[Chih-Horng Kuo] A genomic perspective on prokaryotic taxonomy: Defining genera through gene content differentiation
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Figure. Relationships among representative Mollicutes species. (A) Core-genome phylogeny. (B) Gene content differentiation.
The core of taxonomy lies in grouping and naming organisms, establishing a foundation for biological research and scientific communication. With advancements in genomics, genome sequence analysis has become an essential tool for classifying prokaryotes at the level of species. However, how to apply genome-based analyses to higher taxonomic levels remains a subject of debate in the scientific community.
To address this issue, an international collaborative team led by Dr. Chih-Horng Kuo of the Institute of Plant and Microbial Biology, Academia Sinica, conducted a systematic genomic analysis using species from the class Mollicutes as study materials. The team integrated gene content differentiation analysis, data visualization, and phylogenetic relationships to comprehensively explore how natural taxonomic groups form and correspond to the genus level.
This study revealed that recent taxonomic revisions within the class Mollicutes have tended toward over-splitting. Several of the newly described or emended genera lack clear differentiations in gene content and ecology. Also, some species were misclassified into inappropriate genera. These findings provide a solid basis for future taxonomic revisions, ensuring a more reasonable and precise classification and nomenclature of these important pathogens. Moreover, the bioinformatic concepts and methods developed in this study can be broadly applied to the classification of other prokaryotes or different taxonomic levels.
This work was published in Microbial Genomics, a journal of the Microbiology Society. The authors include Xiao-Hua Yan, Shen-Chian Pei, and Hsi-Ching Yen from Chih-Horng Kuo’s laboratory, along with collaborators from France, Canada, and the United States. Among the team members, Alain Blanchard, Gail E. Gasparich, and Chih-Horng Kuo are members of the Subcommittee on the Taxonomy of Mollicutes under the International Committee on Systematics of Prokaryotes (ICSP). This research project was primarily funded by Academia Sinica.