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Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis
Michael J Tisza1,2, Derek D N Smith1,3, Andrew E Clark4,5
1Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA.
Nature Communications
|July 10, 2023
Summary
Bacterial DNA methylation diversity is vast, particularly in the Bacteroides fragilis group (BFG). Phage gene flow significantly drives this epigenomic variation, impacting host-pathogen interactions.
Area of Science:
- Microbiology
- Epigenetics
- Genomics
Background:
- DNA methylation is crucial for bacterial physiology, including phage defense and virulence.
- Despite known methyltransferases, bacterial epigenomic diversity is largely unexplored.
- The Bacteroides fragilis group (BFG) are key gut commensals and opportunistic pathogens.
Purpose of the Study:
- To investigate the epigenomic diversity within the Bacteroides fragilis group (BFG).
- To identify the sources driving DNA methylation pattern variation in BFG.
Main Methods:
- Pangenomic and panepigenomic analysis of 383 BFG isolates using long-read sequencing.
- Mining of methyltransferase genes and association with prophages.
- Network analysis of gene flow among BFG phages.
Main Results:
- BFG species possess hundreds of DNA methylation motifs, with unique combinations in most isolates.
- Over 6000 methyltransferase genes were identified, with ~1000 linked to intact prophages.
- Significant gene flow among BFG phages suggests a role in driving epigenomic diversity.
Conclusions:
- BFG epigenomes exhibit immense, largely unsampled diversity.
- Bacterial phages are a significant source of variation in BFG DNA methylation patterns.
- Understanding BFG epigenomics is crucial for managing symbiotic roles and multi-drug resistant infections.
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