Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics
Members of the genus <i>Lactobacillus</i> 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 <i>Lactobacillus crispatus</i> in the...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-12-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/1/73 |
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| author | Federico Fontana Giulia Alessandri Gabriele Andrea Lugli Leonardo Mancabelli Giulia Longhi Rosaria Anzalone Alice Viappiani Marco Ventura Francesca Turroni Christian Milani |
| author_facet | Federico Fontana Giulia Alessandri Gabriele Andrea Lugli Leonardo Mancabelli Giulia Longhi Rosaria Anzalone Alice Viappiani Marco Ventura Francesca Turroni Christian Milani |
| author_sort | Federico Fontana |
| collection | DOAJ |
| description | Members of the genus <i>Lactobacillus</i> 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 <i>Lactobacillus crispatus</i> in the vaginal environment has been linked to vaginal health, leading to the widespread use of many <i>L. crispatus</i> strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of <i>L. crispatus</i> taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 <i>L. crispatus</i> strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the <i>L.</i><i>crispatus</i> 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 <i>L. crispatus</i> 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. |
| first_indexed | 2024-03-10T13:40:48Z |
| format | Article |
| id | doaj.art-93614be2e5984661a855812f1977b55e |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T13:40:48Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-93614be2e5984661a855812f1977b55e2023-11-21T03:03:34ZengMDPI AGMicroorganisms2076-26072020-12-01917310.3390/microorganisms9010073Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation ProbioticsFederico Fontana0Giulia Alessandri1Gabriele Andrea Lugli2Leonardo Mancabelli3Giulia Longhi4Rosaria Anzalone5Alice Viappiani6Marco Ventura7Francesca Turroni8Christian Milani9Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyGenProbio s.r.l., 43124 Parma, ItalyGenProbio s.r.l., 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, ItalyMembers of the genus <i>Lactobacillus</i> 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 <i>Lactobacillus crispatus</i> in the vaginal environment has been linked to vaginal health, leading to the widespread use of many <i>L. crispatus</i> strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of <i>L. crispatus</i> taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 <i>L. crispatus</i> strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the <i>L.</i><i>crispatus</i> 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 <i>L. crispatus</i> 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.https://www.mdpi.com/2076-2607/9/1/73comparative genomics<i>Lactobacillus crispatus</i>probiogenomics and vaginal microbiota |
| spellingShingle | Federico Fontana Giulia Alessandri Gabriele Andrea Lugli Leonardo Mancabelli Giulia Longhi Rosaria Anzalone Alice Viappiani Marco Ventura Francesca Turroni Christian Milani Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics Microorganisms comparative genomics <i>Lactobacillus crispatus</i> probiogenomics and vaginal microbiota |
| title | Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics |
| title_full | Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics |
| title_fullStr | Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics |
| title_full_unstemmed | Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics |
| title_short | Probiogenomics Analysis of 97 <i>Lactobacillus</i> <i>crispatus</i> Strains as a Tool for the Identification of Promising Next-Generation Probiotics |
| title_sort | probiogenomics analysis of 97 i lactobacillus i i crispatus i strains as a tool for the identification of promising next generation probiotics |
| topic | comparative genomics <i>Lactobacillus crispatus</i> probiogenomics and vaginal microbiota |
| url | https://www.mdpi.com/2076-2607/9/1/73 |
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