ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias.

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Host DNA depletion is essential for analyzing microbiomes in samples with low microbial DNA content and high host background.
• Identifying microbial DNA in frozen tissue specimens presents practical challenges.
• This study evaluates commercial and novel methods for host DNA depletion in frozen intestinal biopsies.

Purpose of the Study:

• To compare the efficacy and bias of different host DNA depletion methods.
• To assess the suitability of these methods for analyzing microbial DNA in frozen tissues.

Main Methods:

• Evaluation of four commercial host DNA depletion kits.
• Assessment of two novel methods, including chromatin immunoprecipitation (ChIP).
• Application of methods to frozen human and pig intestinal biopsies.
• Analysis using 16S rRNA gene amplicon profiling to assess bias.

Main Results:

• Methods relying on differential lysis introduced substantial taxonomic bias.
• Chromatin immunoprecipitation (ChIP) achieved a 10-fold enrichment of microbial DNA.
• ChIP introduced less bias compared to lysis-based methods, enabling reliable microbiome assessment.

Conclusions:

• ChIP is recommended when significant host DNA depletion and minimal taxonomic bias are required.
• MolYsis or Zymo kits are suitable when a high level of host depletion is prioritized over minimizing taxonomic bias.