Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans ?

Abstract

Thanks to the development of whole-genome sequencing technologies, nowadays researchers have access to rapid, effective, and precise resources for the genetic analysis of prokaryotes. The use of metrics that consider the entire DNA sequence, such as average nucleotide identity and digital DNA-DNA hybridization calculation, in fact, allows better results when compared to single-target gene analysis. However, it is increasingly important to employ reference databases containing correct information with high-quality sequences. The aim of this work is to taxonomically identify an unknown bacterial strain isolated from an ancient Roman amphora. However, it was necessary to resequence the genomes of the reference strains Paenisporosarcina quisquiliarum SK 55 and Psychrobacillus psychrodurans DSM 11713 to obtain correct and more reliable sequences than those available. It was, therefore, possible to uniquely identify the strain Aquil_B6 as Psy. psychrodurans . Also, to obtain further genetic information, given the low number of sequences available for this species, the genome of strain DSM 30747 was sequenced. Further characterization was made to identify the presence of possible genetic characteristic features such as CRISPR-Cas, prophages, resistance factors, and bacteriocins of this species, making a comparison between the available genomes of Paenisporosarcina quisquiliarum SK 55 and Psychrobacillus psychrodurans strains DSM 11713, DSM 30747, and Aquil_B6, to evaluate the impact of time on the evolution of the considered species. IMPORTANCE Since 1988, through the United States government’s founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.