Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake

(2020) Victoria Meslier et al.   GUT

Regulation of intestinal lipid metabolism: current concepts and relevance to disease

(2020) Chih-Wei Ko et al.   Nature Reviews Gastroenterology & Hepatology

Human postprandial responses to food and potential for precision nutrition

(2020) Sarah E. Berry et al.   NATURE MEDICINE

Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts

(2020) Naeimeh Atabaki-Pasdar et al.   PLOS MEDICINE

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

The neuroactive potential of the human gut microbiota in quality of life and depression

(2019) Mireia Valles-Colomer et al.   Nature Microbiology

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

(2019) D B Dhakan et al.   GigaScience

Associations of Probiotic Fermented Milk (PFM) and Yogurt Consumption with Bifidobacterium and Lactobacillus Components of the Gut Microbiota in Healthy Adults

(2019) Noemí Redondo-Useros et al.   Nutrients

Associations of Dietary Cholesterol or Egg Consumption With Incident Cardiovascular Disease and Mortality

(2019) Victor W. Zhong et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

(2019) Francesca De Filippis et al.   Cell Host & Microbe

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study

(2019) Alexander Kurilshikov et al.   CIRCULATION RESEARCH

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Model of personalized postprandial glycemic response to food developed for an Israeli cohort predicts responses in Midwestern American individuals

(2019) Helena Mendes-Soares et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition

(2019) Louise B. Thingholm et al.   Cell Host & Microbe

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

(2019) Adrian Tett et al.   Cell Host & Microbe

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

(2019) Dina Vojinovic et al.   Nature Communications

Seafood Long-Chain n-3 Polyunsaturated Fatty Acids and Cardiovascular Disease: A Science Advisory From the American Heart Association

(2018) Eric B. Rimm et al.   CIRCULATION

Fish consumption and cardiovascular disease related biomarkers: A review of clinical trials

(2018) Filio Petsini et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces

(2018) Mitsuo Sakamoto et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Healthy Plant-Based Diets Are Associated with Lower Risk of All-Cause Mortality in US Adults

(2018) Hyunju Kim et al.   JOURNAL OF NUTRITION

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Microbial modulation of cardiovascular disease

(2018) J. Mark Brown et al.   NATURE REVIEWS MICROBIOLOGY

Consumption of dairy product and its association with total and cause specific mortality – A population-based cohort study and meta-analysis

(2018) Mohsen Mazidi et al.   CLINICAL NUTRITION

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

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

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

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

(2017) Francesco Beghini et al.   ISME Journal

Healthful and Unhealthful Plant-Based Diets and the Risk of Coronary Heart Disease in U.S. Adults

(2017) Ambika Satija et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

The UN Decade of Nutrition, the NOVA food classification and the trouble with ultra-processing

(2017) Carlos Augusto Monteiro et al.   PUBLIC HEALTH NUTRITION

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

Adherence to the Healthy Eating Index and Alternative Healthy Eating Index dietary patterns and mortality from all causes, cardiovascular disease and cancer: a meta-analysis of observational studies

(2016) S. Onvani et al.   JOURNAL OF HUMAN NUTRITION AND DIETETICS

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

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

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

(2016) Marc A. Sze et al.   mBio

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Plant-Based Dietary Patterns and Incidence of Type 2 Diabetes in US Men and Women: Results from Three Prospective Cohort Studies

(2016) Ambika Satija et al.   PLOS MEDICINE

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

(2016) Hailiang Xie et al.   Cell Systems

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

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

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

Metabolite Profiling and Cardiovascular Event Risk: A Prospective Study of 3 Population-Based Cohorts

(2015) P. Wurtz et al.   CIRCULATION

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

(2015) Jingyuan Fu et al.   CIRCULATION RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Intake of saturated and trans unsaturated fatty acids and risk of all cause mortality, cardiovascular disease, and type 2 diabetes: systematic review and meta-analysis of observational studies

(2015) Russell J de Souza et al.   BMJ-British Medical Journal

Are Human Intestinal Eukaryotes Beneficial or Commensals?

(2015) Julius Lukeš et al.   PLoS Pathogens

Intake of saturated and trans unsaturated fatty acids and risk of all cause mortality, cardiovascular disease, and type 2 diabetes: systematic review and meta-analysis of observational studies

(2015) Russell J de Souza et al.   BMJ-British Medical Journal

Greater Healthful Food Variety as Measured by the US Healthy Food Diversity Index Is Associated with Lower Odds of Metabolic Syndrome and its Components in US Adults

(2015) Maya Vadiveloo et al.   JOURNAL OF NUTRITION

Development and evaluation of the US Healthy Food Diversity index

(2014) Maya Vadiveloo et al.   BRITISH JOURNAL OF NUTRITION

Higher Diet Quality Is Associated with Decreased Risk of All-Cause, Cardiovascular Disease, and Cancer Mortality among Older Adults

(2014) Jill Reedy et al.   JOURNAL OF NUTRITION

Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013

(2014) Marie Ng et al.   LANCET

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

A new tool for converting food frequency questionnaire data into nutrient and food group values: FETA research methods and availability

(2014) Angela A Mulligan et al.   BMJ Open

Milk intake and risk of mortality and fractures in women and men: cohort studies

(2014) K. Michaelsson et al.   BMJ-British Medical Journal

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Update of the Healthy Eating Index: HEI-2010

(2013) Patricia M. Guenther et al.   Journal of the Academy of Nutrition and Dietetics

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

U.S. Department of Agriculture and U.S. Department of Health and Human Services, Dietary Guidelines for Americans, 2010. 7th Edition, Washington, DC: U.S. Government Printing Office, January 2011

(2012) Shelley McGuire   Advances in Nutrition

High-fat meal effect on LDL, HDL, and VLDL particle size and number in the Genetics of Lipid-Lowering drugs and diet network (GOLDN): an interventional study

(2011) Mary K Wojczynski et al.   Lipids in Health and Disease

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

General Cardiovascular Risk Profile for Use in Primary Care

(2008) Ralph B. D’Agostino et al.   CIRCULATION

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake

(2008) Leanne Hodson et al.   PROGRESS IN LIPID RESEARCH