Community context reshapes microbial proteomes and reduces functional overlap

Area of Science:

• Microbial ecology
• Systems biology
• Metabolic engineering

Background:

• Microbial communities require strategies to minimize competition and optimize resource utilization for coexistence.
• The precise mechanisms by which microbes execute these ecological strategies within a community context are not well understood.

Purpose of the Study:

• To investigate how bacteria modulate protein abundance in response to specific community members.
• To determine the role of biotic interactions versus abiotic conditions in driving proteomic variation.
• To assess the impact of these expression shifts on functional redundancy, metabolic complementarity, and community productivity.

Main Methods:

• Construction of synthetic gut-derived bacterial consortia.
• Systematic proteomic profiling of individual species within isolate, pairwise, and 4-member communities.
• Exposure of communities to distinct carbon sources to analyze responses.

Main Results:

• Biotic interactions were identified as the primary drivers of proteomic variation, outweighing abiotic factors.
• Bacteria exhibited reproducible, partner-specific protein expression shifts in response to other community members.
• These shifts led to a significant reduction in functional overlap between species.
• Modulation of protein abundance was frequently correlated with increased overall community productivity.

Conclusions:

• Gene expression, specifically protein abundance modulation, is a key mechanism by which microbes implement ecological strategies in complex communities.
• Microbial regulatory plasticity allows for dynamic niche partitioning and stabilization of community structure.
• Understanding these protein-level responses is crucial for predicting and engineering microbial community function.