Genomic characterization of prophage elements in Clostridium clostridioforme : an understudied component of the intestinal microbiome
Humphrey, Suzanne and Marouli, Angeliki and Thümmler, Katja and Mullin, Margaret and Pritchard, Leighton and Wall, Daniel M. (2024) Genomic characterization of prophage elements in Clostridium clostridioforme : an understudied component of the intestinal microbiome. Microbiology, 170 (8). 001486. ISSN 1465-2080 (https://doi.org/10.1099/mic.0.001486)
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Abstract
Genome sequencing of 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 characterize these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. Using PHASTER, PhageScope and manual curation, this work has identified 15 prophages: 4 predicted to be intact, 2 predicted to be defective and 9 which are unclassified. Quantitative PCR (qPCR) analysis revealed spontaneous release of four of the LM41 prophages (φ1, φ2, φ4 and φ10) into the culture supernatant, with virion-like particles visualized using transmission electron microscopy. The majority (12/14) of these particles had morphology akin to podoviruses, which is consistent with morphology predictions for φ1 and φ4. We observed diversity in the lysogeny mechanisms utilized by the prophages, with examples of the classical λ-like CI/Cro system, the ICE 1 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 LM41.
ORCID iDs
Humphrey, Suzanne ORCID: https://orcid.org/0000-0002-9893-3209, Marouli, Angeliki, Thümmler, Katja, Mullin, Margaret, Pritchard, Leighton ORCID: https://orcid.org/0000-0002-8392-2822 and Wall, Daniel M.;-
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Item type: Article ID code: 90211 Dates: DateEvent12 August 2024Published23 July 2024AcceptedFebruary 2024SubmittedSubjects: Science > Microbiology Department: Faculty of Science > Strathclyde Institute of Pharmacy and Biomedical Sciences Depositing user: Pure Administrator Date deposited: 12 Aug 2024 15:31 Last modified: 02 Oct 2024 00:42 Related URLs: URI: https://strathprints.strath.ac.uk/id/eprint/90211