Conducting a microbiome study (Q35208886)

7 August 2017

title

Conducting a microbiome study (English)

1 reference

7 August 2017

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7

1 reference

7 August 2017

Sara C Di Rienzi

2

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Angela C Poole

Angela C Poole

3

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Omry Koren

Omry Koren

4

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Ruth Ley

Ruth E Ley

8

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J Gregory Caporaso

6

J Gregory Caporaso

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7 August 2017

1

Julia K Goodrich

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7 August 2017

5

William A Walters

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7 August 2017

language of work or name

English

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publication date

1 July 2014

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7 August 2017

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7 August 2017

volume

158

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7 August 2017

issue

2

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7 August 2017

page(s)

250-262

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Waste not, want not: why rarefying microbiome data is inadmissible

7 August 2017

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

28 July 2018

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28 July 2018

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Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

28 July 2018

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Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage

28 July 2018

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Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome

28 July 2018

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Gut microbiota drives metabolic disease in immunologically altered mice.

28 July 2018

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Inferring correlation networks from genomic survey data

28 July 2018

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The interplay between the intestinal microbiota and the brain

28 July 2018

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Diversity, stability and resilience of the human gut microbiota

28 July 2018

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Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice

28 July 2018

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Host remodeling of the gut microbiome and metabolic changes during pregnancy

28 July 2018

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Defining the core Arabidopsis thaliana root microbiome

28 July 2018

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Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

28 July 2018

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A framework for human microbiome research

28 July 2018

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Structure, function and diversity of the healthy human microbiome

28 July 2018

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Unlocking the potential of metagenomics through replicated experimental design

28 July 2018

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The application of ecological theory toward an understanding of the human microbiome

28 July 2018

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Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

28 July 2018

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High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature

28 July 2018

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Comparison of storage conditions for human vaginal microbiome studies

28 July 2018

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28 July 2018

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28 July 2018

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Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

28 July 2018

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Experimental and analytical tools for studying the human microbiome

28 July 2018

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Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

28 July 2018

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28 July 2018

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The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine

28 July 2018

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Linking long-term dietary patterns with gut microbial enterotypes

28 July 2018

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28 July 2018

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Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

28 July 2018

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UCHIME improves sensitivity and speed of chimera detection

28 July 2018

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Optimising bacterial DNA extraction from faecal samples: comparison of three methods

28 July 2018

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Moving pictures of the human microbiome

28 July 2018

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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

28 July 2018

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Enterotypes of the human gut microbiome

28 July 2018

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Host-associated and free-living phage communities differ profoundly in phylogenetic composition

28 July 2018

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Removing noise from pyrosequenced amplicons

28 July 2018

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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

28 July 2018

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Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

28 July 2018

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Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans.

28 July 2018

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Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

28 July 2018

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Human oral, gut, and plaque microbiota in patients with atherosclerosis

28 July 2018

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Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

28 July 2018

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Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

28 July 2018

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28 July 2018

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28 July 2018

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Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

28 July 2018

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Viruses in the faecal microbiota of monozygotic twins and their mothers

28 July 2018

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Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

28 July 2018

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Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5

28 July 2018

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Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis

28 July 2018

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Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice

28 July 2018

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

28 July 2018

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Bacterial community variation in human body habitats across space and time

28 July 2018

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Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

28 July 2018

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The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

28 July 2018

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

28 July 2018

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Innate immunity and intestinal microbiota in the development of Type 1 diabetes

28 July 2018

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Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals

28 July 2018

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Evolution of mammals and their gut microbes

28 July 2018

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Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

28 July 2018

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Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

28 July 2018

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Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection

28 July 2018

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Galaxy: a platform for interactive large-scale genome analysis

28 July 2018

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Obesity alters gut microbial ecology

28 July 2018

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Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness

28 July 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

28 July 2018

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Comprehensive human genome amplification using multiple displacement amplification

28 July 2018

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Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants

28 July 2018

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Microbial ecology of the gastrointestinal tract

28 July 2018

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Assessing the human gut microbiota in metabolic diseases

28 July 2018

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Practical innovations for high-throughput amplicon sequencing.

26 September 2018

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Xenobiotics shape the physiology and gene expression of the active human gut microbiome

26 September 2018

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Antibiotics in early life alter the murine colonic microbiome and adiposity

26 September 2018

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The impact of the gut microbiota on human health: an integrative view

26 September 2018

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

26 September 2018

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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

26 September 2018

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Supervised classification of human microbiota

26 September 2018

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Search and clustering orders of magnitude faster than BLAST

26 September 2018

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The UNITE database for molecular identification of fungi--recent updates and future perspectives

26 September 2018

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QIIME allows analysis of high-throughput community sequencing data

26 September 2018

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Galaxy: a web-based genome analysis tool for experimentalists

26 September 2018

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Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase

26 September 2018

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Induction of intestinal Th17 cells by segmented filamentous bacteria

26 September 2018

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A core gut microbiome in obese and lean twins

26 September 2018

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Species divergence and the measurement of microbial diversity

26 September 2018

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Single-cell genomic sequencing using Multiple Displacement Amplification

26 September 2018

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Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5074386

Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5074386

An obesity-associated gut microbiome with increased capacity for energy harvest

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5074386

Microbial ecology: human gut microbes associated with obesity

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5074386

PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5074386

10.1016/J.CELL.2014.06.037

26 September 2018

Identifiers

DOI

1 reference

7 August 2017

1 reference

7 August 2017

1 reference