How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research

Abstract

The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study of microbiomes from all sorts of habitats. Metagenomic sequencing also allowed for a more thorough exploration of prophages, viruses that integrate into bacterial genomes, and how they benefit their hosts. One issue with using open-access metagenomic data is that sequences added to databases often have little to no metadata to work with, so finding enough sequences can be difficult. Many metagenomes have been manually curated but this is a time-consuming process and relies heavily on the uploader to be accurate and thorough when filling in metadata fields and the curators to be working with the same ontologies. Using algorithms to automatically sort metagenomes based on either the taxonomic profile or the functional profile may be a viable solution to the issues with manually curated metagenomes, but it requires that the algorithm is trained on carefully curated datasets and using the most informative profile possible in order to minimize errors.

Keywords: bacteriophage; metagenomics; microbiome.

Figure 1

Plotting the hypothetical rates of lysogeny between the PTL and KTW/PTW dynamics shows how conflicting the hypotheses appear to be (A). However, a recent hypothesis [80] suggests that the previous hypotheses can coexist and PTW overtakes KTW dynamics at high enough bacterial abundances (B).