Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

(2022) Eugeni Belda et al.   GUT

Large-scale association analyses identify host factors influencing human gut microbiome composition

(2021) Alexander Kurilshikov et al.   NATURE GENETICS

Next-generation therapeutic bacteria for treatment of obesity, diabetes, and other endocrine diseases

(2021) Thi Phuong Nam Bui et al.   BEST PRACTICE & RESEARCH CLINICAL ENDOCRINOLOGY & METABOLISM

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

(2021) Lianmin Chen et al.   CELL

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life

(2021) Josefine Roswall et al.   Cell Host & Microbe

Bifidobacteria-mediated immune system imprinting early in life

(2021) Bethany M. Henrick et al.   CELL

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

(2020) Sara Vieira-Silva et al.   NATURE

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes

(2020) Sandra Reitmeier et al.   Cell Host & Microbe

The Gut Microbiota in Prediabetes and Diabetes: A Population-Based Cross-Sectional Study

(2020) Hao Wu et al.   Cell Metabolism

Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits

(2020) Chyn Boon Wong et al.   FEMS MICROBIOLOGY REVIEWS

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study

(2020) Adam G Clooney et al.   GUT

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease

(2020) Francesca De Filippis et al.   CURRENT BIOLOGY

Integration of molecular profiles in a longitudinal wellness profiling cohort

(2020) Abdellah Tebani et al.   Nature Communications

Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes

(2020) Victor Schmidt et al.   mSystems

Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses

(2019) Sara Vieira-Silva et al.   Nature Microbiology

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

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis

(2019) Jeffrey R. Singer et al.   NATURE MEDICINE

Interplay between the human gut microbiome and host metabolism

(2019) Alessia Visconti et al.   Nature Communications

Riboflavin Supplementation in Patients with Crohn’s Disease [the RISE-UP study]

(2019) Julius Z H von Martels et al.   Journal of Crohns & Colitis

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans

(2018) Adil Mardinoglu et al.   Cell Metabolism

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

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

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

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

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

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics

(2017) Mireia Lopez-Siles et al.   ISME Journal

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

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

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Two dynamic regimes in the human gut microbiome

(2017) Sean M. Gibbons et al.   PLoS Computational Biology

Proteobacteria explain significant functional variability in the human gut microbiome

(2017) Patrick H. Bradley et al.   Microbiome

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Stress and stability: applying the Anna Karenina principle to animal microbiomes

(2017) Jesse R. Zaneveld et al.   Nature Microbiology

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Genetic Determinants of the Gut Microbiome in UK Twins

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

Microbiota as Therapeutic Targets

(2016) Ramnik J. Xavier   DIGESTIVE DISEASES

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

(2016) Jun Wang et al.   NATURE GENETICS

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

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

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

(2016) Marc A. Sze et al.   mBio

Gut Bifidobacteria Populations in Human Health and Aging

(2016) Silvia Arboleya et al.   Frontiers in Microbiology

Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

(2016) Anastassia Gorvitovskaia et al.   Microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems

(2015) Christopher E. Lawson et al.   ENVIRONMENTAL MICROBIOLOGY

Proton pump inhibitors alter the composition of the gut microbiota

(2015) Matthew A Jackson et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

The Swedish CArdioPulmonary BioImage Study: objectives and design

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

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

(2014) Anne Salonen et al.   ISME Journal

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

(2014) Fredrik H. Karlsson et al.   PLoS Computational Biology

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

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

(2013) Fredrik H. Karlsson et al.   NATURE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

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

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

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

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases

(2012) M Tanweer Khan et al.   ISME Journal

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Categorization of the gut microbiota: enterotypes or gradients?

(2012) Ian B. Jeffery et al.   NATURE REVIEWS MICROBIOLOGY

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

(2010) Anne Salonen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene

(2009) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE