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Assembly and Tracking of Microbial Community Development within a Microwell Array Platform
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Microbiome assembly is predictable, even with species variation. Nutrient availability and cross-feeding principles explain the structure of microbial communities in soil and plants.

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Area of Science:

  • Microbiology
  • Ecology
  • Systems Biology

Background:

  • Microbiome research faces challenges in predicting community structure from fundamental principles.
  • Ecological processes in natural ecosystems are complex and numerous, hindering theory-to-experiment bridging.

Purpose of the Study:

  • To determine if quantitative ecological principles can explain and predict the taxonomic architecture of microbiomes.
  • To investigate the role of nutrient availability and cross-feeding in microbial community assembly.

Main Methods:

  • Assembly of hundreds of soil- and plant-derived microbiomes was monitored in controlled minimal synthetic media.
  • Generalized classical ecological models to incorporate nonspecific cross-feeding.

Main Results:

  • Both community-level function and coarse-grained taxonomy were highly predictable.
  • Nutrient availability was identified as a key governing factor, despite significant species variability.
  • Nonspecific cross-feeding emerged as a crucial factor in large microbial community assembly.

Conclusions:

  • The complex taxonomic architectures of natural microbiomes are emergent properties of community assembly.
  • Fundamental, quantitative principles, particularly nutrient availability and cross-feeding, can explain microbiome structure.
  • Predictability in microbiome assembly is achievable under controlled conditions.