Hou Shuwen, Jiang Yuesong, Zhang Feng, Cheng Tianfan, Zhao Dan, Yao Jilong, Wen Ping, Jin Lijian, Huang Shi
Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
Division of Stomatology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China.
Front Microbiol. 2025 Jan 24;16:1521108. doi: 10.3389/fmicb.2025.1521108. eCollection 2025.
The microbial composition of human breast milk and infant meconium offers critical insights into the early microbial colonization profile, and it greatly contributes to the infant's immune system and long-term health outcomes. However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.
Here, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).
The accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. Moreover, 2bRAD-M enabled us to identify clinical variables associated with infant microbiota variations and significant changes in microbial diversity across different lactation stages of breast milk.
This study underscores the importance of employing 2bRAD-M in future large-scale and longitudinal studies on maternal and infant microbiomes, thereby enhancing our understanding of microbial colonization in early life stages and demonstrating further translational potential.
人母乳和婴儿胎粪的微生物组成提供了对早期微生物定植概况的关键见解，并且对婴儿的免疫系统和长期健康结果有很大贡献。然而，由于这些样本中微生物生物量较低，使用传统方法分析这些样本通常面临技术挑战和低分辨率的限制。
在此，我们采用IIB型限制性内切酶位点相关DNA测序（2bRAD-M）作为一种简化的宏基因组学方法来解决这些问题并分析物种水平的微生物组成。我们收集了母乳样本、母体粪便和婴儿胎粪，将2bRAD-M的结果与常用的16S rRNA扩增子测序和金标准全宏基因组测序（WMS）的结果进行比较。
2bRAD-M的准确性和稳健性通过其与配对的WMS样本在微生物个体丰度上始终保持高相关性以及在全群落水平上距离较低得到证明。此外，2bRAD-M使我们能够识别与婴儿微生物群变化相关的临床变量以及母乳不同泌乳阶段微生物多样性的显著变化。
本研究强调了在未来关于母婴微生物群的大规模纵向研究中采用2bRAD-M的重要性，从而增进我们对生命早期阶段微生物定植的理解，并展示出进一步的转化潜力。
