Gut microbiota density influences host physiology and is shaped by host and microbial factors

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

(2019) Graham J. Britton et al.   IMMUNITY

Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice

(2018) Sean R. Llewellyn et al.   GASTROENTEROLOGY

Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection

(2018) Tao Zuo et al.   Nature Communications

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

(2018) Eric J. Battaglioli et al.   Science Translational Medicine

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Water activity does not shape the microbiota in the human colon

(2017) Doris Vandeputte et al.   GUT

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte 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

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

(2017) Egle Cekanaviciute et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice

(2017) Giada De Palma et al.   Science Translational Medicine

The Fungal Frontier: A Comparative Analysis of Methods Used in the Study of the Human Gut Mycobiome

(2017) Chloe E. Huseyin et al.   Frontiers in Microbiology

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

(2016) Timothy R. Sampson et al.   CELL

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Sequence-based methods for detecting and evaluating the human gut mycobiome

(2016) M.J. Suhr et al.   LETTERS IN APPLIED MICROBIOLOGY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

Mycobiome: Approaches to analysis of intestinal fungi

(2015) Jie Tang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Neutrophil ageing is regulated by the microbiome

(2015) Dachuan Zhang et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Crosstalk between Muscularis Macrophages and Enteric Neurons Regulates Gastrointestinal Motility

(2014) Paul Andrew Muller et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

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

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

Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice

(2014) Gerold Bongers et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Microbiota-Dependent Crosstalk Between Macrophages and ILC3 Promotes Intestinal Homeostasis

(2014) A. Mortha et al.   SCIENCE

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

(2014) Vijay Shankar et al.   Microbiome

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Complex Interactions Among Diet, Gastrointestinal Transit, and Gut Microbiota in Humanized Mice

(2013) Purna C. Kashyap et al.   GASTROENTEROLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes 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

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

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

(2011) T. Magoc et al.   BIOINFORMATICS

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

The Antibacterial Lectin RegIII  Promotes the Spatial Segregation of Microbiota and Host in the Intestine

(2011) S. Vaishnava et al.   SCIENCE

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

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

The relation between maximal running speed and body mass in terrestrial mammals

(2009) Theodore Garland   JOURNAL OF ZOOLOGY

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY