ArticleScientific reports2019
Improved 18S and 28S rDNA primer sets for NGS-based parasite detection.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 91 citations in OpenAlex.
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- Distinct benthic and planktonic microbial communities within the stratified water column of the perennially ice-covered Lake Joyce, Antarctica.FEMS microbiology ecology · 2026Article
- The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.Microorganisms · 2026Review
- Current and emerging molecular diagnostic approaches in the detection of human parasites.Parasitology research · 2026Review
- High-throughput detection of microeukaryotic parasites in insects using Nanopore sequencing.Microbial genomics · 2026Article
- Optimizing primer selection for microbial diversity studies in freshwater lakes: a comprehensive evaluation of 16S rRNA, 18S rRNA, and ITS gene regions.FEMS microbiology ecology · 2026Article
- Next-Gen intestinal parasite detection: Leveraging metataxonomics for improved diagnosis of intestinal protists and helminths.PloS one · 2026Article
- Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.Frontiers in microbiology · 2026Article
- Enhanced blood parasite species identification using V4-V9 18S rDNA barcoding by universal primers on a nanopore platform.Scientific reports · 2025Article
- 18S/28S rDNA metabarcoding identifies Cryptosporidium parvum and Blastocystis ST1 as the predominant intestinal protozoa in hospital patients from Changchun, Northeast China.Parasites & vectors · 2025Article
- 18S rDNA next-generation sequencing uncovers the biodiversity of Gastrointestinal parasites in Tibetan grazing ruminants in China.BMC veterinary research · 2025Article
- 18S rRNA gene metabarcoding for investigation of gastrointestinal parasite diversity in great cormorants.Scientific reports · 2025Article
- Parasite sedimentary DNA reveals fish introduction into a European high-mountain lake by the seventh century.Nature communications · 2025Article
- Characterizing the Helminth Community of the Mountain Gazelle (Gazella gazella Pallas, 1766) Through DNA Metabarcoding.Acta parasitologica · 2025Article
- Internal transcribed spacers enable species-level Metataxonomic analysis of ciliated protozoa.ISME communications · 2025Article
- Fungal planktonic community related to salinity and temperature in an oligotrophic sea.Frontiers in microbiology · 2025Article
- DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea.Pathogens (Basel, Switzerland) · 2024Article
- Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites.Scientific reports · 2024Article
- Early-life factors shaping the gut microbiota of Common buzzard nestlings.Animal microbiome · 2024Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development and application of next-generation sequencing (NGS) have enabled comprehensive analyses of the microbial community through extensive parallel sequencing. Current analyses of the eukaryotic microbial community are primarily based on polymerase chain reaction amplification of 18S rRNA gene (rDNA) fragments. We found that widely-used 18S rDNA primers can amplify numerous stretches of the bacterial 16S rRNA gene, preventing the high-throughput detection of rare eukaryotic species, particularly in bacteria-rich samples such as faecal material. In this study, we employed in silico and NGS-based analyses of faecal samples to evaluated the existing primers targeting eukaryotic 18S and 28S rDNA in terms of avoiding bacterial read contamination and improving taxonomic coverage for eukaryotes, with a particular emphasis on parasite taxa. Our findings revealed that newly selected primer sets could achieve these objectives, representing an alternative strategy for NGS.
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