Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities (Q34578657)

3 August 2017

title

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

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3 August 2017

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Migun Shakya

1

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Christopher Quince

object named as

Christopher Quince

2

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Mircea Podar

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Mircea Podar

6

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Christopher W Schadt

object named as

Christopher W Schadt

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author name string

James H Campbell

3

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3 August 2017

Zamin K Yang

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3 August 2017

publication date

6 February 2013

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Environmental Microbiology

3 August 2017

published in

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3 August 2017

volume

15

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3 August 2017

issue

6

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3 August 2017

page(s)

1882-1899

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Host genetic and environmental effects on mouse intestinal microbiota.

3 August 2017

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis

7 July 2018

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Taxonomic metagenome sequence assignment with structured output models

7 July 2018

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Reproducibility and quantitation of amplicon sequencing-based detection

7 July 2018

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Removing noise from pyrosequenced amplicons

7 July 2018

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Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

7 July 2018

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

7 July 2018

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Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

7 July 2018

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Examining the global distribution of dominant archaeal populations in soil

7 July 2018

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Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

7 July 2018

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Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

7 July 2018

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Characterization of archaeal community in contaminated and uncontaminated surface stream sediments

7 July 2018

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

7 July 2018

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

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

7 July 2018

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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

7 July 2018

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Mapping the tree of life: progress and prospects

7 July 2018

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

7 July 2018

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Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

7 July 2018

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Polymerase chain reaction primers miss half of rRNA microbial diversity

7 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=3665634

Accurate determination of microbial diversity from 454 pyrosequencing data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

A renaissance for the pioneering 16S rRNA gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Evolution of mammals and their gut microbes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Parallel genomic evolution and metabolic interdependence in an ancient symbiosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

MEGAN analysis of metagenomic data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Comparative metagenomics of microbial communities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Review and re-analysis of domain-specific 16S primers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Environmental Diversity of Bacteria and Archaea

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Bias in template-to-product ratios in multitemplate PCR

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

16S ribosomal DNA amplification for phylogenetic study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3665634

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

7 July 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

Systematic artifacts in metagenomes from complex microbial communities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

Shotgun metaproteomics of the human distal gut microbiota

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

Multiple displacement amplification compromises quantitative analysis of metagenomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12086

21 January 2018

Identifiers

DOI

10.1111/1462-2920.12086

1 reference

3 August 2017

1 reference

3 August 2017

1 reference