Comprehensive and comparative genomic analysis of a novel strain, Peredibacter starrii HCB2-198, to identify features of the genus

The genus Peredibacter is a member of the obligate predatory bacteria Bdellovibrio and like organisms (BALOs). However, there is still a paucity of information because few strains have been isolated, and HCB2-198, a strain of Peredibacter, has been isolated from soil in China. It shares high genomic similarity with Peredibacter starrii A3.12. Thus, HCB2-198 shares some genomic traits with Peredibacter. The complete genome has 3988 coding sequences and a GC content of 42.77. It has a high number of ribosomal structures and biogenesis-associated genes. It contains a larger histone gene with two BD0055 domains. A greater number of histidine kinases and transcription factor regulators exist in Peredibacter strains than in Bdellovibrio strains. A larger DgcC containing a DNA-binding domain such as AtoC, which as antizyme, regulates processes at posttranslational level. A complete set of genes for the metabolism of glycine, serine and threonine were found. nuo gene clusters also have special characteristics. Peredibacter contains 5 distinct BspA proteins that are absent from other predatory strains of Bdellovibrionota. Compared with the 18 representative predatory strains isolated from soils and freshwater, Peredibacter has a high number of specific genes (1344), the absolute majority of which are involved in the metabolism of energy, amino acids, carbohydrates, cofactors, and vitamins in addition to hypothetical proteins. An extensive prey range test revealed that HCB2-198 has a smaller prey range than HD100 does, although it has more MAT proteins, implying that the mechanism for identifying and successfully attacking prey in Peredibacter is still unclear. This study provides the first in-depth genomic characterization of a Peredibacter strain, offering insights into its ecological role, metabolic pathways, and evolutionary history. This genomic analysis is the first complete comprehensive and comparative report of the genus Peredibacter.