajata et al.   JOURNAL OF BACTERIOLOGY

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Bacterial Community Mapping of the Mouse Gastrointestinal Tract

(2013) Shenghua Gu et al.   PLoS One

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

(2013) D. Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Development of intestinal microbiota in infants and its impact on health

(2013) Sebastien Matamoros et al.   TRENDS IN MICROBIOLOGY

Lactocepin Secreted By Lactobacillus Exerts Anti-Inflammatory Effects By Selectively Degrading Proinflammatory Chemokines

(2012) Marie-Anne von Schillde et al.   Cell Host & Microbe

Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection

(2012) Yue Shen et al.   Cell Host & Microbe

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

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

Human milk oligosaccharide consumption by intestinal microbiota

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

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

The role of bacterial outer membrane vesicles for intra- and interspecies delivery

(2012) James Berleman et al.   ENVIRONMENTAL MICROBIOLOGY

Long-term monitoring of the human intestinal microbiota composition

(2012) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

(2012) Kjersti Aagaard et al.   FASEB JOURNAL

Bacteria, Colonic Fermentation, and Gastrointestinal Health

(2012) George T. Macfarlane et al.   JOURNAL OF AOAC INTERNATIONAL

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The impact of nutrition on the human microbiome

(2012) Harry J Flint   NUTRITION REVIEWS

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

Histamine Derived from Probiotic Lactobacillus reuteri Suppresses TNF via Modulation of PKA and ERK Signaling

(2012) Carissa M. Thomas et al.   PLoS One

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Quorum Sensing and Bacterial Social Interactions in Biofilms

(2012) Yung-Hua Li et al.   SENSORS

Host–microbe interactions that facilitate gut colonization by commensal bifidobacteria

(2012) Marco Ventura et al.   TRENDS IN MICROBIOLOGY

Mechanism of Inhibition ofBacillus anthracisSpore Outgrowth by the Lantibiotic Nisin

(2011) Ian M. Gut et al.   ACS Chemical Biology

Bacteriocin Production: a Probiotic Trait?

(2011) Alleson Dobson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative Analysis of Histidine Decarboxylase Gene (hdcA) Transcription and Histamine Production by Streptococcus thermophilus PRI60 under Conditions Relevant to Cheese Making

(2011) Franca Rossi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes

(2011) Christopher M Rath et al.   CURRENT OPINION IN MICROBIOLOGY

A Novel Antiinflammatory Role for the Short-Chain Fatty Acids in Human Labor

(2011) Chiara Voltolini et al.   ENDOCRINOLOGY

Organic acids as antimicrobials to control Salmonella in meat and poultry products

(2011) E. Mani-López et al.   FOOD RESEARCH INTERNATIONAL

The monocarboxylate transporter family-Role and regulation

(2011) Andrew P. Halestrap et al.   IUBMB LIFE

Towards the Human Colorectal Cancer Microbiome

(2011) Julian R. Marchesi et al.   PLoS One

Staphylococcus aureus Produces Membrane-Derived Vesicles That Induce Host Cell Death

(2011) Mamata Gurung et al.   PLoS One

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Characterization of the Serpin-Encoding Gene of Bifidobacterium breve 210B

(2010) F. Turroni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Production of conjugated linoleic acid and conjugated linolenic acid isomers by Bifidobacterium species

(2010) Lara Gorissen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Sodium-coupled electrogenic transport of pyroglutamate (5-oxoproline) via SLC5A8, a monocarboxylate transporter

(2010) Seiji Miyauchi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Central Nervous System Demyelinating Disease Protection by the Human Commensal Bacteroides fragilis Depends on Polysaccharide A Expression

(2010) J. Ochoa-Reparaz et al.   JOURNAL OF IMMUNOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Free fatty acid receptor 2 and nutrient sensing: a proposed role for fibre, fermentable carbohydrates and short-chain fatty acids in appetite regulation

(2010) Michelle L. Sleeth et al.   NUTRITION RESEARCH REVIEWS

Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis

(2010) Y. K. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm

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

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

(2010) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?

(2010) Y. K. Lee et al.   SCIENCE

Probiotic Lactobacillus casei strain Shirota prevents indomethacin-induced small intestinal injury: involvement of lactic acid

(2009) Toshio Watanabe et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Trans-10, cis-12-conjugated linoleic acid reduces the hepatic triacylglycerol content and the leptin mRNA level in adipose tissue in obese Zucker fa/fa rats

(2009) Oddrun A. Gudbrandsen et al.   BRITISH JOURNAL OF NUTRITION

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

(2009) Z. Gao et al.   DIABETES

Individual and co-operative roles of lactic acid and hydrogen peroxide in the killing activity of enteric strain Lactobacillus johnsonii NCC933 and vaginal strain Lactobacillus gasseri KS120.1 against enteric, uropathogenic and vaginosis-associated pathog

(2009) Fabrice Atassi et al.   FEMS MICROBIOLOGY LETTERS

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Entry of Porphyromonas gingivalis Outer Membrane Vesicles into Epithelial Cells Causes Cellular Functional Impairment

(2009) N. Furuta et al.   INFECTION AND IMMUNITY

G Protein-Coupled Receptor 43 Is Essential for Neutrophil Recruitment during Intestinal Inflammation

(2009) C. Sina et al.   JOURNAL OF IMMUNOLOGY

Mechanism of conjugated linoleic acid and vaccenic acid formation in human faecal suspensions and pure cultures of intestinal bacteria

(2009) F. M. McIntosh et al.   MICROBIOLOGY-SGM

Understanding the role of tryptophan and serotonin metabolism in gastrointestinal function

(2009) d. keszthelyi et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Post-Translational Inhibition of IP-10 Secretion in IEC by Probiotic Bacteria: Impact on Chronic Inflammation

(2009) Gabriele Hörmannsperger et al.   PLoS One

The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation

(2009) T. Bansal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human-derived probiotic Lactobacillus reuteri demonstrate antimicrobial activities targeting diverse enteric bacterial pathogens

(2008) Jennifer K. Spinler et al.   ANAEROBE

High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota

(2008) E G Zoetendal et al.   GUT

Cellular expression of a sodium-dependent monocarboxylate transporter (Slc5a8) and the MCT family in the mouse kidney

(2008) Haruko Yanase et al.   HISTOCHEMISTRY AND CELL BIOLOGY

A multifaceted role for polyamines in bacterial pathogens

(2008) Pratik Shah et al.   MOLECULAR MICROBIOLOGY

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

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