Microbial interactions in theory and practice: when are measurements compatible with models?

Area of Science:

• Microbiology
• Theoretical Ecology
• Systems Biology

Background:

• Predictive ecosystem models often rely on organism interactions.
• The generalized Lotka-Volterra (gLV) framework is a common theoretical approach for measuring these interactions.
• Microbial batch cultures are widely used for in vitro studies due to their simplicity and cost-effectiveness.

Purpose of the Study:

• To review theoretical approaches for extracting microbial interaction measurements from experimental data.
• To critically evaluate the suitability of the gLV model for microbial batch cultures.
• To propose alternative experimental and theoretical strategies for microbial ecosystem modeling.

Main Methods:

• Review of theoretical frameworks for ecological modeling.
• Analysis of the assumptions and limitations of the gLV model in the context of microbial batch cultures.
• Exploration of alternative experimental systems (serial-transfer, chemostat) and theoretical models (organism-environment interactions).

Main Results:

• The gLV model's assumptions are often violated in microbial batch cultures, leading to inaccurate interaction estimates.
• Serial-transfer and chemostat systems offer experimental conditions better aligned with gLV model assumptions.
• Explicit organism-environment interaction models provide a more suitable theoretical framework for batch culture dynamics.

Conclusions:

• The gLV model should be avoided for estimating microbial interactions in standard batch cultures.
• Adopting alternative experimental setups and theoretical models will improve the accuracy of microbial ecosystem dynamics predictions.
• These recommendations aim to enhance the experimental and theoretical tractability of microbial model systems.