Meta-pangenome: At the crossroad of pangenomics and metagenomics

Abstract

With the recent technological advancement in cultivation-independent high-throughput sequencing, metagenomes have tremendously improved our ability to characterize the genomic contents of the whole microbial communities. In this chapter, we argue the notion of pangenome can be applied beyond the available genome sequences by leveraging metagenome-assembled genomes, to form a comprehensive representation of the genetic content of a taxonomic group in a particular environment. We present the concept of the meta-pangenome, a representation of the totality of genes belonging to a species identified in multiple metagenomic samplings of a particular habitat. As an essential component in genome-centric pangenome analyses, we emphasize the importance to perform stringent quality assessment and validation to ensure the high quality of metagenomic deconvoluted genomes. This expansion from the traditional pangenome concept to the metapangenome overcomes many of the biases associated with whole-genome sequencing, and addresses the in vivo ecological context to further develop a systems-level understanding of microbial ecosystems.