ArticleEcology and evolution2019
Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments.
Article in Ecology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Comparative Effects of Exogenous Organic Amendments on Rhizosphere Microbial Communities and Soil Properties in Continuous Cropping Watermelon.Microorganisms · 2026Article
- Vertically transmitted bacterivorous nematodes are consistent nest inhabitants in the Azteca-Cecropia ant-plant mutualism.Scientific reports · 2026Article
- Comparative metabarcoding study performed on the mock soil nematode communities, composed of DESS-preserved and freshly extracted nematodes.Journal of nematology · 2026Article
- The shared performance of different COI regions increases the niche breadth detectable from bat guano eDNA.Genetics and molecular biology · 2026Article
- From Mud to Meat: Comparative Metabarcoding Reveals Two Different Evolutionary Paths to Carnivory in a Group of Meiofaunal Annelids.Molecular ecology · 2025Article
- Foodborne Helminths in Imported Fish: Molecular Evidence from Fish Products in the Kazakhstan Market.Foods (Basel, Switzerland) · 2025Article
- Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.PeerJ · 2025Article
- Emerging Trends and Technologies Used for the Identification, Detection, and Characterisation of Plant-Parasitic Nematode Infestation in Crops.Plants (Basel, Switzerland) · 2024Review
- DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea.Pathogens (Basel, Switzerland) · 2024Article
- Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats.Molecular ecology · 2024Article
- VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages.Nature communications · 2024Article
- Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions.ISME communications · 2024Article
- 18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences.Journal of nematology · 2023Article
- Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations.Parasites & vectors · 2023Article
- Article
- Reliability and Utility of Standard Gene Sequence Barcodes for the Identification and Differentiation of Cyst Nematodes of the GenusJournal of nematology · 2022Article
- Ecological and Morphological Differentiation Among COI Haplotype Groups in the Plant Parasitic Nematode SpeciesJournal of nematology · 2022Article
- Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding.Parasites & vectors · 2021Article
- To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography.BMC bioinformatics · 2021Article
- Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology ofMicroorganisms · 2021Article
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species-level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum-specific species-level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read-merging and two clustering algorithms and the cluster-free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus-level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species-level detections, which were, however, associated with higher error rates compared to ASVs. Genus-level assignments using ASVs exhibited higher accuracy and lower error rates compared to species-level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples.
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