Characterisation of prophages in Clostridium clostridioforme: an understudied component of the intestinal microbiome

Abstract

Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterise these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. This work has identified 15 prophages, of which 4 are predicted to be intact, 2 are predicted to be defective, and 9 are unclassified. qPCR analysis revealed spontaneous release of four of the LM41 prophages into the culture supernatant, the majority of which had morphology akin to podoviruses when visualised using Transmission Electron Microscopy. We observed diversity in the lysogeny mechanisms utilised by the prophages, with examples of the classical {lambda}-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system, and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.