ArticleNature methods2024
mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- How to Unmask an Unknown: The Restriction-Modification SystemInternational journal of molecular sciences · 2026Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Bacterial translocation to mesenteric lymph nodes fueling surgical site infections: evidence, technical challenges and future directions.Journal of translational medicine · 2025Review
- Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.ISME communications · 2025Article
- Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications.bioRxiv : the preprint server for biology · 2024Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.Applied and environmental microbiology · 2023Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Registered trials
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