To identify bacteria with highly similar conserved sequences, 16S rDNA cannot provide adequate resolution for comparative sequence analysis; therefore, more DNA sequences and analysis models are required for classification. To develop a rapid identification method, phylogenetic trees based on 16S and gyrB gene sequences were investigated. A strain of Bacillus sp. HX2016004 producing amylase was isolated from soil, and the 16S and gyrB genes of the strain were amplified with universal primers and sequenced. Using BLAST in Genbank, other strains with similar 16S and gyrB genes were selected. Phylogenetic trees based on 16S and gyrB genes were constructed using PAUP* 4.0. In the tree constructed using sequences of both 16S and gyrB genes, strains belonging to the same species were clustered, and the classification structure was accurate. The isolated strain polymerized with Bacillus amyloliquefaciens in the phylogenetic tree. Physiological and biochemical tests verified that the strain belongs to the species B. amyloliquefaciens. Thus, the identification of HX2016004 of B. amyloliquefaciens obtained by the construction of a phylogenetic tree based on the combination of 16S and gyrB genes was accurate, rapid, and simple. Through the analysis of strains with known sequences of 16S and gyrB in Genbank or EZBiocloud, the method was proved to be generally applicable to the identification of Bacillus amyloliquefaciens.
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