Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation

(2018) Alexander Rodriguez-Palacios et al.   Scientific Reports

Inbred Mouse Populations Exhibit Intergenerational Changes in Intestinal Microbiota Composition and Function Following Introduction to a Facility

(2017) Jocelyn M. Choo et al.   Frontiers in Microbiology

Association between the gut microbiota and diet: Fetal life, early childhood, and further life

(2016) Daria A. Kashtanova et al.   NUTRITION

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

Intestinal Microbiota Is Influenced by Gender and Body Mass Index

(2016) Carmen Haro et al.   PLoS One

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism

(2015) Vanessa Leone et al.   Cell Host & Microbe

The gut microbiome in health and in disease

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

Genetic and environmental control of host-gut microbiota interactions

(2015) Elin Org et al.   GENOME RESEARCH

Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation

(2015) Clara Moon et al.   NATURE

Gut microbiota and aging

(2015) P. W. OToole et al.   SCIENCE

Aging and the human gut microbiota—from correlation to causality

(2015) Sitaraman Saraswati et al.   Frontiers in Microbiology

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

(2015) Aaron C. Ericsson et al.   PLoS One

Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time

(2015) Yana Emmy Hoy et al.   PLoS One

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

(2014) Amir Zarrinpar et al.   Cell Metabolism

Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice

(2014) G. B. Rogers et al.   Scientific Reports

Microbial shifts in the aging mouse gut

(2014) Morgan GI Langille et al.   Microbiome

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

(2013) Jonathan McCafferty et al.   ISME Journal

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The role of the immune system in governing host-microbe interactions in the intestine

(2013) Eric M Brown et al.   NATURE IMMUNOLOGY

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle 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

Gut bacteria profiles of Mus musculus at the phylum and family levels are influenced by saturation of dietary fatty acids

(2012) Tianyu Liu et al.   ANAEROBE

The effects of repeated oral gavage on the health of male CD-1 mice

(2012) Regina Arantes-Rodrigues et al.   LAB ANIMAL

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10 −/− mice

(2012) Suzanne Devkota et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Colonization-Induced Host-Gut Microbial Metabolic Interaction

(2011) S. P. Claus et al.   mBio

Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models

(2010) E F Murphy et al.   GUT

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Sex Differences in Pharmacokinetics and Pharmacodynamics

(2009) Offie P. Soldin et al.   CLINICAL PHARMACOKINETICS

Impact of Gut Microbiota on Intestinal and Hepatic Levels of Phase 2 Xenobiotic-Metabolizing Enzymes in the Rat

(2009) W. Meinl et al.   DRUG METABOLISM AND DISPOSITION

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis

(2009) Yunwei Wang et al.   ISME Journal

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

(2008) Ivaylo I. Ivanov et al.   Cell Host & Microbe

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE