Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

• Published in: Frontiers in microbiology Vol. 15; p. 1374708
• Main Authors: Schüler, Miriam A, Daniel, Rolf, Poehlein, Anja
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 21-03-2024
• Subjects: Clostridioides difficile; deoxycholate; Microbiology; mobile genetic element; phage induction; secondary bile salt; temperate phage; deoxycholate; secondary bile salt; Clostridioides difficile; phage induction; mobile genetic element; temperate phage
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2024.1374708

The global pathogen
is a well-studied organism, and researchers work on unraveling its fundamental virulence mechanisms and biology. Prophages have been demonstrated to influence
toxin expression and contribute to the distribution of advantageous genes. All these underline the importance of prophages in
virulence. Although several
prophages were sequenced and characterized, investigations on the entire active virome of a strain are still missing. Phages were mainly isolated after mitomycin C-induction, which does not resemble a natural stressor for
We examined active prophages from different
strains after cultivation in the absence of mitomycin C by sequencing and characterization of particle-protected DNA. Phage particles were collected after standard cultivation, or after cultivation in the presence of the secondary bile salt deoxycholate (DCA). DCA is a natural stressor for
and a potential prophage-inducing agent. We also investigated differences in prophage activity between clinical and non-clinical
strains. Our experiments demonstrated that spontaneous prophage release is common in
and that DCA presence induces prophages. Fourteen different, active phages were identified by this experimental procedure. We could not identify a definitive connection between clinical background and phage activity. However, one phage exhibited distinctively higher activity upon DCA induction in the clinical strain than in the corresponding non-clinical strain, although the phage is identical in both strains. We recorded that enveloped DNA mapped to genome regions with characteristics of mobile genetic elements other than prophages. This pointed to mechanisms of DNA mobility that are not well-studied in
so far. We also detected phage-mediated lateral transduction of bacterial DNA, which is the first described case in
. This study significantly contributes to our knowledge of prophage activity in
and reveals novel aspects of
(phage) biology.