DNA methylation from bacteria & mircobiome using nanopore technology

To battle with bacterial pathogens. Antibiotics resistance poses great risk to public health. To best battle with bacterial pathogens, it is important to discover novel drug targets.
 
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation.  Increasing evidence suggests that bacterial DNA methylation plays important roles in regulating bacterial physiology such as virulence, sporulation, biofilm formation, pathogen-host interaction etc.
 
Bacterial methylomes contain three primary forms of DNA methylation: N6-methyladenine (6 mA), N4-methylcytosine (4mC) and 5-methylcytosine (5mC). The widely used bisulfite sequencing for DNA methylation mapping in mammalian genomes are not effective at resolving bacterial methylomes. Single molecule real-time (SMRT) can effectively map 6mA and 4mC events, and have empowered the study of >4,000 bacterial methylomes in the past ten years. However, SMRT sequencing cannot effectively detect 5mC methylation.
 
In this work, the authors developed a new method that enables nanopore sequencing for broadly applicable methylation discovery. They applied it to individual bacteria and the gut microbiome for reliable methylation discovery. In addition, they demonstrated the use of DNA methylation for high resolution microbiome analysis, mapping mobile genetic elements with their host genomes directly from microbiome samples.

The new method in this work allows researchers to more effectively discover novel DNA methylation from bacterial pathogens, opening new opportunities to discovery novel targets to design new inhibitors.  The new method combines the power of long read sequencing and bacterial DNA methylation to resolve complex microbiome samples into individual species and strains. So, it will also empower higher resolution characterization of human microbiome for medical applications.

By examining three types of DNA methylation in a large diversity of sequence contexts, the authors observed that nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To capture this complexity and enable nanopore sequencing for broadly applicable methylation discovery, they generated a training dataset from an assortment of bacterial species and developed a novel method that couples the identification and fine mapping of the three forms of DNA methylation into a multi-label classification design.'

The authors evaluated the method and then applied it to individual bacteria and mouse gut microbiome for reliable methylation discovery. In addition, they demonstrated in the microbiome analysis the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes, and for the first time, identifying misassembled metagenomic contigs.

https://www.nature.com/articles/s41592-021-01109-3

http://sciencemission.com/site/index.php?page=news&type=view&id=publications%2Fdiscovering-and&filter=22