Abstract
BACKGROUND: Identifying core microbiota is an important step for understanding the key components of microbial communities. Traditional approach that identifies core taxa at the OTU level ignores potential ecological coherence of higher rank taxa. There is a need to develop software that can systematically identify core taxa at and above the species level. RESULTS: Here we developed PhyloCore, an application that uses a phylogeny-based algorithm to identify core taxa at the proper taxonomic levels. It incorporates a number of features that users can set according to their needs. Using multiple gut microbiota as test cases, we demonstrate that PhyloCore is more powerful and flexible than OTU-based approaches. CONCLUSIONS: PhyloCore is a flexible and fast application that identifies core taxa at proper taxonomic levels, making it useful to sequence-based microbial ecology studies. The software is freely available at http://wolbachia.biology.virginia.edu/WuLab/Software.html.