Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa.

ABSTRACT: Advances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the internal transcribed spacer (ITS) gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction. Here, we report a novel bias uncovered during ITS region 2 (ITS2) sequencing of Trichoderma-infected ant fungus gardens and confirmed this bias using mock communities. Abnormally low forward read quality caused Trichoderma ITS2 reads to be computationally filtered before and during read pair merging, thus almost entirely eliminating Tric

SUBMITTER: Kyle KE 

PROVIDER: S-EPMC11784184 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature