Restriction Endonuclease-based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing
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Abstract
Metagenomic sequencing is a swift and powerful tool to ascertain the presence of an organism of interest in a sample. However, sequencing coverage of the organism of interest can be insufficient due to an inundation of reads from irrelevant organisms in the sample. Here, we report a nuclease-based approach to rapidly enrich for DNA from certain organisms, including enterobacteria, based on their differential endogenous modification patterns. We exploit the ability of taxon-specific methylated motifs to resist the action of cognate methylation-sensitive restriction endonucleases that thereby digest unwanted, unmethylated DNA. Subsequently, we use a distributive exonuclease or electrophoretic separation to deplete or exclude the digested fragments, thus, enriching for undigested DNA from the organism of interest. As a proof-of-concept, we apply this method to enrich for the enterobacteria Escherichia coli and Salmonella enterica by 11- to 142-fold from mock metagenomic samples and validate this approach as a versatile means to enrich for genomes of interest in metagenomic samples.
Importance
Pathogens that contaminate the food supply or spread through other means can cause outbreaks that bring devastating repercussions to the health of a populace. Investigations to trace the source of these outbreaks are initiated rapidly but can be drawn out due to the labored methods of pathogen isolation. Metagenomic sequencing can alleviate this hurdle but is often insufficiently sensitive. The approach and implementations detailed here provide a rapid means to enrich for many pathogens involved in foodborne outbreaks, thereby improving the utility of metagenomic sequencing as a tool in outbreak investigations. Additionally, this approach provides a means to broadly enrich for otherwise minute levels of modified DNA which may escape unnoticed in metagenomic samples.
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This looks like a great method for enriching for modified DNA and opens avenues for exploring new DNA modifications. I’m excited by how you captured DNA from bacteriophage T4 as a consequence of its hydroxymethyl cytosine DNA modification. I think you could further strengthen the study by using REMoDE on a complex (non-standardised) microbial community such as found in compost or sewage. This could potentially generate a valuable dataset for insights into microorganisms previously not known to carry DNA modifications, and perhaps also allow for prediction of modifications harbored by their viruses as an anti-defense strategy. I also wonder how the number to restriction sites correlate with enrichment of certain genomes over others - have you looked at this at all? Finally, thanks for creating a tool for this exciting and developing area …
This looks like a great method for enriching for modified DNA and opens avenues for exploring new DNA modifications. I’m excited by how you captured DNA from bacteriophage T4 as a consequence of its hydroxymethyl cytosine DNA modification. I think you could further strengthen the study by using REMoDE on a complex (non-standardised) microbial community such as found in compost or sewage. This could potentially generate a valuable dataset for insights into microorganisms previously not known to carry DNA modifications, and perhaps also allow for prediction of modifications harbored by their viruses as an anti-defense strategy. I also wonder how the number to restriction sites correlate with enrichment of certain genomes over others - have you looked at this at all? Finally, thanks for creating a tool for this exciting and developing area of research!
This is an archived comment originally written by Januka Athukoralage
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This is a really interesting technique, with a lot of potential use cases for exploring genome modification via sequencing. I am most excited about the potential to use this technique to detect phage genome modification in natural samples, as well as to enrich modified phage sequences and promote phage MAG assembly from metagenomes. You could imagine that this would help pull out low coverage phage genomes, if the phage had the right modification. If you want to expand beyond T4, good group of phages to look at next would the the 5hmdU-containing Bacillus phages, like SP8 or SPO1. It doesn’t seem like 5hmdU is as broadly protective against restriction enzymes as T4’s methyl-glucosylation, but you could experiment with boosting the efficiency of protection by treating with sample with a 5hmdU DNA kinase (see here: https://www.ncbi.nlm.nih…
This is a really interesting technique, with a lot of potential use cases for exploring genome modification via sequencing. I am most excited about the potential to use this technique to detect phage genome modification in natural samples, as well as to enrich modified phage sequences and promote phage MAG assembly from metagenomes. You could imagine that this would help pull out low coverage phage genomes, if the phage had the right modification. If you want to expand beyond T4, good group of phages to look at next would the the 5hmdU-containing Bacillus phages, like SP8 or SPO1. It doesn’t seem like 5hmdU is as broadly protective against restriction enzymes as T4’s methyl-glucosylation, but you could experiment with boosting the efficiency of protection by treating with sample with a 5hmdU DNA kinase (see here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653180/ , commercially available through NEB). I hope you keep developing this technique for other types of mods!
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This is a really interesting technique, with a lot of potential use cases for exploring genome modification via sequencing. I am most excited about the potential to use this technique to detect phage genome modification in natural samples, as well as to enrich modified phage sequences and promote phage MAG assembly from metagenomes. You could imagine that this would help pull out low coverage phage genomes, if the phage had the right modification. If you want to expand beyond T4, good group of phages to look at next would the the 5hmdU-containing Bacillus phages, like SP8 or SPO1. It doesn’t seem like 5hmdU is as broadly protective against restriction enzymes as T4’s methyl-glucosylation, but you could experiment with boosting the efficiency of protection by treating with sample with a 5hmdU DNA kinase (see here: https://www.ncbi.nlm.nih…
This is a really interesting technique, with a lot of potential use cases for exploring genome modification via sequencing. I am most excited about the potential to use this technique to detect phage genome modification in natural samples, as well as to enrich modified phage sequences and promote phage MAG assembly from metagenomes. You could imagine that this would help pull out low coverage phage genomes, if the phage had the right modification. If you want to expand beyond T4, good group of phages to look at next would the the 5hmdU-containing Bacillus phages, like SP8 or SPO1. It doesn’t seem like 5hmdU is as broadly protective against restriction enzymes as T4’s methyl-glucosylation, but you could experiment with boosting the efficiency of protection by treating with sample with a 5hmdU DNA kinase (see here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653180/ , commercially available through NEB). I hope you keep developing this technique for other types of mods!
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This looks like a great method for enriching for modified DNA and opens avenues for exploring new DNA modifications. I’m excited by how you captured DNA from bacteriophage T4 as a consequence of its hydroxymethyl cytosine DNA modification. I think you could further strengthen the study by using REMoDE on a complex (non-standardised) microbial community such as found in compost or sewage. This could potentially generate a valuable dataset for insights into microorganisms previously not known to carry DNA modifications, and perhaps also allow for prediction of modifications harbored by their viruses as an anti-defense strategy. I also wonder how the number to restriction sites correlate with enrichment of certain genomes over others - have you looked at this at all? Finally, thanks for creating a tool for this exciting and developing area …
This looks like a great method for enriching for modified DNA and opens avenues for exploring new DNA modifications. I’m excited by how you captured DNA from bacteriophage T4 as a consequence of its hydroxymethyl cytosine DNA modification. I think you could further strengthen the study by using REMoDE on a complex (non-standardised) microbial community such as found in compost or sewage. This could potentially generate a valuable dataset for insights into microorganisms previously not known to carry DNA modifications, and perhaps also allow for prediction of modifications harbored by their viruses as an anti-defense strategy. I also wonder how the number to restriction sites correlate with enrichment of certain genomes over others - have you looked at this at all? Finally, thanks for creating a tool for this exciting and developing area of research!
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