Prophages in Bacteroides fragilis: Distribution and genetic diversity

We evaluated the distribution, epidemiology, and relationships of prophage regions among 500 Bacteroides fragilis group genomes.

Average nucleotide identity (ANI) analysis was carried out to characterize the genome at the species level and phylogenetic analysis was performed to identify the genomic relationship among B. fragilis genomes. Prophages in B. fragilis genomes were performed with PHASTEST and pairwise comparison of prophage regions was performed by using Jspecies.

Prophages were found in 67.6 % (338/500) of B. fragilis genomes with a degree of nucleotide identity >80 % in 54.2 % of these regions. Comparison in the total number of prophages demonstrated that strains belonging to division I showed a higher number of these regions than strains of division II (p < 0.01). Characterization of prophage sequences revealed that strains belonging to division I exhibited a lower conservation degree (i.e. nucleotide identity ≥90 %) of the nucleotide regions than strains belonging to division II (71.88 % vs 90.0 %; p < 0.0001) and strains harbouring toxin-gene showed a lower conservation degree (i.e. nucleotide identity ≥70 %) than toxin-negative strains (70.0 % vs 95.4 %; p < 0.0001).

We demonstrated a wide distribution and high conservation degree of the prophages among B. fragilis genomes. Diversity observed within prophages could reflect the major adaptability of pathogenic strains and that low pressure exerted in the gut of healthy individuals could be related to the high conservation degree of prophage regions in human commensal strains.