ArticlePloS one2015
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.
Article in PloS one, 2015. 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.
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- Characterization of Vaginal Microbiota in Third Trimester Premature Rupture of Membranes Patients through 16S rDNA Sequencing.Pathogens (Basel, Switzerland) · 2022Article
- Analyzing the human gut mycobiome - A short guide for beginners.Computational and structural biotechnology journal · 2022Review
- Identification of the gut microbiota biomarkers associated with heat cycle and failure to enter oestrus in gilts.Microbial biotechnology · 2021Article
- A comprehensive metagenomics framework to characterize organisms relevant for planetary protection.Microbiome · 2021Article
- Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs.Animals : an open access journal from MDPI · 2021Article
- Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites.Frontiers in microbiology · 2021Article
- Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.Animals : an open access journal from MDPI · 2020Article
- The promise and challenge of cancer microbiome research.Genome biology · 2020Review
- MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.Microbiome · 2020Article
- Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?IMA fungus · 2020Article
- The mycobiome of Australian tree hollows in relation to theEcology and evolution · 2019Article
- Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance.GigaScience · 2019Review
- Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation.PloS one · 2019Article
- Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles.Frontiers in microbiology · 2019Article
- Article
- Evaluating the profound effect of gut microbiome on host appetite in pigs.BMC microbiology · 2018Article
- Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding.Scientific reports · 2018Article
- Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.MycoKeys · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities.
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