Conducting a Microbiome Study

[1]  Susan P. Holmes,et al.  Waste Not , Want Not : Why Rarefying Microbiome Data is Inadmissible . October 1 , 2013 , 2013 .

[2]  Nicholas A. Bokulich,et al.  Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate , 2013, Proceedings of the National Academy of Sciences.

[3]  P. Mieczkowski,et al.  Practical innovations for high-throughput amplicon sequencing , 2013, Nature Methods.

[4]  Jens Nielsen,et al.  Assessing the Human Gut Microbiota in Metabolic Diseases , 2013, Diabetes.

[5]  Dan Knights,et al.  Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome , 2013, Gut.

[6]  J. Clemente,et al.  Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice , 2013, Science.

[7]  Brian C. Thomas,et al.  The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria , 2013, eLife.

[8]  J. Clemente,et al.  The Long-Term Stability of the Human Gut Microbiota , 2013 .

[9]  B. Hurwitz,et al.  Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics , 2013, Environmental microbiology.

[10]  S. Tringe,et al.  Diversity and heritability of the maize rhizosphere microbiome under field conditions , 2013, Proceedings of the National Academy of Sciences.

[11]  L. Ursell,et al.  Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor , 2013, Science.

[12]  P. Turnbaugh,et al.  Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome , 2013, Cell.

[13]  Curtis Huttenhower,et al.  A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets , 2013, PLoS Comput. Biol..

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

[15]  Nicholas A. Bokulich,et al.  Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing , 2012, Nature Methods.

[16]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[17]  M. Surette,et al.  The interplay between the intestinal microbiota and the brain , 2012, Nature Reviews Microbiology.

[18]  Larissa B. Thackray,et al.  Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome , 2012, Cell.

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

[20]  Taane G. Clark,et al.  Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice , 2012, PLoS pathogens.

[21]  R. Knight,et al.  Diversity, stability and resilience of the human gut microbiota , 2012, Nature.

[22]  Jonathan Friedman,et al.  Inferring Correlation Networks from Genomic Survey Data , 2012, PLoS Comput. Biol..

[23]  M. Blaser,et al.  Antibiotics in early life alter the murine colonic microbiome and adiposity , 2012, Nature.

[24]  William A. Walters,et al.  Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. , 2012, Cell host & microbe.

[25]  L. T. Angenent,et al.  Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy , 2012, Cell.

[26]  Robert C. Edgar,et al.  Defining the core Arabidopsis thaliana root microbiome , 2012, Nature.

[27]  Rob Knight,et al.  Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys , 2011, The ISME Journal.

[28]  D. Relman,et al.  The Application of Ecological Theory Toward an Understanding of the Human Microbiome , 2012, Science.

[29]  M. Dubinsky,et al.  Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis , 2012, Science.

[30]  Rick L. Stevens,et al.  Unlocking the potential of metagenomics through replicated experimental design , 2012, Nature Biotechnology.

[31]  Mark J. Pallen,et al.  High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature , 2012, PloS one.

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

[33]  P. Gajer,et al.  Comparison of Storage Conditions for Human Vaginal Microbiome Studies , 2012, PloS one.

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

[35]  J. Clemente,et al.  The Impact of the Gut Microbiota on Human Health: An Integrative View , 2012, Cell.

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

[37]  Rob Knight,et al.  Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences , 2012, The ISME Journal.

[38]  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.

[39]  B. Chassaing,et al.  Gut microbiota drives metabolic disease in immunologically altered mice. , 2012, Advances in immunology.

[40]  William A. Walters,et al.  Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys , 2011, The ISME Journal.

[41]  E. Feuille The Antibacterial Lectin RegIII-Gamma Promotes the Spatial Segregation of Microbiota and Host in the Intestine , 2012 .

[42]  Erik S. Wright,et al.  DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences , 2011, Applied and Environmental Microbiology.

[43]  R. Ley,et al.  The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine , 2011, Science.

[44]  F. Bushman,et al.  Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes , 2011, Science.

[45]  David R. Riley,et al.  CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing , 2011, BMC Bioinformatics.

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

[47]  B. S. Manjunath,et al.  The iPlant Collaborative: Cyberinfrastructure for Plant Biology , 2011, Front. Plant Sci..

