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Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes

Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic h...

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Autores principales: Chan, Abigail Hui En, Saralamba, Naowarat, Saralamba, Sompob, Ruangsittichai, Jiraporn, Chaisiri, Kittipong, Limpanont, Yanin, Charoennitiwat, Vachirapong, Thaenkham, Urusa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200835/
https://www.ncbi.nlm.nih.gov/pubmed/35705676
http://dx.doi.org/10.1038/s41598-022-14176-z
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author Chan, Abigail Hui En
Saralamba, Naowarat
Saralamba, Sompob
Ruangsittichai, Jiraporn
Chaisiri, Kittipong
Limpanont, Yanin
Charoennitiwat, Vachirapong
Thaenkham, Urusa
author_facet Chan, Abigail Hui En
Saralamba, Naowarat
Saralamba, Sompob
Ruangsittichai, Jiraporn
Chaisiri, Kittipong
Limpanont, Yanin
Charoennitiwat, Vachirapong
Thaenkham, Urusa
author_sort Chan, Abigail Hui En
collection PubMed
description Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
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spelling pubmed-92008352022-06-17 Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes Chan, Abigail Hui En Saralamba, Naowarat Saralamba, Sompob Ruangsittichai, Jiraporn Chaisiri, Kittipong Limpanont, Yanin Charoennitiwat, Vachirapong Thaenkham, Urusa Sci Rep Article Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies. Nature Publishing Group UK 2022-06-15 /pmc/articles/PMC9200835/ /pubmed/35705676 http://dx.doi.org/10.1038/s41598-022-14176-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Chan, Abigail Hui En
Saralamba, Naowarat
Saralamba, Sompob
Ruangsittichai, Jiraporn
Chaisiri, Kittipong
Limpanont, Yanin
Charoennitiwat, Vachirapong
Thaenkham, Urusa
Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title_full Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title_fullStr Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title_full_unstemmed Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title_short Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
title_sort sensitive and accurate dna metabarcoding of parasitic helminth mock communities using the mitochondrial rrna genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200835/
https://www.ncbi.nlm.nih.gov/pubmed/35705676
http://dx.doi.org/10.1038/s41598-022-14176-z
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