Table 1.

Approaches for defining the core human microbiome.

Approach	Pros	Cons	Examples
Community composition: the core microbiome is described in terms of shared taxa	Relatively simple to implement; can be applied to amplicon studies	Common taxa are usually identified at high taxonomic levels only	[17,28,29,30,31]
Functional profile: definition relies on a set of common functions	Captures the contribution of the core human microbiome to the host and the community	It is difficult to distinguish between human-specific and broad core functions	[9,12,13,26]
Ecology: include taxon abundance, interactions, co-occurrence, and other community-level patterns	Can capture complex patterns in community structure; may be more realistic than community composition alone	Less clear which patterns should be considered; no standard methods and programs are available	[19]
Stability: consider factors that maintain community stability and resilience	Stability is a critical characteristic of the core microbiome that is not captured through community composition alone	Definition is vague; there are no widely accepted methods for evaluating stability and resilience	[32]