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.