Critical assessment of pan-genomic analysis of metagenome-assembled genomes

Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.

Automated summary

The pan-genome analysis of metagenome-assembled genomes (MAGs) can be affected by issues such as fragmentation, incompleteness, and contamination. In this study, the researchers conducted a critical assessment of pan-genomics by comparing the results of complete bacterial genomes and simulated MAGs. The findings show that incompleteness leads to significant loss of core genes, while contamination mainly affects accessory genomes. Lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes can alleviate the loss, but to a limited extent. The study concludes that new pan-genome analysis tools specifically for MAGs are needed.