Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis

Area of Science:

• Microbiology and Ecology
• Computational Biology

Background:

• The core microbiome, defined by consistently present taxa, is crucial for understanding microbial communities.
• Current methods for assigning core microbiome membership are diverse, leading to inconsistencies and ecological interpretation challenges.

Approach:

• Reviewed and applied common core microbiome assignment methods to large datasets.
• Utilized simulations to assess the accuracy of different methods.
• Analyzed the influence of taxon abundance and occupancy distributions on assignment accuracy.

Key Points:

• Core taxa assignments vary significantly depending on the method and data type used.
• Occupancy-based methods demonstrated higher accuracy in identifying true core members.
• Method performance is contingent on the underlying distribution of taxon abundance and occupancy.

Conclusions:

• Inconsistent core microbiome assignments can impact downstream ecological interpretations.
• Occupancy-based methods offer a more reliable approach for core microbiome identification.
• Standardization of methods and data processing is essential for advancing ecological synthesis and reliable microbiome research.