Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome

Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract

(2019) Matthew H. Foley et al.   PLoS Pathogens

Chronic paradoxical sleep deprivation-induced depression­like behavior, energy metabolism and microbial changes in rats

(2019) Weini Ma et al.   LIFE SCIENCES

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Altered fecal microbiota composition in all male aggressor-exposed rodent model simulating features of post-traumatic stress disorder

(2018) Aarti Gautam et al.   JOURNAL OF NEUROSCIENCE RESEARCH

The fecal metabolome as a functional readout of the gut microbiome

(2018) Jonas Zierer et al.   NATURE GENETICS

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

TUDCA: An Agonist of the Bile Acid Receptor GPBAR1/TGR5 With Anti-Inflammatory Effects in Microglial Cells

(2017) Natalia Yanguas-Casás et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Microbiota and reproducibility of rodent models

(2017) Craig L Franklin et al.   LAB ANIMAL

3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

(2017) Ivan Protsyuk et al.   Nature Protocols

The sleep-deprived human brain

(2017) Adam J. Krause et al.   NATURE REVIEWS NEUROSCIENCE

Human and rat gut microbiome composition is maintained following sleep restriction

(2017) Shirley L. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Bile Acid Signaling Pathways from the Enterohepatic Circulation to the Central Nervous System

(2017) Kim L. Mertens et al.   Frontiers in Neuroscience

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Sleep Disturbance Immediately Prior to Trauma Predicts Subsequent Psychiatric Disorder

(2017) Richard A. Bryant et al.   SLEEP

Microbiota-induced obesity requires farnesoid X receptor

(2016) Ava Parséus et al.   GUT

Multiple classifier systems for automatic sleep scoring in mice

(2016) Vance Gao et al.   JOURNAL OF NEUROSCIENCE METHODS

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis?

(2016) Roman M. Stilling et al.   NEUROCHEMISTRY INTERNATIONAL

Immunization with a heat-killed preparation of the environmental bacteriumMycobacterium vaccaepromotes stress resilience in mice

(2016) Stefan O. Reber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Triterpenoid herbal saponins enhance beneficial bacteria, decrease sulfate-reducing bacteria, modulate inflammatory intestinal microenvironment and exert cancer preventive effects in ApcMin/+ mice

(2016) Lei Chen et al.   Oncotarget

Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals

(2016) Christian Benedict et al.   Molecular Metabolism

Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk

(2016) Kalaimathi Govindarajan et al.   PLoS One

Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice

(2016) Valeriy A. Poroyko et al.   Scientific Reports

Why Sleep Is Important for Health: A Psychoneuroimmunology Perspective

(2015) Michael R. Irwin   Annual Review of Psychology

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood

(2015) Laura Steenbergen et al.   BRAIN BEHAVIOR AND IMMUNITY

Host–microbe interactions and the enteric nervous system: a new connection?

(2015) Katrina Ray   Nature Reviews Gastroenterology & Hepatology

Sleep quality but not sleep quantity effects on cortisol responses to acute psychosocial stress

(2015) Sarah M. Bassett et al.   STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS

Sleep Disturbance during Military Deployment

(2015) Alan L. Peterson et al.   MILITARY MEDICINE

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

(2014) Filipe De Vadder et al.   CELL

Beyond intestinal soap—bile acids in metabolic control

(2014) Folkert Kuipers et al.   Nature Reviews Endocrinology

Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut

(2014) S. A. Joyce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Absence of the gut microbiota enhances anxiety-like behavior and neuroendocrine response to acute stress in rats

(2014) Michèle Crumeyrolle-Arias et al.   PSYCHONEUROENDOCRINOLOGY

Effects of recovery sleep after one work week of mild sleep restriction on interleukin-6 and cortisol secretion and daytime sleepiness and performance

(2013) Slobodanka Pejovic et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Effect of on-call-related sleep deprivation on physicians′ mood and alertness

(2013) SirajO Wali et al.   Annals of Thoracic Medicine

Identification of the metabolites of anti-inflammatory compound clematichinenoside AR in rat intestinal microflora

(2013) Feng Li et al.   BIOMEDICAL CHROMATOGRAPHY

Homeostasis in Intestinal Epithelium Is Orchestrated by the Circadian Clock and Microbiota Cues Transduced by TLRs

(2013) Atish Mukherji et al.   CELL

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Partial Sleep Restriction Activates Immune Response-Related Gene Expression Pathways: Experimental and Epidemiological Studies in Humans

(2013) Vilma Aho et al.   PLoS One

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity

(2013) Fei Li et al.   Nature Communications

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

(2012) John F. Cryan et al.   NATURE REVIEWS NEUROSCIENCE

Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice

(2012) Betty W. Ma et al.   PLoS One

The Intestinal Microbiota Affect Central Levels of Brain-Derived Neurotropic Factor and Behavior in Mice

(2011) Premysl Bercik et al.   GASTROENTEROLOGY

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

(2011) Daniel McDonald et al.   ISME Journal

The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut-brain communication

(2011) P. Bercik et al.   NEUROGASTROENTEROLOGY AND MOTILITY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Variable selection using random forests

(2010) Robin Genuer et al.   PATTERN RECOGNITION LETTERS

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

(2010) Nadja Larsen et al.   PLoS One

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

(2010) M. Vijay-Kumar et al.   SCIENCE

A Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable Bowel Syndrome

(2009) Caroline Codling et al.   DIGESTIVE DISEASES AND SCIENCES

The Bile Acid Receptor FXR Is a Modulator of Intestinal Innate Immunity

(2009) P. Vavassori et al.   JOURNAL OF IMMUNOLOGY

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Sleep deprivation worsens inflammation and delays recovery in a mouse model of colitis

(2009) Yueming Tang et al.   SLEEP MEDICINE

Targeting bile-acid signalling for metabolic diseases

(2008) Charles Thomas et al.   NATURE REVIEWS DRUG DISCOVERY

Cardiovascular, Inflammatory, and Metabolic Consequences of Sleep Deprivation

(2008) Janet M. Mullington et al.   PROGRESS IN CARDIOVASCULAR DISEASES