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

Anna-Ursula Happel,Rémy Froissart,Heather B Jaspan,Hoyam Gamieldien,Arvind Varsani,Jo-Ann S Passmore,Darren Martin,Brian R Kullin

doi:10.3390/microorganisms10020214

Abstract

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.

Highlights

Bacterial vaginosis (BV) is a common adverse condition in women of reproductive age [1,2]
Genomes of Lactobacillaceae genera commonly present within live therapeutics for vaginal health that were available on 1 June 2019 were downloaded from the NCBI RefSeq assembly database (Table S1), including genomes of Lactobacillus acidophilus (n = 37), Lactobacillus crispatus (n = 91), Lactobacillus gasseri (n = 29), Lactobacillus helveticus (n = 53), Lactobacillus iners (n = 21), Lactobacillus jensenii (n = 18), Limosilactobacillus mucosae (n = 11), Lactiplantibacillus plantarum (n = 434), Limosilactobacillus reuteri (n = 125), Lacticaseibacillus rhamnosus (n = 149), Ligilactobacillus salivarius (n = 82) and Limosilactobacillus vaginalis (n = 3)
We selected the following species as they are commonly found in the female genital tract (FGT) and/or present in commercial probiotics marketed for FGT use: 30 Lactobacillus acidophilus, 70 Lactobacillus crispatus, 25 Lactobacillus gasseri, 49 Lactobacillus helveticus, 19 Lactobacillus iners, 16 Lactobacillus jensenii, 10 Limosilactobacillus mucosae, 344 Lactiplantibacillus plantarum, 116 Limosilactobacillus reuteri, 139 Lacticaseibacillus rhamnosus, 77 Ligilactobacillus salivarius and 2 Limosilactobacillus vaginalis genomes

Summary

Introduction

Bacterial vaginosis (BV) is a common adverse condition in women of reproductive age [1,2]. Are considered to be ideal probiotic candidates for treating BV as they produce antibacterial metabolites [8,9,10], lower vaginal pH [9,11,12], inhibit the adhesion and growth of non-optimal bacteria [12,13,14], and modulate innate immunity [11,12,15] Probiotic therapies, those targeted at the promotion of women’s reproductive health, have gained increasing interest in the past few years amongst both the scientific community [16] and the general public [17,18]. Whether all Lactobacillaceae genera, species, or strains make safe and effective probiotics for promoting vaginal health remains a pertinent question

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