ArticleEcology and evolution2015
Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods.
Article in Ecology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 160 citations in OpenAlex.
- Fungal community dynamics associated with the outbreaks of sugarcane root rot disease.Microbiology spectrum · 2024Article
- A comprehensive guide to assess gut mycobiome and its role in pathogenesis and treatment of inflammatory bowel disease.Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology · 2024Review
- Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.PloS one · 2024Article
- Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology.iScience · 2023Article
- Effect of marker-free transgenic Chlamydomonas on the control of Aedes mosquito population and on plankton.Parasites & vectors · 2023Article
- Control of Aedes mosquito populations using recombinant microalgae expressing short hairpin RNAs and their effect on plankton.PLoS neglected tropical diseases · 2023Article
- Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane.Frontiers in microbiology · 2023Article
- Mycoheterotrophic plants preferentially target arbuscular mycorrhizal fungi that are highly connected to autotrophic plants.The New phytologist · 2022Article
- Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem.Scientific reports · 2022Article
- Untangling the Rhizosphere Bacterial Community Composition and Response of Soil Physiochemical Properties to Different Nitrogen Applications in Sugarcane Field.Frontiers in microbiology · 2022Article
- How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?Ecology and evolution · 2021Article
- Chronic consumption of sweeteners in mice and its effect on the immune system and the small intestine microbiotaBiomedica : revista del Instituto Nacional de Salud · 2021Article
- Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers.Molecular ecology · 2021Article
- A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region.Royal Society open science · 2021Article
- Isolation and Identification of Dominant Bacteria From Black Soldier Fly Larvae (Frontiers in microbiology · 2021Article
- Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach.Scientific reports · 2020Article
- Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance.GigaScience · 2019Review
- Impacts of long-term elevated atmospheric COMolecular ecology · 2019Article
- Probing the active fraction of soil microbiomes using BONCAT-FACS.Nature communications · 2019Article
- Molecular diet analysis finds an insectivorous desert bat community dominated by resource sharing despite diverse echolocation and foraging strategies.Ecology and evolution · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60-5068 OTUs) and three orders of magnitude for the natural community (22-22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive.
Indexed as
Identifiers
What OpenQuestion holds
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.