Microbiome Structure and Function: A New Framework for Interpreting Data

Area of Science:

• Microbiome research
• Systems biology
• Ecology

Background:

• The microbiome field generates vast amounts of data on structure and function.
• Interpreting this data requires clear definitions of
• structure
• and
• function
• .

Purpose of the Study:

• To propose a conceptual clarification for interpreting microbiome data.
• To distinguish between different notions of microbiome structure and function.
• To provide methodological guidance for microbiome research.

Main Methods:

• Conceptual analysis of existing microbiome research.
• Linking different data types (sequence, biochemical, network, taxonomic) to specific functional interpretations.
• Distinguishing between potential biochemical activities, causal roles, and selected effects.

Main Results:

• Sequence data relates to potential biochemical activities.
• Biochemical agents relate to actual biochemical activities.
• Interaction networks relate to causal roles.
• Taxonomic communities and their dynamics relate to selected effects.

Conclusions:

• A clear distinction between structure and function is crucial for interpreting microbiome data.
• This conceptual framework has significant methodological implications for microbiome research.
• Future research must more directly address notions of function in the microbiome.