Toward quantitative metabarcoding

Amplicon‐sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon‐sequencing studies—known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments...

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Bibliographic Details
Published in:Ecology (Durham) Vol. 104; no. 2; pp. e3906 - n/a
Main Authors: Shelton, Andrew Olaf, Gold, Zachary J., Jensen, Alexander J., D′Agnese, Erin, Andruszkiewicz Allan, Elizabeth, Van Cise, Amy, Gallego, Ramón, Ramón‐Laca, Ana, Garber‐Yonts, Maya, Parsons, Kim, Kelly, Ryan P.
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 01.02.2023
Ecological Society of America
Subjects:
amplicon sequencing
bias adjustment
Biodiversity
community structure
compositional analysis
Conserved sequence
Deoxyribonucleic acid
diet analysis
DNA
DNA - genetics
DNA barcoding
DNA Barcoding, Taxonomic - methods
Ecology
Environmental DNA
microbiome
Microbiomes
Microbiota
Mixtures
Nucleotide sequence
Polymerase chain reaction
Public health
Reaction mechanisms
Sequences
amplicon sequencing
bias adjustment
diet analysis
community structure
environmental DNA
compositional analysis
ISSN:0012-9658, 1939-9170, 1939-9170
Online Access:Get full text
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Summary:Amplicon‐sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon‐sequencing studies—known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture—struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon‐sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
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ISSN:0012-9658
1939-9170
1939-9170
DOI:10.1002/ecy.3906