TY - JOUR
T1 - Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
AU - Frøslev, Tobias Guldberg
AU - Kjøller, Rasmus
AU - Bruun, Hans Henrik
AU - Ejrnæs, Rasmus
AU - Brunbjerg, Ane Kirstine
AU - Pietroni, Carlotta
AU - Hansen, Anders Johannes
PY - 2017/10/30
Y1 - 2017/10/30
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85032577891&partnerID=8YFLogxK
U2 - 10.1038/s41467-017-01312-x
DO - 10.1038/s41467-017-01312-x
M3 - Journal article
C2 - 29084957
AN - SCOPUS:85032577891
VL - 8
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 1188
ER -