Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis

[1]  J. Venter,et al.  A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome , 2016, Scientific Reports.

[2]  P. O’Toole,et al.  Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants , 2016, Microbiome.

[3]  J. Choo,et al.  Sample storage conditions significantly influence faecal microbiome profiles , 2015, Scientific Reports.

[4]  M. Gorzelak,et al.  Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool , 2015, PloS one.

[5]  P. Savelkoul,et al.  The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects , 2015, PloS one.

[6]  Stephen Wilcox,et al.  An inducible lentiviral guide RNA platform enables the identification of tumor-essential genes and tumor-promoting mutations in vivo. , 2015, Cell reports.

[7]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[8]  R. Hayes,et al.  Comparison of methods for fecal microbiome biospecimen collection , 2014, BMC Microbiology.

[9]  Yan Mei,et al.  The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA , 2014, Genome Biology.

[10]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[11]  T. Jones,et al.  Environmental determinants of islet autoimmunity (ENDIA): a pregnancy to early life cohort study in children at-risk of type 1 diabetes , 2013, BMC Pediatrics.

[12]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[13]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[14]  T. Klaenhammer,et al.  Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage , 2012, PloS one.

[15]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[16]  C. Manichanh,et al.  Storage conditions of intestinal microbiota matter in metagenomic analysis , 2012, BMC Microbiology.

[17]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[18]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[19]  J. Clemente,et al.  Human gut microbiome viewed across age and geography , 2012, Nature.

[20]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[21]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[22]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[23]  S. Massart,et al.  Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa , 2010, Proceedings of the National Academy of Sciences.

[24]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[25]  Rob Knight,et al.  Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. , 2010, FEMS microbiology letters.

[26]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[27]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[28]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[29]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[30]  G. Casella,et al.  Influence of Fecal Sample Storage on Bacterial Community Diversity , 2009, The open microbiology journal.

[31]  L. Pozza,et al.  OMNIgene®•GUT enables reliable collection of high quality fecal samples for gut microbiome studies , 2014 .

[32]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010 .

[33]  Methodology article , 2002 .