This scientific opinion article challenges the way we evaluate the “completeness” of metagenome-assembled genomes (MAGs). The authors highlight that high-quality scores can create the impression of a complete genome, while important genomic regions — such as mobile elements, plasmids, and gene clusters involved in specialized molecule production — may still be missing.

By comparing MAGs with reference genomes, they demonstrate that these missing pieces can affect our understanding of microbial adaptation, evolution, and functional diversity. The authors propose distinguishing between marker-based completeness and true biological completeness, which better represents the recovery of traits needed to interpret microbial biology.

In short: a genome can look “complete” based on numbers, but still miss key pieces of information needed to understand microbial life.

https://doi.org/10.3389/fmicb.2026.1884628