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Deferred Growth Inhibition Assay to Quantify the Effect of Bacteria-derived Antimicrobials on Competition
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Intraspecies warfare restricts strain coexistence in human skin microbiomes
Christopher P Mancuso1,2, Jacob S Baker1,2, Evan B Qu1,2
1Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Nature Microbiology
|June 30, 2025
Summary
Intraspecies warfare, or "self vs. self" bacterial conflict, significantly limits strain engraftment in the human skin microbiome. Understanding these conflicts is key for developing effective probiotic therapies.
Area of Science:
- Microbiology
- Systems Biology
- Genomics
Background:
- Microbiome engraftment is poorly understood.
- Metabolic competition is a known barrier, but other factors exist.
Purpose of the Study:
- Investigate intraspecies warfare as a barrier to strain engraftment in the human skin microbiome.
- Determine the role of intraspecies competition in microbial community structure.
Main Methods:
- Genomic analysis of Staphylococcus epidermidis isolates.
- High-throughput agar competition assays profiling 14,884 pairwise interactions.
- Analysis of isolates from 18 individuals across 6 families.
Main Results:
- Intraspecies antagonisms are abundant, mechanistically diverse, and independent of strain relatedness.
- Antagonisms are significantly depleted within individuals, indicating in vivo relevance.
- Antimicrobial production and resistance vary, suggesting fitness trade-offs.
Conclusions:
- Intraspecies warfare is a major barrier to bacterial strain coexistence.
- Understanding these conflicts is essential for engineering stable microbial communities.
- Accounting for intraspecies warfare is crucial for designing durable probiotic therapeutics.
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