Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions

Area of Science:

• Microbiology
• Systems Biology
• Metabolic Engineering

Background:

• Multi-strain probiotics offer enhanced gut microbiota stability and host health benefits compared to single strains.
• Understanding strain interactions, resource competition, and biofilm effects in probiotics is crucial but largely unexplored.
• Metabolic functionality and interactions of probiotics require comprehensive assessment across diverse growth conditions.

Purpose of the Study:

• To develop and apply an integrated experimental and computational approach for assessing probiotic metabolic functionality and interactions.
• To investigate the cooperative or competitive dynamics between Lactobacillus reuteri and Saccharomyces boulardii.
• To characterize the production potential of beneficial compounds by these probiotic strains.

Main Methods:

• Utilized co-culture assays combined with genome-scale metabolic modeling.
• Employed multivariate data analysis and systems biology techniques.
• Integrated data-driven and knowledge-driven approaches to analyze microbial consortia.

Main Results:

• Demonstrated a mixed cooperative-antagonistic interaction between Lactobacillus reuteri and Saccharomyces boulardii, primarily driven by resource competition.
• Observed increased individual exchange but decreased net production of amino acids and short-chain fatty acids.
• Characterized the metabolic fingerprint and production potential of these probiotic strains.

Conclusions:

• The developed integrative approach effectively explores microbial metabolic fingerprints of biotechnological interest.
• Multifaceted equilibria in simple microbial consortia can be captured using this strategy.
• Findings provide insights into probiotic strain interactions relevant for gut health and biotechnological applications.