COREMIC: a web-tool to search for a niche associated CORE MICrobiome

Area of Science:

• Ecology
• Microbiology
• Bioinformatics

Background:

• Soil harbors immense microbial diversity, with thousands of species per gram.
• Understanding microbial niche partitioning and habitat-microbe relationships is crucial but poorly understood.
• Existing methods for identifying core microbiomes are limited.

Purpose of the Study:

• To develop a systems-biology approach for mining databases to identify core microbiomes.
• To create a user-friendly, statistically robust web tool (COREMIC) for identifying habitat-specific microbes.
• To investigate niche partitioning and habitat-function relationships.

Main Methods:

• Utilized a systems-biology approach to mine existing databases.
• Developed the COREMIC web tool using Google App Engine.
• Employed statistical criteria (presence in >90% samples, FDR q-val <0.05%) and an outgroup for identification.

Main Results:

• Identified a core switchgrass rhizosphere microbiome across diverse soil environments.
• Observed core bacteria including *Lysobacter spp.*, *Mesorhizobium spp.*, and *Chitinophagaceae*.
• These taxa are associated with antibiotic production and plant growth promotion.

Conclusions:

• COREMIC effectively identifies key habitat-specific microbes using available databases.
• The tool serves as a hypothesis-generating or confirmatory resource for understanding microbial ecology.
• COREMIC facilitates research into habitat-microbe relationships and potential biotechnological applications.