Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

(2017) Catherine Igartua et al.   Microbiome

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke

(2017) Kazuo Yamashiro et al.   PLoS One

@MInter: automated text-mining of microbial interactions

(2016) Kun Ming Kenneth Lim et al.   BIOINFORMATICS

The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease

(2016) David N. O’Dwyer et al.   JOURNAL OF IMMUNOLOGY

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

(2016) Anastassia Gorvitovskaia et al.   Microbiome

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

(2016) Antoine M. Snijders et al.   Nature Microbiology

Quantitative Imaging of Gut Microbiota Spatial Organization

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

Intake ofLactobacillus reuteriImproves Incretin and Insulin Secretion in Glucose-Tolerant Humans: A Proof of Concept

(2015) Marie-Christine Simon et al.   DIABETES CARE

Diet strongly influences the gut microbiota of surgeonfishes

(2015) Sou Miyake et al.   MOLECULAR ECOLOGY

Antihypertensive effects of probioticsLactobacillusstrains in spontaneously hypertensive rats

(2015) Manuel Gómez-Guzmán et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Noninvasive monitoring of infection and rejection after lung transplantation

(2015) Iwijn De Vlaminck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity

(2015) Ningwen Tai et al.   REVIEWS IN ENDOCRINE & METABOLIC DISORDERS

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection

(2015) Jason L. Kubinak et al.   Nature Communications

Circulating microbial RNA and health

(2015) Ross Ka-Kit Leung et al.   Scientific Reports

Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma

(2014) Meabh Beatty et al.   BMC GENOMICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Probiotic Administration Attenuates Myocardial Hypertrophy and Heart Failure After Myocardial Infarction in the Rat

(2014) Xiaohong Tracey Gan et al.   Circulation-Heart Failure

Interactions Between the Intestinal Microbiome and Liver Diseases

(2014) Bernd Schnabl et al.   GASTROENTEROLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

(2014) Jun Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Links between diet, gut microbiota composition and gut metabolism

(2014) Harry J. Flint et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

Commensal microbes and interferon-  determine persistence of enteric murine norovirus infection

(2014) M. T. Baldridge et al.   SCIENCE

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Complex host genetics influence the microbiome in inflammatory bowel disease

(2014) Dan Knights et al.   Genome Medicine

Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

(2014) Muriel Vayssier-Taussat et al.   Frontiers in Cellular and Infection Microbiology

Sources, isolation, characterisation and evaluation of probiotics

(2013) Luis Fontana et al.   BRITISH JOURNAL OF NUTRITION

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

(2013) Giulia Marchetti et al.   CLINICAL MICROBIOLOGY REVIEWS

Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia

(2013) Bojana Bogovič Matijašić et al.   EUROPEAN JOURNAL OF NUTRITION

An update on the use and investigation of probiotics in health and disease

(2013) Mary Ellen Sanders et al.   GUT

Altered profile of human gut microbiome is associated with cirrhosis and its complications

(2013) Jasmohan S. Bajaj et al.   JOURNAL OF HEPATOLOGY

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Circulating bacterial-derived DNA fragments as a marker * of systemic inflammation in peritoneal dialysis

(2013) B. C.-H. Kwan et al.   NEPHROLOGY DIALYSIS TRANSPLANTATION

Metagenomic Analyses of Alcohol Induced Pathogenic Alterations in the Intestinal Microbiome and the Effect of Lactobacillus rhamnosus GG Treatment

(2013) Lara Bull-Otterson et al.   PLoS One

Bacteroides fragilis polysaccharide A is necessary and sufficient for acute activation of intestinal sensory neurons

(2013) Yu-Kang Mao et al.   Nature Communications

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers

(2012) María Isabel Queipo-Ortuño et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Colonic microbiome is altered in alcoholism

(2012) Ece A. Mutlu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Alcohol Metabolism

(2012) Arthur I. Cederbaum   Clinics in Liver Disease

ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation

(2012) Tatsuo Hashimoto et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity

(2012) Jorge Henao-Mejia et al.   NATURE

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Defining the human microbiome

(2012) Luke K Ursell et al.   NUTRITION REVIEWS

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits

(2012) Autumn M. McKnite et al.   PLoS One

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

(2012) Margaret L. Zupancic et al.   PLoS One

The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota?

(2012) Kai Wang et al.   PLoS One

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

Chimpanzees and humans harbour compositionally similar gut enterotypes

(2012) Andrew H. Moeller et al.   Nature Communications

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Treating Clostridium difficile Infection With Fecal Microbiota Transplantation

(2011) Johan S. Bakken et al.   Clinical Gastroenterology and Hepatology

Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults

(2011) S.-K. Li et al.   CLINICAL MICROBIOLOGY AND INFECTION

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Characterization of fecal microbial communities in patients with liver cirrhosis

(2011) Yanfei Chen et al.   HEPATOLOGY

Probiotic properties of Lactobacillus plantarum CECT 7315 and CECT 7316 isolated from faeces of healthy children

(2011) M. Bosch et al.   LETTERS IN APPLIED MICROBIOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Identification of an innate T helper type 17 response to intestinal bacterial pathogens

(2011) Kaoru Geddes et al.   NATURE MEDICINE

Comparative Analysis of Korean Human Gut Microbiota by Barcoded Pyrosequencing

(2011) Young-Do Nam et al.   PLoS One

Successful Transmission of a Retrovirus Depends on the Commensal Microbiota

(2011) M. Kane et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Caspase deficiency alters the murine gut microbiome

(2011) B M Brinkman et al.   Cell Death & Disease

Synbiotics prevent asthma-like symptoms in infants with atopic dermatitis

(2010) L. B. van der Aa et al.   ALLERGY

Effect of mother’s weight on infant’s microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy

(2010) Maria Carmen Collado et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Enteric dysbiosis associated with a mouse model of alcoholic liver disease

(2010) Arthur W. Yan et al.   HEPATOLOGY

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

(2010) Nadja Larsen et al.   PLoS One

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

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

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inadequate Clearance of Translocated Bacterial Products in HIV-Infected Humanized Mice

(2010) Ursula Hofer et al.   PLoS Pathogens

Intestinal Dysbiosis: A Possible Mechanism of Alcohol-Induced Endotoxemia and Alcoholic Steatohepatitis in Rats

(2009) Ece Mutlu et al.   ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Plasma Levels of Bacterial DNA Correlate with Immune Activation and the Magnitude of Immune Restoration in Persons with Antiretroviral‐Treated HIV Infection

(2009) Wei Jiang et al.   JOURNAL OF INFECTIOUS DISEASES

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

(2009) Kendle M. Maslowski et al.   NATURE

Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients

(2009) Angèle PM Kerckhoffs et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Human Immunodeficiency Virus-Related Microbial Translocation and Progression of Hepatitis C

(2008) Ashwin Balagopal et al.   GASTROENTEROLOGY

Chylomicrons promote intestinal absorption of lipopolysaccharides

(2008) Sarbani Ghoshal et al.   JOURNAL OF LIPID RESEARCH

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE