COREMIC

COREMIC identifies habitat-specific core microbiomes by mining public microbial sequence databases and applying statistical criteria to detect taxa consistently associated with a target habitat.

Key Features:

• Database Mining Capabilities: Mines public microbial sequence databases and applies systems-biology approaches to explore habitat–microbe relationships.
• Statistical Rigor: Applies conservative criteria including presence in >90% of habitat samples and Fisher's exact test with false discovery rate (FDR) control (reported <0.05%).
• Hypothesis Generation and Confirmation: Supports generating hypotheses about microbial roles (for example, plant growth promotion or antibiotic production) and confirming taxa consistently associated with a habitat.

Scientific Applications:

• Core microbiome identification: Identifies taxa consistently associated with specific habitats across diverse environments, as demonstrated for the switchgrass rhizosphere.
• Functional inference: Facilitates linking identified core taxa to potential ecological functions, exemplified by associations with Lysobacter spp., Mesorhizobium spp., and members of the Chitinophagaceae.

Methodology:

Compares microbial communities from target habitats against outgroup samples, uses a presence threshold of >90% and Fisher's exact test with FDR control (reported <0.05%), and in the case study compared 31 switchgrass rhizosphere samples to 28 non-switchgrass samples to identify core taxa.