PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. (Q33228737)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16332901%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

title

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

1 reference

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10 January 2020

1 reference

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10 January 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16332901%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

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10 January 2020

author name string

Ramahi Sarma-Rupavtarm

series ordinal

1 reference

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10 January 2020

language of work or name

English

0 references

publication date

1 December 2005

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Applied and Environmental Microbiology

10 January 2020

published in

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10 January 2020

volume

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10 January 2020

issue

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10 January 2020

page(s)

8966-8969

1 reference

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Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae).

10 January 2020

cites work

1 reference

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14 July 2018

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Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

14 July 2018

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Reevaluation and reduction of a PCR bias caused by reannealing of templates.

14 July 2018

1 reference

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Fine-scale phylogenetic architecture of a complex bacterial community.

14 July 2018

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Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.

14 July 2018

1 reference

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Environmental genome shotgun sequencing of the Sargasso Sea

14 July 2018

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ARB: a software environment for sequence data

14 July 2018

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A newly discovered Roseobacter cluster in temperate and polar oceans

14 July 2018

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Diversity and Abundance of Uncultured Cytophaga -Like Bacteria in the Delaware Estuary

14 July 2018

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Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts

14 July 2018

1 reference

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SAR11 clade dominates ocean surface bacterioplankton communities.

14 July 2018

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Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Counting the uncountable: statistical approaches to estimating microbial diversity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Bias in template-to-product ratios in multitemplate PCR

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Chimeric cDNA clones: a novel PCR artifact

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Modeling of heteroduplex formation during PCR from mixtures of DNA templates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Genotypic diversity within a natural coastal bacterioplankton population.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1317340

The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16332901

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/AEM.71.12.8966-8969.2005

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16332901%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16332901%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

PubMed publication ID

16332901

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16332901%20AND%20SRC:MED&resulttype=core&format=json