Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

(2019) Afshin Beheshti et al.   Jove-Journal of Visualized Experiments

Behavior of mice aboard the International Space Station

(2019) April E. Ronca et al.   Scientific Reports

Understanding sequencing data as compositions: an outlook and review

(2018) Thomas P Quinn et al.   BIOINFORMATICS

Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study

(2018) Afshin Beheshti et al.   Scientific Reports

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome

(2018) Anupriya Tripathi et al.   mSystems

GeneLab: Omics database for spaceflight experiments

(2018) Shayoni Ray et al.   BIOINFORMATICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Microbiome Datasets Are Compositional: And This Is Not Optional

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

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome

(2017) David Casero et al.   Microbiome

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Microbiome-wide association studies link dynamic microbial consortia to disease

(2016) Jack A. Gilbert et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Changes in mitochondrial homeostasis and redox status in astronauts following long stays in space

(2016) Hiroko P. Indo et al.   Scientific Reports

Spaceflight impairs antigen-specific tolerance induction in vivo and increases inflammatory cytokines

(2015) Tammy T. Chang et al.   FASEB JOURNAL

Fluid shifts, vasodilatation and ambulatory blood pressure reduction during long duration spaceflight

(2015) Peter Norsk et al.   JOURNAL OF PHYSIOLOGY-LONDON

Feasibility of a Short-Arm Centrifuge for Mouse Hypergravity Experiments

(2015) Hironobu Morita et al.   PLoS One

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches

(2015) Stefan J. Green et al.   PLoS One

Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis

(2015) Lauren E. Ritchie et al.   PLoS One

Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea

(2014) Isabel Moreno-Indias et al.   EUROPEAN RESPIRATORY JOURNAL

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

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

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

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Spaceflight Environment Induces Mitochondrial Oxidative Damage in Ocular Tissue

(2013) Xiao W. Mao et al.   RADIATION RESEARCH

High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation

(2013) P. V. Moonsamy et al.   TISSUE ANTIGENS

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Gut Microbiota Composition Is Correlated to Grid Floor Induced Stress and Behavior in the BALB/c Mouse

(2012) Katja Maria Bangsgaard Bendtsen et al.   PLoS One

Coarse, but not finely ground, dietary fibre increases intestinal Firmicutes:Bacteroidetes ratio and reduces diarrhoea induced by experimental infection in piglets

(2011) Francesc Molist et al.   BRITISH JOURNAL OF NUTRITION

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

(2011) Seth M. Bybee et al.   Genome Biology and Evolution

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

(2011) Daniel McDonald et al.   ISME Journal

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

Principal component analysis for compositional data with outliers

(2009) Peter Filzmoser et al.   ENVIRONMETRICS

Mammalian polyamine metabolism and function

(2009) Anthony E. Pegg   IUBMB LIFE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols