Interactions between species introduce spurious associations in microbiome studies

Oscillospira and related bacteria - From metagenomic species to metabolic features

(2017) Uri Gophna et al.   ENVIRONMENTAL MICROBIOLOGY

Variable habitat conditions drive species covariation in the human microbiota

(2017) Charles K. Fisher et al.   PLoS Computational Biology

Periodontal Bacteria in the Genital Tract: Are They Related to Adverse Pregnancy Outcome?

(2017) M.A. Cassini et al.   INTERNATIONAL JOURNAL OF IMMUNOPATHOLOGY AND PHARMACOLOGY

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

(2016) Kenichiro Takahashi et al.   DIGESTION

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population

(2016) Silan Gu et al.   MICROBES AND INFECTION

Microbiome-wide association studies link dynamic microbial consortia to disease

(2016) Jack A. Gilbert et al.   NATURE

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Universality of human microbial dynamics

(2016) Amir Bashan et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

(2016) John Chu et al.   Nature Chemical Biology

Local equilibrium in bird flocks

(2016) Thierry Mora et al.   Nature Physics

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers

(2016) Ryan S. Schwarz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota

(2016) Feng Wang et al.   Cell Reports

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data

(2016) Patricio Jeraldo et al.   Frontiers in Microbiology

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp.

(2016) Kaisa Hiippala et al.   Frontiers in Microbiology

The Gut Microbiota in Immune-Mediated Inflammatory Diseases

(2016) Jessica D. Forbes et al.   Frontiers in Microbiology

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis

(2016) Sabrina Duranti et al.   Scientific Reports

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study

(2016) Christian Milani et al.   Scientific Reports

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

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

(2015) K. Z. Coyte et al.   SCIENCE

Interactions between the intestinal microbiota and bile acids in gallstones patients

(2015) Nirit Keren et al.   Environmental Microbiology Reports

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

(2015) Richard R. Stein et al.   PLoS Computational Biology

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection

(2015) Joshua S. Son et al.   PLoS One

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

(2014) Helen Kettle et al.   ENVIRONMENTAL MICROBIOLOGY

Arthritis susceptibility and the gut microbiome

(2014) Veena Taneja   FEBS LETTERS

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

(2014) Jotham Suez et al.   NATURE

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Gut Microbiome in Down Syndrome

(2014) Elena Biagi et al.   PLoS One

Faecalibacterium prausnitzii Inhibits Interleukin-17 to Ameliorate Colorectal Colitis in Rats

(2014) Mingming Zhang et al.   PLoS One

Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity

(2013) Samuel B. Brusca et al.   CURRENT OPINION IN RHEUMATOLOGY

Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis

(2013) Xinyun Qiu et al.   Journal of Crohns & Colitis

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Human intestinal microbiota composition is associated with local and systemic inflammation in obesity

(2013) Froukje J. Verdam et al.   Obesity

The Microaerophilic Microbiota of De-Novo Paediatric Inflammatory Bowel Disease: The BISCUIT Study

(2013) Richard Hansen et al.   PLoS One

Characterization of the Gut-Associated Microbiome in Inflammatory Pouch Complications Following Ileal Pouch-Anal Anastomosis

(2013) Andrea D. Tyler et al.   PLoS One

Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder

(2013) Lv Wang et al.   Molecular Autism

Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH

(2012) Lixin Zhu et al.   HEPATOLOGY

Microbiota conservation and BMI signatures in adult monozygotic twins

(2012) Sebastian Tims et al.   ISME Journal

Microbial Dysbiosis in Pediatric Patients with Crohn's Disease

(2012) N. O. Kaakoush et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2012) Junjie Qin et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Contributions of the microbial hydrogen economy to colonic homeostasis

(2012) Franck Carbonero et al.   Nature Reviews Gastroenterology & Hepatology

Application of Novel PCR-Based Methods for Detection, Quantitation, and Phylogenetic Characterization of Sutterella Species in Intestinal Biopsy Samples from Children with Autism and Gastrointestinal Disturbances

(2012) B. L. Williams et al.   mBio

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

(2011) Reiner Jumpertz et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Treating Clostridium difficile Infection With Fecal Microbiota Transplantation

(2011) Johan S. Bakken et al.   Clinical Gastroenterology and Hepatology

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

(2011) M. Joossens et al.   GUT

Characterization of the Gastrointestinal Microbiota in Health and Inflammatory Bowel Disease

(2011) Peter De Cruz et al.   INFLAMMATORY BOWEL DISEASES

The microbiome-gut-brain axis: from bowel to behavior

(2011) J. F. Cryan et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Behavior of QQ-Plots and Genomic Control in Studies of Gene-Environment Interaction

(2011) Arend Voorman et al.   PLoS One

A Comprehensive Evaluation of Colonic Mucosal Isolates of Sutterella wadsworthensis from Inflammatory Bowel Disease

(2011) Indrani Mukhopadhya et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Butyrate production in phylogenetically diverse Firmicutes isolated from the chicken caecum

(2011) Venessa Eeckhaut et al.   Microbial Biotechnology

Assessment of psychotropic-like properties of a probiotic formulation ( Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects

(2010) Michaël Messaoudi et al.   BRITISH JOURNAL OF NUTRITION

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Bacteria Associated with Immunoregulatory Cells in Mice

(2009) L. L. Presley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Low counts of Faecalibacterium prausnitzii in colitis microbiota

(2009) H. Sokol et al.   INFLAMMATORY BOWEL DISEASES

Inferring species interactions in tropical forests

(2009) I. Volkov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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