Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater

(2019) Julien Tap et al.   Scientific Reports

Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation

(2019) Jingi Bae et al.   Clinical Proteomics

Impacts of the Human Gut Microbiome on Therapeutics

(2018) Yoshiki Vázquez-Baeza et al.   Annual Review of Pharmacology and Toxicology

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

(2018) Julia Hassa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD

(2018) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

Integrative omics for health and disease

(2018) Konrad J. Karczewski et al.   NATURE REVIEWS GENETICS

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods

(2018) Courtney N. Passow et al.   Molecular Ecology Resources

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research

(2017) Sebastian Menke et al.   Frontiers in Microbiology

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

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

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

(2016) R. Heyer et al.   Biotechnology for Biofuels

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

(2016) Eric W. Deutsch et al.   NUCLEIC ACIDS RESEARCH

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

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

(2016) Se Jin Song et al.   mSystems

Effect of short-term room temperature storage on the microbial community in infant fecal samples

(2016) Yong Guo et al.   Scientific Reports

Multiorganismal Insects: Diversity and Function of Resident Microorganisms

(2015) Angela E. Douglas   Annual Review of Entomology

Unraveling the Hygiene Hypothesis of helminthes and autoimmunity: origins, pathophysiology, and clinical applications

(2015) Mathilde Versini et al.   BMC Medicine

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeks

(2015) Vanessa L. Hale et al.   JOURNAL OF MICROBIOLOGICAL METHODS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

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

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities

(2015) Shaman Narayanasamy et al.   Microbial Biotechnology

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

(2015) Fiona Fouhy et al.   PLoS One

Picking Vanished Proteins from the Void: How to Collect and Ship/Share Extremely Dilute Proteins in a Reproducible and Highly Efficient Manner

(2014) Florian Bonn et al.   ANALYTICAL CHEMISTRY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

Gut Microbiome and Multiple Sclerosis

(2014) Pavan Bhargava et al.   Current Neurology and Neuroscience Reports

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years?

(2014) Georgina L Hold   WORLD JOURNAL OF GASTROENTEROLOGY

Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection

(2014) F Drissi et al.   Nutrition & Diabetes

A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia

(2013) Natalya Yutin et al.   ENVIRONMENTAL MICROBIOLOGY

Consumption of Fermented Milk Product With Probiotic Modulates Brain Activity

(2013) Kirsten Tillisch et al.   GASTROENTEROLOGY

Beyond gene expression: The impact of protein post-translational modifications in bacteria

(2013) Joel A. Cain et al.   Journal of Proteomics

Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis

(2013) Robert A Koeth et al.   NATURE MEDICINE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

(2013) M. I. Smith et al.   SCIENCE

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

(2012) Thomas Schneider et al.   ISME Journal

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

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

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

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

(2011) Reiner Jumpertz et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Assessment of psychotropic-like properties of a probiotic formulation ( Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects

(2010) Michaël Messaoudi et al.   BRITISH JOURNAL OF NUTRITION

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles

(2009) Paul Wilmes et al.   CURRENT OPINION IN MICROBIOLOGY

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

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH