Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns

Using sewage for surveillance of antimicrobial resistance

(2020) Frank M. Aarestrup et al.   SCIENCE

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

(2020) Q. R. Ducarmon et al.   mSystems

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

(2019) Rene S. Hendriksen et al.   Nature Communications

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

(2019) Philipp Rausch et al.   Microbiome

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

(2018) Marina Panek et al.   Scientific Reports

The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis

(2018) Luisa K. Hallmaier-Wacker et al.   Scientific Reports

Impact of sample processing on human airways microbial metagenomes

(2017) Lutz Wiehlmann et al.   JOURNAL OF BIOTECHNOLOGY

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

(2017) Thomas Nordahl Petersen et al.   PLoS One

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data

(2016) Ran Blekhman et al.   Scientific Reports

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

(2016) Berith E. Knudsen et al.   mSystems

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

(2016) Se Jin Song et al.   mSystems

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

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

(2015) Roberto Flores et al.   Microbiome

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

(2015) Danyta I. Tedjo et al.   PLoS One

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles

(2014) Jun Hang et al.   Microbiome

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML)

(2008) Renzo Kottmann et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY