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

While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available genomes using Phaster, Phigaro, Phispy, Prop...

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Bibliographic Details
Published in:Microorganisms (Basel) 2022-01, Vol.10 (2), p.214
Main Authors: Happel, Anna-Ursula, Kullin, Brian R, Gamieldien, Hoyam, Jaspan, Heather B, Varsani, Arvind, Martin, Darren, Passmore, Jo-Ann S, Froissart, Rémy
Format: Article
Language:English
Subjects:
Algorithms
antibiotic resistant genes
Antibiotics
Antimicrobial resistance
Bacteria
Bacteriology
bacteriophages
Datasets
Genes
genital
Genomes
Gynecology and obstetrics
Human health and pathology
Infectious diseases
Lactobacillaceae
Life Sciences
Microbiology and Parasitology
Microbiomes
Microbiota
Probiotics
Prophages
Proteins
Santé publique et épidémiologie
Vagina
Virulence
virulence factor
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Summary:While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available 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 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 or families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while 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 prophages in live biotherapeutics.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms10020214