Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories

In their recent study, Espinoza et al. employ genome-resolved metagenomics to investigate supragingival plaque metagenomes of 88 individuals (1). The 34 metagenome-assembled genomes (MAGs) that the authors report include those that resolve to clades that have largely evaded cultivation efforts, such as Gracilibacteria (formerly GN02) and Saccharibacteria (formerly TM7) of the recently described Candidate Phyla Radiation (2). Generating new genomic insights into the understudied members of the human oral cavity is of critical importance for a comprehensive understanding of the microbial ecology and functioning of this biome, and we acknowledge the contribution of the authors on this front. However, the redundant occurrence of bacterial single-copy core genes suggests that more than half of the MAGs that Espinoza et al. report are composite genomes that do not meet the recent quality guidelines suggested by the community (3). Composite genomes that aggregate sequences originating from multiple distinct populations can yield misleading insights when treated and reported as single genomes (4). To briefly demonstrate their composite nature, we refined some of the key …