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Longitudinal phage-bacteria dynamics in the early life gut microbiome
Michael J Tisza1,2, Richard E Lloyd1,2, Kristi Hoffman1,2
1The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
Nature Microbiology
|January 24, 2025
Summary
Infant gut phage communities are more diverse and transient than bacterial ones, with changes linked to type 1 diabetes risk. Phage data enhances microbiome analysis, revealing phage-bacteria interactions in early life.
Area of Science:
- Microbiology
- Virology
- Human Microbiome Research
Background:
- Infant gut microbial colonization is crucial but phage dynamics remain understudied.
- Limited data and tools hinder analysis of phage communities in early life.
Purpose of the Study:
- To analyze phage community dynamics during infant gut colonization.
- To develop bioinformatics tools for simultaneous phage and bacterial analysis.
- To investigate the impact of phage-bacteria interactions on early life microbiome development.
Main Methods:
- Reanalyzed 12,262 longitudinal infant gut shotgun sequencing samples from the TEDDY study.
- Developed a phage genome catalogue (49,111 taxa) using Marker-MAGu.
- Integrated phage marker genes into MetaPhlAn 4 for co-analysis with bacterial data.
Main Results:
- Children host hundreds of diverse, transient phages, accumulating more over time than bacteria.
- Type 1 diabetes correlated with slower bacterial and viral community changes in toddlers.
- Phage data improved country discrimination in machine learning models.
- Observed phage ecological succession correlated with host bacteria.
Conclusions:
- Phage communities are dynamic and individual-specific, yet follow successional trends linked to bacterial hosts.
- Understanding phage-bacteria interactions is key to deciphering early life microbiome development.
- This study provides a valuable resource for microbiome research.
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