The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies (Q21146713)

17 August 2022

6

Myrna G Serrano

Myrna G

Serrano

1 reference

17 August 2022

14

Gregory A

Buck

Gregory A Buck

1 reference

17 August 2022

5

Jennifer M

Fettweis

Jennifer M Fettweis

1 reference

17 August 2022

3

Michael D

Harwich

Michael D Harwich

1 reference

17 August 2022

9

Bernice

Huang

Bernice Huang

1 reference

17 August 2022

10

Philippe

Girerd

Philippe Girerd

1 reference

17 August 2022

8

Nihar U

Sheth

Nihar U Sheth

1 reference

17 August 2022

12

Jerome F

Strauss

Jerome F Strauss

1 reference

17 August 2022

J Paul Brooks

1

J Paul

Brooks

1 reference

17 August 2022

David J Edwards

series ordinal

2

author given names

David J

author last names

Edwards

1 reference

17 August 2022

Maria C Rivera

series ordinal

4

author given names

Maria C

author last names

Rivera

1 reference

17 August 2022

Robert A Reris

series ordinal

7

author given names

Robert A

author last names

Reris

1 reference

Creative Commons Attribution 2.0 Generic

17 August 2022

language of work or name

English

0 references

publication date

2015

0 references

published in

BMC Microbiology

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volume

15

0 references

issue

1

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page(s)

66

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copyright license

start time

21 March 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ggplot2

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4433096

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/s12866-015-0351-6

0 references

cites work

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

19 March 2017

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Human gut microbiota: repertoire and variations

19 March 2017

1 reference

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Vaginal microbiome of reproductive-age women

19 March 2017

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Unlocking the potential of metagenomics through replicated experimental design

19 March 2017

1 reference

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

19 March 2017

1 reference

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Microbial culturomics: paradigm shift in the human gut microbiome study

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

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

7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Differential abundance analysis for microbial marker-gene surveys

7 April 2017

1 reference

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The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Species-level classification of the vaginal microbiome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Genomic sequence analysis and characterization of Sneathia amnii sp. nov

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Polymerase chain reaction primers miss half of rRNA microbial diversity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Accurate determination of microbial diversity from 454 pyrosequencing data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Predicting failure rate of PCR in large genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Bias in template-to-product ratios in multitemplate PCR

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Bias and artifacts in multitemplate polymerase chain reactions (PCR).

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

High GC contents of primer 5'-end increases reaction efficiency in polymerase chain reaction.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Assessment of bias associated with incomplete extraction of microbial DNA from soil.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Use of a D-optimal mixture design to estimate the effects of diverse chloride salts on the growth parameters of Lactobacillus pentosus.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Use of a D-optimal design with constrains to quantify the effects of the mixture of sodium, potassium, calcium and magnesium chloride salts on the growth parameters of Saccharomyces cerevisiae.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Mixture design as a first step for optimization of fermentation medium for cutinase production from Colletotrichum lindemuthianum.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Optimization of Streptomyces peucetius var. caesius N47 cultivation and epsilon-rhodomycinone production using experimental designs and response surface methods

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4433096

Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows

29 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12866-015-0351-6

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1186/S12866-015-0351-6

1 reference

1172314

0 references

1172314

1 reference

1 reference

1 reference