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. 2017 Oct 30;8(1):1188.
doi: 10.1038/s41467-017-01312-x.

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Affiliations

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Tobias Guldberg Frøslev et al. Nat Commun. .

Abstract

DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Fig. 1
Fig. 1
Effects of curation with the LULU algorithm for clustering methods at 97% level. OTU table metrics before (red = raw) and after (blue = curated) curation with LULU. a correspondence of OTU (plant ITS2 sequence data) richness vs. plant richness for each of the 130 sampling sites, b total number of OTUs compared to total plant species recorded (564 species, dashed line), c percentage of OTUs having taxonomically redundant annotation, d OTU β-diversity (total richness/mean site richness) compared to plant β-diversity (17.23, dashed line), e distribution of best reference database (GenBank) match for OTUs retained and discarded by LULU
Fig. 2
Fig. 2
LULU curation workflow. (1) The user constructs an OTU table. (2) The user constructs a match list. (3) OTU table and match list is fed to the LULU algorithm

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