Metabarcoding of pathogenic parasites based on copro-DNA analysis of wild animals in South Korea

Choi, Jun Ho; Kim, Soo Lim; Yoo, Dong Kyun; Yi, Myung-hee; Oh, Singeun; Kim, Myungjun; Yun, Sohyeon; Yong, Tai-Soon; Choe, Seongjun; Lee, Jong Koo; Kim, Ju Yeong

doi:10.1016/j.heliyon.2024.e30059

Heliyon

2024

DOI: 10.1016/j.heliyon.2024.e30059

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Metabarcoding of pathogenic parasites based on copro-DNA analysis of wild animals in South Korea

Jun Ho Choi,

Soo Lim Kim,

Dong Kyun Yoo

et al.

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2024

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Cited by 2 publications

References 52 publications

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Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites

Kang,

Choi,

Kim

et al. 2024

Sci Rep

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Recent advancements in next-generation sequencing (NGS) technologies have created new opportunities for comprehensive screening of multiple parasite species. In this study, we cloned the 18 S rDNA V9 region of 11 species of intestinal parasites into plasmids. Equal amounts and concentrations of these 11 plasmids were pooled, and amplicon NGS targeting the 18 S rDNA V9 region was performed using the Illumina iSeq 100 platform. A total of 434,849 reads were identified, and all 11 parasite species were detected, although the number of output reads for each parasite varied. The read count ratio, in descending order, was as follows: Clonorchis sinensis , 17.2%; Entamoeba histolytica , 16.7%; Dibothriocephalus latus , 14.4%; Trichuris trichiura , 10.8%; Fasciola hepatica , 8.7%; Necator americanus , 8.5%; Paragonimus westermani , 8.5%; Taenia saginata , 7.1%; Giardia intestinalis , 5.0%; Ascaris lumbricoides , 1.7%; and Enterobius vermicularis , 0.9%. We found that the DNA secondary structures showed a negative association with the number of output reads. Additionally, variations in the amplicon PCR annealing temperature affected the relative abundance of output reads for each parasite. These findings can be applied to improve parasite detection methodologies and ultimately enhance efforts to control and prevent intestinal parasitic infections. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-024-76304-1.

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Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites

Kang,

Choi,

Kim

et al. 2024

Sci Rep

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DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea

Alkathiri,

Lee,

Ahn

et al. 2024

Pathogens

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The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.

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Metabarcoding of pathogenic parasites based on copro-DNA analysis of wild animals in South Korea

Cited by 2 publications

References 52 publications

Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites

Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites

DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea

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