Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them.

ABSTRACT: The importance of rarefying ecological or amplicon sequencing data to a standardized level of diversity coverage for reliable diversity comparisons across samples is well recognized. However, the importance of diversity coverage, i.e. the fraction of the genomic diversity of a sample sequenced, in comparative shotgun metagenomic studies remains frequently overlooked. Using both in silico and natural metagenomes from a wide range of environments, we demonstrate that uneven metagenome coverage can result in misleading biological conclusions, particularly for identifying differentially abundant features, i.e. groups of genes or genomes assigned to the same protein family or taxonomic rank, respectively, and for comparing diversity between samples. The main underlying cause is that not

SUBMITTER: Aldeguer-Riquelme B 

PROVIDER: S-EPMC12477595 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature