Temperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut

ABSTRACT

Ruminococcus gnavus is a prevalent gut microbe reported to occur in higher abundance among individuals with inflammatory bowel disease (IBD). This study reports the isolation and characterization of six bacteriophages (phages) isolated from human fecal material and environmental samples that infect this species. Isolated phages have a siphovirus morphology, with genomes ranging between 36.5 and 37.8 kbp. Genome analysis indicates that the phages have a temperate lifestyle, which was confirmed by their ability to form lysogens on their host bacterial species. In contrast to the finding that phages lyse their host in liquid medium, results from a mouse trial indicate these phages can co-exist with the host bacterium in the gut without causing a significant reduction of R. gnavus. The bacterial counts in the feces of phage-treated mice did not significantly differ in the presence of phage. Furthermore, analysis of publicly available gut virome sequence data indicates a high abundance of these phages among individuals suffering from IBD. This work provides the first insight into how phages interact with R. gnavus in the human gut microbiome.

KEYWORDS:

• Ruminococcus gnavus
• bacteriophage
• mouse trial
• inflammatory bowel disease

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Authors’ contributions

C.B. and E.V.K. performed bioinformatics, analyzed results and wrote the manuscript; E.V.K. and A.N.S. conducted wet lab work; L.S. performed genomic sequencing of R. gnavus strains; C.M.H. designed and performed the mouse trail; B.G. & L.A.D. managed the project; R.P.R., A.N.S. and C.H. secured funding and supervised the project. All authors reviewed and edited the manuscript.

Consent for publication

The manuscript does not contain any individual personal data in any form.

Ethics approval and Consent to participate

The studies involving human participants were reviewed and approved by the Cork Research Ethics Committee.

Availability of data and materials

The genomes of bacteria used are freely available on the NCBI website, accession numbers are provided in Table 1.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2194794.

Additional information

Funding

This research was conducted with the financial support of Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273 (Colin Hill & Paul Ross), a Science Foundation Ireland’s Spokes Programme which is co-funded under the European Regional Development Fund under Grant Number SFI/14/SP APC/B3032, and a research grant from Janssen Biotech, Inc (Colin Hill & Paul Ross). Andrey Shkoporov was supported by a Wellcome Trust Research Career Development Fellowship [220646/Z/20/Z], and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 101001684). This research was funded in whole, or in part, by the Wellcome Trust [220646/Z/20/Z]. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.