The long-term genetic stability and individual specificity of the human gut microbiome

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

(2020) Sara Vieira-Silva et al.   NATURE

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

(2020) Lianmin Chen et al.   Nature Communications

Genetic and Microbial Associations to Plasma and Fecal Bile Acids in Obesity Relate to Plasma Lipids and Liver Fat Content

(2020) Lianmin Chen et al.   Cell Reports

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Structural variation in the gut microbiome associates with host health

(2019) David Zeevi et al.   NATURE

Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates

(2019) A.C.M. Veloo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Longitudinal multi-omics of host–microbe dynamics in prediabetes

(2019) Wenyu Zhou et al.   NATURE

Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease

(2019) Koichi Kikuchi et al.   Nature Communications

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

(2018) Moran Yassour et al.   Cell Host & Microbe

Association between hippuric acid and left ventricular hypertrophy in maintenance hemodialysis patients

(2018) Teng-Hung Yu et al.   CLINICA CHIMICA ACTA

A system biology perspective on environment–host–microbe interactions

(2018) Lianmin Chen et al.   HUMAN MOLECULAR GENETICS

The importance of cohort studies in the post-GWAS era

(2018) Cisca Wijmenga et al.   NATURE GENETICS

Gut microbiota derived metabolites in cardiovascular health and disease

(2018) Zeneng Wang et al.   Protein & Cell

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

(2018) Tommi Vatanen et al.   NATURE

Temporal development of the gut microbiome in early childhood from the TEDDY study

(2018) Christopher J. Stewart et al.   NATURE

Species-level functional profiling of metagenomes and metatranscriptomes

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

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

(2018) Arnau Vich Vila et al.   Science Translational Medicine

Antibiotic resistance: a rundown of a global crisis

(2018) Bilal Aslam et al.   Infection and Drug Resistance

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

(2018) Tommi Vatanen et al.   Nature Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice

(2017) Eveliina Munukka et al.   ISME Journal

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

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

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Real friends:Faecalibacterium prausnitziisupports mucosal immune homeostasis

(2015) Mathias W Hornef et al.   GUT

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics

(2015) Ettje F Tigchelaar et al.   BMJ Open

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Probiotic Bifidobacterium species: potential beneficial effects in diarrheal disorders. Focus on “Probiotic Bifidobacterium species stimulate human SLC26A3 gene function and expression in intestinal epithelial cells”

(2014) Debolina Ray et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Cohort Profile: LifeLines, a three-generation cohort study and biobank

(2014) Salome Scholtens et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Faecalibacterium prausnitzii and human intestinal health

(2013) S Miquel et al.   CURRENT OPINION IN MICROBIOLOGY

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

(2013) A. Everard 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

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Normal and Pathologic Concentrations of Uremic Toxins

(2012) F. Duranton et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.

(2012) Ajay Kumar Mishra et al.   Standards in Genomic Sciences

High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

(2011) Tobias Fuhrer et al.   ANALYTICAL CHEMISTRY

Bacterial transport of sulfate, molybdate, and related oxyanions

(2011) Esther Aguilar-Barajas et al.   BIOMETALS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

(2011) M. Joossens et al.   GUT

Effects of Melatonin and Pycnogenol on Small Artery Structure and Function in Spontaneously Hypertensive Rats

(2010) Rita Rezzani et al.   HYPERTENSION

Erythropoietic Response and Outcomes in Kidney Disease and Type 2 Diabetes

(2010) Scott D. Solomon et al.   NEW ENGLAND JOURNAL OF MEDICINE