In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health

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dc.contributor.authorHappel, Anna-Ursula
dc.contributor.authorKullin, Brian R
dc.contributor.authorGamieldien, Hoyam
dc.contributor.authorJaspan, Heather B
dc.contributor.authorVarsani, Arvind
dc.contributor.authorMartin, Darren
dc.contributor.authorPassmore, Jo-Ann S
dc.contributor.authorFroissart, Rémy
dc.date.accessioned2022-04-09T17:04:55Z
dc.date.available2022-04-09T17:04:55Z
dc.date.issued2022-01-20
dc.date.updated2022-02-24T14:50:17Z
dc.description.abstractWhile live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics.en_US
dc.identifierdoi: 10.3390/microorganisms10020214
dc.identifier.apacitationHappel, A., Kullin, B. R., Gamieldien, H., Jaspan, H. B., Varsani, A., Martin, D., ... Froissart, R. (2022). In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. <i>Microorganisms</i>, 10(2), 214. http://hdl.handle.net/11427/36319en_ZA
dc.identifier.chicagocitationHappel, Anna-Ursula, Brian R Kullin, Hoyam Gamieldien, Heather B Jaspan, Arvind Varsani, Darren Martin, Jo-Ann S Passmore, and Rémy Froissart "In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health." <i>Microorganisms</i> 10, 2. (2022): 214. http://hdl.handle.net/11427/36319en_ZA
dc.identifier.citationHappel, A., Kullin, B.R., Gamieldien, H., Jaspan, H.B., Varsani, A., Martin, D., Passmore, J.S. & Froissart, R. et al. 2022. In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. <i>Microorganisms.</i> 10(2):214. http://hdl.handle.net/11427/36319en_ZA
dc.identifier.ris TY - Journal Article AU - Happel, Anna-Ursula AU - Kullin, Brian R AU - Gamieldien, Hoyam AU - Jaspan, Heather B AU - Varsani, Arvind AU - Martin, Darren AU - Passmore, Jo-Ann S AU - Froissart, Rémy AB - While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics. DA - 2022-01-20 DB - OpenUCT DP - University of Cape Town IS - 2 J1 - Microorganisms LK - https://open.uct.ac.za PY - 2022 T1 - In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health TI - In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health UR - http://hdl.handle.net/11427/36319 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/36319
dc.identifier.vancouvercitationHappel A, Kullin BR, Gamieldien H, Jaspan HB, Varsani A, Martin D, et al. In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. Microorganisms. 2022;10(2):214. http://hdl.handle.net/11427/36319.en_ZA
dc.language.isoenen_US
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_US
dc.publisher.facultyFaculty of Health Sciencesen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceMicroorganismsen_US
dc.source.journalissue2en_US
dc.source.journalvolume10en_US
dc.source.pagination214en_US
dc.source.urihttps://www.mdpi.com/journal/microorganisms
dc.titleIn Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Healthen_US
dc.typeJournal Articleen_US
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