Taxonomy Analysis in Bacteria Kingdom based on Protein Domain: A Comparison Study

Wang, Boqian; Zhou, Jianglin; Jin, Yuan; Hu, Mingda; Zhao, Yunxiang; Wang, Xin; Yang, Haoyi; Gong, Xingfei; Zhang, Fengwei; Zhang, Zehan; Kang, Fuqiang; Liang, Long; Yue, Junjie; Ren, Hongguang

It is important to conduct taxonomy research on the bacteria kingdom for deeper understanding, which can utilize the conserved genes, 16s rRNA, protein domain, and so on. Among them, the methods based on the protein domain has a direct relationship with phenotype. However, these methods still lack analysis of their biological significance, models evaluation and the comparison of taxonomy results. To this end, we propose a complete framework to standardize the process for taxonomy problem based on the protein functional domain. By applying it to bacteria kingdom and comparing the results with the NCBI taxonomy, we point out the most appropriate method in each step of the framework and evaluate models according to the biological significance. Finally, taxonomy suggestions and recommendations are proposed based on the phylogenetic tree generated by the framework with the most appropriate combination. Significance Statement We standardize a framework to confirmed the feasibility of utilizing protein domain to carry out bacterial taxonomy research. Furthermore, we filter out the best solution that generates the most appropriate classification result and drill down to the biological significant of the algorithms it depends on. Finally, we put forward suggestions on bacteria taxonomy modification based on our classification results.