Inclusion of database outgroups improves accuracy of fungal meta-amplicon taxonomic assignments

Abstract

Meta-amplicon studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other non-fungal environmental sequences that are amplified during PCR are inherently assigned taxonomy by these same databases, possibly leading to ambiguous non-fungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including non-fungal outgroups in a fungal taxonomic database to aid in detecting and removing these non-target amplicons. We processed 15 publicly available fungal meta-amplicon data sets and discovered that roughly 40% of the reads from these studies were not fungal, though they were assigned as Fungus sp. when using a database without non-fungal outgroups. We discuss implications for meta-amplicon studies and recommend assigning taxonomy using a database with outgroups to better detect these non-fungal amplicons.