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

• DOI: 10.7717/peerj.4395
• Publication Date: 2018-02-15T09:18:41Z
• Authors: Richard R. Rodrigues; Nyle C. Rodgers; Xiaowei Wu; Mark A. Williams
• Keywords: Human Microbiome Project

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram soil. Understanding how this sorted selected into habitat niches a major focus ecology biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases show it can be answer questions related the core microbiome habitat-microbe relationships. By making use burgeoning growth databases, our tool “COREMIC” meets great need in search for understanding niche partitioning habitat-function The work unique, furthermore, because provides user-friendly statistically robust web-tool ( http://coremic2.appspot.com or http://core-mic.com ), developed using Google App Engine, help process database mining identify “core microbiome” associated with given habitat. case study presented data 31 switchgrass rhizosphere community habitats across diverse set soil sampling environments. methodology utilizes an outgroup 28 non-switchgrass (other grasses forbs) microbiome. Even (five environments), conservative statistical criteria (presence more than 90% samples FDR q -val <0.05% Fisher’s exact test) bacteria observed. These included, among others, closely taxa Lysobacter spp., Mesorhizobium spp , Chitinophagaceae . have been shown functions production bacterial fungal antibiotics plant promotion. COREMIC as hypothesis generating confirmatory that shows potential identifying may important functioning (e.g. host plant). study, conclusion, key habitat-specific microbes samples, currently available unique freely software.