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Resource availability structures microbial competition through genomic niche partitioning.

Célio Dias Santos-Júnior1,2,3, Maria Camila Escobar4,5, Paula Huber3,6

  • 1Department of Agricultural Product Quality Safety and Nutrition Health, Hubei Hongshan Laboratory, Wuhan 430070, China.

Proceedings of the National Academy of Sciences of the United States of America
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PubMed
Summary
This summary is machine-generated.

Microbial competition shapes ecosystems. A new metric, CaCo, quantifies competition potential from genomic data, revealing niche overlap increases in resource-rich environments like the human gut.

Keywords:
metabolic competitionmetagenome assembled genomesniche overlapphylogenetic relatednessresource gradient

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Area of Science:

  • Microbial Ecology
  • Genomics
  • Macroecology

Background:

  • Microbial competition for resources is a key driver of biodiversity and ecosystem function.
  • Quantifying microbial competition from genomic data has been a significant challenge.

Purpose of the Study:

  • Introduce CaCo, a scalable metric to quantify microbial niche overlap and competition potential using metagenomic data.
  • Analyze macroecological patterns of microbial competition across diverse biomes.

Main Methods:

  • Developed CaCo metric transforming carbohydrate-active enzyme profiles into Resource Partitioning Scores (RPS).
  • Analyzed 14,691 metagenome-assembled genomes from ocean, freshwater, soil, and human gut microbiomes.
  • Validated CaCo using BIOLOG phenotypes, synthetic cocultures, and interaction gradients.

Main Results:

  • Revealed a macroecological gradient: niche overlap increases from specialists in oligotrophic oceans to generalists in carbon-rich environments.
  • Phylogenetic signals suggest closely related taxa exhibit more intense competition.
  • CaCo accurately predicted competitive exclusion and niche breadth.

Conclusions:

  • CaCo effectively bridges genomic potential with ecological reality in microbial communities.
  • Resource availability significantly shapes microbial competition and community structure.
  • The study provides a novel tool for predicting microbial interactions and community dynamics.