Deciphering functional redundancy in the human microbiome.

Area of Science:

• Microbiome Research
• Systems Biology
• Evolutionary Biology

Background:

• Human microbiome's gene content is conserved despite variable species composition, suggesting functional redundancy.
• Functional redundancy is hypothesized to ensure microbiome stability and resilience, but lacks quantitative testing.
• The evolutionary origins of functional redundancy remain unclear.

Purpose of the Study:

• Investigate the basis of functional redundancy in the human microbiome.
• Analyze the genomic content network's topological features.
• Model genome evolution to understand functional redundancy drivers.
• Assess functional redundancy's impact on fecal microbiota transplantation (FMT).

Main Methods:

• Analysis of the human microbiome's genomic content network (microbe-gene bipartite graph).
• Development of a simple genome evolution model.
• Examination of topological network features.
• Analysis of pre-FMT and post-FMT microbiota data from published studies.

Main Results:

• The genomic content network exhibits topological features promoting high functional redundancy.
• Moderate selection pressure and high horizontal gene transfer rates are crucial for generating such networks.
• High functional redundancy in recipient microbiota impedes donor microbiota engraftment during FMT.

Conclusions:

• Functional redundancy in the human microbiome is shaped by specific ecological and evolutionary processes.
• Network topology and evolutionary dynamics (selection, HGT) contribute to functional redundancy.
• Functional redundancy influences microbiome resilience and inter-microbiota interactions, impacting FMT success.