ArticleMicrobiome2018
A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 37 citations in OpenAlex.
- Detection of Echinococcus multilocularis in coyotes in Washington State, USA highlights need for increased wildlife surveillance.PLoS neglected tropical diseases · 2026Article
- High-throughput detection of microeukaryotic parasites in insects using Nanopore sequencing.Microbial genomics · 2026Article
- Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.Animal microbiome · 2025Article
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- Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae.Parasite (Paris, France) · 2024Article
- Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing.International journal for parasitology. Parasites and wildlife · 2023Article
- Investigation of Parasitic Nematodes Detected in the Feces of Wild Carnivores in the Eastern Qinghai-Tibet Plateau, China.Pathogens (Basel, Switzerland) · 2022Article
- The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease.Inflammatory bowel diseases · 2022Review
- Metabarcoding options to study eukaryotic endoparasites of birds.Ecology and evolution · 2021Article
- Article
- Target acquired: transcriptional regulators as drug targets for protozoan parasites.International journal for parasitology · 2021Review
- High Frequency ofJournal of fungi (Basel, Switzerland) · 2021Article
- Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing.Microbiome · 2021Article
- Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia.Current research in parasitology & vector-borne diseases · 2021Article
- Relative contributions of various endogenous and exogenous factors to the mosquito microbiota.Parasites & vectors · 2020Article
- SPDB: a specialized database and web-based analysis platform for swine pathogens.Database : the journal of biological databases and curation · 2020Article
- Improved 18S and 28S rDNA primer sets for NGS-based parasite detection.Scientific reports · 2019Article
- A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundSeveral of the most devastating human diseases are caused by eukaryotic parasites transmitted by arthropod vectors or through food and water contamination. These pathogens only represent a fraction of all unicellular eukaryotes and helminths that are present in the environment and many uncharacterized organisms might have subtle but pervasive effects on health, including by modifying the microbiome where they reside. Unfortunately, while we have modern molecular tools to characterize bacterial and, to a lesser extent, fungal communities, we lack suitable methods to comprehensively investigate and characterize most unicellular eukaryotes and helminths: the detection of these organisms often relies on microscopy that cannot differentiate related organisms, while molecular assays can only detect the pathogens specifically tested.
resultsHere, we describe a novel sequencing-based assay, akin to bacterial 16S rRNA sequencing, that enables high-throughput detection and characterization of a wide range of unicellular eukaryotes and helminths, including those from taxonomical groups containing all common human parasites. We designed and evaluated taxon-specific PCR primer pairs that selectively amplify all species from eight taxonomical groups (Apicomplexa, Amoeba, Diplomonadida, Kinetoplastida, Parabasalia, Nematoda, Platyhelminthes, and Microsporidia). We then used these primers to screen DNA extracted from clinical, biological, and environmental samples, and after next-generation sequencing, identified both known and previously undescribed organisms from most taxa targeted.
conclusionsThis novel high-throughput assay enables comprehensive detection and identification of eukaryotic parasites and related organisms, from a wide range of complex biological and environmental samples. This approach can be easily deployed to many settings and will efficiently complement existing methods and provide a holistic perspective on the microbiome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.