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Analyzing diversity of reverse-transcriptase-containing viruses through global metagenomics

Viral reverse transcriptase (RT) plays a critical role in replication (e.g., retroviruses, that reverse transcribe RNA templates into complementary DNA) and genome mutations (e.g., diversity-generating retroelements in bacteriophages). In contrast to retroviruses, bacterial viruses (bacteriophages) use RT not for genome replication, but for viral gene variation within diversity-generating retroelements (DGRs) or for other diverse biological functions (e.g., CRISPR-RT).

DGRs are critical for host adaptation in bacteriophages, especially those that are abundant in mammalian gut ecosystems. By promoting mutations in host-attachment-related genes (e.g., tail and spike proteins), DGRs enhance the ability of bacteriophages to adapt to their bacterial hosts, contributing to the shaping of gut bacterial communities. Despite the wide functional diversity of viral RTs, our understanding of them remains limited.

Recently, the research team led by Min Wang at the College of Marine Life Sciences, Ocean University of China, published a study titled "" on hLife. The study highlights the pivotal roles of viral-encoded RTs in evolution, microbial ecology, and host interactions.

Using high-throughput sequencing and bioinformatics approaches, the study identified 76,077 viral RT sequences from 7,377 global metagenomes across diverse environments. The biogeographic distribution of these viral genomes revealed their widespread presence in natural environments such as soil, wastewater, freshwater, and marine ecosystems, as well as their close association with animal hosts. A significant proportion of viral RT sequences were derived from the human gut, emphasizing the critical role of these viruses in maintaining the stability of human gut microbiota.

Based on rigorous phylogenetic inference, the study defined seven evolutionary clades of viral RTs, including the retrovirus clade, the giant virus clade, the bacteriophage DGRs clade, the bacterial Group II intron clade, the bacterial retrons clade, and two newly identified clades. These clades exhibit distinct monophyletic groupings, that correlate with their biological functions and taxonomic ranks, indicating diverse evolutionary trajectories and functional specialization of viral RTs. The two newly defined clades suggest unexplored functions of viral RTs, providing valuable insights for future antiviral strategies and biotechnological applications.

Through comparative genomic analyses, the study identified 78 unique viral clusters composed exclusively of RT-encoding bacteriophages. In the clustering network, RT-encoding bacteriophages were grouped into three major communities, each characterized by distinct host features.

The three largest communities were associated with Bacillota, Pseudomonadota, and Bacteroidota, respectively. These viral clusters also exhibited habitat-specific patterns. Most clusters were restricted to host-associated environments, but 151 clusters were shared across different habitats, suggesting that certain RT-encoding bacteriophages may migrate between environments via their infected hosts.

Integration of RT-encoding bacteriophages into host genomes through lysogenic infection is common. This study identified numerous prophages encoding RTs in the complete or nearly complete genomes of 383 prokaryotes spanning 10 phyla. Most of these prophages originated from the bacteriophage DGRs clade and were widely associated with genera belonging to Bacteroidota, Bacillota, and Pseudomonadota.

Among them, Bacteroidota was identified as the primary host lineage, encompassing 17 genera and 4,461 prophages encoding RTs. Over half of these prophages were shared across different genera, indicating frequent cross-genera infections by Bacteroidota-associated bacteriophages. Given the importance of Bacteroidota in the human gut microbiota, these findings suggest that RT-encoding bacteriophages may contribute to the adaptation of Bacteroidota to the gut environment.

In conclusion, this study provides a systematic exploration and comprehensive analysis of viral RTs, revealing their evolutionary and functional diversity. These findings contribute to the development of novel genetic tools and therapeutic targets. The research advances our understanding of virus-microbe interactions in the environment and highlights the role of viruses in maintaining the stability of the human gut microbiota.