Summary
This narrative review comprehensively examines host DNA depletion strategies essential for accurate plant microbiome metagenomic analysis. The authors evaluate established techniques including physical separation and enzymatic approaches, as well as advanced methods such as magnetic bead capture and nanopore sequencing, whilst identifying efficiency and specificity gaps in current practice. The review proposes emerging innovations, particularly CRISPR–Cas9 and chromatin immunoprecipitation approaches, to address limitations and enable more precise, cost-effective microbial characterisation in crop and soil systems.
UK applicability
These methodological advances are directly applicable to UK agricultural research programmes seeking to characterise soil and plant-associated microbiomes for crop improvement and sustainable farming. Enhanced host DNA depletion techniques would improve the quality of microbiome data underpinning UK-based research into soil health, disease resistance and agroecological innovation.
Key measures
Comparative assessment of physical separation techniques (filtration, gradient centrifugation), selective lysis, enzymatic treatments, targeted sequence capture, methylation-based enrichment, nanopore selective sequencing, CRISPR–Cas9 and chromatin immunoprecipitation methods
Outcomes reported
The review systematically catalogues current and emerging host DNA depletion strategies for plant microbiome studies, evaluating their efficiency, specificity and applicability. It identifies current methodological limitations and proposes novel approaches including CRISPR–Cas9 and chromatin immunoprecipitation-based methods to improve microbial enrichment.
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