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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Systems Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1521108

Unveiling Early-life Microbial Colonization Profile through Characterizing Low-Biomass Maternal-infant Microbiomes by 2bRAD-M

Provisionally accepted
Shuwen Hou Shuwen Hou 1Yuesong Jiang Yuesong Jiang 1Feng Zhang Feng Zhang 2Tianfan Cheng Tianfan Cheng 1Dan Zhao Dan Zhao 3Jilong Yao Jilong Yao 2Ping Wen Ping Wen 2Lijian Jin Lijian Jin 1Shi Huang Shi Huang 1*
  • 1 The University of Hong Kong, Pokfulam, Hong Kong, SAR China
  • 2 Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
  • 3 Beijing Stomatological Hospital, Capital Medical University, Beijing, Beijing Municipality, China

The final, formatted version of the article will be published soon.

    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.

    Keywords: breast milk, Meconium, low-biomass microbiota, 2bRAD-M, early-life microbiome

    Received: 01 Nov 2024; Accepted: 09 Jan 2025.

    Copyright: © 2025 Hou, Jiang, Zhang, Cheng, Zhao, Yao, Wen, Jin and Huang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Shi Huang, The University of Hong Kong, Pokfulam, Hong Kong, SAR China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.