Defining and quantifying the core microbiome: Challenges and prospects.

Area of Science:

• Microbial Ecology
• Microbiome Research
• Bioinformatics

Background:

• The 'core microbiome' concept identifies characteristic microbial taxa within a host or environment.
• Current quantification methods lack consensus, leading to inconsistencies in research.
• The term is widely used but its practical measurement remains debated.

Purpose of the Study:

• To review the history and diverse metrics used for quantifying the core microbiome.
• To identify limitations and biases associated with current quantification approaches.
• To advocate for standardized metrics in microbiome research.

Main Methods:

• Literature review of studies using core microbiome quantification.
• Analysis of various metrics, including occurrence and abundance cutoffs.
• Examination of taxonomic levels from phyla to amplicon sequence variants (ASVs).

Main Results:

• A wide range of metrics are empirically applied, often with arbitrary cutoffs.
• Common metrics are susceptible to sampling and other biases.
• Inconsistent quantification hinders comparative microbiome studies.

Conclusions:

• Standardized metrics are crucial for accurate core microbiome quantification.
• Addressing biases in quantification is necessary for robust ecological and functional interpretations.
• Developing consistent methods will advance hypothesis testing in microbiome science.