An online atlas of human plasma metabolite signatures of gut microbiome composition

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

(2021) Francesco Asnicar et al.   NATURE MEDICINE

Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial

(2021) Noel T. Mueller et al.   DIABETES CARE

Combinatorial, additive and dose-dependent drug–microbiome associations

(2021) Sofia K. Forslund et al.   NATURE

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

(2020) Arnau Vich Vila et al.   Nature Communications

Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents

(2020) Xifan Wang et al.   GUT

Serum metabolites reflecting gut microbiome alpha diversity predict type 2 diabetes

(2020) Cristina Menni et al.   Gut Microbes

Gut microbiota in human metabolic health and disease

(2020) Yong Fan et al.   NATURE REVIEWS MICROBIOLOGY

Associations between untargeted plasma metabolomic signatures and gut microbiota composition in the Milieu Intérieur population of healthy adults

(2020) Valentin Partula et al.   BRITISH JOURNAL OF NUTRITION

The Malmö Offspring Study (MOS): design, methods and first results

(2020) Louise Brunkwall et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Effects of Coffee and Its Components on the Gastrointestinal Tract and the Brain–Gut Axis

(2020) Amaia Iriondo-DeHond et al.   Nutrients

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

(2019) Edoardo Pasolli et al.   CELL

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

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

(2019) Alexander Kurilshikov et al.   CIRCULATION RESEARCH

Extensive transmission of microbes along the gastrointestinal tract

(2019) Thomas SB Schmidt et al.   eLife

Blood metabolome predicts gut microbiome α-diversity in humans

(2019) Tomasz Wilmanski et al.   NATURE BIOTECHNOLOGY

Interplay between the human gut microbiome and host metabolism

(2019) Alessia Visconti et al.   Nature Communications

Plasma metabolite biomarkers of boiled and filtered coffee intake and their association with type 2 diabetes risk

(2019) L. Shi et al.   JOURNAL OF INTERNAL MEDICINE

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

(2019) Dina Vojinovic et al.   Nature Communications

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

Effect of metformin on plasma metabolite profile in the Copenhagen Insulin and Metformin Therapy (CIMT) trial

(2018) N. Safai et al.   DIABETIC MEDICINE

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

Could Fecal Phenylacetic and Phenylpropionic Acids Be Used as Indicators of Health Status?

(2018) Isabel Gutiérrez-Díaz et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

(2017) Hao Wu et al.   NATURE MEDICINE

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Coffee consumption and health: umbrella review of meta-analyses of multiple health outcomes

(2017) Robin Poole et al.   BMJ-British Medical Journal

p-Cresyl Sulfate

(2017) Tessa Gryp et al.   Toxins

Coffee consumption and health: umbrella review of meta-analyses of multiple health outcomes

(2017) Robin Poole et al.   BMJ-British Medical Journal

A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression

(2016) Shuanghong Jiang et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Effect of metformin therapy on circulating amino acids in a randomized trial: the CAMERA study

(2016) D. Preiss et al.   DIABETIC MEDICINE

Microbiota-Derived Phenylacetylglutamine Associates with Overall Mortality and Cardiovascular Disease in Patients with CKD

(2016) R. Poesen et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

The Swedish CArdioPulmonary BioImage Study: objectives and design

(2015) G. Bergström et al.   JOURNAL OF INTERNAL MEDICINE

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

New Biomarkers of Coffee Consumption Identified by the Non-Targeted Metabolomic Profiling of Cohort Study Subjects

(2014) Joseph A. Rothwell et al.   PLoS One

A New Equation to Estimate Glomerular Filtration Rate

(2013) Andrew S. Levey et al.   ANNALS OF INTERNAL MEDICINE

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrated, Nontargeted Ultrahigh Performance Liquid Chromatography/Electrospray Ionization Tandem Mass Spectrometry Platform for the Identification and Relative Quantification of the Small-Molecule Complement of Biological Systems

(2009) Anne M. Evans et al.   ANALYTICAL CHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The streptococcal inhibitor of complement (SIC) protectsStreptococcus pyogenes  from bacteriocin-like inhibitory substance (BLIS) fromStreptococcus salivarius

(2009) Masaaki Minami et al.   FEMS MICROBIOLOGY LETTERS

Bile acids: regulation of synthesis

(2009) John Y. L. Chiang   JOURNAL OF LIPID RESEARCH

Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm

(2008) S. B. I. Luppens et al.   Oral microbiology and immunology

Uremic Toxins: What Are They? An Integrated Overview of Pathobiology and Classification

(2007) Richard J. Glassock   JOURNAL OF RENAL NUTRITION