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Data from: Scrutinizing key steps for reliable metabarcoding of environmental samples

Citation

Alberdi, Antton; Aizpurua, Ostaizka; Gilbert, M. Thomas P.; Bohmann, Kristine (2018), Data from: Scrutinizing key steps for reliable metabarcoding of environmental samples, Dryad, Dataset, https://doi.org/10.5061/dryad.g14k2

Abstract

1. Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis pipelines to ensure reliable results. We explore how decisions regarding study design, laboratory work and bioinformatic processing affect the final results, and provide guidelines for reliable study of environmental samples. 2. We evaluate the performance of four primer sets targeting COI and 16S regions characterising arthropod diversity in bat faecal samples, and investigate how metabarcoding results are affected by parameters including: i) number of PCR replicates per sample, ii) sequencing depth, iii) PCR replicate processing strategy (i.e. either additively, by combining the sequences obtained from the PCR replicates, or restrictively, by only retaining sequences that occur in multiple PCR replicates for each sample), iv) minimum copy number for sequences to be retained, v) chimera removal, and vi) similarity thresholds for OTU clustering. Lastly, we measure within- and between-taxa dissimilarities when using sequences from public databases to determine the most appropriate thresholds for OTU clustering and taxonomy assignment. 3. Our results show that the use of multiple primer sets reduces taxonomic biases and increases taxonomic coverage. Taxonomic profiles resulting from each primer set are principally affected by how many PCR replicates are carried out per sample and how sequences are filtered across them, the sequence copy number threshold and the OTU clustering threshold. We also report considerable diversity differences between PCR replicates from each sample. Sequencing depth increases the dissimilarity between PCR replicates unless the bioinformatic strategies to remove allegedly artefactual sequences are adjusted according to the number of analysed sequences. Finally, we show that the appropriate identity thresholds for OTU clustering and taxonomy assignment differ between target markers. 4. Metabarcoding of complex environmental samples ideally requires i) investigation of whether more than one primer sets targeting the same taxonomic group is needed to offset the effect of primer biases, ii) more than one PCR replicate per sample, iii) bioinformatic processing approaches of sequences that balance diversity detection with removal of artificial sequences, and iv) empirical selection of OTU clustering and taxonomy assignment thresholds tailored to each genetic marker and the obtained taxa.

Usage Notes

Location

Europe