Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M
IntroductionThe 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 challe...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1521108/full |
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| author | Shuwen Hou Yuesong Jiang Feng Zhang Tianfan Cheng Dan Zhao Jilong Yao Ping Wen Ping Wen Lijian Jin Shi Huang |
| author_facet | Shuwen Hou Yuesong Jiang Feng Zhang Tianfan Cheng Dan Zhao Jilong Yao Ping Wen Ping Wen Lijian Jin Shi Huang |
| author_sort | Shuwen Hou |
| collection | DOAJ |
| description | IntroductionThe 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.MethodsHere, 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).ResultsThe 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.DiscussionThis 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. |
| format | Article |
| id | doaj-art-0560206d03eb4fa6b6724cdc2a044118 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-0560206d03eb4fa6b6724cdc2a0441182025-01-24T07:13:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-01-011610.3389/fmicb.2025.15211081521108Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-MShuwen Hou0Yuesong Jiang1Feng Zhang2Tianfan Cheng3Dan Zhao4Jilong Yao5Ping Wen6Ping Wen7Lijian Jin8Shi Huang9Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, ChinaDivision of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, ChinaDivision of Stomatology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, ChinaDivision of Periodontology and Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, ChinaDepartment of Implant Dentistry, Beijing Stomatological Hospital, Capital Medical University, Beijing, ChinaDivision of Obstetrics and Gynecology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, ChinaInstitute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, ChinaShenzhen Key Laboratory of Maternal and Child Health and Diseases, Shenzhen, ChinaDivision of Periodontology and Implant Dentistry, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, ChinaDivision of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, ChinaIntroductionThe 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.MethodsHere, 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).ResultsThe 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.DiscussionThis 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.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1521108/fullbreast milkmeconiumlow-biomass microbiota2bRAD-Mearly-life microbiome |
| spellingShingle | Shuwen Hou Yuesong Jiang Feng Zhang Tianfan Cheng Dan Zhao Jilong Yao Ping Wen Ping Wen Lijian Jin Shi Huang Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M Frontiers in Microbiology breast milk meconium low-biomass microbiota 2bRAD-M early-life microbiome |
| title | Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M |
| title_full | Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M |
| title_fullStr | Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M |
| title_full_unstemmed | Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M |
| title_short | Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M |
| title_sort | unveiling early life microbial colonization profile through characterizing low biomass maternal infant microbiomes by 2brad m |
| topic | breast milk meconium low-biomass microbiota 2bRAD-M early-life microbiome |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1521108/full |
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