Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome

Abstract

Nucleotide sequence similarity, including k-mer plasmid composition, has been used for prediction of plasmid evolutionary host range, representing the hosts in which a plasmid has replicated at some point during its evolutionary history. However, the relationships between the bacterial taxa of experimentally identified transconjugants and the predicted evolutionary host ranges are poorly understood. Here, four different PromA group plasmids showing different k-mer compositions were used as model plasmids. Filter mating assays were performed with a donor harbouring plasmids and recipients of bacterial communities extracted from environmental samples. A broad range of transconjugants was obtained with different bacterial taxa. A calculation of the dissimilarities in k-mer compositions as Mahalanobis distance between the plasmid and its sequenced transconjugant chromosomes revealed that each plasmid and transconjugant were significantly more similar than the plasmid and other non-transconjugant chromosomes. These results indicate that plasmids with different k-mer compositions clearly have different host ranges to which the plasmid will be transferred and replicated. The similarity of the nucleotide compositions could be used for predicting not only the plasmid evolutionary host range but also future host ranges.

Microbial evolution through horizontal gene transfer by mobile genetic elements

“…Additionally, the host information of bacteriophages and plasmids is particularly inadequate. Several attempts have been made to predict hosts by analysing the dissimilarities in sequence information between the plasmid and its host (Suzuki et al, 2008(Suzuki et al, , 2010Tokuda et al, 2020Tokuda et al, , 2023. Recently, machine learning-based tools, including PlasmidHostFinder, have been developed to predict the host of a plasmid based on its sequence (Aytan-Aktug et al, 2022).…”