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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Benjamin R Macadangdang1,2, Yanling Wang3, Cora L Woodward2
1Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA.
Science (New York, N.Y.)
|October 9, 2025
Summary
Diversity-generating retroelements (DGRs) in the gut microbiota rapidly evolve bacterial proteins. These DGRs are transferred between species, especially to infants, shaping microbial communities.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Diversity-generating retroelements (DGRs) are known to accelerate evolution by diversifying proteins.
- The human gut microbiota has a high density of DGRs, suggesting adaptive roles.
- Bacteroides species are key members of the human gut microbiota.
Purpose of the Study:
- To identify and characterize DGRs in human-associated Bacteroides species.
- To investigate the function and transfer of these DGRs.
- To understand the role of DGRs in shaping host-associated microbial communities.
Main Methods:
- Bioinformatic identification of >1100 distinct DGRs in Bacteroides species.
- Analysis of DGR activity and targets, including type V pili.
- Horizontal gene transfer analysis and competition assays in gnotobiotic mice.
- Comparative analysis of >2700 DGRs across phyla in mother-infant pairs.
Main Results:
- A subset of Bacteroides DGRs diversifies adhesive proteins of type V pili.
- Bacteroides DGRs are horizontally transferred across species and exhibit variable activity levels.
- DGRs preferentially alter ligand-binding residues, and specific sequences are enriched during bacterial competition.
- Bacteroides DGRs are disproportionately transferred to vaginally delivered infants and actively diversify.
Conclusions:
- Bacteroides DGRs contribute to microbial adaptation and evolution within the human gut.
- Horizontal transfer of DGRs, particularly to infants, plays a significant role in shaping the gut microbiome.
- Targeted genome plasticity via DGRs is a key factor in host-associated microbial community dynamics.
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