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High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion
Yuesong Jiang1, Jiang Liu2, Yufeng Zhang1
1Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
NPJ Biofilms and Microbiomes
|November 28, 2025
Summary
A new method, 2bRAD-M, efficiently analyzes human microbiota in samples with high host DNA. This reduced sequencing approach bypasses host DNA depletion, offering a practical solution for microbiome research.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Characterizing human microbiota is vital for understanding host-microbe interactions.
- High host DNA context (HoC) presents a significant challenge in analyzing host-dominated samples.
- Existing host DNA depletion methods suffer from DNA loss and require immediate sample processing.
Purpose of the Study:
- To introduce 2bRAD-M, a reduced metagenomic sequencing method for efficient host-microbe analysis.
- To enable microbiome analysis without prior host DNA depletion.
- To provide a practical and efficient solution for samples with high host DNA context.
Main Methods:
- Development and validation of 2bRAD-M, a reduced metagenomic sequencing technique.
- Application of 2bRAD-M to mock samples with >90% human DNA.
- Comparative analysis of 2bRAD-M with whole metagenome sequencing (WMS) on saliva and oral cancer samples.
- Utilizing 2bRAD-M in an early childhood caries (ECC) study.
Main Results:
- 2bRAD-M achieved over 93% in AUPR and L2 similarity on mock samples.
- 2bRAD-M profiles closely matched WMS profiles in saliva and oral cancer samples.
- In saliva samples, 2bRAD-M captured diurnal and host-specific patterns using only 5-10% of sequencing effort.
- 2bRAD-M identified key bacterial indicators in an ECC study, distinguishing ECC from healthy subjects with an AUC of 0.92.
Conclusions:
- 2bRAD-M provides high-resolution microbial profiles without the need for host DNA depletion.
- The method is validated for its efficiency and accuracy in host-dominated samples.
- 2bRAD-M offers a practical and cost-effective alternative for microbiome research challenged by high host DNA.
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