Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets.

In the past decade, metagenomics studies of microbial communities have added billions of sequences to the databases. This extensive amount of data and information has the potential to widen our understanding of the functioning of microbial communities and their roles in the environment. A fundamental step in this process is the functional and taxonomic profiling of the metagenomes, through an accurate gene annotation. This gene-level information can then be placed in the genomic context of metagenome-assembled genomes. Then, on a broader level, we can place this combined data into the context of a pangenome and start characterizing core and accessory gene sets. In this chapter, we provide a workflow to create an annotated gene catalog and to identify core sets of genes in the context of a pangenome. The first section will focus on the methods to provide metagenomic genes with accurate annotations. The second part will describe how to combine the gene catalog information with metagenome-assembled genomes and how to use both to build and investigate a pangenome.