Identification of diversity-generating retroelements in human microbiomes

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Diversity-generating retroelements (DGRs) enhance host evolution through a specialized reverse transcription process.
• DGRs, first found in Bordetella phage, are predicted in diverse viral and bacterial species.
• A minimal DGR system includes RTase, template (TR), and variable region (VR) genes.

Purpose of the Study:

• To develop a computational tool (DGRscan) for identifying DGR systems.
• To survey DGR systems within the human microbiome.
• To identify novel DGR-associated target genes.

Main Methods:

• Developed DGRscan for de novo and similarity-based DGR identification.
• Applied DGRscan to Human Microbiome Project (HMP) datasets.
• Analyzed identified DGR systems and their putative target genes.

Main Results:

• Identified 271 non-redundant DGR systems in the human microbiome, doubling the known count.
• Discovered 651 putative target genes potentially diversified by DGRs.
• Found DGRs are frequent in human-associated bacteria but rare in individual genomes.

Conclusions:

• DGRscan is effective for discovering DGR systems in large datasets.
• The human microbiome harbors a significant, previously uncharacterized DGR repertoire.
• This study provides functional insights into numerous unannotated genes involved in DGR systems.