Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies (Q35766366)

10 August 2017

Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies (English)

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10 August 2017

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3

Joël Doré

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10 August 2017

Vincent Thomas

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author name string

James Clark

series ordinal

2

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PubMed ID

26347019

10 August 2017

language of work or name

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8 September 2015

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10 August 2017

20

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based on heuristic

inferred from page(s)

published in

Future Microbiology

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10 August 2017

10

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10 August 2017

1485-1504

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10 August 2017

9

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Richness of human gut microbiome correlates with metabolic markers

10 August 2017

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The neglected organ: bacterial flora has a crucial immunostimulatory role

21 January 2018

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The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations.

21 January 2018

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

21 January 2018

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Antibiotic treatments and microbes in the gut.

21 January 2018

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Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility

21 January 2018

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Effect of metformin on metabolic improvement and gut microbiota

21 January 2018

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Exercise and associated dietary extremes impact on gut microbial diversity

21 January 2018

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Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans

21 January 2018

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Diet rapidly and reproducibly alters the human gut microbiome

21 January 2018

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Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study

21 January 2018

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Temporal variability is a personalized feature of the human microbiome

21 January 2018

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Molecular analysis of the gut microbiota of identical twins with Crohn's disease

21 January 2018

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Comparative study of bacterial groups within the human cecal and fecal microbiota

21 January 2018

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Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples

21 January 2018

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The approach to sample acquisition and its impact on the derived human fecal microbiome and VOC metabolome

21 January 2018

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Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD.

21 January 2018

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The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

21 January 2018

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Survival in hostile territory: the microbiota of the stomach

21 January 2018

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Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

21 January 2018

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A crypt-specific core microbiota resides in the mouse colon

21 January 2018

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Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon.

21 January 2018

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

21 January 2018

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Functional biostructure of colonic microbiota (central fermenting area, germinal stock area and separating mucus layer) in healthy subjects and patients with diarrhea treated with Saccharomyces boulardii

21 January 2018

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The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

21 January 2018

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Processing faecal samples: a step forward for standards in microbial community analysis

21 January 2018

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Stool form scale as a useful guide to intestinal transit time

21 January 2018

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The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations.

21 January 2018

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Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis.

21 January 2018

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Storage conditions of intestinal microbiota matter in metagenomic analysis

21 January 2018

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

21 January 2018

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

21 January 2018

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Relating the metatranscriptome and metagenome of the human gut.

21 January 2018

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Demonstration of a frozen sample aliquotter to prepare plasma and serum aliquots without thawing frozen parent samples

21 January 2018

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Feasibility of self-collection of fecal specimens by randomly sampled women for health-related studies of the gut microbiome

21 January 2018

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

21 January 2018

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Comparison of methods for fecal microbiome biospecimen collection

21 January 2018

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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

21 January 2018

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Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

21 January 2018

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The human gut virome: inter-individual variation and dynamic response to diet

21 January 2018

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Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach.

21 January 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

21 January 2018

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Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction.

21 January 2018

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The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

21 January 2018

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A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples

21 January 2018

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Comparison of the QIAsymphony automated nucleic acid extraction and PCR setup platforms with NucliSens easyMAG and Corbett CAS-1200 liquid handling station for the detection of enteric pathogens in fecal samples.

21 January 2018

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Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

21 January 2018

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Ribosomal Database Project: data and tools for high throughput rRNA analysis

21 January 2018

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rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

21 January 2018

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Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity

21 January 2018

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Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance

21 January 2018

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The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses

21 January 2018

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Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas

21 January 2018

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CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

21 January 2018

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Evaluation of 16S rDNA-based community profiling for human microbiome research

21 January 2018

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A core human microbiome as viewed through 16S rRNA sequence clusters

21 January 2018

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Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.

21 January 2018

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Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium

21 January 2018

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Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers

21 January 2018

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Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

21 January 2018

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PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

21 January 2018

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How many 16S-based studies should be included in a metagenomic conference? It may be a matter of etymology.

21 January 2018

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cpnDB: a chaperonin sequence database

21 January 2018

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Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers.

21 January 2018

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Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail

21 January 2018

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A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity

21 January 2018

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Metagenomic analysis of the human distal gut microbiome

21 January 2018

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Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

21 January 2018

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A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

21 January 2018

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Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

21 January 2018

1 reference

A metagenome-wide association study of gut microbiota in type 2 diabetes

21 January 2018

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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

21 January 2018

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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

21 January 2018

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Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms

21 January 2018

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Developing a metagenomic view of xenobiotic metabolism

21 January 2018

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Genomic variation landscape of the human gut microbiome

21 January 2018

1 reference

Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities

21 January 2018

1 reference

Resident viruses and their interactions with the immune system

21 January 2018

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

21 January 2018

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Fecal excretion of human deoxyribonucleic acid as an index of inflammatory activity in ulcerative colitis.

21 January 2018

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Library preparation methods for next-generation sequencing: tone down the bias

21 January 2018

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Dual RNA-seq of pathogen and host

21 January 2018

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A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

21 January 2018

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Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection

21 January 2018

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A user's guide to quantitative and comparative analysis of metagenomic datasets

21 January 2018

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Analytical tools and databases for metagenomics in the next-generation sequencing era

21 January 2018

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Technology: The $1,000 genome

21 January 2018

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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

21 January 2018

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A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 January 2018

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First FDA authorization for next-generation sequencer

21 January 2018

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High-throughput sequencing technologies

21 January 2018

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Field guide to next-generation DNA sequencers

21 January 2018

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Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform

21 January 2018

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

21 January 2018

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Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling

21 January 2018

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Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

21 January 2018

1 reference

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

21 January 2018

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Assessment of metagenomic assembly using simulated next generation sequencing data

21 January 2018

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An extensive evaluation of read trimming effects on Illumina NGS data analysis

21 January 2018

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Assessment of quality control approaches for metagenomic data analysis

21 January 2018

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Quality control of microbiota metagenomics by k-mer analysis

21 January 2018

1 reference

https://opencitations.net/index/coci/api/v1/citations/10.1128/MR.51.2.221-271.1987

21 January 2018

1 reference

18 October 2022

Identifiers

DOI

10.2217/FMB.15.87

1 reference

10 August 2017

1 reference

PubMed ID

26347019