Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 23, Issue 4, Pages -Publisher
MDPI
DOI: 10.3390/ijms23042181
Keywords
high throughput sequencing; human microbiome; host DNA depletion; clinical metagenomics
Funding
- National Key R&D Program of China [2020YFA0509200/2020YFA0509203]
- RGC Theme-based Res Scheme Hong Kong [T21-705/20-N]
- RGC Collaborative Research Fund [C4039-19GF, C7065-18GF]
- RGC-GRF Hong Kong [14163817]
- Vice-Chancellor's Discretionary Fund Chinese University of Hong Kong
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Whole genome metagenomic sequencing is a powerful technology that allows the identification of all genes from different organisms in a complex sample. However, the presence of excessive host DNA poses a challenge in metagenomic studies, and various methods have been developed to remove host DNA and improve microbial detection sensitivity.
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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