Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies

Sodium butyrate attenuates high-fat diet-induced steatohepatitis in mice by improving gut microbiota and gastrointestinal barrier

(2017) Da Zhou et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants

(2017) Wendy S.W. Wong et al.   Microbiome

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

(2016) Emily Vogtmann et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L.

(2016) Sachi Tanaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Epidemiologic studies of the human microbiome and cancer

(2016) Emily Vogtmann et al.   BRITISH JOURNAL OF CANCER

Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies

(2016) E. Loftfield et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

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

(2016) Kenichiro Takahashi et al.   DIGESTION

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State

(2016) Hong Lin et al.   Scientific Reports

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies

(2015) R. Sinha et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

(2015) Roberto Berni Canani et al.   ISME Journal

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Gut mucosal microbiome across stages of colorectal carcinogenesis

(2015) Geicho Nakatsu et al.   Nature Communications

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Collection media and delayed freezing effects on microbial composition of human stool

(2015) Roberto Flores et al.   Microbiome

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

(2015) Fiona Fouhy et al.   PLoS One

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Relating the metatranscriptome and metagenome of the human gut

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

A targeted metabolomic protocol for short-chain fatty acids and branched-chain amino acids

(2013) Xiaojiao Zheng et al.   Metabolomics

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

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

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences

(2012) Roberto Flores et al.   EUROPEAN JOURNAL OF CLINICAL INVESTIGATION

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

(2012) Martin Iain Bahl et al.   FEMS MICROBIOLOGY LETTERS

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

(2012) J Gregory Caporaso et al.   ISME Journal

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Daniel McDonald et al.   ISME Journal

Human intestinal microbiota: cross-talk with the host and its potential role in colorectal cancer

(2010) Marco Candela et al.   CRITICAL REVIEWS IN MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Obesity and the human microbiome

(2009) Ruth E Ley   CURRENT OPINION IN GASTROENTEROLOGY

Panorganismal Gut Microbiome−Host Metabolic Crosstalk

(2009) Francois-Pierre J. Martin et al.   JOURNAL OF PROTEOME RESEARCH

Serum Metabolite Profiling of Human Colorectal Cancer Using GC−TOFMS and UPLC−QTOFMS

(2009) Yunping Qiu et al.   JOURNAL OF PROTEOME RESEARCH

Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces

(2007) Jordan M. Nechvatal et al.   JOURNAL OF MICROBIOLOGICAL METHODS