[48]  R. Knight,et al.  Moving pictures of the human microbiome , 2011, Genome Biology.

[49]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[50]  Emily S. Charlson,et al.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications , 2011, Nature Biotechnology.

[51]  K. Krogfelt,et al.  Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods , 2011, The open microbiology journal.

[52]  R. Knight,et al.  Supervised classification of human microbiota. , 2011, FEMS microbiology reviews.

[53]  B. Haas,et al.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. , 2011, Genome research.

[54]  R. Knight,et al.  Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition , 2011, PloS one.

[55]  William A. Walters,et al.  Experimental and analytical tools for studying the human microbiome , 2011, Nature Reviews Genetics.

[56]  T. Fennell,et al.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.

[57]  Russell J. Davenport,et al.  Removing Noise From Pyrosequenced Amplicons , 2011, BMC Bioinformatics.

[58]  Vincent J. Denef,et al.  Strain-resolved community genomic analysis of gut microbial colonization in a premature infant , 2010, Proceedings of the National Academy of Sciences.

[59]  N. Socci,et al.  Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. , 2010, The Journal of clinical investigation.

[60]  Rob Knight,et al.  Human oral, gut, and plaque microbiota in patients with atherosclerosis , 2010, Proceedings of the National Academy of Sciences.

[61]  Min Zhang,et al.  Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors , 2010, Proceedings of the National Academy of Sciences.

[62]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[63]  D. Relman,et al.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation , 2010, Proceedings of the National Academy of Sciences.

[64]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[65]  R. Knight,et al.  Microbial community resemblance methods differ in their ability to detect biologically relevant patterns , 2010, Nature Methods.

[66]  F. Bushman,et al.  Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags , 2010, BMC Microbiology.

[67]  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.

[68]  Janne Nikkilä,et al.  Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. , 2010, Journal of microbiological methods.

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

[70]  R. Ley,et al.  Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5 , 2010, Science.

[71]  Andy F. S. Taylor,et al.  The UNITE database for molecular identification of fungi--recent updates and future perspectives. , 2010, The New phytologist.

[72]  I. Wilson,et al.  Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice , 2010, PloS one.

[73]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

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

[75]  R. Knight,et al.  Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution , 2010, Nature Methods.

[76]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[77]  Dan R. Littman,et al.  Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria , 2009, Cell.

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

[79]  Daniel J. G. Lahr,et al.  Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. , 2009, BioTechniques.

[80]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[81]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[82]  A. Reverter,et al.  Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals. , 2009, Veterinary microbiology.

[83]  Les Dethlefsen,et al.  The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing , 2008, PLoS biology.

[84]  R. Ley,et al.  Innate immunity and intestinal microbiota in the development of Type 1 diabetes , 2008, Nature.

[85]  R. Knight,et al.  Species divergence and the measurement of microbial diversity. , 2008, FEMS microbiology reviews.

[86]  R. Knight,et al.  Evolution of Mammals and Their Gut Microbes , 2008, Science.

[87]  R. Knight,et al.  Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex , 2008, Nature Methods.

[88]  Wendy S. Garrett,et al.  Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System , 2007, Cell.

[89]  Roger S Lasken,et al.  Single-cell genomic sequencing using Multiple Displacement Amplification. , 2007, Current opinion in microbiology.

[90]  Rita Sipos,et al.  Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. , 2007, FEMS microbiology ecology.

[91]  Yang Liu,et al.  Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases , 2007, Emerging infectious diseases.

[92]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[93]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[94]  Jeffrey I. Gordon,et al.  Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection , 2006, Cell.

[95]  Vanja Klepac-Ceraj,et al.  PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample , 2005, Applied and Environmental Microbiology.

[96]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[97]  F. Bäckhed,et al.  Obesity alters gut microbial ecology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[98]  J. Handelsman,et al.  Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness , 2005, Applied and Environmental Microbiology.

[99]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[100]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[101]  Norman R. Pace,et al.  Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants , 1998, Applied and Environmental Microbiology.

[102]  AC Tose Cell , 1993, Cell.

[103]  D. Savage Microbial ecology of the gastrointestinal tract. , 1977, Annual review of microbiology.