Description: Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we developed WAAFLE : a W orkflow to A nnotate A ssemblies and F ind L GT E vents.
WAAFLE integrates gene sequence homology and taxonomic provenance to identify metagenomic contigs explained by pairs of microbial clades but not by single clades (i.e. putative LGTs). More specifically, for each locus in a contig, WAAFLE identifies the best hit to each species in a pangenome database. WAAFLE then looks for a species whose minimum per-locus score exceeds a lenient homology threshold (k1). If one or more species meet this criterion, then the contig is assigned to the species with the best average score. Otherwise, the process is repeated for pairs of species. If all per-locus scores for a pair of species exceed a stringent homology threshold (k2), then the contig is considered a putative LGT between those species.
Tiffany Y. Hsu, Eric A. Franzosa, Dennis Wong, Chengwei Luo, Robert G. Beiko, Morgan Langille, Curtis Huttenhower. The landscape of novel lateral gene transfer events in the human microbiome.