How quantitative is metabarcoding: A meta‐analytical approach

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to...

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Vydané v:Molecular ecology Ročník 28; číslo 2; s. 420 - 430
Hlavní autori: Lamb, Philip D., Hunter, Ewan, Pinnegar, John K., Creer, Simon, Davies, Richard G., Taylor, Martin I.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Blackwell Publishing Ltd 01.01.2019
John Wiley and Sons Inc
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ISSN:0962-1083, 1365-294X, 1365-294X
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Abstract Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
AbstractList Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p  < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
Author Hunter, Ewan
Pinnegar, John K.
Taylor, Martin I.
Creer, Simon
Davies, Richard G.
Lamb, Philip D.
AuthorAffiliation 4 School of Biological Sciences Bangor University Bangor UK
3 Cefas Lowestoft UK
2 School of Environmental Sciences University of East Anglia Norwich UK
1 School of Biological Sciences University of East Anglia Norwich UK
AuthorAffiliation_xml – name: 1 School of Biological Sciences University of East Anglia Norwich UK
– name: 4 School of Biological Sciences Bangor University Bangor UK
– name: 3 Cefas Lowestoft UK
– name: 2 School of Environmental Sciences University of East Anglia Norwich UK
Author_xml – sequence: 1
  givenname: Philip D.
  orcidid: 0000-0003-3748-8241
  surname: Lamb
  fullname: Lamb, Philip D.
  email: p.lamb@uea.ac.uk
  organization: University of East Anglia
– sequence: 2
  givenname: Ewan
  surname: Hunter
  fullname: Hunter, Ewan
  organization: Cefas
– sequence: 3
  givenname: John K.
  surname: Pinnegar
  fullname: Pinnegar, John K.
  organization: Cefas
– sequence: 4
  givenname: Simon
  surname: Creer
  fullname: Creer, Simon
  organization: Bangor University
– sequence: 5
  givenname: Richard G.
  surname: Davies
  fullname: Davies, Richard G.
  organization: University of East Anglia
– sequence: 6
  givenname: Martin I.
  orcidid: 0000-0002-3858-0712
  surname: Taylor
  fullname: Taylor, Martin I.
  organization: University of East Anglia
BackLink https://www.ncbi.nlm.nih.gov/pubmed/30408260$$D View this record in MEDLINE/PubMed
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Issue 2
Keywords meta-analysis
biomass
metabarcoding
next-generation sequencing
high-throughput sequencing
Language English
License Attribution
2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Snippet Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA....
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StartPage 420
SubjectTerms biomass
Deoxyribonucleic acid
DNA
DNA barcoding
Ecological monitoring
Environmental DNA
high‐throughput sequencing
Meta-analysis
metabarcoding
Moderators
next‐generation sequencing
Sequences
Special Issue: Species Interactions, Ecological Networks and Community Dynamics
uncertainty
variance
Title How quantitative is metabarcoding: A meta‐analytical approach
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fmec.14920
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Volume 28
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