Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding

Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ and cost‐effective tool to determine animal diets. Here, we summarize the trends of fecal metabarcodin...

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Veröffentlicht in:Environmental DNA (Hoboken, N.J.) Jg. 2; H. 4; S. 391 - 406
Hauptverfasser: Ando, Haruko, Mukai, Haruka, Komura, Taketo, Dewi, Tungga, Ando, Masaki, Isagi, Yuji
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Hoboken John Wiley & Sons, Inc 01.10.2020
Wiley
Schlagworte:
Bioinformatics
Cloning
Deoxyribonucleic acid
Diet
DNA
DNA sequencing
Endangered & extinct species
Ethanol
fecal samples
Feces
Food
metabarcoding
methodology
Research methodology
trend
Trends
Trophic relationships
ISSN:2637-4943, 2637-4943
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Abstract Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ and cost‐effective tool to determine animal diets. Here, we summarize the trends of fecal metabarcoding studies as well as methodological characteristics using 155 original papers published from 2009 to March 2020. We calculated the frequencies of the methods and conditions used in each experimental procedure and bioinformatics approach. Mammals were the major target taxa for fecal metabarcoding. A few methods or conditions dominated each procedure: sampling, DNA extraction, PCR, sequencing, and bioinformatics, which might be specialized for metabarcoding of degraded fecal DNA. However, the disadvantages of common methods were noted in some studies, and further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance. This review will help fecal metabarcode users, especially new scientists who are considering using fecal metabarcoding in their studies, understand the process and common methods of fecal metabarcoding. We also hope this review will facilitate further technical improvements in this method. We summarize the trends of fecal metabarcoding studies as well as methodological characteristics. Mammals were the major target taxa. A few methods or conditions dominated each procedure, which might be specialized for metabarcoding of degraded fecal DNA. However, further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance.
AbstractList Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ and cost‐effective tool to determine animal diets. Here, we summarize the trends of fecal metabarcoding studies as well as methodological characteristics using 155 original papers published from 2009 to March 2020. We calculated the frequencies of the methods and conditions used in each experimental procedure and bioinformatics approach. Mammals were the major target taxa for fecal metabarcoding. A few methods or conditions dominated each procedure: sampling, DNA extraction, PCR, sequencing, and bioinformatics, which might be specialized for metabarcoding of degraded fecal DNA. However, the disadvantages of common methods were noted in some studies, and further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance. This review will help fecal metabarcode users, especially new scientists who are considering using fecal metabarcoding in their studies, understand the process and common methods of fecal metabarcoding. We also hope this review will facilitate further technical improvements in this method. We summarize the trends of fecal metabarcoding studies as well as methodological characteristics. Mammals were the major target taxa. A few methods or conditions dominated each procedure, which might be specialized for metabarcoding of degraded fecal DNA. However, further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance.
Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ and cost‐effective tool to determine animal diets. Here, we summarize the trends of fecal metabarcoding studies as well as methodological characteristics using 155 original papers published from 2009 to March 2020. We calculated the frequencies of the methods and conditions used in each experimental procedure and bioinformatics approach. Mammals were the major target taxa for fecal metabarcoding. A few methods or conditions dominated each procedure: sampling, DNA extraction, PCR, sequencing, and bioinformatics, which might be specialized for metabarcoding of degraded fecal DNA. However, the disadvantages of common methods were noted in some studies, and further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance. This review will help fecal metabarcode users, especially new scientists who are considering using fecal metabarcoding in their studies, understand the process and common methods of fecal metabarcoding. We also hope this review will facilitate further technical improvements in this method.
Abstract Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ and cost‐effective tool to determine animal diets. Here, we summarize the trends of fecal metabarcoding studies as well as methodological characteristics using 155 original papers published from 2009 to March 2020. We calculated the frequencies of the methods and conditions used in each experimental procedure and bioinformatics approach. Mammals were the major target taxa for fecal metabarcoding. A few methods or conditions dominated each procedure: sampling, DNA extraction, PCR, sequencing, and bioinformatics, which might be specialized for metabarcoding of degraded fecal DNA. However, the disadvantages of common methods were noted in some studies, and further optimizations are required to obtain more accurate dietary data with high taxonomic resolution and quantitative performance. This review will help fecal metabarcode users, especially new scientists who are considering using fecal metabarcoding in their studies, understand the process and common methods of fecal metabarcoding. We also hope this review will facilitate further technical improvements in this method.
Author Komura, Taketo
Mukai, Haruka
Isagi, Yuji
Ando, Haruko
Ando, Masaki
Dewi, Tungga
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  surname: Isagi
  fullname: Isagi, Yuji
  organization: Kyoto University
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Snippet Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been accepted...
Abstract Fine‐scale estimation of trophic interactions is an important subject in the field of ecology. Diet analysis based on fecal DNA metabarcoding has been...
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SubjectTerms Bioinformatics
Cloning
Deoxyribonucleic acid
Diet
DNA
DNA sequencing
Endangered & extinct species
Ethanol
fecal samples
Feces
Food
metabarcoding
methodology
Research methodology
trend
Trends
Trophic relationships
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Title Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding
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