• Isolation of a Novel Phage with Activity against Streptococcus mutans Biofilms

      Dalmasso, Marion; de Haas, Eric; Neve, Horst; Strain, Ronan; Cousin, Fabien J.; Stockdale, Stephen R.; Ross, R Paul; Hill, Colin; Science Foundation Ireland; SFI/12/RC/2273 (PLOS, 23/09/2015)
      Streptococcus mutans is one of the principal agents of caries formation mainly, because of its ability to form biofilms at the tooth surface. Bacteriophages (phages) are promising antimicrobial agents that could be used to prevent or treat caries formation by S. mutans. The aim of this study was to isolate new S. mutans phages and to characterize their antimicrobial properties. A new phage, ɸAPCM01, was isolated from a human saliva sample. Its genome was closely related to the only two other available S. mutans phage genomes, M102 and M102AD. ɸAPCM01 inhibited the growth of S. mutans strain DPC6143 within hours in broth and in artificial saliva at multiplicity of infections as low as 2.5x10-5. In the presence of phage ɸAPCM01 the metabolic activity of a S. mutans biofilm was reduced after 24 h of contact and did not increased again after 48 h, and the live cells in the biofilm decreased by at least 5 log cfu/ml. Despite its narrow host range, this newly isolated S. mutans phage exhibits promising antimicrobial properties.
    • Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

      McCann, Angela; Ryan, Feargal J.; Stockdale, Stephen R.; Dalmasso, Marion; Blake, Tony; Ryan, C. Anthony; STANTON, CATHERINE; Mills, Susan; Ross, Paul R.; Hill, Colin; et al. (PeerJ, 2018-05-07)
      Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
    • ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

      Shkoporov, Andrey N.; Khokhlova, Ekaterina V.; Fitzgerald, C. Brian; Stockdale, Stephen R.; Draper, Lorraine A.; Hill, Colin; Ross, R Paul; Science Foundation Ireland; Janssen Biotech, Inc.; SFI/12/RC/2273; et al. (Nature Publishing Group, 2018-11-14)
      CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks.