Rethinking Alpha Diversity in Marker-Gene Microbiome Studies: Dominance Matters More Than Richness

Area of Science:

• Microbial ecology
• Biodiversity analysis
• Bioinformatics

Background:

• Marker-gene sequencing is prevalent for studying microbial communities.
• Alpha diversity metrics are widely used to assess biodiversity patterns.
• Existing metrics face challenges with microbial richness and taxon detectability.

Purpose of the Study:

• To critically evaluate conceptual and methodological limitations of alpha diversity metrics in marker-gene studies.
• To address the interpretation of microbial richness and dominance.
• To propose an improved framework for ecological inference in microbiome research.

Main Methods:

• Conceptual analysis of alpha diversity metrics.
• Methodological critique of marker-gene sequencing assumptions.
• Review of ecological inference in microbiome studies.

Main Results:

• Alpha diversity metrics often reflect dominance shifts rather than true richness in marker-gene data.
• Limitations include the open-ended nature of microbial richness and uneven taxon detectability.
• Common assumptions underlying these metrics frequently fail.

Conclusions:

• Re-evaluating alpha diversity metrics is crucial for accurate microbiome research.
• A dominance-centered perspective enhances ecological inference.
• Improved interpretation is needed to avoid misinterpretations in biodiversity patterns.