Probiogenomics Analysis of 97 Lactobacillus crispatus Strains as a Tool for the Identification of Promising Next-Generation Probiotics.

Federico Fontana,Francesca Turroni,Giulia Longhi,Christian Milani,Rosaria Anzalone,Giulia Alessandri,Gabriele Andrea Lugli,Marco Ventura,Alice Viappiani,Leonardo Mancabelli

doi:10.3390/microorganisms9010073

Federico Fontana, Francesca Turroni + Show 8 more

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https://doi.org/10.3390/microorganisms9010073

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Journal: Microorganisms	Publication Date: Dec 30, 2020
Citations: 14	License type: CC BY 4.0

Affiliation: University of Parma

Abstract

Members of the genus Lactobacillus represent the most common colonizers of the human vagina and are well-known for preserving vaginal health and contrasting the colonization of opportunistic pathogens. Remarkably, high abundance of Lactobacillus crispatus in the vaginal environment has been linked to vaginal health, leading to the widespread use of many L. crispatus strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of L. crispatus taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 L. crispatus strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the L. crispatus pan-genome and core-genome followed by a comprehensive phylogenetic analysis based on the predicted core genes that revealed clustering based on ecological origin. Subsequently, a genomics-targeted approach, i.e., probiogenomics analysis, was applied for in-depth analysis of the eight L. crispatus strains of human origin sequenced in this study. In detail their genetic repertoire was screened for strain-specific genes responsible for phenotypic features that may guide the identification of optimal candidates for next-generation probiotics. The latter includes bacteriocin production, carbohydrates transport and metabolism, as well as a range of features that may be responsible for improved ecological fitness. In silico results regarding the genetic repertoire involved in carbohydrate metabolism were also validated by growth assays on a range of sugars, leading to the selection of putative novel probiotic strains.

Highlights

IntroductionThe host-associated microbiota is considered a primary contributor to the healthy status of many human compartments, such as the gastrointestinal tract (GIT) and the urogenital tract [1]
Using InterProscan [20], RapSearch2 [21] and NCBI CDD analysis [22], we evaluated the presence of functional domains conserved within the unique genes present in the eight strains of L. crispatus isolated from human vagina present in our L. crispatus bacterial stock
We performed a comprehensive comparative genomics an a probiogenomics approach was used to investigate the genetic potential of the eight L. crispatus strains isolated from humans and sequenced in this study in order to identify putative novel probiotics for the treatment of vaginal dysbiosis

Summary

Introduction

The host-associated microbiota is considered a primary contributor to the healthy status of many human compartments, such as the gastrointestinal tract (GIT) and the urogenital tract [1]. Regarding the latter, recent literature revealed that the vaginal microbiota is fundamental in both biological and chemical homeostasis [2]. Recent literature revealed that the vaginal microbiota is fundamental in both biological and chemical homeostasis [2] In this context, it is well-known that bacteria harbored by the vaginal environment participate in maintaining a low pH, which on average should range between 3.8 and 4.5 in a healthy condition [3]. Among the dominant bacterial genera observed in the vaginal microbiota, the most prevalent are LAB

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