Genomic diversity and clade clustering of Burkholderia pseudomallei and B. thailandensis prophages with soil-derived phages

Abstract

Most studies on bacteriophages (phages) of the Gram-negative bacterium Burkholderia pseudomallei rely on in silico predictions and thus underestimate the true diversity of phages. Analysis of the whole genome sequences of culturable prophages induced from B. pseudomallei and B. thailandensis, along with their free Burkholderia phages isolated from soils in Thailand, identified six novel groups of Burkholderia phages, surpassing in silico expectations. The analysis also indicated that soil-dwelling phages may have originated from lysogenic B. pseudomallei strains. Free phages isolated from soil showed high nucleotide similarity to prophage sequences in B. pseudomallei, including phages previously cultured from melioidosis patients’ hemocultures, indicating that similar phage types occur in both environmental and clinical sources. Phylogenomic analysis also revealed close genomic relatedness between prophages from B. thailandensis and B. pseudomallei, although the biological significance remains unknown. Together, these findings refine our understanding of the genomic diversity and ecological patterns of Burkholderia phages.