Evaluating the core microbiota in complex communities: A systematic investigation.

Area of Science:

• Microbiology
• Ecology
• Bioinformatics

Background:

• Complex microbial communities, like those in marine sponges, present analytical challenges due to high species diversity.
• Transient microorganisms add complexity, leading to the increasing popularity of the 'core microbiota' approach focusing on stable members.

Purpose of the Study:

• To systematically evaluate how different definitions of a core microbiota impact study conclusions.
• To assess the robustness of the core microbiota approach in complex marine sponge ecosystems.

Main Methods:

• Utilized complex marine sponge microbiotas for analysis.
• Systematically evaluated various factors used to define a core microbiota.
• Assessed impacts on alpha-diversity, beta-diversity, host specificity, environmental quality, and ecological networks.

Main Results:

• Significant differences in alpha- and beta-diversity were observed with certain core definitions, but not all.
• Conclusions regarding host specificity and environmental quality were largely unaffected by core definition changes.
• Perception of bacterial ecological networks within sponges remained consistent across all applied core definitions.

Conclusions:

• The core microbiota approach is surprisingly robust for comparing microbiotas, especially in closely related samples.
• While careful interpretation is still needed, the core microbiota concept provides a reliable framework for microbial community analysis.