A method for selectively enriching microbial DNA from contaminating vertebrate host DNA

Area of Science:

• Genomics
• Microbiology
• Molecular Biology

Background:

• DNA sequencing of biological samples often contains a significant amount of host DNA, overshadowing microbial DNA.
• This excess host DNA complicates the analysis of microbial communities (microbiomes).

Purpose of the Study:

• To develop and validate a method for enriching microbial DNA by removing host DNA from various biological samples.
• To assess the effectiveness of the methyl-CpG binding domain-Fc fusion protein (MBD-Fc) method in host DNA depletion and microbial DNA enrichment.

Main Methods:

• Utilized a methyl-CpG binding domain (MBD) fused to the Fc region of a human antibody (MBD-Fc) for DNA separation.
• Employed protein A paramagnetic beads to create an enrichment complex for one-step host DNA removal.
• Applied the MBD-Fc method to DNA samples from human saliva, human blood, a mock malaria-infected blood sample, and a black molly fish.

Main Results:

• Achieved a 50-fold decrease in host genome-derived sequence reads.
• Observed an 8-11.5-fold increase in bacterial and Plasmodium DNA sequence reads.
• Demonstrated that bacterial species diversity and relative abundance were conserved, with Shannon-Wiener diversity indices remaining similar before and after enrichment.

Conclusions:

• The MBD-Fc method provides an effective one-step approach for enriching microbial DNA by depleting host DNA.
• This technique is applicable across diverse sample types, including saliva, blood, and fish DNA.
• The MBD-Fc enrichment holds significant promise for advancing targeted microbiome sequence analysis.