Conjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important.
Here, we outline two related methods to identify conjugative elements in the human gut microbiome. Conjugative systems can effectively be identified from metagenomic assemblies either using a curated sets of profile hidden Markov models or by searching against large-scale databases, such as UniRef90. Both methods were successful at identifying type IV conjugative systems with profile hidden Markov models being faster, but less sensitive than alignment to the UniRef database. Finally, we demonstrate that the majority of assembled conjugative elements are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in "high-quality" metagenomic bins.
Analysis of the human gut microbiome by shotgun metagenomic sequencing has revealed numerous connections to human health outcomes. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines. We suggest that analysis of type IV conjugative systems should be added to the current metagenomic analysis approaches as they contain much information that could explain differences between cohorts.