Prophage-mediated genome differentiation of the Salmonella Derby ST71 population

Abstract

Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella .

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers

“…Certain bacterial species that are widely distributed in various environments usually have an open pan-genome, in which new genes can confer beneficial effects for environmental adaptation [ 47 ]. On the other hand, species that tend to occupy limited habitats frequently have a closed pan-genome because they do not need to respond to many environmental changes [ 48 , 49 ]. Our results demonstrated that L. salivarius species harbor a closed pan-genome, similar to that in L. ruminis [ 50 ].…”

“…The higher abundance of GT2 and GT8 families in the strains from badgers may benefit the host by regulating gut microbiota homeostasis through the production of polysaccharides [ 59 ]. Besides plasmids, prophages are an important source of the gene gain events which play a critical role in bacterial population evolution [ 49 ]. Most of the prophage sequences identified in these badger-originated strains did not show high similarity to other analyzed L. salivarius genomes (Fig.…”

“…The information of the identified prophages in the genomes were listed in Table S 5 . The prophage sequences were clustered to groups using cd-hit-est with parameter -c 0.9 [ 49 , 77 ]. The plasmids were clustered to groups using the mob_typer method implemented in mob-suite with default parameters [ 78 ].…”

Analyses ofXenorhabdus griffiniaegenomes reveal two distinct sub-species that display intra-species variation due to prophages

“…to be highly variable and differentially conserved among strains, making them key drivers of genome diversification and useful markers for serovar typing [126,127], Similarly, we conclude that in X. griffiniae prophages are major drivers of subspeciation and strain differentiation.…”

“…Moreover, X. griffiniae prophage regions reduced pairwise dDDH values among them by three percentage points. In Salmonella enterica prophage sequences have been shown to be highly variable and differentially conserved among strains, making them key drivers of genome diversification and useful markers for serovar typing [126, 127], Similarly, we conclude that in X. griffiniae prophages are major drivers of subspeciation and strain differentiation.…”