High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion

Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.

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Publication Details

Journal
npj Biofilms and Microbiomes
Published
2025-11-28
DOI
https://doi.org/10.1038/s41522-025-00851-2
Citations
2
Primary Topic
Oral microbiology and periodontitis research
Type
article
Field-Weighted Citation Impact
2.93
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article

High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion

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2 citations
npj Biofilms and Microbiomes
Oral microbiology and periodontitis research
2.93
article

High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion

Tao Ding, Yu-Xiong Su, Qianya Niu, Zhenjiang Zech Xu, Shi Huang, Lisha Zhou, Gao Zhang, Yufeng Zhang, Enoch Kao, Jiang Liu, Yongxin Liu, Fei Teng, Xiuping Wang, Yuesong Jiang, Shuwen Hou, Yu Liu
article en
2 citations

Abstract

Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.

npj Biofilms and MicrobiomesVol. 11(1)
Nanchang University (CN), Sun Yat-sen University (CN), Agricultural Genomics Institute at Shenzhen (CN), Chinese Academy of Agricultural Sciences (CN), Ministry of Agriculture and Rural Affairs (CN), State Key Laboratory of Food Science and Technology (CN), University of Hong Kong (HK)
Openalex Percentile: Top 8%
Oral microbiology and periodontitis research
2.93
DOIOpen Access PDFOpenAlex
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