Characterising functional redundancy in microbiome communities via relative entropy

Area of Science:

• Microbiome research
• Systems biology
• Metagenomics

Background:

• High microbiome diversity is linked to human health, potentially due to functional redundancy.
• Quantifying functional redundancy and interdependency in microbial communities is crucial for understanding this link.

Purpose of the Study:

• To conceptualize and operationalize functional redundancy at a single-trait level.
• To investigate the relationship between species diversity and functional redundancy.
• To explore the connection between microbiome functional redundancy and host metabolomics.

Main Methods:

• Utilized an information-theoretic approach based on relative entropy.
• Applied constraint-based microbiome community modeling to fecal metagenomic data.
• Integrated host fecal metabolome data.

Main Results:

• The relationship between species diversity and functional redundancy depends on trait rarity and interdependencies.
• Functional redundancy measures correlate with host metabolomic profiles.
• Colorectal cancer patients exhibit higher species-species functional interdependencies.
• Inflammatory bowel disease (IBD) patients show increased functional redundancy for specific metabolites (e.g., hydrogen sulfide) despite decreased species diversity.

Conclusions:

• Formalized the concept of functional redundancy in microbial communities.
• Demonstrated the utility of functional redundancy measures in real microbiome data.
• Highlighted the potential of functional redundancy to provide insights beyond species diversity in health and disease.