Related Experiment Video
Updated: May 22, 2025
Bacteriophage Effectiveness for Biocontrol of Foodborne Pathogens Evaluated via High-Throughput Settings
Published on: August 19, 2021
Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces
Hanpeng Liao1, Chang Wen1, Dan Huang2
1Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Background:
Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.
Results:
Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.
Conclusion:
Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.
Insights
Phages targeting keystone bacteria like Streptomyces can reduce antibiotic resistance genes (ARGs) in soil. This phage-based approach offers a novel strategy to control the environmental spread of antimicrobial resistance.
Area of Science:
- Environmental microbiology
- Microbiome engineering
- Antimicrobial resistance
Background:
- Antimicrobial resistance (AMR) is a global health threat, with antibiotic resistance genes (ARGs) spreading beyond clinical settings.
- Understanding and mitigating ARG spread in non-clinical environments, such as soil, is crucial to prevent food web contamination.
Purpose of the Study:
- To investigate the potential of bacteriophages (phages) to control ARG maintenance and dissemination in soil environments.
- To identify keystone bacterial taxa critical for ARG persistence and explore phage-based strategies for microbiome modification.
Main Methods:
- Utilized multi-omics approaches (metagenomics, metatranscriptomics, viromics, metabolomics) and direct experimentation.
- Analyzed phages from activated sludge for their impact on soil microbiome composition and ARG abundance.
- Enriched Streptomyces-specific phage consortia and tested their efficacy across diverse soil samples.
Main Results:
- Phages from activated sludge modulated soil microbiomes, reducing ARG levels and altering bacterial community structure.
- The abundance and activity of the Streptomyces genus, a key reservoir for ARGs, were significantly reduced.
- Enriched Streptomyces-specific phages consistently decreased ARG abundances across 48 soil samples, demonstrating predictable resistome control.
Conclusions:
- Bacterial keystone taxa play a critical role in maintaining and spreading ARGs in soil.
- Metagenomics-informed phage consortia can predictably regulate soil microbiome function and mitigate ARG prevalence.
- Phages can be employed as 'ecosystem engineers' for environmental resistome management.
