Abundance-occupancy distributions to prioritize core microbiome membership


Core microbiomes are the consistent features of a dataset that are hypothesized to reflect underlying functional relationships with the host. A review of the recent plant-microbiome literature reveals a variety of study-specific approaches used to define the core, which presents a challenge to building a general plant-microbiome framework. Abundance-occupancy distributions, used in macroecology to describe changes in community diversity over space, offer an ecological approach for prioritizing core membership for both spatial and temporal studies. Additionally, neutral models fit to the abundance-occupancy distributions can provide insights into deterministically selected core members. We provide examples and code to systematically explore a core plant microbiome from abundance-occupancy distributions.

Current Opinion in Microbiology (in review)