  Background: In the metagenome assembly of a microbiome community, we may
think abundant species would be easier to assemble due to their deeper
coverage. However, this conjucture is rarely tested. We often do not know how
many abundant species we are missing and do not have an approach to recover
these species.
  Results: Here we proposed k-mer based and 16S RNA based methods to measure
the completeness of metagenome assembly. We showed that even with PacBio
High-Fidelity (HiFi) reads, abundant species are often not assembled as high
strain diversity may lead to fragmented contigs. We developed a novel algorithm
to recover abundant metagenome-assembled genomes (MAGs) by identifying circular
assembly subgraphs. Our algorithm is reference-free and complement to standard
metagenome binning. Evaluated on 14 real datasets, it rescued many abundant
species that would be missing with existing methods.
  Conclusions: Our work stresses the importance of metagenome completeness
which is often overlooked before. Our algorithm generates more circular MAGs
and moves a step closer to the complete representation of microbiome
communities.
