(Q34075659)

30 July 2017

title

Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing (English)

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30 July 2017

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Shunsuke Takahashi

1

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30 July 2017

Junko Tomita

2

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30 July 2017

Kaori Nishioka

3

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30 July 2017

Takayoshi Hisada

4

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30 July 2017

Miyuki Nishijima

5

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30 July 2017

language of work or name

English

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publication date

21 August 2014

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30 July 2017

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30 July 2017

volume

9

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30 July 2017

issue

8

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30 July 2017

page(s)

e105592

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Creative Commons Attribution 4.0 International

30 July 2017

copyright license

start time

21 August 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

massive parallel sequencing

1 reference

based on heuristic

inferred from title

cites work

The choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

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

5 July 2018

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Effects of environmental variation and spatial distance on bacteria, archaea and viruses in sub-polar and arctic waters

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Bacterial and archaeal diversity in sediments of west Lake Bonney, McMurdo Dry Valleys, Antarctica

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Culture-dependent and -independent investigations of microbial diversity on urinary catheters

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Next-generation sequencing technologies for environmental DNA research

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Bacterial, archaeal and fungal succession in the forefield of a receding glacier

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

The Western English Channel contains a persistent microbial seed bank

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Culture-independent characterization of archaeal biodiversity in swine confinement building bioaerosols

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Quantitative effects of position and type of single mismatch on single base primer extension.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

What is the extent of prokaryotic diversity?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Host-bacterial mutualism in the human intestine

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Molecular ecological analysis of the gastrointestinal microbiota: a review.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

The RDP-II (Ribosomal Database Project).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

'Touchdown' PCR to circumvent spurious priming during gene amplification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Archaea in coastal marine environments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140814

Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations.

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0105592

A method for the absolute quantification of cDNA using real-time PCR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0105592

Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0105592

Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0105592

Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0105592

Changes in microbiota population during fermentation of narezushi as revealed by pyrosequencing analysis

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25144201

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0105592

1 reference

release_eeroa3zl6faerdn5q3pjhzn7yq

30 July 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/eeroa3zl6faerdn5q3pjhzn7yq

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

4140814

1 reference

30 July 2017

1 reference