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

The gut microbiome in health and in disease

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

Regularization Paths for Generalized Linear Models via Coordinate Descent

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

Effect of Metformin on Metabolic Improvement and Gut Microbiota

(2014) Heetae Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits

(2014) Filipe De Vadder et al.   CELL

Gut Dysbiosis and Detection of “Live Gut Bacteria” in Blood of Japanese Patients With Type 2 Diabetes

(2014) Junko Sato et al.   DIABETES CARE

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

(2014) J. Gerritsen et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Metformin—mode of action and clinical implications for diabetes and cancer

(2014) Ida Pernicova et al.   Nature Reviews Endocrinology

Novel Gut-Based Pharmacology of Metformin in Patients with Type 2 Diabetes Mellitus

(2014) Antonella Napolitano et al.   PLoS One

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

Lifestyle Interventions for Patients With and at Risk for Type 2 Diabetes

(2013) Elizabeth Sumamo Schellenberg et al.   ANNALS OF INTERNAL MEDICINE

Metformin Retards Aging in C. elegans by Altering Microbial Folate and Methionine Metabolism

(2013) Filipe Cabreiro et al.   CELL

An increase in theAkkermansiaspp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice

(2013) Na-Ri Shin et al.   GUT

A gut prediction

(2013) Willem M. de Vos et al.   NATURE

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

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Human Gut Microbiota Changes Reveal the Progression of Glucose Intolerance

(2013) Xiuying Zhang et al.   PLoS One

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

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

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

A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens)

(2012) Falk Hildebrand et al.   BMC GENOMICS

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

(2012) Junjie Qin et al.   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Effect of susceptibility to enterotoxigenic Escherichia coli F4 and of dietary tryptophan on gut microbiota diversity observed in healthy young pigs

(2012) Stefano Messori et al.   VETERINARY MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

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

(2010) Nadja Larsen et al.   PLoS One

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

(2009) Thomas Abeel et al.   BIOINFORMATICS